| Previous changeset 60:9645d995fb3c (2018-10-24) Next changeset 62:e6c4f3e96e47 (2019-01-17) |
|
Commit message:
Updated package according to recommendations. |
|
modified:
bin/Rcall.pm bin/align.pm bin/css/bootstrap-responsive.css bin/css/bootstrap-table.css bin/css/bootstrap.css bin/html.pm bin/js/bootstrap-table.js bin/js/bootstrap.min.js bin/js/filter.js bin/js/jquery.js bin/ppp.pm bin/resize.pm bin/sRNAPipe.pl bin/subgroups.pm sRNAPipe.xml test-data/TE-file-small.fa test-data/dmel-all-rRNA-r6.03.fasta test-data/dmel-all-sn-snoRNA-r6.03.fasta test-data/dmel-all-tRNA-r6.03.fasta test-data/genome-small.fa test-data/mirbase-21-dme-hairpins-16jul2015.fa test-data/reads-sample-small.fastq test-data/transcripts-file-small.fa tool-data/bwa_index.loc.sample tool_data_table_conf.xml.sample |
|
added:
README.rst test-data/fastq_dir/reads-sample-small.fastq-bonafide_reads-TEs.fastq test-data/fastq_dir/reads-sample-small.fastq-bonafide_reads-TEs_uni.fastq test-data/fastq_dir/reads-sample-small.fastq-bonafide_reads-genome.fastq test-data/fastq_dir/reads-sample-small.fastq-bonafide_reads-genome_uni.fastq test-data/fastq_dir/reads-sample-small.fastq-bonafide_reads-transcripts.fastq test-data/fastq_dir/reads-sample-small.fastq-bonafide_reads-transcripts_uni.fastq test-data/fastq_dir/reads-sample-small.fastq-miRNAs-TEs_uni.fastq test-data/fastq_dir/reads-sample-small.fastq-miRNAs-genome.fastq test-data/fastq_dir/reads-sample-small.fastq-miRNAs-genome_uni.fastq test-data/fastq_dir/reads-sample-small.fastq-miRNAs-transcripts.fastq test-data/fastq_dir/reads-sample-small.fastq-miRNAs-transcripts_uni.fastq test-data/fastq_dir/reads-sample-small.fastq-piRNAs-TEs.fastq test-data/fastq_dir/reads-sample-small.fastq-piRNAs-TEs_uni.fastq test-data/fastq_dir/reads-sample-small.fastq-piRNAs-genome.fastq test-data/fastq_dir/reads-sample-small.fastq-piRNAs-genome_uni.fastq test-data/fastq_dir/reads-sample-small.fastq-piRNAs-transcripts.fastq test-data/fastq_dir/reads-sample-small.fastq-piRNAs-transcripts_uni.fastq test-data/fastq_dir/reads-sample-small.fastq-siRNAs-TEs.fastq test-data/fastq_dir/reads-sample-small.fastq-siRNAs-TEs_uni.fastq test-data/fastq_dir/reads-sample-small.fastq-siRNAs-genome.fastq test-data/fastq_dir/reads-sample-small.fastq-siRNAs-genome_uni.fastq test-data/fastq_dir/reads-sample-small.fastq-siRNAs-transcripts.fastq test-data/fastq_dir/reads-sample-small.fastq-siRNAs-transcripts_uni.fastq test-data/fastq_dir/reads-sample-small.fastq_all_mappers.fastq test-data/fastq_dir/reads-sample-small.fastq_unique_mappers.fastq test-data/fastq_dir/reads-sample-small.fastq_unmapped.fastq test-data/res.html test-data/res_files/css/bootstrap-responsive.css test-data/res_files/css/bootstrap-table.css test-data/res_files/css/bootstrap.css test-data/res_files/js/bootstrap-table.js test-data/res_files/js/bootstrap.min.js test-data/res_files/js/filter.js test-data/res_files/js/jquery.galleriffic.js test-data/res_files/js/jquery.js test-data/res_files/js/jquery.opacityrollover.js test-data/res_files/reads-sample-small.fastq-bonafide_reads-TEs.html test-data/res_files/reads-sample-small.fastq-bonafide_reads-genome.html test-data/res_files/reads-sample-small.fastq-bonafide_reads-transcripts.html test-data/res_files/reads-sample-small.fastq-miRNAs-TEs.html test-data/res_files/reads-sample-small.fastq-miRNAs-genome.html test-data/res_files/reads-sample-small.fastq-miRNAs-transcripts.html test-data/res_files/reads-sample-small.fastq-piRNAs-PPP.html test-data/res_files/reads-sample-small.fastq-piRNAs-TEs.html test-data/res_files/reads-sample-small.fastq-piRNAs-genome.html test-data/res_files/reads-sample-small.fastq-piRNAs-transcripts.html test-data/res_files/reads-sample-small.fastq-siRNAs-TEs.html test-data/res_files/reads-sample-small.fastq-siRNAs-genome.html test-data/res_files/reads-sample-small.fastq-siRNAs-transcripts.html test-data/res_files/reads-sample-small.fastq-sub.html test-data/res_files/reads-sample-small.fastq.html test-data/res_files/reads-sample-small.fastq/dataset_35117_18-29.fastq test-data/res_files/reads-sample-small.fastq/genome/Gviz/rand/chrom_1.png test-data/res_files/reads-sample-small.fastq/genome/Gviz/rand/chrom_2.png test-data/res_files/reads-sample-small.fastq/genome/Gviz/rand/chrom_3.png test-data/res_files/reads-sample-small.fastq/genome/Gviz/rand/chrom_4.png test-data/res_files/reads-sample-small.fastq/genome/Gviz/rand/chrom_5.png test-data/res_files/reads-sample-small.fastq/genome/Gviz/rand/chrom_6.png test-data/res_files/reads-sample-small.fastq/genome/Gviz/unique/chrom_1.png test-data/res_files/reads-sample-small.fastq/genome/Gviz/unique/chrom_2.png test-data/res_files/reads-sample-small.fastq/genome/Gviz/unique/chrom_3.png test-data/res_files/reads-sample-small.fastq/genome/Gviz/unique/chrom_4.png test-data/res_files/reads-sample-small.fastq/genome/Gviz/unique/chrom_5.png test-data/res_files/reads-sample-small.fastq/genome/Gviz/unique/chrom_6.png test-data/res_files/reads-sample-small.fastq/genome/distribution.png test-data/res_files/reads-sample-small.fastq/genome/distribution.txt test-data/res_files/reads-sample-small.fastq/genome/dup_mapnum.txt test-data/res_files/reads-sample-small.fastq/genome/dup_nonmapp.txt test-data/res_files/reads-sample-small.fastq/genome/dup_unique.txt test-data/res_files/reads-sample-small.fastq/genome/reads-sample-small.fastq_18-29_minus.bedgraph test-data/res_files/reads-sample-small.fastq/genome/reads-sample-small.fastq_18-29_plus.bedgraph test-data/res_files/reads-sample-small.fastq/genome/reads-sample-small.fastq_18-29_sorted.bam test-data/res_files/reads-sample-small.fastq/genome/reads-sample-small.fastq_18-29_unique_minus.bedgraph test-data/res_files/reads-sample-small.fastq/genome/reads-sample-small.fastq_18-29_unique_plus.bedgraph test-data/res_files/reads-sample-small.fastq/genome/reads-sample-small.fastq_18-29_unique_sorted.bam test-data/res_files/reads-sample-small.fastq/size/duplicates.txt test-data/res_files/reads-sample-small.fastq/size/histogram.png test-data/res_files/reads-sample-small.fastq/size/reads_size.txt test-data/res_files/reads-sample-small.fastq/subgroups/PPPartners/BATUMI_I.html test-data/res_files/reads-sample-small.fastq/subgroups/PPPartners/BATUMI_I/antisens.txt test-data/res_files/reads-sample-small.fastq/subgroups/PPPartners/BATUMI_I/antisensPPP.txt test-data/res_files/reads-sample-small.fastq/subgroups/PPPartners/BATUMI_I/histogram.png test-data/res_files/reads-sample-small.fastq/subgroups/PPPartners/BATUMI_I/overlap_size.txt test-data/res_files/reads-sample-small.fastq/subgroups/PPPartners/BATUMI_I/sens.txt test-data/res_files/reads-sample-small.fastq/subgroups/PPPartners/BATUMI_I/sensPPP.txt test-data/res_files/reads-sample-small.fastq/subgroups/PPPartners/BATUMI_LTR.html test-data/res_files/reads-sample-small.fastq/subgroups/PPPartners/BATUMI_LTR/antisens.txt test-data/res_files/reads-sample-small.fastq/subgroups/PPPartners/BATUMI_LTR/antisensPPP.txt test-data/res_files/reads-sample-small.fastq/subgroups/PPPartners/BATUMI_LTR/histogram.png test-data/res_files/reads-sample-small.fastq/subgroups/PPPartners/BATUMI_LTR/overlap_size.txt test-data/res_files/reads-sample-small.fastq/subgroups/PPPartners/BATUMI_LTR/sens.txt test-data/res_files/reads-sample-small.fastq/subgroups/PPPartners/BATUMI_LTR/sensPPP.txt test-data/res_files/reads-sample-small.fastq/subgroups/PPPartners/BS2.html test-data/res_files/reads-sample-small.fastq/subgroups/PPPartners/BS2/antisens.txt test-data/res_files/reads-sample-small.fastq/subgroups/PPPartners/BS2/antisensPPP.txt test-data/res_files/reads-sample-small.fastq/subgroups/PPPartners/BS2/histogram.png test-data/res_files/reads-sample-small.fastq/subgroups/PPPartners/BS2/overlap_size.txt test-data/res_files/reads-sample-small.fastq/subgroups/PPPartners/BS2/sens.txt test-data/res_files/reads-sample-small.fastq/subgroups/PPPartners/BS2/sensPPP.txt test-data/res_files/reads-sample-small.fastq/subgroups/PPPartners/DMCR1A.html test-data/res_files/reads-sample-small.fastq/subgroups/PPPartners/DMCR1A/antisens.txt test-data/res_files/reads-sample-small.fastq/subgroups/PPPartners/DMCR1A/antisensPPP.txt test-data/res_files/reads-sample-small.fastq/subgroups/PPPartners/DMCR1A/histogram.png test-data/res_files/reads-sample-small.fastq/subgroups/PPPartners/DMCR1A/overlap_size.txt test-data/res_files/reads-sample-small.fastq/subgroups/PPPartners/DMCR1A/sens.txt test-data/res_files/reads-sample-small.fastq/subgroups/PPPartners/DMCR1A/sensPPP.txt test-data/res_files/reads-sample-small.fastq/subgroups/PPPartners/DMRT1B.html test-data/res_files/reads-sample-small.fastq/subgroups/PPPartners/DMRT1B/antisens.txt test-data/res_files/reads-sample-small.fastq/subgroups/PPPartners/DMRT1B/antisensPPP.txt test-data/res_files/reads-sample-small.fastq/subgroups/PPPartners/DMRT1B/histogram.png test-data/res_files/reads-sample-small.fastq/subgroups/PPPartners/DMRT1B/overlap_size.txt test-data/res_files/reads-sample-small.fastq/subgroups/PPPartners/DMRT1B/sens.txt test-data/res_files/reads-sample-small.fastq/subgroups/PPPartners/DMRT1B/sensPPP.txt test-data/res_files/reads-sample-small.fastq/subgroups/PPPartners/FW.html test-data/res_files/reads-sample-small.fastq/subgroups/PPPartners/FW/antisens.txt test-data/res_files/reads-sample-small.fastq/subgroups/PPPartners/FW/antisensPPP.txt test-data/res_files/reads-sample-small.fastq/subgroups/PPPartners/FW/histogram.png test-data/res_files/reads-sample-small.fastq/subgroups/PPPartners/FW/overlap_size.txt test-data/res_files/reads-sample-small.fastq/subgroups/PPPartners/FW/sens.txt test-data/res_files/reads-sample-small.fastq/subgroups/PPPartners/FW/sensPPP.txt test-data/res_files/reads-sample-small.fastq/subgroups/PPPartners/G6_DM.html test-data/res_files/reads-sample-small.fastq/subgroups/PPPartners/G6_DM/antisens.txt test-data/res_files/reads-sample-small.fastq/subgroups/PPPartners/G6_DM/antisensPPP.txt test-data/res_files/reads-sample-small.fastq/subgroups/PPPartners/G6_DM/histogram.png test-data/res_files/reads-sample-small.fastq/subgroups/PPPartners/G6_DM/overlap_size.txt test-data/res_files/reads-sample-small.fastq/subgroups/PPPartners/G6_DM/sens.txt test-data/res_files/reads-sample-small.fastq/subgroups/PPPartners/G6_DM/sensPPP.txt test-data/res_files/reads-sample-small.fastq/subgroups/PPPartners/Gypsy2-LTR_DM.html test-data/res_files/reads-sample-small.fastq/subgroups/PPPartners/Gypsy2-LTR_DM/antisens.txt test-data/res_files/reads-sample-small.fastq/subgroups/PPPartners/Gypsy2-LTR_DM/antisensPPP.txt test-data/res_files/reads-sample-small.fastq/subgroups/PPPartners/Gypsy2-LTR_DM/histogram.png test-data/res_files/reads-sample-small.fastq/subgroups/PPPartners/Gypsy2-LTR_DM/overlap_size.txt test-data/res_files/reads-sample-small.fastq/subgroups/PPPartners/Gypsy2-LTR_DM/sens.txt test-data/res_files/reads-sample-small.fastq/subgroups/PPPartners/Gypsy2-LTR_DM/sensPPP.txt test-data/res_files/reads-sample-small.fastq/subgroups/PPPartners/I_DM.html test-data/res_files/reads-sample-small.fastq/subgroups/PPPartners/I_DM/antisens.txt test-data/res_files/reads-sample-small.fastq/subgroups/PPPartners/I_DM/antisensPPP.txt test-data/res_files/reads-sample-small.fastq/subgroups/PPPartners/I_DM/histogram.png test-data/res_files/reads-sample-small.fastq/subgroups/PPPartners/I_DM/overlap_size.txt test-data/res_files/reads-sample-small.fastq/subgroups/PPPartners/I_DM/sens.txt test-data/res_files/reads-sample-small.fastq/subgroups/PPPartners/I_DM/sensPPP.txt test-data/res_files/reads-sample-small.fastq/subgroups/PPPartners/MAX_I.html test-data/res_files/reads-sample-small.fastq/subgroups/PPPartners/MAX_I/antisens.txt test-data/res_files/reads-sample-small.fastq/subgroups/PPPartners/MAX_I/antisensPPP.txt test-data/res_files/reads-sample-small.fastq/subgroups/PPPartners/MAX_I/histogram.png test-data/res_files/reads-sample-small.fastq/subgroups/PPPartners/MAX_I/overlap_size.txt test-data/res_files/reads-sample-small.fastq/subgroups/PPPartners/MAX_I/sens.txt test-data/res_files/reads-sample-small.fastq/subgroups/PPPartners/MAX_I/sensPPP.txt test-data/res_files/reads-sample-small.fastq/subgroups/PPPartners/MAX_LTR.html test-data/res_files/reads-sample-small.fastq/subgroups/PPPartners/MAX_LTR/antisens.txt test-data/res_files/reads-sample-small.fastq/subgroups/PPPartners/MAX_LTR/antisensPPP.txt test-data/res_files/reads-sample-small.fastq/subgroups/PPPartners/MAX_LTR/histogram.png test-data/res_files/reads-sample-small.fastq/subgroups/PPPartners/MAX_LTR/overlap_size.txt test-data/res_files/reads-sample-small.fastq/subgroups/PPPartners/MAX_LTR/sens.txt test-data/res_files/reads-sample-small.fastq/subgroups/PPPartners/MAX_LTR/sensPPP.txt test-data/res_files/reads-sample-small.fastq/subgroups/PPPartners/PROTOP.html test-data/res_files/reads-sample-small.fastq/subgroups/PPPartners/PROTOP/antisens.txt test-data/res_files/reads-sample-small.fastq/subgroups/PPPartners/PROTOP/antisensPPP.txt test-data/res_files/reads-sample-small.fastq/subgroups/PPPartners/PROTOP/histogram.png test-data/res_files/reads-sample-small.fastq/subgroups/PPPartners/PROTOP/overlap_size.txt test-data/res_files/reads-sample-small.fastq/subgroups/PPPartners/PROTOP/sens.txt test-data/res_files/reads-sample-small.fastq/subgroups/PPPartners/PROTOP/sensPPP.txt test-data/res_files/reads-sample-small.fastq/subgroups/PPPartners/ppp.txt test-data/res_files/reads-sample-small.fastq/subgroups/TEs.fai test-data/res_files/reads-sample-small.fastq/subgroups/TEs.sam_aln.err test-data/res_files/reads-sample-small.fastq/subgroups/TEs.sam_samse.err test-data/res_files/reads-sample-small.fastq/subgroups/bonafide_reads/Gviz_TEs/BATUMI_I.png test-data/res_files/reads-sample-small.fastq/subgroups/bonafide_reads/Gviz_TEs/BATUMI_LTR.png test-data/res_files/reads-sample-small.fastq/subgroups/bonafide_reads/Gviz_TEs/BS2.png test-data/res_files/reads-sample-small.fastq/subgroups/bonafide_reads/Gviz_TEs/DMCR1A.png test-data/res_files/reads-sample-small.fastq/subgroups/bonafide_reads/Gviz_TEs/DMRT1B.png test-data/res_files/reads-sample-small.fastq/subgroups/bonafide_reads/Gviz_TEs/FW.png test-data/res_files/reads-sample-small.fastq/subgroups/bonafide_reads/Gviz_TEs/G6_DM.png test-data/res_files/reads-sample-small.fastq/subgroups/bonafide_reads/Gviz_TEs/Gypsy2-LTR_DM.png test-data/res_files/reads-sample-small.fastq/subgroups/bonafide_reads/Gviz_TEs/I_DM.png test-data/res_files/reads-sample-small.fastq/subgroups/bonafide_reads/Gviz_TEs/MAX_I.png test-data/res_files/reads-sample-small.fastq/subgroups/bonafide_reads/Gviz_TEs/MAX_LTR.png test-data/res_files/reads-sample-small.fastq/subgroups/bonafide_reads/Gviz_TEs/PROTOP.png test-data/res_files/reads-sample-small.fastq/subgroups/bonafide_reads/Gviz_genome/rand/chrom_1.png test-data/res_files/reads-sample-small.fastq/subgroups/bonafide_reads/Gviz_genome/rand/chrom_2.png test-data/res_files/reads-sample-small.fastq/subgroups/bonafide_reads/Gviz_genome/rand/chrom_4.png test-data/res_files/reads-sample-small.fastq/subgroups/bonafide_reads/Gviz_genome/rand/chrom_5.png test-data/res_files/reads-sample-small.fastq/subgroups/bonafide_reads/Gviz_genome/rand/chrom_6.png test-data/res_files/reads-sample-small.fastq/subgroups/bonafide_reads/Gviz_genome/unique/chrom_1.png test-data/res_files/reads-sample-small.fastq/subgroups/bonafide_reads/Gviz_genome/unique/chrom_2.png test-data/res_files/reads-sample-small.fastq/subgroups/bonafide_reads/Gviz_genome/unique/chrom_4.png test-data/res_files/reads-sample-small.fastq/subgroups/bonafide_reads/Gviz_genome/unique/chrom_5.png test-data/res_files/reads-sample-small.fastq/subgroups/bonafide_reads/Gviz_genome/unique/chrom_6.png test-data/res_files/reads-sample-small.fastq/subgroups/bonafide_reads/bonafide_reads-TEs_minus.bedgraph test-data/res_files/reads-sample-small.fastq/subgroups/bonafide_reads/bonafide_reads-TEs_plus.bedgraph test-data/res_files/reads-sample-small.fastq/subgroups/bonafide_reads/bonafide_reads-TEs_reads_counts.txt test-data/res_files/reads-sample-small.fastq/subgroups/bonafide_reads/bonafide_reads-TEs_reads_counts_mismatches.txt test-data/res_files/reads-sample-small.fastq/subgroups/bonafide_reads/bonafide_reads-TEs_reads_counts_nomismatches.txt test-data/res_files/reads-sample-small.fastq/subgroups/bonafide_reads/bonafide_reads-TEs_sorted.bam test-data/res_files/reads-sample-small.fastq/subgroups/bonafide_reads/bonafide_reads-TEs_unique_sorted.bam test-data/res_files/reads-sample-small.fastq/subgroups/bonafide_reads/bonafide_reads-genome_minus.bedgraph test-data/res_files/reads-sample-small.fastq/subgroups/bonafide_reads/bonafide_reads-genome_plus.bedgraph test-data/res_files/reads-sample-small.fastq/subgroups/bonafide_reads/bonafide_reads-genome_sorted.bam test-data/res_files/reads-sample-small.fastq/subgroups/bonafide_reads/bonafide_reads-genome_unique_minus.bedgraph test-data/res_files/reads-sample-small.fastq/subgroups/bonafide_reads/bonafide_reads-genome_unique_plus.bedgraph test-data/res_files/reads-sample-small.fastq/subgroups/bonafide_reads/bonafide_reads-genome_unique_sorted.bam test-data/res_files/reads-sample-small.fastq/subgroups/bonafide_reads/bonafide_reads-transcripts_reads_counts.txt test-data/res_files/reads-sample-small.fastq/subgroups/bonafide_reads/bonafide_reads-transcripts_sorted.bam test-data/res_files/reads-sample-small.fastq/subgroups/bonafide_reads/bonafide_reads-transcripts_unique_sorted.bam test-data/res_files/reads-sample-small.fastq/subgroups/miRNAs.sam_aln.err test-data/res_files/reads-sample-small.fastq/subgroups/miRNAs.sam_samse.err test-data/res_files/reads-sample-small.fastq/subgroups/miRNAs/Gviz_genome/rand/chrom_3.png test-data/res_files/reads-sample-small.fastq/subgroups/miRNAs/Gviz_genome/unique/chrom_3.png test-data/res_files/reads-sample-small.fastq/subgroups/miRNAs/miRNAs-TEs_minus.bedgraph test-data/res_files/reads-sample-small.fastq/subgroups/miRNAs/miRNAs-TEs_plus.bedgraph test-data/res_files/reads-sample-small.fastq/subgroups/miRNAs/miRNAs-TEs_reads_counts.txt test-data/res_files/reads-sample-small.fastq/subgroups/miRNAs/miRNAs-TEs_reads_counts_mismatches.txt test-data/res_files/reads-sample-small.fastq/subgroups/miRNAs/miRNAs-TEs_reads_counts_nomismatches.txt test-data/res_files/reads-sample-small.fastq/subgroups/miRNAs/miRNAs-TEs_sorted.bam test-data/res_files/reads-sample-small.fastq/subgroups/miRNAs/miRNAs-TEs_unique_sorted.bam test-data/res_files/reads-sample-small.fastq/subgroups/miRNAs/miRNAs-genome_minus.bedgraph test-data/res_files/reads-sample-small.fastq/subgroups/miRNAs/miRNAs-genome_plus.bedgraph test-data/res_files/reads-sample-small.fastq/subgroups/miRNAs/miRNAs-genome_sorted.bam test-data/res_files/reads-sample-small.fastq/subgroups/miRNAs/miRNAs-genome_unique_minus.bedgraph test-data/res_files/reads-sample-small.fastq/subgroups/miRNAs/miRNAs-genome_unique_plus.bedgraph test-data/res_files/reads-sample-small.fastq/subgroups/miRNAs/miRNAs-genome_unique_sorted.bam test-data/res_files/reads-sample-small.fastq/subgroups/miRNAs/miRNAs-transcripts_reads_counts.txt test-data/res_files/reads-sample-small.fastq/subgroups/miRNAs/miRNAs-transcripts_sorted.bam test-data/res_files/reads-sample-small.fastq/subgroups/miRNAs/miRNAs-transcripts_unique_sorted.bam test-data/res_files/reads-sample-small.fastq/subgroups/miRNAs/miRNAs_reads_counts.txt test-data/res_files/reads-sample-small.fastq/subgroups/piRNAs/Gviz_TEs/BATUMI_I.png test-data/res_files/reads-sample-small.fastq/subgroups/piRNAs/Gviz_TEs/BATUMI_LTR.png test-data/res_files/reads-sample-small.fastq/subgroups/piRNAs/Gviz_TEs/BS2.png test-data/res_files/reads-sample-small.fastq/subgroups/piRNAs/Gviz_TEs/DMCR1A.png test-data/res_files/reads-sample-small.fastq/subgroups/piRNAs/Gviz_TEs/DMRT1B.png test-data/res_files/reads-sample-small.fastq/subgroups/piRNAs/Gviz_TEs/FW.png test-data/res_files/reads-sample-small.fastq/subgroups/piRNAs/Gviz_TEs/G6_DM.png test-data/res_files/reads-sample-small.fastq/subgroups/piRNAs/Gviz_TEs/Gypsy2-LTR_DM.png test-data/res_files/reads-sample-small.fastq/subgroups/piRNAs/Gviz_TEs/I_DM.png test-data/res_files/reads-sample-small.fastq/subgroups/piRNAs/Gviz_TEs/MAX_I.png test-data/res_files/reads-sample-small.fastq/subgroups/piRNAs/Gviz_TEs/MAX_LTR.png test-data/res_files/reads-sample-small.fastq/subgroups/piRNAs/Gviz_TEs/PROTOP.png test-data/res_files/reads-sample-small.fastq/subgroups/piRNAs/Gviz_genome/rand/chrom_1.png test-data/res_files/reads-sample-small.fastq/subgroups/piRNAs/Gviz_genome/rand/chrom_2.png test-data/res_files/reads-sample-small.fastq/subgroups/piRNAs/Gviz_genome/rand/chrom_4.png test-data/res_files/reads-sample-small.fastq/subgroups/piRNAs/Gviz_genome/rand/chrom_6.png test-data/res_files/reads-sample-small.fastq/subgroups/piRNAs/Gviz_genome/unique/chrom_1.png test-data/res_files/reads-sample-small.fastq/subgroups/piRNAs/Gviz_genome/unique/chrom_2.png test-data/res_files/reads-sample-small.fastq/subgroups/piRNAs/Gviz_genome/unique/chrom_4.png test-data/res_files/reads-sample-small.fastq/subgroups/piRNAs/Gviz_genome/unique/chrom_6.png test-data/res_files/reads-sample-small.fastq/subgroups/piRNAs/piRNAs-TEs_minus.bedgraph test-data/res_files/reads-sample-small.fastq/subgroups/piRNAs/piRNAs-TEs_plus.bedgraph test-data/res_files/reads-sample-small.fastq/subgroups/piRNAs/piRNAs-TEs_reads_counts.txt test-data/res_files/reads-sample-small.fastq/subgroups/piRNAs/piRNAs-TEs_reads_counts_mismatches.txt test-data/res_files/reads-sample-small.fastq/subgroups/piRNAs/piRNAs-TEs_reads_counts_nomismatches.txt test-data/res_files/reads-sample-small.fastq/subgroups/piRNAs/piRNAs-TEs_sorted.bam test-data/res_files/reads-sample-small.fastq/subgroups/piRNAs/piRNAs-TEs_unique_sorted.bam test-data/res_files/reads-sample-small.fastq/subgroups/piRNAs/piRNAs-genome_minus.bedgraph test-data/res_files/reads-sample-small.fastq/subgroups/piRNAs/piRNAs-genome_plus.bedgraph test-data/res_files/reads-sample-small.fastq/subgroups/piRNAs/piRNAs-genome_sorted.bam test-data/res_files/reads-sample-small.fastq/subgroups/piRNAs/piRNAs-genome_unique_minus.bedgraph test-data/res_files/reads-sample-small.fastq/subgroups/piRNAs/piRNAs-genome_unique_plus.bedgraph test-data/res_files/reads-sample-small.fastq/subgroups/piRNAs/piRNAs-genome_unique_sorted.bam test-data/res_files/reads-sample-small.fastq/subgroups/piRNAs/piRNAs-transcripts_reads_counts.txt test-data/res_files/reads-sample-small.fastq/subgroups/piRNAs/piRNAs-transcripts_sorted.bam test-data/res_files/reads-sample-small.fastq/subgroups/piRNAs/piRNAs-transcripts_unique_sorted.bam test-data/res_files/reads-sample-small.fastq/subgroups/pie_chart.png test-data/res_files/reads-sample-small.fastq/subgroups/repartition.txt test-data/res_files/reads-sample-small.fastq/subgroups/siRNAs/Gviz_TEs/BATUMI_I.png test-data/res_files/reads-sample-small.fastq/subgroups/siRNAs/Gviz_TEs/BATUMI_LTR.png test-data/res_files/reads-sample-small.fastq/subgroups/siRNAs/Gviz_TEs/BS2.png test-data/res_files/reads-sample-small.fastq/subgroups/siRNAs/Gviz_TEs/DMCR1A.png test-data/res_files/reads-sample-small.fastq/subgroups/siRNAs/Gviz_TEs/DMRT1B.png test-data/res_files/reads-sample-small.fastq/subgroups/siRNAs/Gviz_TEs/FW.png test-data/res_files/reads-sample-small.fastq/subgroups/siRNAs/Gviz_TEs/G6_DM.png test-data/res_files/reads-sample-small.fastq/subgroups/siRNAs/Gviz_TEs/Gypsy2-LTR_DM.png test-data/res_files/reads-sample-small.fastq/subgroups/siRNAs/Gviz_TEs/I_DM.png test-data/res_files/reads-sample-small.fastq/subgroups/siRNAs/Gviz_TEs/MAX_I.png test-data/res_files/reads-sample-small.fastq/subgroups/siRNAs/Gviz_TEs/MAX_LTR.png test-data/res_files/reads-sample-small.fastq/subgroups/siRNAs/Gviz_TEs/PROTOP.png test-data/res_files/reads-sample-small.fastq/subgroups/siRNAs/Gviz_genome/rand/chrom_1.png test-data/res_files/reads-sample-small.fastq/subgroups/siRNAs/Gviz_genome/rand/chrom_2.png test-data/res_files/reads-sample-small.fastq/subgroups/siRNAs/Gviz_genome/rand/chrom_4.png test-data/res_files/reads-sample-small.fastq/subgroups/siRNAs/Gviz_genome/rand/chrom_5.png test-data/res_files/reads-sample-small.fastq/subgroups/siRNAs/Gviz_genome/rand/chrom_6.png test-data/res_files/reads-sample-small.fastq/subgroups/siRNAs/Gviz_genome/unique/chrom_1.png test-data/res_files/reads-sample-small.fastq/subgroups/siRNAs/Gviz_genome/unique/chrom_2.png test-data/res_files/reads-sample-small.fastq/subgroups/siRNAs/Gviz_genome/unique/chrom_4.png test-data/res_files/reads-sample-small.fastq/subgroups/siRNAs/Gviz_genome/unique/chrom_5.png test-data/res_files/reads-sample-small.fastq/subgroups/siRNAs/Gviz_genome/unique/chrom_6.png test-data/res_files/reads-sample-small.fastq/subgroups/siRNAs/siRNAs-TEs_minus.bedgraph test-data/res_files/reads-sample-small.fastq/subgroups/siRNAs/siRNAs-TEs_plus.bedgraph test-data/res_files/reads-sample-small.fastq/subgroups/siRNAs/siRNAs-TEs_reads_counts.txt test-data/res_files/reads-sample-small.fastq/subgroups/siRNAs/siRNAs-TEs_reads_counts_mismatches.txt test-data/res_files/reads-sample-small.fastq/subgroups/siRNAs/siRNAs-TEs_reads_counts_nomismatches.txt test-data/res_files/reads-sample-small.fastq/subgroups/siRNAs/siRNAs-TEs_sorted.bam test-data/res_files/reads-sample-small.fastq/subgroups/siRNAs/siRNAs-TEs_unique_sorted.bam test-data/res_files/reads-sample-small.fastq/subgroups/siRNAs/siRNAs-genome_minus.bedgraph test-data/res_files/reads-sample-small.fastq/subgroups/siRNAs/siRNAs-genome_plus.bedgraph test-data/res_files/reads-sample-small.fastq/subgroups/siRNAs/siRNAs-genome_sorted.bam test-data/res_files/reads-sample-small.fastq/subgroups/siRNAs/siRNAs-genome_unique_minus.bedgraph test-data/res_files/reads-sample-small.fastq/subgroups/siRNAs/siRNAs-genome_unique_plus.bedgraph test-data/res_files/reads-sample-small.fastq/subgroups/siRNAs/siRNAs-genome_unique_sorted.bam test-data/res_files/reads-sample-small.fastq/subgroups/siRNAs/siRNAs-transcripts_reads_counts.txt test-data/res_files/reads-sample-small.fastq/subgroups/siRNAs/siRNAs-transcripts_sorted.bam test-data/res_files/reads-sample-small.fastq/subgroups/siRNAs/siRNAs-transcripts_unique_sorted.bam test-data/res_files/reads-sample-small.fastq/subgroups/transcripts.fai test-data/res_files/reads-sample-small.fastq/subgroups/transcripts.sam_aln.err test-data/res_files/reads-sample-small.fastq/subgroups/transcripts.sam_samse.err test-data/res_files/report.txt |
|
removed:
README.md |
| b |
| diff -r 9645d995fb3c -r 9185ca0a7b43 README.md --- a/README.md Wed Oct 24 07:40:20 2018 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,57 +0,0 @@ -# sRNAPipe -a GALAXY-based pipeline for bioinformatic in-depth exploration of small RNA-seq data - -Description -============= - -The field of small RNA is one of the most investigated research areas since they were shown to regulate gene expression and play essential roles in fundamental biological processes. -sRNAPipe a computational pipeline (sRNAPipe: small RNA pipeline) based on the Galaxy framework that takes as input a fastq file of small RNA-seq reads and performs successive steps of mapping to categories of genomic sequences: microRNAs, gene transcripts, small nuclear RNAs, ribosomal RNAs, transfer RNAs and transposable elements. It also provides individual mapping and counting for chromosomes, gene transcripts and transposable elements, normalization, small RNA length analysis and plotting of the data along genomic coordinates to build publication-quality graphs and figures. sRNAPipe evaluates 10-nucleotide 5’-overlaps of reads on opposite strands to test ping-pong amplification for putative PIWI-interacting RNAs, providing numbers of overlaps and corresponding z-scores. - - - -Prerequisites -============= - -1. Unix system with A Galaxy server (release july 2014 or later installed) - -2. Some tools are used by sRNAPipe and must be installed and added to the Path. - - * Bwa aligner: you can obtain it here: https://sourceforge.net/projects/bio-bwa/files/ . Please download version 0.7.12-r1039 or higher - * BedTools powerful toolset for genome arithmetic is also needed. It should be found here: http://bedtools.readthedocs.io/en/latest/ . We recommend to use v2.24.0 or higher. - * Samtools : you can obtain it here : https://sourceforge.net/projects/samtools/files/samtools/1.5/. Please download version 1.5 - -3. Perl version higher than 5.1 is needed with packages : "perl-statistics", "Parallel::ForkManager", "Statistics::R", "Getopt::Long" , "String::Random", "File::Copy::Recursive" and "Math::CDF" installed. - -4. R project version higher than 3.1 is needed with libraries "plotrix", "bioconductor-sushi", "RColorBrewer" and "ggplot2" installed. You can find respectively these libraries here: https://cran.r-project.org/web/packages/plotrix/index.html and https://bioconductor.org/packages/release/bioc/html/Sushi.html and https://cran.r-project.org/web/packages/RColorBrewer/index.html and https://cran.r-project.org/web/packages/ggplot2/index.html - -Installation -============= - -The process has to be completed by an administrator of your Galaxy server to install sRNAPipe. - -1. Download sRNAPipe -You can find sRNAPipe here: https://github.com/brassetjensen/sRNAPipe - -2. Put the tool into Galaxy's tools directory -You need to add files into tools/ directory , where all tool-related files are stored, within your Galaxy installation. - -3. Make Galaxy aware of the new tool sRNAPipe -Now that the tool and its definition file are ready, the final step is to make Galaxy aware of the new files. -Galaxy recognizes installed tools by reading the tool_conf.xml tool configuration file. Thus, letting Galaxy know about the new tool is as easy as adding a few lines to the tool_conf.xml file located in the config/ directory of the Galaxy installation. New tools can either be added to existing sections or added to new sections defined in the following way: - -```xml - <section name="NewTools" id="mTools"> - <tool file="sRNAPipe.xml" /> - </section> -``` - - 4. Start or Restart Galaxy to use it. - - User Manual -============= - - <object data="https://github.com/brassetjensen/sRNAPipe/blob/master/sRNAPipe_User_Manual.pdf" type="application/pdf" width="700px" height="700px"> - <embed src="https://github.com/brassetjensen/sRNAPipe/blob/master/sRNAPipe_User_Manual.pdf"> - This browser does not support PDFs. Please download the PDF to view it: <a href="https://github.com/brassetjensen/sRNAPipe/blob/master/sRNAPipe_User_Manual.pdf">Download PDF</a>.</p> - </embed> -</object> |
| b |
| diff -r 9645d995fb3c -r 9185ca0a7b43 README.rst --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/README.rst Wed Jan 16 08:18:13 2019 -0500 |
| b |
| @@ -0,0 +1,63 @@ + +sRNAPipe +======== + +A GALAXY-based pipeline for bioinformatic in-depth exploration of small RNA-seq data + +Description +=========== + +The field of small RNA is one of the most investigated research areas since they were shown to regulate gene expression and play essential roles in fundamental biological processes. +sRNAPipe a computational pipeline (sRNAPipe: small RNA pipeline) based on the Galaxy framework that takes as input a fastq file of small RNA-seq reads and performs successive steps of mapping to categories of genomic sequences: microRNAs, gene transcripts, small nuclear RNAs, ribosomal RNAs, transfer RNAs and transposable elements. It also provides individual mapping and counting for chromosomes, gene transcripts and transposable elements, normalization, small RNA length analysis and plotting of the data along genomic coordinates to build publication-quality graphs and figures. sRNAPipe evaluates 10-nucleotide 5’-overlaps of reads on opposite strands to test ping-pong amplification for putative PIWI-interacting RNAs, providing numbers of overlaps and corresponding z-scores. + +Prerequisites +============= + +1. Unix system with A Galaxy server (release july 2014 or later installed) + +2. Some tools are used by sRNAPipe and must be installed and added to the Path. + + + * Bwa aligner: you can obtain it here: https://sourceforge.net/projects/bio-bwa/files/ . Please download version 0.7.12-r1039 or higher + * BedTools powerful toolset for genome arithmetic is also needed. It should be found here: http://bedtools.readthedocs.io/en/latest/ . We recommend to use v2.24.0 or higher. + * Samtools : you can obtain it here : https://sourceforge.net/projects/samtools/files/samtools/1.5/. Please download version 1.5 + +3. Perl version higher than 5.1 is needed with packages : "perl-statistics", "Parallel::ForkManager", "Statistics::R", "Getopt::Long" , "String::Random", "File::Copy::Recursive" and "Math::CDF" installed. + +4. R project version higher than 3.1 is needed with libraries "plotrix", "bioconductor-sushi", "RColorBrewer" and "ggplot2" installed. You can find respectively these libraries here: https://cran.r-project.org/web/packages/plotrix/index.html and https://bioconductor.org/packages/release/bioc/html/Sushi.html and https://cran.r-project.org/web/packages/RColorBrewer/index.html and https://cran.r-project.org/web/packages/ggplot2/index.html + +Installation +============ + +The process has to be completed by an administrator of your Galaxy server to install sRNAPipe. + + +1. Download sRNAPipe + You can find sRNAPipe here: https://github.com/brassetjensen/sRNAPipe + +2. Put the tool into Galaxy's tools directory + You need to add files into tools/ directory , where all tool-related files are stored, within your Galaxy installation. + +3. Make Galaxy aware of the new tool sRNAPipe + Now that the tool and its definition file are ready, the final step is to make Galaxy aware of the new files. + Galaxy recognizes installed tools by reading the tool_conf.xml tool configuration file. Thus, letting Galaxy know about the new tool is as easy as adding a few lines to the tool_conf.xml file located in the config/ directory of the Galaxy installation. New tools can either be added to existing sections or added to new sections defined in the following way: + +.. code-block:: xml + + <section name="NewTools" id="mTools"> + <tool file="sRNAPipe.xml" /> + </section> + +4. Start or Restart Galaxy to use it. + +User Manual +=========== + + .. raw:: html + + <object data="https://github.com/brassetjensen/sRNAPipe/blob/master/sRNAPipe_User_Manual.pdf" type="application/pdf" width="700px" height="700px"> + <embed src="https://github.com/brassetjensen/sRNAPipe/blob/master/sRNAPipe_User_Manual.pdf"> + This browser does not support PDFs. Please download the PDF to view it: <a href="https://github.com/brassetjensen/sRNAPipe/blob/master/sRNAPipe_User_Manual.pdf">Download PDF</a>.</p> + </embed> + </object> + |
| b |
| diff -r 9645d995fb3c -r 9185ca0a7b43 bin/Rcall.pm --- a/bin/Rcall.pm Wed Oct 24 07:40:20 2018 -0400 +++ b/bin/Rcall.pm Wed Jan 16 08:18:13 2019 -0500 |
| [ |
| b'@@ -1,136 +1,136 @@\n-package Rcall;\r\n-\r\n-use strict;\r\n-use warnings;\r\n-use Statistics::R;\r\n-\r\n-use Exporter;\r\n-our @ISA = qw(Exporter);\r\n-our @EXPORT_OK = qw( &histogram &pie_chart &bg_to_png );\r\n-\r\n-sub histogram\r\n-{\r\n- my ($size_hashR, $out_png, $size) = @_;\r\n- my (@abs, @ord);\r\n- my $i = 0;\r\n- foreach my $k (sort {$a <=> $b} keys %{$size_hashR})\r\n- {\r\n- my $percentage = 0;\r\n- $percentage = $size_hashR->{$k} * 100 / $size if $size != 0;\r\n- $abs[$i] = $k ; $ord[$i] = $percentage; $i++;\r\n- }\r\n- my $abs = join (",", @abs );\r\n- my $ord = join (",", @ord );\r\n- if (scalar(@abs) != 0)\r\n- {\r\n-\r\n- my $R = Statistics::R->new();\r\n- $R->startR;\r\n- $R->send(\r\n- qq`library(ggplot2)\r\n- percentage = c($ord)\r\n- size =c($abs)\r\n- min = min(size) \r\n- max = max(size) \r\n- dat = data.frame(size,percentage)\r\n- png(filename=\\"$out_png\\", width = 640, height = 640)\r\n- c = ggplot(dat,aes(size,percentage))\r\n- c + geom_bar(stat="identity") + scale_x_continuous(breaks=min:max)+theme( axis.text.x = element_text(angle=90, hjust=0.5, size=20), axis.text.y = element_text( size=20 ), axis.title.x = element_text( size=25, face="bold"), axis.title.y = element_text( size=25, face="bold") )\r\n- dev.off()`);\r\n- $R->stopR();\r\n-\r\n- }\r\n-}\r\n-\r\n-sub bg_to_png\r\n-{\r\n- my ( $fai, $bgP, $bgM, $dir, $sb ) = @_;\r\n- my $R = Statistics::R->new();\r\n- $R->startR;\r\n- $R->send( \r\n- qq`library(\'Sushi\')\r\n- fai =read.table("$fai")\r\n- if ( file.info("$bgP")\\$size !=0 )\r\n- {\r\n- bgP = read.table("$bgP")\r\n- } else { bgP = data.frame(factor(),integer()) }\r\n-\r\n- if ( file.info("$bgM")\\$size !=0 )\r\n- {\r\n- bgM = read.table("$bgM")\r\n- } else { bgM = data.frame(factor(),integer()) }\r\n-\r\n- f_both = function(chr,end) {\r\n- jpeg( paste0("$dir",as.character(chr),".png"), quality=100)\r\n- par(mfrow=c(2,1),mar=c(1,10,1,3))\r\n- plotBedgraph(bgP, chrom=chr,chromstart=0,chromend=end,transparency=.50, color=SushiColors(2)(2)[1])\r\n- axis(side=2,las=2,tcl=.2)\r\n- mtext("Scaled Read Depth",side=2,line=4,cex=1,font=2)\r\n- plotBedgraph(bgM, chrom=chr,chromstart=0,chromend=end,transparency=.50, flip=TRUE, color=SushiColors(2)(2)[2]) \r\n- labelgenome(chrom=chr,chromstart=0,chromend=end,side=3,n=3,scale="$sb", line=0, chromline = 0.5, scaleline = 0.5, scaleadjust =1.05, chromadjust = -0.4)\r\n- axis(side=2,las=2,tcl=.2,at=pretty(par("yaxp")[c(1,2)]),labels=-1*pretty(par("yaxp")[c(1,2)]))\r\n- mtext("Scaled Read Depth",side=2,line=4.5,cex=1,font=2)\r\n- dev.off() \r\n- }\r\n-\r\n- f_plus = function(chr,end) {\r\n- jpeg( paste0("$dir",as.character(chr),".png"), quality=100)\r\n- plotBedgraph(bgP, chrom=chr,chromstart=0,chromend=end,transparency=.50, color=SushiColors(2)(2)[1])\r\n- labelgenome(chrom=chr,chromstart=0,chromend=end,n=3,scale="$sb", line=0, chromline = 0.5, scaleline = 0.5, scaleadjust =1.05, chromadjust = -0.4)\r\n- axis(side=2,las=2,tcl=.2)\r\n- mtext("Scaled Read Depth",side=2,line=4,cex=1,font=2)\r\n- dev.off()\r\n- }\r\n-\r\n- f_minus = function(chr,end) {\r\n- jpeg( paste0("$dir",as.character(chr),".png"), quality=100)\r\n- plotBedgraph(bgM, chrom=chr,chromstart=0,chromend=end,transparency=.50, flip=TRUE, color=SushiColors(2)(2)[2]) \r\n- labelgenome(chrom=chr,chromstart=0,chromend=end,n=3,scale="$sb", line=0, chromline = 0.5, scaleline = 0.5, scaleadjust =1.05, chromadjust = -0.4)\r\n- axis(side=2,las=2,tcl=.2,at=pretty(par("yaxp")[c(1,2)]),labels=-1*pretty(par("yaxp")[c(1,2)]))\r\n- mtext("Scaled Read Depth",side=2,line=4.5,cex=1,font=2)\r\n- dev.off()\r\n- }\r\n-\r\n- fai_b = fai[fai\\$V1 %in% intersect(bgM\\$V1,bgP\\$V1), ]\r\n- mapply( f_both, fai_b\\$V1, fai_b\\$V2)\r\n-\r\n- fai_p = fai[fai\\$V1 %in% setdiff(bgP\\$V1,bgM\\$V1), ]\r\n- mapply( f_plus, fai_p\\$V1, fai_p\\$V2)\r\n-\r\n- fai_m = fai[fai\\$V1 %in% setdiff(bgM\\$V1,bgP\\$V1), ]\r\n- mapply( f_minus, fai_m\\$V1, fai_m\\$V2) `);\r\n-\r\n- $R->stopR();\r\n-}\r\n-\r\n-sub pie_chart\r\n-{\r\n- my $dir = shift;\r\n- my $in = $dir.\'repart'..b'e)\n+ png(filename=\\"$out_png\\", width = 640, height = 640)\n+ c = ggplot(dat,aes(size,percentage))\n+ c + geom_bar(stat="identity") + scale_x_continuous(breaks=min:max)+theme( axis.text.x = element_text(angle=90, hjust=0.5, size=20), axis.text.y = element_text( size=20 ), axis.title.x = element_text( size=25, face="bold"), axis.title.y = element_text( size=25, face="bold") )\n+ dev.off()`);\n+ $R->stopR();\n+\n+ }\n+}\n+\n+sub bg_to_png\n+{\n+ my ( $fai, $bgP, $bgM, $dir, $sb ) = @_;\n+ my $R = Statistics::R->new();\n+ $R->startR;\n+ $R->send(\n+ qq`library(\'Sushi\')\n+ fai =read.table("$fai")\n+ if ( file.info("$bgP")\\$size !=0 )\n+ {\n+ bgP = read.table("$bgP")\n+ } else { bgP = data.frame(factor(),integer()) }\n+\n+ if ( file.info("$bgM")\\$size !=0 )\n+ {\n+ bgM = read.table("$bgM")\n+ } else { bgM = data.frame(factor(),integer()) }\n+\n+ f_both = function(chr,end) {\n+ jpeg( paste0("$dir",as.character(chr),".png"), quality=100)\n+ par(mfrow=c(2,1),mar=c(1,10,1,3))\n+ plotBedgraph(bgP, chrom=chr,chromstart=0,chromend=end,transparency=.50, color=SushiColors(2)(2)[1])\n+ axis(side=2,las=2,tcl=.2)\n+ mtext("Scaled Read Depth",side=2,line=4,cex=1,font=2)\n+ plotBedgraph(bgM, chrom=chr,chromstart=0,chromend=end,transparency=.50, flip=TRUE, color=SushiColors(2)(2)[2])\n+ labelgenome(chrom=chr,chromstart=0,chromend=end,side=3,n=3,scale="$sb", line=0, chromline = 0.5, scaleline = 0.5, scaleadjust =1.05, chromadjust = -0.4)\n+ axis(side=2,las=2,tcl=.2,at=pretty(par("yaxp")[c(1,2)]),labels=-1*pretty(par("yaxp")[c(1,2)]))\n+ mtext("Scaled Read Depth",side=2,line=4.5,cex=1,font=2)\n+ dev.off()\n+ }\n+\n+ f_plus = function(chr,end) {\n+ jpeg( paste0("$dir",as.character(chr),".png"), quality=100)\n+ plotBedgraph(bgP, chrom=chr,chromstart=0,chromend=end,transparency=.50, color=SushiColors(2)(2)[1])\n+ labelgenome(chrom=chr,chromstart=0,chromend=end,n=3,scale="$sb", line=0, chromline = 0.5, scaleline = 0.5, scaleadjust =1.05, chromadjust = -0.4)\n+ axis(side=2,las=2,tcl=.2)\n+ mtext("Scaled Read Depth",side=2,line=4,cex=1,font=2)\n+ dev.off()\n+ }\n+\n+ f_minus = function(chr,end) {\n+ jpeg( paste0("$dir",as.character(chr),".png"), quality=100)\n+ plotBedgraph(bgM, chrom=chr,chromstart=0,chromend=end,transparency=.50, flip=TRUE, color=SushiColors(2)(2)[2])\n+ labelgenome(chrom=chr,chromstart=0,chromend=end,n=3,scale="$sb", line=0, chromline = 0.5, scaleline = 0.5, scaleadjust =1.05, chromadjust = -0.4)\n+ axis(side=2,las=2,tcl=.2,at=pretty(par("yaxp")[c(1,2)]),labels=-1*pretty(par("yaxp")[c(1,2)]))\n+ mtext("Scaled Read Depth",side=2,line=4.5,cex=1,font=2)\n+ dev.off()\n+ }\n+\n+ fai_b = fai[fai\\$V1 %in% intersect(bgM\\$V1,bgP\\$V1), ]\n+ mapply( f_both, fai_b\\$V1, fai_b\\$V2)\n+\n+ fai_p = fai[fai\\$V1 %in% setdiff(bgP\\$V1,bgM\\$V1), ]\n+ mapply( f_plus, fai_p\\$V1, fai_p\\$V2)\n+\n+ fai_m = fai[fai\\$V1 %in% setdiff(bgM\\$V1,bgP\\$V1), ]\n+ mapply( f_minus, fai_m\\$V1, fai_m\\$V2) `);\n+\n+ $R->stopR();\n+}\n+\n+sub pie_chart\n+{\n+ my $dir = shift;\n+ my $in = $dir.\'repartition.txt\';\n+ my $out = $dir.\'pie_chart.png\';\n+\n+ my $R = Statistics::R->new();\n+ $R->startR;\n+ $R->send(\n+ qq`\n+ library(plotrix)\n+ library(RColorBrewer)\n+ R =read.table("$in",header=T)\n+ values = round(R\\$percentage)\n+ keys = R\\$type\n+ lab = paste(values, "%", sep="")\n+ png("$out")\n+ colors <- brewer.pal(7,"Paired")\n+ pie(values, col=colors, labels=lab, clockwise=TRUE)\n+ legend("bottom", legend = keys, fill=colors, bty="n", ncol = 3)\n+ par(mai = c(0,0,0,0))\n+ layout(c(1,2),heights=c(0.3,1))\n+ plot.new()\n+ legend("bottom", legend = keys, fill=colors, bty="n",ncol = 3)\n+ pie(values, col=colors, labels=lab, clockwise=TRUE)\n+ dev.off()`\n+ );\n+ $R->stopR();\n+}\n+\n+1;\n' |
| b |
| diff -r 9645d995fb3c -r 9185ca0a7b43 bin/align.pm --- a/bin/align.pm Wed Oct 24 07:40:20 2018 -0400 +++ b/bin/align.pm Wed Jan 16 08:18:13 2019 -0500 |
| [ |
| b'@@ -1,552 +1,551 @@\n-package align;\r\n-\r\n-use strict;\r\n-use warnings;\r\n-use File::Basename;\r\n-use String::Random;\r\n-\r\n-use FindBin;\r\n-use lib $FindBin::Bin;\r\n-use Rcall qw ( histogram );\r\n-\r\n-use Exporter;\r\n-our @ISA = qw( Exporter );\r\n-our @EXPORT = qw( &rpms_rpkm_te &BWA_call &to_build &get_unique &sam_sorted_bam &get_hash_alignment &sam_to_bam_bg &sam_count &sam_count_mis &rpms_rpkm &get_fastq_seq &extract_sam );\r\n-\r\n-sub to_build\r\n-{\r\n- my ( $toBuildTabP, $log, $newdir ) = @_;\r\n-\r\n- foreach my $pairs ( @{ $toBuildTabP } ) \r\n- {\r\n- if ( $pairs->[0] == 1 ) \r\n- { \r\n- my $sym = $newdir.basename(${$pairs->[1]}).\'_symlink.fa\';\r\n- symlink( ${$pairs->[1]}, $sym );\r\n- ${$pairs->[1]} = $sym;\r\n- build_index ( ${$pairs->[1]}, $log );\r\n- } \r\n- }\r\n-}\r\n-\r\n-sub build_index\r\n-{\r\n-\tmy $to_index = shift;\r\n-\tmy $log = shift;\r\n-\tmy $index_log = $to_index.\'_index.err\';\r\n-\t`bwa index \'$to_index\' 2> \'$index_log\'`;\r\n-\tprint $log "Creating index for $to_index\\n";\r\n-}\r\n-\r\n-sub get_unique\r\n-{\r\n-\tmy ( $sam, $s_uni, $out_prefix, $col_prefix, $details, $report ) = @_;\r\n-\r\n-\tmy $fout = $col_prefix.\'_all_mappers.fastq\'; \r\n-\tmy $funi = $col_prefix.\'_unique_mappers.fastq\';\r\n-\tmy $frej = $col_prefix.\'_unmapped.fastq\';\r\n-\t\r\n- my $repartition = $out_prefix.\'distribution.txt\';\r\n-\tmy $png_rep = $out_prefix.\'distribution.png\';\r\n-\tmy ( %duplicates, %genome_hits) ;\r\n-\r\n-\t#alignement to the first reference\r\n-\tmy @return = sam_parse( $sam, $fout, $funi, $frej, $s_uni, \\%duplicates, \\%genome_hits, $report );\r\n-\tmy $ref_fai = $return[4];\r\n-\tmy $mappers = $return[5];\r\n-\tmy $mappers_uni = $return[6];\r\n-\tmy $size_mappedHashR = $return[7];\r\n-\r\n-\tif ( $details == 1 )\r\n-\t{\r\n-\t\t#print number of duplicates and hits number\r\n-\t\tmy ($pourcentage, $total) =(0,0);\r\n-\r\n-\t\t$total += $_ foreach values %{$size_mappedHashR};\r\n-\t\topen (my $rep, \'>\'.$repartition) || die "cannot create $repartition $!\\n";\r\n-\t\tprint $rep "size\\tnumber\\tpercentage\\n";\r\n-\t\tforeach my $k (sort{$a cmp $b} keys (%{$size_mappedHashR}))\r\n-\t\t{\r\n-\t\t\t$pourcentage = 0;\r\n-\t\t\t$pourcentage = $size_mappedHashR->{$k} / $total * 100 unless $total ==0;\r\n-\r\n-\t\t\tprint $rep "$k\\t$size_mappedHashR->{$k}\\t";\r\n-\t\t\tprintf $rep "%.2f\\n",$pourcentage;\r\n-\t\t}\r\n-\r\n-\t\thistogram($size_mappedHashR, $png_rep, $total);\r\n-\r\n-\r\n-\t\tmy $dup = $out_prefix.\'dup_mapnum.txt\';\r\n-\t\tmy $dup_u = $out_prefix .\'dup_unique.txt\';\r\n-\t\tmy $dup_r = $out_prefix .\'dup_nonmapp.txt\';\r\n-\t\topen(my $tab,">".$dup) || die "cannot open output txt file\\n";\r\n-\t\topen(my $tab_r,">".$dup_r) || die "cannot open output txt file\\n";\r\n-\t\topen(my $tab_u,">".$dup_u) || die "cannot open output txt file\\n";\r\n-\t\tprint $tab "sequence\\tcount\\tmapnum\\n";\r\n-\t\tprint $tab_u "sequence\\tcount\\n";\r\n-\t\tprint $tab_r "sequence\\tcount\\n";\r\n-\t\tforeach my $k (sort {$duplicates{$b} <=> $duplicates{$a}}keys %duplicates)\r\n-\t\t{\r\n-\t\t\t$duplicates{$k} = 0 unless exists($duplicates{$k});\r\n-\t\t\t$genome_hits{$k} = 0 unless exists($genome_hits{$k});\r\n-\t\t\tif ($genome_hits{$k} != 0) { print $tab $k."\\t".$duplicates{$k}."\\t".$genome_hits{$k}."\\n"; }\r\n-\t\t\telse {print $tab_r $k."\\t".$duplicates{$k}."\\n";}\r\n-\t\t\tif ($genome_hits{$k} == 1) { print $tab_u $k."\\t".$duplicates{$k}."\\n"; }\r\n-\t\t}\r\n-\tclose $dup; close $dup_r; close $dup_u;\r\n-\t}\r\n-\treturn ( $ref_fai, $mappers, $mappers_uni );\r\n-}\r\n-\r\n-sub sam_parse\r\n-{\r\n-\tmy ( $sam, $fastq_accepted, $fastq_accepted_unique, $fastq_rejected, $sam_unique, $duplicate_hashR, $best_hit_number_hashR, $report ) = @_ ;\r\n-\tmy ($reads, $mappers, $mappersUnique, @garbage, %size_num, %size_num_spe, %number, %numberSens, %numberReverse, %unique_number, %numberNM, %numberM, %size);\r\n-\t$mappers = $mappersUnique = $reads = 0;\r\n-\r\n-\topen my $fic, \'<\', $sam || die "cannot open $sam $!\\n";\r\n-\topen my $accepted, \'>\', $fastq_accepted || die "cannot create $fastq_accepted $! \\n";\r\n-\topen my $unique, \'>\', $fastq_accepted_unique || die "cannot create $fastq_accepted_unique $! \\n";\r\n-\topen my $rejected, \'>\', $fastq_rejected || die "cannot create $fastq_re'..b'> \'$samse_err\' > \'$sam\'\\n";\n+ `bwa aln -t $number_of_cpus -n $mismatches \'$index\' \'$fastq\' 2> \'$aln_err\' | bwa samse $index /dev/stdin \'$fastq\' 2> \'$samse_err\' > \'$sam\' `;\n+}\n+\n+sub rpms_rpkm\n+{\n+ my ( $counthashR, $sizehashR, $mapped, $out_file, $piRNA_number, $miRNA_number, $bonafide_number ) =@_;\n+ open(my $out, ">".$out_file) || die "cannot open normalized file $! \\n";\n+ print $out "ID\\treads counts\\tRPKM";\n+ print $out "\\tper million of piRNAs" if ($piRNA_number != 0);\n+ print $out "\\tper million of miRNAs" if ($miRNA_number != 0);\n+ print $out "\\tper million of bonafide reads" if ($bonafide_number != 0);\n+ print $out "\\n";\n+ foreach my $k ( sort keys %{$counthashR} )\n+ {\n+ my ($rpkm, $pirna, $mirna, $bonafide) = (0,0,0,0);\n+ \n+ $rpkm = ( $counthashR->{$k} * 1000000000) / ( $sizehashR->{$k} * $mapped) if ( $sizehashR->{$k} * $mapped) != 0 ;\n+ print $out $k."\\t".$counthashR->{$k}."\\t"; printf $out "%.2f",$rpkm;\n+ \n+ if ($piRNA_number != 0 )\n+ {\n+ $pirna = ( $counthashR->{$k} * 1000000) / $piRNA_number;\n+ printf $out "\\t%.2f",$pirna;\n+ }\n+ if ($miRNA_number != 0 )\n+ {\n+ $mirna = ( $counthashR->{$k} * 1000000) / $miRNA_number;\n+ printf $out "\\t%.2f",$mirna;\n+ }\n+ if ($bonafide_number != 0 )\n+ {\n+ $bonafide = ( $counthashR->{$k} * 1000000) / $bonafide_number;\n+ printf $out "\\t%.2f",$bonafide;\n+ }\n+ print $out "\\n";\n+ }\n+ close $out;\n+}\n+\n+sub extract_sam\n+{\n+ my ( $hashRef, $sam_in, $sam_out, $sam_uni_out, $fastq_out, $fastq_uni_out ) = @_;\n+ \n+ open my $s_in, \'<\', $sam_in || die "cannot open $sam_in file $!\\n";\n+\n+ open my $f_out, \'>\', $fastq_out || die "cannot create $fastq_out $!\\n";\n+ open my $f_uni_out, \'>\', $fastq_uni_out || die "cannot create $fastq_uni_out $!\\n";\n+ \n+ open my $s_out, \'>\', $sam_out || die "cannot create $sam_out file $!\\n" if defined ($hashRef);\n+ open my $s_uni_out, \'>\', $sam_uni_out || die "cannot create $sam_uni_out file $!\\n";\n+\n+ my $sequence = \'\';\n+ while(<$s_in>)\n+ {\n+ if ($_ =~ /^\\@[A-Za-z][A-Za-z](\\t[A-Za-z][A-Za-z0-9]:[ -~]+)+$/ || $_ =~ /^\\@CO\\t.*/ )\n+ {\n+ print $s_out $_ if defined ($hashRef);\n+ print $s_uni_out $_;\n+ next;\n+ }\n+ my @line = split (/\\t/,$_);\n+ $sequence = $line[0];\n+ if ( (! defined ($hashRef) )|| ( exists $hashRef->{$sequence} && $hashRef->{$sequence} == 1 ) )\n+ {\n+ my $arn = $line[9];\n+ if ($line[1] & 16)\n+ {\n+ $arn =reverse($arn);\n+ $arn =~ tr/atgcuATGCU/tacgaTACGA/;\n+ }\n+\n+ if ( ( $line[1] == 16 || $line[1] == 0 ) )\n+ {\n+ print $f_out "\\@".$line[0]."\\n".$arn."\\n+\\n".$line[10]."\\n" ;\n+ print $s_out $_ if defined ($hashRef);\n+ if ( $line[11] eq "XT:A:U" )\n+ {\n+ print $f_uni_out "\\@".$line[0]."\\n".$arn."\\n+\\n".$line[10]."\\n" ;\n+ print $s_uni_out $_ ;\n+ }\n+ }\n+ }\n+ }\n+ close $s_in; close $s_out if defined ($hashRef);\n+ close $s_uni_out; close $f_out; close $f_uni_out;\n+}\n+\n+sub get_fastq_seq\n+{\n+ my $fastq = shift;\n+ my %hash; my $cmp = 0;\n+\n+ open my $fic, \'<\', $fastq || die "cannot open input file $! \\n";\n+ while(<$fic>)\n+ {\n+ chomp $_;\n+ $cmp++;\n+ if ($cmp % 4 == 1)\n+ {\n+ die "file do not contain a @ at line $cmp\\n" unless ($_ =~ /^\\@/ );\n+ if ($_ =~ /^\\@(.*)\\s.*/) { $hash{$1} = 1;}\n+ elsif ($_ =~ /^\\@(.*)/) { $hash{$1} = 1;}\n+ }\n+ elsif ($cmp % 4 == 3 )\n+ {\n+ die "file do not contain a + at line $cmp\\n" unless $_ =~ /^\\+/;\n+ }\n+ }\n+ close $fic;\n+ return \\%hash;\n+}\n+\n+1;\n' |
| b |
| diff -r 9645d995fb3c -r 9185ca0a7b43 bin/css/bootstrap-responsive.css --- a/bin/css/bootstrap-responsive.css Wed Oct 24 07:40:20 2018 -0400 +++ b/bin/css/bootstrap-responsive.css Wed Jan 16 08:18:13 2019 -0500 |
| [ |
| b'@@ -1,1109 +1,1109 @@\n-/*!\r\n- * Bootstrap Responsive v2.3.2\r\n- *\r\n- * Copyright 2012 Twitter, Inc\r\n- * Licensed under the Apache License v2.0\r\n- * http://www.apache.org/licenses/LICENSE-2.0\r\n- *\r\n- * Designed and built with all the love in the world @twitter by @mdo and @fat.\r\n- */\r\n-\r\n-.clearfix {\r\n- *zoom: 1;\r\n-}\r\n-\r\n-.clearfix:before,\r\n-.clearfix:after {\r\n- display: table;\r\n- line-height: 0;\r\n- content: "";\r\n-}\r\n-\r\n-.clearfix:after {\r\n- clear: both;\r\n-}\r\n-\r\n-.hide-text {\r\n- font: 0/0 a;\r\n- color: transparent;\r\n- text-shadow: none;\r\n- background-color: transparent;\r\n- border: 0;\r\n-}\r\n-\r\n-.input-block-level {\r\n- display: block;\r\n- width: 100%;\r\n- min-height: 30px;\r\n- -webkit-box-sizing: border-box;\r\n- -moz-box-sizing: border-box;\r\n- box-sizing: border-box;\r\n-}\r\n-\r\n-@-ms-viewport {\r\n- width: device-width;\r\n-}\r\n-\r\n-.hidden {\r\n- display: none;\r\n- visibility: hidden;\r\n-}\r\n-\r\n-.visible-phone {\r\n- display: none !important;\r\n-}\r\n-\r\n-.visible-tablet {\r\n- display: none !important;\r\n-}\r\n-\r\n-.hidden-desktop {\r\n- display: none !important;\r\n-}\r\n-\r\n-.visible-desktop {\r\n- display: inherit !important;\r\n-}\r\n-\r\n-@media (min-width: 768px) and (max-width: 979px) {\r\n- .hidden-desktop {\r\n- display: inherit !important;\r\n- }\r\n- .visible-desktop {\r\n- display: none !important ;\r\n- }\r\n- .visible-tablet {\r\n- display: inherit !important;\r\n- }\r\n- .hidden-tablet {\r\n- display: none !important;\r\n- }\r\n-}\r\n-\r\n-@media (max-width: 767px) {\r\n- .hidden-desktop {\r\n- display: inherit !important;\r\n- }\r\n- .visible-desktop {\r\n- display: none !important;\r\n- }\r\n- .visible-phone {\r\n- display: inherit !important;\r\n- }\r\n- .hidden-phone {\r\n- display: none !important;\r\n- }\r\n-}\r\n-\r\n-.visible-print {\r\n- display: none !important;\r\n-}\r\n-\r\n-@media print {\r\n- .visible-print {\r\n- display: inherit !important;\r\n- }\r\n- .hidden-print {\r\n- display: none !important;\r\n- }\r\n-}\r\n-\r\n-@media (min-width: 1200px) {\r\n- .row {\r\n- margin-left: -30px;\r\n- *zoom: 1;\r\n- }\r\n- .row:before,\r\n- .row:after {\r\n- display: table;\r\n- line-height: 0;\r\n- content: "";\r\n- }\r\n- .row:after {\r\n- clear: both;\r\n- }\r\n- [class*="span"] {\r\n- float: left;\r\n- min-height: 1px;\r\n- margin-left: 30px;\r\n- }\r\n- .container,\r\n- .navbar-static-top .container,\r\n- .navbar-fixed-top .container,\r\n- .navbar-fixed-bottom .container {\r\n- width: 1170px;\r\n- }\r\n- .span12 {\r\n- width: 1170px;\r\n- }\r\n- .span11 {\r\n- width: 1070px;\r\n- }\r\n- .span10 {\r\n- width: 970px;\r\n- }\r\n- .span9 {\r\n- width: 870px;\r\n- }\r\n- .span8 {\r\n- width: 770px;\r\n- }\r\n- .span7 {\r\n- width: 670px;\r\n- }\r\n- .span6 {\r\n- width: 570px;\r\n- }\r\n- .span5 {\r\n- width: 470px;\r\n- }\r\n- .span4 {\r\n- width: 370px;\r\n- }\r\n- .span3 {\r\n- width: 270px;\r\n- }\r\n- .span2 {\r\n- width: 170px;\r\n- }\r\n- .span1 {\r\n- width: 70px;\r\n- }\r\n- .offset12 {\r\n- margin-left: 1230px;\r\n- }\r\n- .offset11 {\r\n- margin-left: 1130px;\r\n- }\r\n- .offset10 {\r\n- margin-left: 1030px;\r\n- }\r\n- .offset9 {\r\n- margin-left: 930px;\r\n- }\r\n- .offset8 {\r\n- margin-left: 830px;\r\n- }\r\n- .offset7 {\r\n- margin-left: 730px;\r\n- }\r\n- .offset6 {\r\n- margin-left: 630px;\r\n- }\r\n- .offset5 {\r\n- margin-left: 530px;\r\n- }\r\n- .offset4 {\r\n- margin-left: 430px;\r\n- }\r\n- .offset3 {\r\n- margin-left: 330px;\r\n- }\r\n- .offset2 {\r\n- margin-left: 230px;\r\n- }\r\n- .offset1 {\r\n- margin-left: 130px;\r\n- }\r\n- .row-fluid {\r\n- width: 100%;\r\n- *zoom: 1;\r\n- }\r\n- .row-fluid:before,\r\n- .row-fluid:after {\r\n- display: table;\r\n- line-height: 0;\r\n- content: "";\r\n- }\r\n- .row-fluid:after {\r\n- clear: both;\r\n- }\r\n- .row-fluid [class*="span"] {\r\n- display: block;\r\n- float: left;\r\n- width: 100%;\r\n- min-height: 30px;\r\n- margin-left: 2.564102564102564%;\r\n- *margin-left: 2.5109110747408616%;\r\n- -webkit-box-sizing: border-box;\r\n- -moz-box-sizing: border-box;\r\n- box-sizing: border-box;\r\n- }\r\n- .r'..b'tic;\n+ }\n+}\n+\n+@media (max-width: 979px) {\n+ body {\n+ padding-top: 0;\n+ }\n+ .navbar-fixed-top,\n+ .navbar-fixed-bottom {\n+ position: static;\n+ }\n+ .navbar-fixed-top {\n+ margin-bottom: 20px;\n+ }\n+ .navbar-fixed-bottom {\n+ margin-top: 20px;\n+ }\n+ .navbar-fixed-top .navbar-inner,\n+ .navbar-fixed-bottom .navbar-inner {\n+ padding: 5px;\n+ }\n+ .navbar .container {\n+ width: auto;\n+ padding: 0;\n+ }\n+ .navbar .brand {\n+ padding-right: 10px;\n+ padding-left: 10px;\n+ margin: 0 0 0 -5px;\n+ }\n+ .nav-collapse {\n+ clear: both;\n+ }\n+ .nav-collapse .nav {\n+ float: none;\n+ margin: 0 0 10px;\n+ }\n+ .nav-collapse .nav > li {\n+ float: none;\n+ }\n+ .nav-collapse .nav > li > a {\n+ margin-bottom: 2px;\n+ }\n+ .nav-collapse .nav > .divider-vertical {\n+ display: none;\n+ }\n+ .nav-collapse .nav .nav-header {\n+ color: #777777;\n+ text-shadow: none;\n+ }\n+ .nav-collapse .nav > li > a,\n+ .nav-collapse .dropdown-menu a {\n+ padding: 9px 15px;\n+ font-weight: bold;\n+ color: #777777;\n+ -webkit-border-radius: 3px;\n+ -moz-border-radius: 3px;\n+ border-radius: 3px;\n+ }\n+ .nav-collapse .btn {\n+ padding: 4px 10px 4px;\n+ font-weight: normal;\n+ -webkit-border-radius: 4px;\n+ -moz-border-radius: 4px;\n+ border-radius: 4px;\n+ }\n+ .nav-collapse .dropdown-menu li + li a {\n+ margin-bottom: 2px;\n+ }\n+ .nav-collapse .nav > li > a:hover,\n+ .nav-collapse .nav > li > a:focus,\n+ .nav-collapse .dropdown-menu a:hover,\n+ .nav-collapse .dropdown-menu a:focus {\n+ background-color: #f2f2f2;\n+ }\n+ .navbar-inverse .nav-collapse .nav > li > a,\n+ .navbar-inverse .nav-collapse .dropdown-menu a {\n+ color: #999999;\n+ }\n+ .navbar-inverse .nav-collapse .nav > li > a:hover,\n+ .navbar-inverse .nav-collapse .nav > li > a:focus,\n+ .navbar-inverse .nav-collapse .dropdown-menu a:hover,\n+ .navbar-inverse .nav-collapse .dropdown-menu a:focus {\n+ background-color: #111111;\n+ }\n+ .nav-collapse.in .btn-group {\n+ padding: 0;\n+ margin-top: 5px;\n+ }\n+ .nav-collapse .dropdown-menu {\n+ position: static;\n+ top: auto;\n+ left: auto;\n+ display: none;\n+ float: none;\n+ max-width: none;\n+ padding: 0;\n+ margin: 0 15px;\n+ background-color: transparent;\n+ border: none;\n+ -webkit-border-radius: 0;\n+ -moz-border-radius: 0;\n+ border-radius: 0;\n+ -webkit-box-shadow: none;\n+ -moz-box-shadow: none;\n+ box-shadow: none;\n+ }\n+ .nav-collapse .open > .dropdown-menu {\n+ display: block;\n+ }\n+ .nav-collapse .dropdown-menu:before,\n+ .nav-collapse .dropdown-menu:after {\n+ display: none;\n+ }\n+ .nav-collapse .dropdown-menu .divider {\n+ display: none;\n+ }\n+ .nav-collapse .nav > li > .dropdown-menu:before,\n+ .nav-collapse .nav > li > .dropdown-menu:after {\n+ display: none;\n+ }\n+ .nav-collapse .navbar-form,\n+ .nav-collapse .navbar-search {\n+ float: none;\n+ padding: 10px 15px;\n+ margin: 10px 0;\n+ border-top: 1px solid #f2f2f2;\n+ border-bottom: 1px solid #f2f2f2;\n+ -webkit-box-shadow: inset 0 1px 0 rgba(255, 255, 255, 0.1), 0 1px 0 rgba(255, 255, 255, 0.1);\n+ -moz-box-shadow: inset 0 1px 0 rgba(255, 255, 255, 0.1), 0 1px 0 rgba(255, 255, 255, 0.1);\n+ box-shadow: inset 0 1px 0 rgba(255, 255, 255, 0.1), 0 1px 0 rgba(255, 255, 255, 0.1);\n+ }\n+ .navbar-inverse .nav-collapse .navbar-form,\n+ .navbar-inverse .nav-collapse .navbar-search {\n+ border-top-color: #111111;\n+ border-bottom-color: #111111;\n+ }\n+ .navbar .nav-collapse .nav.pull-right {\n+ float: none;\n+ margin-left: 0;\n+ }\n+ .nav-collapse,\n+ .nav-collapse.collapse {\n+ height: 0;\n+ overflow: hidden;\n+ }\n+ .navbar .btn-navbar {\n+ display: block;\n+ }\n+ .navbar-static .navbar-inner {\n+ padding-right: 10px;\n+ padding-left: 10px;\n+ }\n+}\n+\n+@media (min-width: 980px) {\n+ .nav-collapse.collapse {\n+ height: auto !important;\n+ overflow: visible !important;\n+ }\n+}\n' |
| b |
| diff -r 9645d995fb3c -r 9185ca0a7b43 bin/css/bootstrap-table.css --- a/bin/css/bootstrap-table.css Wed Oct 24 07:40:20 2018 -0400 +++ b/bin/css/bootstrap-table.css Wed Jan 16 08:18:13 2019 -0500 |
| [ |
| b"@@ -1,313 +1,313 @@\n-/**\r\n- * @author zhixin wen <wenzhixin2010@gmail.com>\r\n- * version: 1.11.1\r\n- * https://github.com/wenzhixin/bootstrap-table/\r\n- */\r\n-\r\n-.bootstrap-table .table {\r\n- margin-bottom: 0 !important;\r\n- border-bottom: 1px solid #dddddd;\r\n- border-collapse: collapse !important;\r\n- border-radius: 1px;\r\n-}\r\n-\r\n-.bootstrap-table .table:not(.table-condensed),\r\n-.bootstrap-table .table:not(.table-condensed) > tbody > tr > th,\r\n-.bootstrap-table .table:not(.table-condensed) > tfoot > tr > th,\r\n-.bootstrap-table .table:not(.table-condensed) > thead > tr > td,\r\n-.bootstrap-table .table:not(.table-condensed) > tbody > tr > td,\r\n-.bootstrap-table .table:not(.table-condensed) > tfoot > tr > td {\r\n- padding: 8px;\r\n-}\r\n-\r\n-.bootstrap-table .table.table-no-bordered > thead > tr > th,\r\n-.bootstrap-table .table.table-no-bordered > tbody > tr > td {\r\n- border-right: 2px solid transparent;\r\n-}\r\n-\r\n-.bootstrap-table .table.table-no-bordered > tbody > tr > td:last-child {\r\n- border-right: none;\r\n-}\r\n-\r\n-.fixed-table-container {\r\n- position: relative;\r\n- clear: both;\r\n- border: 1px solid #dddddd;\r\n- border-radius: 4px;\r\n- -webkit-border-radius: 4px;\r\n- -moz-border-radius: 4px;\r\n-}\r\n-\r\n-.fixed-table-container.table-no-bordered {\r\n- border: 1px solid transparent;\r\n-}\r\n-\r\n-.fixed-table-footer,\r\n-.fixed-table-header {\r\n- overflow: hidden;\r\n-}\r\n-\r\n-.fixed-table-footer {\r\n- border-top: 1px solid #dddddd;\r\n-}\r\n-\r\n-.fixed-table-body {\r\n- overflow-x: auto;\r\n- overflow-y: auto;\r\n- height: 100%;\r\n-}\r\n-\r\n-.fixed-table-container table {\r\n- width: 100%;\r\n-}\r\n-\r\n-.fixed-table-container thead th {\r\n- height: 0;\r\n- padding: 0;\r\n- margin: 0;\r\n- border-left: 1px solid #dddddd;\r\n-}\r\n-\r\n-.fixed-table-container thead th:focus {\r\n- outline: 0 solid transparent;\r\n-}\r\n-\r\n-.fixed-table-container thead th:first-child {\r\n- border-left: none;\r\n- border-top-left-radius: 4px;\r\n- -webkit-border-top-left-radius: 4px;\r\n- -moz-border-radius-topleft: 4px;\r\n-}\r\n-\r\n-.fixed-table-container thead th .th-inner,\r\n-.fixed-table-container tbody td .th-inner {\r\n- padding: 8px;\r\n- line-height: 24px;\r\n- vertical-align: top;\r\n- overflow: hidden;\r\n- text-overflow: ellipsis;\r\n- white-space: nowrap;\r\n-}\r\n-\r\n-.fixed-table-container thead th .sortable {\r\n- cursor: pointer;\r\n- background-position: right;\r\n- background-repeat: no-repeat;\r\n- padding-right: 30px;\r\n-}\r\n-\r\n-.fixed-table-container thead th .both {\r\n- background-image: url('data:image/png;base64,iVBORw0KGgoAAAANSUhEUgAAABMAAAATCAQAAADYWf5HAAAAkElEQVQoz7X QMQ5AQBCF4dWQSJxC5wwax1Cq1e7BAdxD5SL+Tq/QCM1oNiJidwox0355mXnG/DrEtIQ6azioNZQxI0ykPhTQIwhCR+BmBYtlK7kLJYwWCcJA9M4qdrZrd8pPjZWPtOqdRQy320YSV17OatFC4euts6z39GYMKRPCTKY9UnPQ6P+GtMRfGtPnBCiqhAeJPmkqAAAAAElFTkSuQmCC');\r\n-}\r\n-\r\n-.fixed-table-container thead th .asc {\r\n- background-image: url('data:image/png;base64,iVBORw0KGgoAAAANSUhEUgAAABMAAAATCAYAAAByUDbMAAAAZ0lEQVQ4y2NgGLKgquEuFxBPAGI2ahhWCsS/gDibUoO0gPgxEP8H4ttArEyuQYxAPBdqEAxPBImTY5gjEL9DM+wTENuQahAvEO9DMwiGdwAxOymGJQLxTyD+jgWDxCMZRsEoGAVoAADeemwtPcZI2wAAAABJRU5ErkJggg==');\r\n-}\r\n-\r\n-.fixed-table-container thead th .desc {\r\n- background-image: url('data:image/png;base64,iVBORw0KGgoAAAANSUhEUgAAABMAAAATCAYAAAByUDbMAAAAZUlEQVQ4y2NgGAWjYBSggaqGu5FA/BOIv2PBIPFEUgxjB+IdQPwfC94HxLykus4GiD+hGfQOiB3J8SojEE9EM2wuSJzcsFMG4ttQgx4DsRalkZENxL+AuJQaMcsGxBOAmGvopk8AVz1sLZgg0bsAAAAASUVORK5CYII= ');\r\n-}\r\n-\r\n-.fixed-table-container th.detail {\r\n- width: 30px;\r\n-}\r\n-\r\n-.fixed-table-container tbody td {\r\n- border-left: 1px solid #dddddd;\r\n-}\r\n-\r\n-.fixed-table-container tbody tr:first-child td {\r\n- border-top: none;\r\n-}\r\n-\r\n-.fixed-table-container tbody td:first-child {\r\n- border-left: none;\r\n-}\r\n-\r\n-/* the same color with .active */\r\n-.fixed-table-container tbody .selected td {\r\n- background-color: #f5f5f5;\r\n-}\r\n-\r\n-.fixed-table-container .bs-checkbox {\r\n- text-align: center;\r\n-}\r\n-\r\n-.fixed-table-contain"..b'solid #dddddd;\n+}\n+\n+.fixed-table-container tbody tr:first-child td {\n+ border-top: none;\n+}\n+\n+.fixed-table-container tbody td:first-child {\n+ border-left: none;\n+}\n+\n+/* the same color with .active */\n+.fixed-table-container tbody .selected td {\n+ background-color: #f5f5f5;\n+}\n+\n+.fixed-table-container .bs-checkbox {\n+ text-align: center;\n+}\n+\n+.fixed-table-container .bs-checkbox .th-inner {\n+ padding: 8px 0;\n+}\n+\n+.fixed-table-container input[type="radio"],\n+.fixed-table-container input[type="checkbox"] {\n+ margin: 0 auto !important;\n+}\n+\n+.fixed-table-container .no-records-found {\n+ text-align: center;\n+}\n+\n+.fixed-table-pagination div.pagination,\n+.fixed-table-pagination .pagination-detail {\n+ margin-top: 10px;\n+ margin-bottom: 10px;\n+}\n+\n+.fixed-table-pagination div.pagination .pagination {\n+ margin: 0;\n+}\n+\n+.fixed-table-pagination .pagination a {\n+ padding: 6px 12px;\n+ line-height: 1.428571429;\n+}\n+\n+.fixed-table-pagination .pagination-info {\n+ line-height: 34px;\n+ margin-right: 5px;\n+}\n+\n+.fixed-table-pagination .btn-group {\n+ position: relative;\n+ display: inline-block;\n+ vertical-align: middle;\n+}\n+\n+.fixed-table-pagination .dropup .dropdown-menu {\n+ margin-bottom: 0;\n+}\n+\n+.fixed-table-pagination .page-list {\n+ display: inline-block;\n+}\n+\n+.fixed-table-toolbar .columns-left {\n+ margin-right: 5px;\n+}\n+\n+.fixed-table-toolbar .columns-right {\n+ margin-left: 5px;\n+}\n+\n+.fixed-table-toolbar .columns label {\n+ display: block;\n+ padding: 3px 20px;\n+ clear: both;\n+ font-weight: normal;\n+ line-height: 1.428571429;\n+}\n+\n+.fixed-table-toolbar .bs-bars,\n+.fixed-table-toolbar .search,\n+.fixed-table-toolbar .columns {\n+ position: relative;\n+ margin-top: 10px;\n+ margin-bottom: 10px;\n+ line-height: 34px;\n+}\n+\n+.fixed-table-pagination li.disabled a {\n+ pointer-events: none;\n+ cursor: default;\n+}\n+\n+.fixed-table-loading {\n+ display: none;\n+ position: absolute;\n+ top: 42px;\n+ right: 0;\n+ bottom: 0;\n+ left: 0;\n+ z-index: 99;\n+ background-color: #fff;\n+ text-align: center;\n+}\n+\n+.fixed-table-body .card-view .title {\n+ font-weight: bold;\n+ display: inline-block;\n+ min-width: 30%;\n+ text-align: left !important;\n+}\n+\n+/* support bootstrap 2 */\n+.fixed-table-body thead th .th-inner {\n+ box-sizing: border-box;\n+}\n+\n+.table th, .table td {\n+ vertical-align: middle;\n+ box-sizing: border-box;\n+}\n+\n+.fixed-table-toolbar .dropdown-menu {\n+ text-align: left;\n+ max-height: 300px;\n+ overflow: auto;\n+}\n+\n+.fixed-table-toolbar .btn-group > .btn-group {\n+ display: inline-block;\n+ margin-left: -1px !important;\n+}\n+\n+.fixed-table-toolbar .btn-group > .btn-group > .btn {\n+ border-radius: 0;\n+}\n+\n+.fixed-table-toolbar .btn-group > .btn-group:first-child > .btn {\n+ border-top-left-radius: 4px;\n+ border-bottom-left-radius: 4px;\n+}\n+\n+.fixed-table-toolbar .btn-group > .btn-group:last-child > .btn {\n+ border-top-right-radius: 4px;\n+ border-bottom-right-radius: 4px;\n+}\n+\n+.bootstrap-table .table > thead > tr > th {\n+ vertical-align: bottom;\n+ border-bottom: 1px solid #ddd;\n+}\n+\n+/* support bootstrap 3 */\n+.bootstrap-table .table thead > tr > th {\n+ padding: 0;\n+ margin: 0;\n+}\n+\n+.bootstrap-table .fixed-table-footer tbody > tr > td {\n+ padding: 0 !important;\n+}\n+\n+.bootstrap-table .fixed-table-footer .table {\n+ border-bottom: none;\n+ border-radius: 0;\n+ padding: 0 !important;\n+}\n+\n+.bootstrap-table .pull-right .dropdown-menu {\n+ right: 0;\n+ left: auto;\n+}\n+\n+/* calculate scrollbar width */\n+p.fixed-table-scroll-inner {\n+ width: 100%;\n+ height: 200px;\n+}\n+\n+div.fixed-table-scroll-outer {\n+ top: 0;\n+ left: 0;\n+ visibility: hidden;\n+ width: 200px;\n+ height: 150px;\n+ overflow: hidden;\n+}\n+\n+/* for get correct heights */\n+.fixed-table-toolbar:after, .fixed-table-pagination:after {\n+ content: "";\n+ display: block;\n+ clear: both;\n+}\n' |
| b |
| diff -r 9645d995fb3c -r 9185ca0a7b43 bin/css/bootstrap.css --- a/bin/css/bootstrap.css Wed Oct 24 07:40:20 2018 -0400 +++ b/bin/css/bootstrap.css Wed Jan 16 08:18:13 2019 -0500 |
| [ |
| b'@@ -1,6167 +1,6167 @@\n-/*!\r\n- * Bootstrap v2.3.2\r\n- *\r\n- * Copyright 2012 Twitter, Inc\r\n- * Licensed under the Apache License v2.0\r\n- * http://www.apache.org/licenses/LICENSE-2.0\r\n- *\r\n- * Designed and built with all the love in the world @twitter by @mdo and @fat.\r\n- */\r\n-\r\n-.clearfix {\r\n- *zoom: 1;\r\n-}\r\n-\r\n-.clearfix:before,\r\n-.clearfix:after {\r\n- display: table;\r\n- line-height: 0;\r\n- content: "";\r\n-}\r\n-\r\n-.clearfix:after {\r\n- clear: both;\r\n-}\r\n-\r\n-.hide-text {\r\n- font: 0/0 a;\r\n- color: transparent;\r\n- text-shadow: none;\r\n- background-color: transparent;\r\n- border: 0;\r\n-}\r\n-\r\n-.input-block-level {\r\n- display: block;\r\n- width: 100%;\r\n- min-height: 30px;\r\n- -webkit-box-sizing: border-box;\r\n- -moz-box-sizing: border-box;\r\n- box-sizing: border-box;\r\n-}\r\n-\r\n-article,\r\n-aside,\r\n-details,\r\n-figcaption,\r\n-figure,\r\n-footer,\r\n-header,\r\n-hgroup,\r\n-nav,\r\n-section {\r\n- display: block;\r\n-}\r\n-\r\n-audio,\r\n-canvas,\r\n-video {\r\n- display: inline-block;\r\n- *display: inline;\r\n- *zoom: 1;\r\n-}\r\n-\r\n-audio:not([controls]) {\r\n- display: none;\r\n-}\r\n-\r\n-html {\r\n- font-size: 100%;\r\n- -webkit-text-size-adjust: 100%;\r\n- -ms-text-size-adjust: 100%;\r\n-}\r\n-\r\n-a:focus {\r\n- outline: thin dotted #333;\r\n- outline: 5px auto -webkit-focus-ring-color;\r\n- outline-offset: -2px;\r\n-}\r\n-\r\n-a:hover,\r\n-a:active {\r\n- outline: 0;\r\n-}\r\n-\r\n-sub,\r\n-sup {\r\n- position: relative;\r\n- font-size: 75%;\r\n- line-height: 0;\r\n- vertical-align: baseline;\r\n-}\r\n-\r\n-sup {\r\n- top: -0.5em;\r\n-}\r\n-\r\n-sub {\r\n- bottom: -0.25em;\r\n-}\r\n-\r\n-img {\r\n- width: auto\\9;\r\n- height: auto;\r\n- max-width: 100%;\r\n- vertical-align: middle;\r\n- border: 0;\r\n- -ms-interpolation-mode: bicubic;\r\n-}\r\n-\r\n-#map_canvas img,\r\n-.google-maps img {\r\n- max-width: none;\r\n-}\r\n-\r\n-button,\r\n-input,\r\n-select,\r\n-textarea {\r\n- margin: 0;\r\n- font-size: 100%;\r\n- vertical-align: middle;\r\n-}\r\n-\r\n-button,\r\n-input {\r\n- *overflow: visible;\r\n- line-height: normal;\r\n-}\r\n-\r\n-button::-moz-focus-inner,\r\n-input::-moz-focus-inner {\r\n- padding: 0;\r\n- border: 0;\r\n-}\r\n-\r\n-button,\r\n-html input[type="button"],\r\n-input[type="reset"],\r\n-input[type="submit"] {\r\n- cursor: pointer;\r\n- -webkit-appearance: button;\r\n-}\r\n-\r\n-label,\r\n-select,\r\n-button,\r\n-input[type="button"],\r\n-input[type="reset"],\r\n-input[type="submit"],\r\n-input[type="radio"],\r\n-input[type="checkbox"] {\r\n- cursor: pointer;\r\n-}\r\n-\r\n-input[type="search"] {\r\n- -webkit-box-sizing: content-box;\r\n- -moz-box-sizing: content-box;\r\n- box-sizing: content-box;\r\n- -webkit-appearance: textfield;\r\n-}\r\n-\r\n-input[type="search"]::-webkit-search-decoration,\r\n-input[type="search"]::-webkit-search-cancel-button {\r\n- -webkit-appearance: none;\r\n-}\r\n-\r\n-textarea {\r\n- overflow: auto;\r\n- vertical-align: top;\r\n-}\r\n-\r\n-@media print {\r\n- * {\r\n- color: #000 !important;\r\n- text-shadow: none !important;\r\n- background: transparent !important;\r\n- box-shadow: none !important;\r\n- }\r\n- a,\r\n- a:visited {\r\n- text-decoration: underline;\r\n- }\r\n- a[href]:after {\r\n- content: " (" attr(href) ")";\r\n- }\r\n- abbr[title]:after {\r\n- content: " (" attr(title) ")";\r\n- }\r\n- .ir a:after,\r\n- a[href^="javascript:"]:after,\r\n- a[href^="#"]:after {\r\n- content: "";\r\n- }\r\n- pre,\r\n- blockquote {\r\n- border: 1px solid #999;\r\n- page-break-inside: avoid;\r\n- }\r\n- thead {\r\n- display: table-header-group;\r\n- }\r\n- tr,\r\n- img {\r\n- page-break-inside: avoid;\r\n- }\r\n- img {\r\n- max-width: 100% !important;\r\n- }\r\n- @page {\r\n- margin: 0.5cm;\r\n- }\r\n- p,\r\n- h2,\r\n- h3 {\r\n- orphans: 3;\r\n- widows: 3;\r\n- }\r\n- h2,\r\n- h3 {\r\n- page-break-after: avoid;\r\n- }\r\n-}\r\n-\r\n-body {\r\n- margin: 0;\r\n- font-family: "Helvetica Neue", Helvetica, Arial, sans-serif;\r\n- font-size: 14px;\r\n- line-height: 20px;\r\n- color: #333333;\r\n- background-color: #ffffff;\r\n-}\r\n-\r\n-a {\r\n- color: #0088cc;\r\n- text-decoration: none;\r\n-}\r\n-\r\n-a:hover,\r\n-a:focus {\r\n- color: #005580;\r\n- text-decoration: underline;\r\n-}\r\n-\r\n-.img-rounded {\r\n- -webkit'..b', 255, 0.15) 25%, transparent 25%, transparent 50%, rgba(255, 255, 255, 0.15) 50%, rgba(255, 255, 255, 0.15) 75%, transparent 75%, transparent);\n+ background-image: linear-gradient(45deg, rgba(255, 255, 255, 0.15) 25%, transparent 25%, transparent 50%, rgba(255, 255, 255, 0.15) 50%, rgba(255, 255, 255, 0.15) 75%, transparent 75%, transparent);\n+}\n+\n+.accordion {\n+ margin-bottom: 20px;\n+}\n+\n+.accordion-group {\n+ margin-bottom: 2px;\n+ border: 1px solid #e5e5e5;\n+ -webkit-border-radius: 4px;\n+ -moz-border-radius: 4px;\n+ border-radius: 4px;\n+}\n+\n+.accordion-heading {\n+ border-bottom: 0;\n+}\n+\n+.accordion-heading .accordion-toggle {\n+ display: block;\n+ padding: 8px 15px;\n+}\n+\n+.accordion-toggle {\n+ cursor: pointer;\n+}\n+\n+.accordion-inner {\n+ padding: 9px 15px;\n+ border-top: 1px solid #e5e5e5;\n+}\n+\n+.carousel {\n+ position: relative;\n+ margin-bottom: 20px;\n+ line-height: 1;\n+}\n+\n+.carousel-inner {\n+ position: relative;\n+ width: 100%;\n+ overflow: hidden;\n+}\n+\n+.carousel-inner > .item {\n+ position: relative;\n+ display: none;\n+ -webkit-transition: 0.6s ease-in-out left;\n+ -moz-transition: 0.6s ease-in-out left;\n+ -o-transition: 0.6s ease-in-out left;\n+ transition: 0.6s ease-in-out left;\n+}\n+\n+.carousel-inner > .item > img,\n+.carousel-inner > .item > a > img {\n+ display: block;\n+ line-height: 1;\n+}\n+\n+.carousel-inner > .active,\n+.carousel-inner > .next,\n+.carousel-inner > .prev {\n+ display: block;\n+}\n+\n+.carousel-inner > .active {\n+ left: 0;\n+}\n+\n+.carousel-inner > .next,\n+.carousel-inner > .prev {\n+ position: absolute;\n+ top: 0;\n+ width: 100%;\n+}\n+\n+.carousel-inner > .next {\n+ left: 100%;\n+}\n+\n+.carousel-inner > .prev {\n+ left: -100%;\n+}\n+\n+.carousel-inner > .next.left,\n+.carousel-inner > .prev.right {\n+ left: 0;\n+}\n+\n+.carousel-inner > .active.left {\n+ left: -100%;\n+}\n+\n+.carousel-inner > .active.right {\n+ left: 100%;\n+}\n+\n+.carousel-control {\n+ position: absolute;\n+ top: 40%;\n+ left: 15px;\n+ width: 40px;\n+ height: 40px;\n+ margin-top: -20px;\n+ font-size: 60px;\n+ font-weight: 100;\n+ line-height: 30px;\n+ color: #ffffff;\n+ text-align: center;\n+ background: #222222;\n+ border: 3px solid #ffffff;\n+ -webkit-border-radius: 23px;\n+ -moz-border-radius: 23px;\n+ border-radius: 23px;\n+ opacity: 0.5;\n+ filter: alpha(opacity=50);\n+}\n+\n+.carousel-control.right {\n+ right: 15px;\n+ left: auto;\n+}\n+\n+.carousel-control:hover,\n+.carousel-control:focus {\n+ color: #ffffff;\n+ text-decoration: none;\n+ opacity: 0.9;\n+ filter: alpha(opacity=90);\n+}\n+\n+.carousel-indicators {\n+ position: absolute;\n+ top: 15px;\n+ right: 15px;\n+ z-index: 5;\n+ margin: 0;\n+ list-style: none;\n+}\n+\n+.carousel-indicators li {\n+ display: block;\n+ float: left;\n+ width: 10px;\n+ height: 10px;\n+ margin-left: 5px;\n+ text-indent: -999px;\n+ background-color: #ccc;\n+ background-color: rgba(255, 255, 255, 0.25);\n+ border-radius: 5px;\n+}\n+\n+.carousel-indicators .active {\n+ background-color: #fff;\n+}\n+\n+.carousel-caption {\n+ position: absolute;\n+ right: 0;\n+ bottom: 0;\n+ left: 0;\n+ padding: 15px;\n+ background: #333333;\n+ background: rgba(0, 0, 0, 0.75);\n+}\n+\n+.carousel-caption h4,\n+.carousel-caption p {\n+ line-height: 20px;\n+ color: #ffffff;\n+}\n+\n+.carousel-caption h4 {\n+ margin: 0 0 5px;\n+}\n+\n+.carousel-caption p {\n+ margin-bottom: 0;\n+}\n+\n+.hero-unit {\n+ padding: 60px;\n+ margin-bottom: 30px;\n+ font-size: 18px;\n+ font-weight: 200;\n+ line-height: 30px;\n+ color: inherit;\n+ background-color: #eeeeee;\n+ -webkit-border-radius: 6px;\n+ -moz-border-radius: 6px;\n+ border-radius: 6px;\n+}\n+\n+.hero-unit h1 {\n+ margin-bottom: 0;\n+ font-size: 60px;\n+ line-height: 1;\n+ letter-spacing: -1px;\n+ color: inherit;\n+}\n+\n+.hero-unit li {\n+ line-height: 30px;\n+}\n+\n+.pull-right {\n+ float: right;\n+}\n+\n+.pull-left {\n+ float: left;\n+}\n+\n+.hide {\n+ display: none;\n+}\n+\n+.show {\n+ display: block;\n+}\n+\n+.invisible {\n+ visibility: hidden;\n+}\n+\n+.affix {\n+ position: fixed;\n+}\n' |
| b |
| diff -r 9645d995fb3c -r 9185ca0a7b43 bin/html.pm --- a/bin/html.pm Wed Oct 24 07:40:20 2018 -0400 +++ b/bin/html.pm Wed Jan 16 08:18:13 2019 -0500 |
| [ |
| b'@@ -1,910 +1,910 @@\n-package html;\r\n-\r\n-use strict;\r\n-use warnings;\r\n-use File::Basename;\r\n-\r\n-use Exporter;\r\n-our @ISA = qw( Exporter );\r\n-our @EXPORT_OK = qw( &main_page &details_pages &menu_page &ppp_page );\r\n-\r\n-sub main_page\r\n-{\r\n- my ( $dir, $file, $list_mainTabP, $current, $ma, $ma_uni, $dir_root ) = @_;\r\n- my ( $futHashP, $uniqueTabP, $randTabP, $pngTabP ) = get_genome ( $dir, $dir_root );\r\n-\r\n- open my $h, \'>\', $file || die "cannot create $file $!\\n";\r\n- header ( $h );\r\n- navbar ( $h, $list_mainTabP, $current );\r\n- print $h "<div class=\\"container\\"><p><a class=\\"btn\\" href=\\"$current-sub.html\\">View details »</a></p></div>\\n";\r\n- futurette( $h, $current, $pngTabP, $futHashP );\r\n- print $h "<div class=\\"container\\"><h2>mappers #: $ma</h2><h2>unique mappers #: $ma_uni</h2> </div>\\n";\r\n- carousel2( $h, $uniqueTabP, $randTabP, $dir_root );\r\n- footer($h);\r\n- close $h;\r\n-}\r\n-\r\n-sub menu_page\r\n-{\r\n- my ( $dir, $file, $list_mainTabP, $current, $min, $max, $simin, $simax, $pimin, $pimax, $dir_root ) = @_;\r\n- my $html_ref = $1 if $dir =~ /$dir_root(.*)/;\r\n- open my $h, \'>\', $file || die "cannot create $file $!\\n";\r\n- header($h);\r\n- navbar ( $h, $list_mainTabP, $current );\r\n- span( $h, $current, $min, $max, $simin, $simax, $pimin, $pimax );\r\n- print $h " <div class=\\"container\\"> <div class=\\"row text-center\\"> <img src=\\"$html_ref/pie_chart.png\\"/><br />\\n";\r\n- print $h " <A HREF=\\"$html_ref/repartition.txt\\">text file</A><br/>\\n </div></div>";\r\n- footer($h);\r\n- close $h;\r\n-}\r\n-\r\n-sub details_pages\r\n-{\r\n- my ( $dir_details, $prefix, $list_mainTabP, $current, $misTE, $dir_root, $ppp ) = @_;\r\n- my ($Hex, $HTE, $HG, $NonUniTE, $NonUniG, $UniG ) = get_subgroups( $dir_details, $current, $misTE, $dir_root );\r\n-\r\n- my $html_ref = $1.\'-PPP.html\' if $prefix =~ /$dir_root(.*)/;\r\n- open my $h, \'>\', $prefix.\'-TEs.html\' || die "cannot create $prefix-TEs.html $!\\n";\r\n- header($h);\r\n- navbar ( $h, $list_mainTabP, $current );\r\n- if ( $prefix =~ /piRNAs$/ && $ppp eq \'true\' )\r\n- {\r\n- print $h " <div class=\\"container\\">";\r\n- print $h " <p><a class=\\"btn\\" href=\\"$html_ref\\">Ping Pong Partners</a></p>\\n";\r\n- print $h "</div>";\r\n- }\r\n- fut($h,\'Transposable elements\',$HTE);\r\n- carousel($h,$NonUniTE,$dir_root);\r\n- footer($h);\r\n- close $h;\r\n-\r\n- open $h, \'>\', $prefix.\'-genome.html\' || die "cannot create $prefix-genome.html $!\\n";\r\n- header($h);\r\n- navbar ( $h, $list_mainTabP, $current );\r\n- fut($h,\'Genome\',$HG);\r\n- carousel2($h,$UniG, $NonUniG,$dir_root);\r\n- footer($h);\r\n- close $h;\r\n-\r\n- open $h, \'>\', $prefix.\'-transcripts.html\' || die "cannot create $prefix-transcripts.html $!\\n";\r\n- header($h);\r\n- navbar ( $h, $list_mainTabP, $current );\r\n- fut($h,\'transcripts\',$Hex);\r\n- footer($h);\r\n- close $h;\r\n-}\r\n-\r\n-sub ppp_page\r\n-{\r\n- my ( $dir, $file, $list_mainTabP, $current, $ppp, $dir_root ) = @_;\r\n-\r\n- my $ppp_file = $ppp.\'ppp.txt\';\r\n- open my $h, \'>\', $file || die "cannot create $file $!\\n";\r\n- header($h);\r\n- navbar ( $h, $list_mainTabP, $current );\r\n- print $h \'<div class="container"> <table class="wb-tables table table-striped table-hover">\'."\\n";\r\n- print $h \'<thead>\r\n- <tr>\r\n- <th data-sortable="true">ID</th>\r\n- <th data-sortable="true">overlap sum</th>\r\n- <th data-sortable="true">ten overlap sum</th>\r\n- <th data-sortable="true">mean</th>\r\n- <th data-sortable="true">standard deviation</th>\r\n- \t<th data-sortable="true">z-score</th>\r\n- \t<th data-sortable="true">p-value</th>\r\n-\t</tr>\r\n- </thead>\r\n- <tbody>\';\r\n-\r\n- open my $f, \'<\', $ppp_file || die "cannot open $ppp_file $!\\n";\r\n- while ( <$f> )\r\n- {\r\n- chomp;\r\n- print $h \'<tr>\';\r\n- my ( $id, $sum, $ten, $mean, $sd, $zscore, $prob) = split /\\t/, $_;\r\n- if( -d "$ppp/$id" )\r\n- {\r\n- my $sub_html = $ppp.$id.\'.html\';\r\n- my $sub_html_ref = $1.$id if $ppp =~ /$dir_root(.*)/;\r\n- print $h "<td> <a href=\\"$sub_html_ref.html\\">$id</a> </td>";\r\n-\r\n- open my $sub, \'>\', $sub_h'..b'\n+ my ($dir, $name) = @_;\n+ my (@out,@group);\n+ my $group = "\'$dir\'".\'/\'."\'$name\'".\'-subgroups-bonafide_reads-TE-*distribution-*.png\';\n+ @group = glob $group;\n+ foreach (my $g =0; $g <= $#group; $g++)\n+ {\n+ if ($group[$g] =~ /.*($name-subgroups-bonafide_reads-TE-.*distribution-.*\\.png)/ )\n+ {\n+ my $tmp = $1;\n+ push @out, $1;\n+ }\n+ }\n+ return (\\@out);\n+}\n+\n+sub get_PPP\n+{\n+ my ($dir,$name) = @_;\n+ my (%distri,@group);\n+ my $group = "\'$dir\'".\'/\'."\'$name\'".\'-subgroups-bonafide_reads-TE-PPPartners-*\';\n+ @group = glob $group;\n+\n+ foreach (my $g =0; $g <= $#group; $g++)\n+ {\n+ if ($group[$g] =~ /.*($name-subgroups-bonafide_reads-TE-PPPartners-.*)/ )\n+ {\n+ my $tmp = $1;\n+ if ($tmp =~ /PPPartners-(.*?)-sens\\.txt$/)\n+ {\n+ $distri{$1} = [\'\',\'\',\'\',\'\',\'\',\'\'] unless exists $distri{$1};\n+ $distri{$1}->[0] = $tmp;\n+ }\n+ elsif ($tmp =~ /PPPartners-(.*?)-antisens\\.txt$/)\n+ {\n+ $distri{$1} = [\'\',\'\',\'\',\'\',\'\',\'\'] unless exists $distri{$1};\n+ $distri{$1}->[1] = $tmp;\n+ }\n+ elsif ($tmp =~ /PPPartners-(.*?)-sensPPP\\.txt$/)\n+ {\n+ $distri{$1} = [\'\',\'\',\'\',\'\',\'\',\'\'] unless exists $distri{$1};\n+ $distri{$1}->[2] = $tmp;\n+ }\n+ elsif ($tmp =~ /PPPartners-(.*?)-antisensPPP\\.txt$/)\n+ {\n+ $distri{$1} = [\'\',\'\',\'\',\'\',\'\',\'\'] unless exists $distri{$1};\n+ $distri{$1}->[3] = $tmp;\n+ }\n+ elsif ($tmp =~ /PPPartners-(.*?)-overlap_size\\.txt$/)\n+ {\n+ $distri{$1} = [\'\',\'\',\'\',\'\',\'\',\'\'] unless exists $distri{$1};\n+ $distri{$1}->[4] = $tmp;\n+ }\n+ elsif ($tmp =~ /PPPartners-(.*?)-histogram\\.png$/)\n+ {\n+ $distri{$1} = [\'\',\'\',\'\',\'\',\'\',\'\'] unless exists $distri{$1};\n+ $distri{$1}->[5] = $tmp;\n+ }\n+ }\n+ }\n+ return \\%distri;\n+}\n+\n+sub PPPrint\n+{\n+ my ($h, $hash) = @_;\n+ my $cmp = 0;\n+\n+ print $h "<div class=\\"container\\">\\n";\n+ print $h "<div class=\\"row text-center\\">";\n+ while ( my ($k,$v) = each %{$hash} )\n+ {\n+ print $h "</div><div class=\\"row text-center\\">" if $cmp != 0 && $cmp % 2 == 0;\n+ print $h "\n+ \n+ <div class=\\"span6\\">\n+ <h2>$k</h2>\n+ <p class=\\"featurette-p\\"> <img src=\\"$v->[5]\\"/></p>\n+ <p class=\\"featurette-p\\"><a href=\\"$v->[4]\\">ping pong signature</a></p>\n+ <p class=\\"featurette-p\\"><a href=\\"$v->[2]\\">sense reads with PPP</a></p>\n+ <p class=\\"featurette-p\\"><a href=\\"$v->[3]\\">reverse reads with PPP</a></p>\n+ <p class=\\"featurette-p\\"><a href=\\"$v->[0]\\">sense reads without PPP</a></p>\n+ <p class=\\"featurette-p\\"><a href=\\"$v->[1]\\">reverse reads without PPP</a></p>\n+ </div>\n+ ";\n+ $cmp++;\n+ }\n+\n+ print $h "</div></div>";\n+}\n+\n+sub printDistri\n+{\n+ my ($h, $tab) = @_;\n+ my ($txt, $name);\n+ my $cmp = 0;\n+ print $h "<div class=\\"container\\">\\n";\n+ print $h "<div class=\\"row text-center\\">";\n+ foreach my $k (@{$tab})\n+ {\n+ if ($k =~ /(.*)-(.*)\\.png$/)\n+ {\n+ $txt = $1.\'-\'.$2.\'.txt\';\n+ $name = $2;\n+ }\n+ print $h "</div><div class=\\"row text-center\\">" if $cmp != 0 && $cmp % 2 == 0;\n+ print $h "\n+ \n+ <div class=\\"span6\\">\n+ <h2>$name</h2>\n+ <p> <img src=\\"$k\\"/></p>\n+ <p class=\\"featurette-p\\"><a href=\\"$txt\\">text file</a></p>\n+ </div>\n+ ";\n+ $cmp++;\n+ }\n+\n+ print $h "</div></div>";\n+}\n+\n+sub mapnum\n+{\n+ my $dupmapnum = shift;\n+ my $dupnum_genome = shift;\n+ open (my $dupTE, $dupmapnum) || die "cannot open ".$dupmapnum."\\n";\n+ my %dupnum_TE = ();\n+ my $header = <$dupTE>;\n+ while (<$dupTE>)\n+ {\n+ chomp $_;\n+ my @dupline = split /\\t/, $_;\n+ $dupnum_TE{$dupline[0]} = $dupline[2];\n+ }\n+ close $dupTE;\n+ open (my $du_TE, \'>\'.$dupmapnum) || die "cannot open to write ".$dupmapnum."\\n";\n+ print $du_TE "sequence\\tduplicate\\tgenome map num\\tmap num\\n";\n+ while (my ($k, $v) = each %dupnum_TE )\n+ {\n+ my $hashRef = ${$dupnum_genome}{$k};\n+ print $du_TE "$k\\t$hashRef->[0]\\t$hashRef->[1]\\t$v\\n";\n+ }\n+ close $du_TE;\n+}\n+\n+1;\n' |
| b |
| diff -r 9645d995fb3c -r 9185ca0a7b43 bin/js/bootstrap-table.js --- a/bin/js/bootstrap-table.js Wed Oct 24 07:40:20 2018 -0400 +++ b/bin/js/bootstrap-table.js Wed Jan 16 08:18:13 2019 -0500 |
| [ |
| b"@@ -1,3094 +1,3094 @@\n-/**\r\n- * @author zhixin wen <wenzhixin2010@gmail.com>\r\n- * version: 1.11.1\r\n- * https://github.com/wenzhixin/bootstrap-table/\r\n- */\r\n-\r\n-(function ($) {\r\n- 'use strict';\r\n-\r\n- // TOOLS DEFINITION\r\n- // ======================\r\n-\r\n- var cachedWidth = null;\r\n-\r\n- // it only does '%s', and return '' when arguments are undefined\r\n- var sprintf = function (str) {\r\n- var args = arguments,\r\n- flag = true,\r\n- i = 1;\r\n-\r\n- str = str.replace(/%s/g, function () {\r\n- var arg = args[i++];\r\n-\r\n- if (typeof arg === 'undefined') {\r\n- flag = false;\r\n- return '';\r\n- }\r\n- return arg;\r\n- });\r\n- return flag ? str : '';\r\n- };\r\n-\r\n- var getPropertyFromOther = function (list, from, to, value) {\r\n- var result = '';\r\n- $.each(list, function (i, item) {\r\n- if (item[from] === value) {\r\n- result = item[to];\r\n- return false;\r\n- }\r\n- return true;\r\n- });\r\n- return result;\r\n- };\r\n-\r\n- var getFieldIndex = function (columns, field) {\r\n- var index = -1;\r\n-\r\n- $.each(columns, function (i, column) {\r\n- if (column.field === field) {\r\n- index = i;\r\n- return false;\r\n- }\r\n- return true;\r\n- });\r\n- return index;\r\n- };\r\n-\r\n- // http://jsfiddle.net/wenyi/47nz7ez9/3/\r\n- var setFieldIndex = function (columns) {\r\n- var i, j, k,\r\n- totalCol = 0,\r\n- flag = [];\r\n-\r\n- for (i = 0; i < columns[0].length; i++) {\r\n- totalCol += columns[0][i].colspan || 1;\r\n- }\r\n-\r\n- for (i = 0; i < columns.length; i++) {\r\n- flag[i] = [];\r\n- for (j = 0; j < totalCol; j++) {\r\n- flag[i][j] = false;\r\n- }\r\n- }\r\n-\r\n- for (i = 0; i < columns.length; i++) {\r\n- for (j = 0; j < columns[i].length; j++) {\r\n- var r = columns[i][j],\r\n- rowspan = r.rowspan || 1,\r\n- colspan = r.colspan || 1,\r\n- index = $.inArray(false, flag[i]);\r\n-\r\n- if (colspan === 1) {\r\n- r.fieldIndex = index;\r\n- // when field is undefined, use index instead\r\n- if (typeof r.field === 'undefined') {\r\n- r.field = index;\r\n- }\r\n- }\r\n-\r\n- for (k = 0; k < rowspan; k++) {\r\n- flag[i + k][index] = true;\r\n- }\r\n- for (k = 0; k < colspan; k++) {\r\n- flag[i][index + k] = true;\r\n- }\r\n- }\r\n- }\r\n- };\r\n-\r\n- var getScrollBarWidth = function () {\r\n- if (cachedWidth === null) {\r\n- var inner = $('<p/>').addClass('fixed-table-scroll-inner'),\r\n- outer = $('<div/>').addClass('fixed-table-scroll-outer'),\r\n- w1, w2;\r\n-\r\n- outer.append(inner);\r\n- $('body').append(outer);\r\n-\r\n- w1 = inner[0].offsetWidth;\r\n- outer.css('overflow', 'scroll');\r\n- w2 = inner[0].offsetWidth;\r\n-\r\n- if (w1 === w2) {\r\n- w2 = outer[0].clientWidth;\r\n- }\r\n-\r\n- outer.remove();\r\n- cachedWidth = w1 - w2;\r\n- }\r\n- return cachedWidth;\r\n- };\r\n-\r\n- var calculateObjectValue = function (self, name, args, defaultValue) {\r\n- var func = name;\r\n-\r\n- if (typeof name === 'string') {\r\n- // support obj.func1.func2\r\n- var names = name.split('.');\r\n-\r\n- if (names.length > 1) {\r\n- func = window;\r\n- $.each(names, function (i, f) {\r\n- func = func[f];\r\n- });\r\n- } else {\r\n- func = window[name];\r\n- "..b' i < trs.length; i++) {\n+ this.expandRow_(true, $(trs[i]).data("index"));\n+ }\n+ }\n+ };\n+\n+ BootstrapTable.prototype.collapseAllRows = function (isSubTable) {\n+ if (isSubTable) {\n+ this.expandRow_(false, 0);\n+ } else {\n+ var trs = this.$body.children();\n+ for (var i = 0; i < trs.length; i++) {\n+ this.expandRow_(false, $(trs[i]).data("index"));\n+ }\n+ }\n+ };\n+\n+ BootstrapTable.prototype.updateFormatText = function (name, text) {\n+ if (this.options[sprintf(\'format%s\', name)]) {\n+ if (typeof text === \'string\') {\n+ this.options[sprintf(\'format%s\', name)] = function () {\n+ return text;\n+ };\n+ } else if (typeof text === \'function\') {\n+ this.options[sprintf(\'format%s\', name)] = text;\n+ }\n+ }\n+ this.initToolbar();\n+ this.initPagination();\n+ this.initBody();\n+ };\n+\n+ // BOOTSTRAP TABLE PLUGIN DEFINITION\n+ // =======================\n+\n+ var allowedMethods = [\n+ \'getOptions\',\n+ \'getSelections\', \'getAllSelections\', \'getData\',\n+ \'load\', \'append\', \'prepend\', \'remove\', \'removeAll\',\n+ \'insertRow\', \'updateRow\', \'updateCell\', \'updateByUniqueId\', \'removeByUniqueId\',\n+ \'getRowByUniqueId\', \'showRow\', \'hideRow\', \'getHiddenRows\',\n+ \'mergeCells\',\n+ \'checkAll\', \'uncheckAll\', \'checkInvert\',\n+ \'check\', \'uncheck\',\n+ \'checkBy\', \'uncheckBy\',\n+ \'refresh\',\n+ \'resetView\',\n+ \'resetWidth\',\n+ \'destroy\',\n+ \'showLoading\', \'hideLoading\',\n+ \'showColumn\', \'hideColumn\', \'getHiddenColumns\', \'getVisibleColumns\',\n+ \'showAllColumns\', \'hideAllColumns\',\n+ \'filterBy\',\n+ \'scrollTo\',\n+ \'getScrollPosition\',\n+ \'selectPage\', \'prevPage\', \'nextPage\',\n+ \'togglePagination\',\n+ \'toggleView\',\n+ \'refreshOptions\',\n+ \'resetSearch\',\n+ \'expandRow\', \'collapseRow\', \'expandAllRows\', \'collapseAllRows\',\n+ \'updateFormatText\'\n+ ];\n+\n+ $.fn.bootstrapTable = function (option) {\n+ var value,\n+ args = Array.prototype.slice.call(arguments, 1);\n+\n+ this.each(function () {\n+ var $this = $(this),\n+ data = $this.data(\'bootstrap.table\'),\n+ options = $.extend({}, BootstrapTable.DEFAULTS, $this.data(),\n+ typeof option === \'object\' && option);\n+\n+ if (typeof option === \'string\') {\n+ if ($.inArray(option, allowedMethods) < 0) {\n+ throw new Error("Unknown method: " + option);\n+ }\n+\n+ if (!data) {\n+ return;\n+ }\n+\n+ value = data[option].apply(data, args);\n+\n+ if (option === \'destroy\') {\n+ $this.removeData(\'bootstrap.table\');\n+ }\n+ }\n+\n+ if (!data) {\n+ $this.data(\'bootstrap.table\', (data = new BootstrapTable(this, options)));\n+ }\n+ });\n+\n+ return typeof value === \'undefined\' ? this : value;\n+ };\n+\n+ $.fn.bootstrapTable.Constructor = BootstrapTable;\n+ $.fn.bootstrapTable.defaults = BootstrapTable.DEFAULTS;\n+ $.fn.bootstrapTable.columnDefaults = BootstrapTable.COLUMN_DEFAULTS;\n+ $.fn.bootstrapTable.locales = BootstrapTable.LOCALES;\n+ $.fn.bootstrapTable.methods = allowedMethods;\n+ $.fn.bootstrapTable.utils = {\n+ sprintf: sprintf,\n+ getFieldIndex: getFieldIndex,\n+ compareObjects: compareObjects,\n+ calculateObjectValue: calculateObjectValue,\n+ getItemField: getItemField,\n+ objectKeys: objectKeys,\n+ isIEBrowser: isIEBrowser\n+ };\n+\n+ // BOOTSTRAP TABLE INIT\n+ // =======================\n+\n+ $(function () {\n+ $(\'[data-toggle="table"]\').bootstrapTable();\n+ });\n+})(jQuery);\n' |
| b |
| diff -r 9645d995fb3c -r 9185ca0a7b43 bin/js/bootstrap.min.js --- a/bin/js/bootstrap.min.js Wed Oct 24 07:40:20 2018 -0400 +++ b/bin/js/bootstrap.min.js Wed Jan 16 08:18:13 2019 -0500 |
| [ |
| b'@@ -1,6 +1,6 @@\n-/**\r\n-* Bootstrap.js v2.3.2 by @fat & @mdo\r\n-* Copyright 2013 Twitter, Inc.\r\n-* http://www.apache.org/licenses/LICENSE-2.0.txt\r\n-*/\r\n+/**\n+* Bootstrap.js v2.3.2 by @fat & @mdo\n+* Copyright 2013 Twitter, Inc.\n+* http://www.apache.org/licenses/LICENSE-2.0.txt\n+*/\n !function(e){"use strict";e(function(){e.support.transition=function(){var e=function(){var e=document.createElement("bootstrap"),t={WebkitTransition:"webkitTransitionEnd",MozTransition:"transitionend",OTransition:"oTransitionEnd otransitionend",transition:"transitionend"},n;for(n in t)if(e.style[n]!==undefined)return t[n]}();return e&&{end:e}}()})}(window.jQuery),!function(e){"use strict";var t=\'[data-dismiss="alert"]\',n=function(n){e(n).on("click",t,this.close)};n.prototype.close=function(t){function s(){i.trigger("closed").remove()}var n=e(this),r=n.attr("data-target"),i;r||(r=n.attr("href"),r=r&&r.replace(/.*(?=#[^\\s]*$)/,"")),i=e(r),t&&t.preventDefault(),i.length||(i=n.hasClass("alert")?n:n.parent()),i.trigger(t=e.Event("close"));if(t.isDefaultPrevented())return;i.removeClass("in"),e.support.transition&&i.hasClass("fade")?i.on(e.support.transition.end,s):s()};var r=e.fn.alert;e.fn.alert=function(t){return this.each(function(){var r=e(this),i=r.data("alert");i||r.data("alert",i=new n(this)),typeof t=="string"&&i[t].call(r)})},e.fn.alert.Constructor=n,e.fn.alert.noConflict=function(){return e.fn.alert=r,this},e(document).on("click.alert.data-api",t,n.prototype.close)}(window.jQuery),!function(e){"use strict";var t=function(t,n){this.$element=e(t),this.options=e.extend({},e.fn.button.defaults,n)};t.prototype.setState=function(e){var t="disabled",n=this.$element,r=n.data(),i=n.is("input")?"val":"html";e+="Text",r.resetText||n.data("resetText",n[i]()),n[i](r[e]||this.options[e]),setTimeout(function(){e=="loadingText"?n.addClass(t).attr(t,t):n.removeClass(t).removeAttr(t)},0)},t.prototype.toggle=function(){var e=this.$element.closest(\'[data-toggle="buttons-radio"]\');e&&e.find(".active").removeClass("active"),this.$element.toggleClass("active")};var n=e.fn.button;e.fn.button=function(n){return this.each(function(){var r=e(this),i=r.data("button"),s=typeof n=="object"&&n;i||r.data("button",i=new t(this,s)),n=="toggle"?i.toggle():n&&i.setState(n)})},e.fn.button.defaults={loadingText:"loading..."},e.fn.button.Constructor=t,e.fn.button.noConflict=function(){return e.fn.button=n,this},e(document).on("click.button.data-api","[data-toggle^=button]",function(t){var n=e(t.target);n.hasClass("btn")||(n=n.closest(".btn")),n.button("toggle")})}(window.jQuery),!function(e){"use strict";var t=function(t,n){this.$element=e(t),this.$indicators=this.$element.find(".carousel-indicators"),this.options=n,this.options.pause=="hover"&&this.$element.on("mouseenter",e.proxy(this.pause,this)).on("mouseleave",e.proxy(this.cycle,this))};t.prototype={cycle:function(t){return t||(this.paused=!1),this.interval&&clearInterval(this.interval),this.options.interval&&!this.paused&&(this.interval=setInterval(e.proxy(this.next,this),this.options.interval)),this},getActiveIndex:function(){return this.$active=this.$element.find(".item.active"),this.$items=this.$active.parent().children(),this.$items.index(this.$active)},to:function(t){var n=this.getActiveIndex(),r=this;if(t>this.$items.length-1||t<0)return;return this.sliding?this.$element.one("slid",function(){r.to(t)}):n==t?this.pause().cycle():this.slide(t>n?"next":"prev",e(this.$items[t]))},pause:function(t){return t||(this.paused=!0),this.$element.find(".next, .prev").length&&e.support.transition.end&&(this.$element.trigger(e.support.transition.end),this.cycle(!0)),clearInterval(this.interval),this.interval=null,this},next:function(){if(this.sliding)return;return this.slide("next")},prev:function(){if(this.sliding)return;return this.slide("prev")},slide:function(t,n){var r=this.$element.find(".item.active"),i=n||r[t](),s=this.interval,o=t=="next"?"left":"right",u=t=="next"?"first":"last",a=this,f;this.sliding=!0,s&&this.pause(),i=i.leng'..b',next:function(t){var n=this.$menu.find(".active").removeClass("active"),r=n.next();r.length||(r=e(this.$menu.find("li")[0])),r.addClass("active")},prev:function(e){var t=this.$menu.find(".active").removeClass("active"),n=t.prev();n.length||(n=this.$menu.find("li").last()),n.addClass("active")},listen:function(){this.$element.on("focus",e.proxy(this.focus,this)).on("blur",e.proxy(this.blur,this)).on("keypress",e.proxy(this.keypress,this)).on("keyup",e.proxy(this.keyup,this)),this.eventSupported("keydown")&&this.$element.on("keydown",e.proxy(this.keydown,this)),this.$menu.on("click",e.proxy(this.click,this)).on("mouseenter","li",e.proxy(this.mouseenter,this)).on("mouseleave","li",e.proxy(this.mouseleave,this))},eventSupported:function(e){var t=e in this.$element;return t||(this.$element.setAttribute(e,"return;"),t=typeof this.$element[e]=="function"),t},move:function(e){if(!this.shown)return;switch(e.keyCode){case 9:case 13:case 27:e.preventDefault();break;case 38:e.preventDefault(),this.prev();break;case 40:e.preventDefault(),this.next()}e.stopPropagation()},keydown:function(t){this.suppressKeyPressRepeat=~e.inArray(t.keyCode,[40,38,9,13,27]),this.move(t)},keypress:function(e){if(this.suppressKeyPressRepeat)return;this.move(e)},keyup:function(e){switch(e.keyCode){case 40:case 38:case 16:case 17:case 18:break;case 9:case 13:if(!this.shown)return;this.select();break;case 27:if(!this.shown)return;this.hide();break;default:this.lookup()}e.stopPropagation(),e.preventDefault()},focus:function(e){this.focused=!0},blur:function(e){this.focused=!1,!this.mousedover&&this.shown&&this.hide()},click:function(e){e.stopPropagation(),e.preventDefault(),this.select(),this.$element.focus()},mouseenter:function(t){this.mousedover=!0,this.$menu.find(".active").removeClass("active"),e(t.currentTarget).addClass("active")},mouseleave:function(e){this.mousedover=!1,!this.focused&&this.shown&&this.hide()}};var n=e.fn.typeahead;e.fn.typeahead=function(n){return this.each(function(){var r=e(this),i=r.data("typeahead"),s=typeof n=="object"&&n;i||r.data("typeahead",i=new t(this,s)),typeof n=="string"&&i[n]()})},e.fn.typeahead.defaults={source:[],items:8,menu:\'<ul class="typeahead dropdown-menu"></ul>\',item:\'<li><a href="#"></a></li>\',minLength:1},e.fn.typeahead.Constructor=t,e.fn.typeahead.noConflict=function(){return e.fn.typeahead=n,this},e(document).on("focus.typeahead.data-api",\'[data-provide="typeahead"]\',function(t){var n=e(this);if(n.data("typeahead"))return;n.typeahead(n.data())})}(window.jQuery),!function(e){"use strict";var t=function(t,n){this.options=e.extend({},e.fn.affix.defaults,n),this.$window=e(window).on("scroll.affix.data-api",e.proxy(this.checkPosition,this)).on("click.affix.data-api",e.proxy(function(){setTimeout(e.proxy(this.checkPosition,this),1)},this)),this.$element=e(t),this.checkPosition()};t.prototype.checkPosition=function(){if(!this.$element.is(":visible"))return;var t=e(document).height(),n=this.$window.scrollTop(),r=this.$element.offset(),i=this.options.offset,s=i.bottom,o=i.top,u="affix affix-top affix-bottom",a;typeof i!="object"&&(s=o=i),typeof o=="function"&&(o=i.top()),typeof s=="function"&&(s=i.bottom()),a=this.unpin!=null&&n+this.unpin<=r.top?!1:s!=null&&r.top+this.$element.height()>=t-s?"bottom":o!=null&&n<=o?"top":!1;if(this.affixed===a)return;this.affixed=a,this.unpin=a=="bottom"?r.top-n:null,this.$element.removeClass(u).addClass("affix"+(a?"-"+a:""))};var n=e.fn.affix;e.fn.affix=function(n){return this.each(function(){var r=e(this),i=r.data("affix"),s=typeof n=="object"&&n;i||r.data("affix",i=new t(this,s)),typeof n=="string"&&i[n]()})},e.fn.affix.Constructor=t,e.fn.affix.defaults={offset:0},e.fn.affix.noConflict=function(){return e.fn.affix=n,this},e(window).on("load",function(){e(\'[data-spy="affix"]\').each(function(){var t=e(this),n=t.data();n.offset=n.offset||{},n.offsetBottom&&(n.offset.bottom=n.offsetBottom),n.offsetTop&&(n.offset.top=n.offsetTop),t.affix(n)})})}(window.jQuery);\n\\ No newline at end of file\n' |
| b |
| diff -r 9645d995fb3c -r 9185ca0a7b43 bin/js/filter.js --- a/bin/js/filter.js Wed Oct 24 07:40:20 2018 -0400 +++ b/bin/js/filter.js Wed Jan 16 08:18:13 2019 -0500 |
| [ |
| @@ -1,20 +1,20 @@ -function search(input) { - // Declare variables - var elt, filter, uls, li, a, i; - elt = input.parentElement; - filter = input.value.toUpperCase(); - uls = elt.getElementsByClassName('thumbs'); - - // Loop through all list items, and hide those who don't match the search query - for (j = 0; j < uls.length; j++) { - li = uls[j].getElementsByTagName('li'); - for (i = 0; i < li.length; i++) { - a = li[i].getElementsByTagName("a")[0]; - if (a.innerHTML.toUpperCase().indexOf(filter) > -1) { - li[i].style.display = ""; - } else { - li[i].style.display = "none"; - } - } - } -} +function search(input) { + // Declare variables + var elt, filter, uls, li, a, i; + elt = input.parentElement; + filter = input.value.toUpperCase(); + uls = elt.getElementsByClassName('thumbs'); + + // Loop through all list items, and hide those who don't match the search query + for (j = 0; j < uls.length; j++) { + li = uls[j].getElementsByTagName('li'); + for (i = 0; i < li.length; i++) { + a = li[i].getElementsByTagName("a")[0]; + if (a.innerHTML.toUpperCase().indexOf(filter) > -1) { + li[i].style.display = ""; + } else { + li[i].style.display = "none"; + } + } + } +} |
| b |
| diff -r 9645d995fb3c -r 9185ca0a7b43 bin/js/jquery.js --- a/bin/js/jquery.js Wed Oct 24 07:40:20 2018 -0400 +++ b/bin/js/jquery.js Wed Jan 16 08:18:13 2019 -0500 |
| [ |
| b'@@ -1,5 +1,5 @@\n-/*! jQuery v1.9.1 | (c) 2005, 2012 jQuery Foundation, Inc. | jquery.org/license\r\n-//@ sourceMappingURL=jquery.min.map\r\n-*/(function(e,t){var n,r,i=typeof t,o=e.document,a=e.location,s=e.jQuery,u=e.$,l={},c=[],p="1.9.1",f=c.concat,d=c.push,h=c.slice,g=c.indexOf,m=l.toString,y=l.hasOwnProperty,v=p.trim,b=function(e,t){return new b.fn.init(e,t,r)},x=/[+-]?(?:\\d*\\.|)\\d+(?:[eE][+-]?\\d+|)/.source,w=/\\S+/g,T=/^[\\s\\uFEFF\\xA0]+|[\\s\\uFEFF\\xA0]+$/g,N=/^(?:(<[\\w\\W]+>)[^>]*|#([\\w-]*))$/,C=/^<(\\w+)\\s*\\/?>(?:<\\/\\1>|)$/,k=/^[\\],:{}\\s]*$/,E=/(?:^|:|,)(?:\\s*\\[)+/g,S=/\\\\(?:["\\\\\\/bfnrt]|u[\\da-fA-F]{4})/g,A=/"[^"\\\\\\r\\n]*"|true|false|null|-?(?:\\d+\\.|)\\d+(?:[eE][+-]?\\d+|)/g,j=/^-ms-/,D=/-([\\da-z])/gi,L=function(e,t){return t.toUpperCase()},H=function(e){(o.addEventListener||"load"===e.type||"complete"===o.readyState)&&(q(),b.ready())},q=function(){o.addEventListener?(o.removeEventListener("DOMContentLoaded",H,!1),e.removeEventListener("load",H,!1)):(o.detachEvent("onreadystatechange",H),e.detachEvent("onload",H))};b.fn=b.prototype={jquery:p,constructor:b,init:function(e,n,r){var i,a;if(!e)return this;if("string"==typeof e){if(i="<"===e.charAt(0)&&">"===e.charAt(e.length-1)&&e.length>=3?[null,e,null]:N.exec(e),!i||!i[1]&&n)return!n||n.jquery?(n||r).find(e):this.constructor(n).find(e);if(i[1]){if(n=n instanceof b?n[0]:n,b.merge(this,b.parseHTML(i[1],n&&n.nodeType?n.ownerDocument||n:o,!0)),C.test(i[1])&&b.isPlainObject(n))for(i in n)b.isFunction(this[i])?this[i](n[i]):this.attr(i,n[i]);return this}if(a=o.getElementById(i[2]),a&&a.parentNode){if(a.id!==i[2])return r.find(e);this.length=1,this[0]=a}return this.context=o,this.selector=e,this}return e.nodeType?(this.context=this[0]=e,this.length=1,this):b.isFunction(e)?r.ready(e):(e.selector!==t&&(this.selector=e.selector,this.context=e.context),b.makeArray(e,this))},selector:"",length:0,size:function(){return this.length},toArray:function(){return h.call(this)},get:function(e){return null==e?this.toArray():0>e?this[this.length+e]:this[e]},pushStack:function(e){var t=b.merge(this.constructor(),e);return t.prevObject=this,t.context=this.context,t},each:function(e,t){return b.each(this,e,t)},ready:function(e){return b.ready.promise().done(e),this},slice:function(){return this.pushStack(h.apply(this,arguments))},first:function(){return this.eq(0)},last:function(){return this.eq(-1)},eq:function(e){var t=this.length,n=+e+(0>e?t:0);return this.pushStack(n>=0&&t>n?[this[n]]:[])},map:function(e){return this.pushStack(b.map(this,function(t,n){return e.call(t,n,t)}))},end:function(){return this.prevObject||this.constructor(null)},push:d,sort:[].sort,splice:[].splice},b.fn.init.prototype=b.fn,b.extend=b.fn.extend=function(){var e,n,r,i,o,a,s=arguments[0]||{},u=1,l=arguments.length,c=!1;for("boolean"==typeof s&&(c=s,s=arguments[1]||{},u=2),"object"==typeof s||b.isFunction(s)||(s={}),l===u&&(s=this,--u);l>u;u++)if(null!=(o=arguments[u]))for(i in o)e=s[i],r=o[i],s!==r&&(c&&r&&(b.isPlainObject(r)||(n=b.isArray(r)))?(n?(n=!1,a=e&&b.isArray(e)?e:[]):a=e&&b.isPlainObject(e)?e:{},s[i]=b.extend(c,a,r)):r!==t&&(s[i]=r));return s},b.extend({noConflict:function(t){return e.$===b&&(e.$=u),t&&e.jQuery===b&&(e.jQuery=s),b},isReady:!1,readyWait:1,holdReady:function(e){e?b.readyWait++:b.ready(!0)},ready:function(e){if(e===!0?!--b.readyWait:!b.isReady){if(!o.body)return setTimeout(b.ready);b.isReady=!0,e!==!0&&--b.readyWait>0||(n.resolveWith(o,[b]),b.fn.trigger&&b(o).trigger("ready").off("ready"))}},isFunction:function(e){return"function"===b.type(e)},isArray:Array.isArray||function(e){return"array"===b.type(e)},isWindow:function(e){return null!=e&&e==e.window},isNumeric:function(e){return!isNaN(parseFloat(e))&&isFinite(e)},type:function(e){return null==e?e+"":"object"==typeof e||"function"==typeof e?l[m.call(e)]||"object":typeof e},isPlainObject:function(e){if(!e||"object"!==b.type(e)||e.nodeType||b.isWindow(e))return!1;try{if(e.constructor&&!y.call(e,"constructor")&&!y.call(e.constructor.prototype,"isPrototypeOf")'..b' ir(e,t){var n,r={height:e},i=0;for(t=t?1:0;4>i;i+=2-t)n=Zt[i],r["margin"+n]=r["padding"+n]=e;return t&&(r.opacity=r.width=e),r}b.each({slideDown:ir("show"),slideUp:ir("hide"),slideToggle:ir("toggle"),fadeIn:{opacity:"show"},fadeOut:{opacity:"hide"},fadeToggle:{opacity:"toggle"}},function(e,t){b.fn[e]=function(e,n,r){return this.animate(t,e,n,r)}}),b.speed=function(e,t,n){var r=e&&"object"==typeof e?b.extend({},e):{complete:n||!n&&t||b.isFunction(e)&&e,duration:e,easing:n&&t||t&&!b.isFunction(t)&&t};return r.duration=b.fx.off?0:"number"==typeof r.duration?r.duration:r.duration in b.fx.speeds?b.fx.speeds[r.duration]:b.fx.speeds._default,(null==r.queue||r.queue===!0)&&(r.queue="fx"),r.old=r.complete,r.complete=function(){b.isFunction(r.old)&&r.old.call(this),r.queue&&b.dequeue(this,r.queue)},r},b.easing={linear:function(e){return e},swing:function(e){return.5-Math.cos(e*Math.PI)/2}},b.timers=[],b.fx=rr.prototype.init,b.fx.tick=function(){var e,n=b.timers,r=0;for(Xn=b.now();n.length>r;r++)e=n[r],e()||n[r]!==e||n.splice(r--,1);n.length||b.fx.stop(),Xn=t},b.fx.timer=function(e){e()&&b.timers.push(e)&&b.fx.start()},b.fx.interval=13,b.fx.start=function(){Un||(Un=setInterval(b.fx.tick,b.fx.interval))},b.fx.stop=function(){clearInterval(Un),Un=null},b.fx.speeds={slow:600,fast:200,_default:400},b.fx.step={},b.expr&&b.expr.filters&&(b.expr.filters.animated=function(e){return b.grep(b.timers,function(t){return e===t.elem}).length}),b.fn.offset=function(e){if(arguments.length)return e===t?this:this.each(function(t){b.offset.setOffset(this,e,t)});var n,r,o={top:0,left:0},a=this[0],s=a&&a.ownerDocument;if(s)return n=s.documentElement,b.contains(n,a)?(typeof a.getBoundingClientRect!==i&&(o=a.getBoundingClientRect()),r=or(s),{top:o.top+(r.pageYOffset||n.scrollTop)-(n.clientTop||0),left:o.left+(r.pageXOffset||n.scrollLeft)-(n.clientLeft||0)}):o},b.offset={setOffset:function(e,t,n){var r=b.css(e,"position");"static"===r&&(e.style.position="relative");var i=b(e),o=i.offset(),a=b.css(e,"top"),s=b.css(e,"left"),u=("absolute"===r||"fixed"===r)&&b.inArray("auto",[a,s])>-1,l={},c={},p,f;u?(c=i.position(),p=c.top,f=c.left):(p=parseFloat(a)||0,f=parseFloat(s)||0),b.isFunction(t)&&(t=t.call(e,n,o)),null!=t.top&&(l.top=t.top-o.top+p),null!=t.left&&(l.left=t.left-o.left+f),"using"in t?t.using.call(e,l):i.css(l)}},b.fn.extend({position:function(){if(this[0]){var e,t,n={top:0,left:0},r=this[0];return"fixed"===b.css(r,"position")?t=r.getBoundingClientRect():(e=this.offsetParent(),t=this.offset(),b.nodeName(e[0],"html")||(n=e.offset()),n.top+=b.css(e[0],"borderTopWidth",!0),n.left+=b.css(e[0],"borderLeftWidth",!0)),{top:t.top-n.top-b.css(r,"marginTop",!0),left:t.left-n.left-b.css(r,"marginLeft",!0)}}},offsetParent:function(){return this.map(function(){var e=this.offsetParent||o.documentElement;while(e&&!b.nodeName(e,"html")&&"static"===b.css(e,"position"))e=e.offsetParent;return e||o.documentElement})}}),b.each({scrollLeft:"pageXOffset",scrollTop:"pageYOffset"},function(e,n){var r=/Y/.test(n);b.fn[e]=function(i){return b.access(this,function(e,i,o){var a=or(e);return o===t?a?n in a?a[n]:a.document.documentElement[i]:e[i]:(a?a.scrollTo(r?b(a).scrollLeft():o,r?o:b(a).scrollTop()):e[i]=o,t)},e,i,arguments.length,null)}});function or(e){return b.isWindow(e)?e:9===e.nodeType?e.defaultView||e.parentWindow:!1}b.each({Height:"height",Width:"width"},function(e,n){b.each({padding:"inner"+e,content:n,"":"outer"+e},function(r,i){b.fn[i]=function(i,o){var a=arguments.length&&(r||"boolean"!=typeof i),s=r||(i===!0||o===!0?"margin":"border");return b.access(this,function(n,r,i){var o;return b.isWindow(n)?n.document.documentElement["client"+e]:9===n.nodeType?(o=n.documentElement,Math.max(n.body["scroll"+e],o["scroll"+e],n.body["offset"+e],o["offset"+e],o["client"+e])):i===t?b.css(n,r,s):b.style(n,r,i,s)},n,a?i:t,a,null)}})}),e.jQuery=e.$=b,"function"==typeof define&&define.amd&&define.amd.jQuery&&define("jquery",[],function(){return b})})(window);\n\\ No newline at end of file\n' |
| b |
| diff -r 9645d995fb3c -r 9185ca0a7b43 bin/ppp.pm --- a/bin/ppp.pm Wed Oct 24 07:40:20 2018 -0400 +++ b/bin/ppp.pm Wed Jan 16 08:18:13 2019 -0500 |
| [ |
| b'@@ -1,230 +1,230 @@\n-package ppp;\r\n-\r\n-use strict;\r\n-use warnings;\r\n-use FindBin;\r\n-use lib $FindBin::Bin;\r\n-use Rcall qw ( histogram );\r\n-use Math::CDF;\r\n-\r\n-use Exporter;\r\n-our @ISA = qw( Exporter );\r\n-our @EXPORT_OK = qw( &ping_pong_partners );\r\n-\r\n-sub ping_pong_partners\r\n-{\r\n- my ( $TE_fai, $sam, $dir, $max ) = @_;\r\n- my ( $hashRef, $dupRef, $hasPpp ) = count_mapped ( $TE_fai, $sam );\r\n- my ( %num_per_overlap_size, $overlap_number, $reverseR, $begRev, $endRev, $sensR, $begSens, $endSens, $snum, $rnum, $overlap );\r\n- my ( $SP, $AP, $SN, $AN, $txt );\r\n- my $flag = 0;\r\n- my @distri_overlap = (); my @overlaps_names = ();\r\n-\r\n- open my $ppp_f, \'>\', $dir."ppp.txt" || die "cannot create ppp.txt $!\\n";\r\n- foreach my $k ( sort keys %{$hashRef} )\r\n- {\r\n- my $v = $hashRef->{$k};\r\n- my $TE_dir = $dir.$k.\'/\';\r\n-\r\n- %num_per_overlap_size = (); $overlap_number = 0;\r\n- $flag = 0;\r\n- for ( my $i = 0; $i <= $#{$v->[1]} ; $i++ )\r\n- {\r\n- $reverseR = ${$v->[1]}[$i] ;\r\n- $begRev = $reverseR->[0];\r\n- $endRev = $begRev + length($reverseR->[1]) - 1;\r\n-\r\n- my $revR = reverse($reverseR->[1]);\r\n- $revR =~ tr/atgcuATGCU/tacgaTACGA/;\r\n-\r\n- for ( my $j = 0; $j <= $#{$v->[0]}; $j++ )\r\n- {\r\n- $sensR = ${$v->[0]}[$j];\r\n- $begSens = $sensR->[0];\r\n- $endSens = $begSens + length($sensR->[1]) - 1;\r\n-\r\n- if ( $begSens <= $endRev && $endSens > $endRev )\r\n- {\r\n- $flag = 1;\r\n- mkdir $TE_dir;\r\n- open $txt, \'>\', $TE_dir.\'overlap_size.txt\' || die "cannot open repartition\\n";\r\n-\r\n- $overlap = $endRev - $begSens + 1;\r\n- $snum = $dupRef->{$sensR->[0].$sensR->[1].$sensR->[2].$sensR->[3]};\r\n- $rnum = $dupRef->{$reverseR->[0].$reverseR->[1].$reverseR->[2].$reverseR->[3]};\r\n-\r\n- if ( $overlap == 10 )\r\n- {\r\n- $hasPpp->{ $sensR->[0].$sensR->[1].$sensR->[2].$sensR->[3] } = 1;\r\n- $hasPpp->{ $reverseR->[0].$reverseR->[1].$reverseR->[2].$reverseR->[3] } = 1;\r\n- }\r\n- next if $overlap > $max;\r\n- if ( $snum < $rnum )\r\n- {\r\n- $num_per_overlap_size{$overlap} += $snum;\r\n- $overlap_number += $snum;\r\n- }\r\n- else\r\n- {\r\n- $num_per_overlap_size{$overlap} += $rnum ;\r\n- $overlap_number += $rnum ;\r\n- }\r\n- }\r\n- }\r\n- }\r\n- if ( $max != 0 )\r\n- {\r\n- my @overlaps = ();\r\n- push @overlaps_names, $k;\r\n- for my $i (1..$max)\r\n- {\r\n- $num_per_overlap_size{$i} = 0 unless exists( $num_per_overlap_size{$i} );\r\n- push @overlaps, $num_per_overlap_size{$i};\r\n- }\r\n- push @distri_overlap, \\@overlaps;\r\n- }\r\n-\r\n- if ( $flag == 1 )\r\n- {\r\n- open $AP, \'>\', $TE_dir."antisensPPP.txt" || die "cannot create antisensPPP\\n";\r\n- open $AN, \'>\', $TE_dir."antisens.txt" || die "cannot create antisens\\n";\r\n- for ( my $i = 0; $i <= $#{$v->[1]} ; $i++ )\r\n- {\r\n- $reverseR = ${$v->[1]}[$i] ;\r\n- my $revR = reverse($reverseR->[1]);\r\n- $revR =~ tr/atgcuATGCU/tacgaTACGA/;\r\n- $rnum = $dupRef->{$reverseR->[0].$reverseR->[1].$reverseR->[2].$reverseR->[3]};\r\n- if ( $hasPpp->{ $reverseR->[0].$reverseR->[1].$reverseR->[2].$reverseR->[3] } == 1 )\r\n- {\r\n- print $AP ">$reverseR->[0]|$reverseR->[2]|$reverseR->[3]|$rnum\\n$revR\\n";\r\n- }\r\n- else\r\n- {\r\n- print $AN ">$reverseR->[0]|$reverseR->[2]|$reverseR->[3]|$rnum\\n$revR\\n";\r\n- }\r\n- }\r\n- close $AP; close $AN;\r\n-\r\n- open $SP, \'>\', $TE_dir."sensPPP.txt" || die "cannot create sensPPP\\n";\r\n- open $SN, \'>\', $TE_dir."sens.txt" || die "cannot create sens\\n";\r\n- for ( my $j = 0; $j <= $#{$v->[0]}; $j++ )\r\n- {\r\n- $sensR = ${$v->[0]}[$j];\r\n- $snum = $dupRef->{$sensR->[0].$sensR->[1].$sensR->[2].$sensR->[3]};\r\n- if ( $hasPpp->{ $sensR->[0].$sensR->[1].$sensR->[2].$sensR'..b' open $SP, \'>\', $TE_dir."sensPPP.txt" || die "cannot create sensPPP\\n";\n+ open $SN, \'>\', $TE_dir."sens.txt" || die "cannot create sens\\n";\n+ for ( my $j = 0; $j <= $#{$v->[0]}; $j++ )\n+ {\n+ $sensR = ${$v->[0]}[$j];\n+ $snum = $dupRef->{$sensR->[0].$sensR->[1].$sensR->[2].$sensR->[3]};\n+ if ( $hasPpp->{ $sensR->[0].$sensR->[1].$sensR->[2].$sensR->[3] } == 1 )\n+ {\n+ print $SP ">$sensR->[0]|$sensR->[2]|$sensR->[3]|$snum\\n$sensR->[1]\\n";\n+ }\n+ else\n+ {\n+ print $SN ">$sensR->[0]|$sensR->[2]|$sensR->[3]|$snum\\n$sensR->[1]\\n";\n+ }\n+ }\n+ close $SP; close $SN;\n+\n+ my $histo_png = $TE_dir.\'histogram.png\';\n+ histogram( \\%num_per_overlap_size, $histo_png, $overlap_number );\n+ print $txt "size\\tnumber\\tpercentage of the total overlap number\\n";\n+ foreach my $k ( sort {$a <=> $b} keys %num_per_overlap_size )\n+ {\n+ my $percentage = 0;\n+ $percentage = $num_per_overlap_size{$k} * 100 / $overlap_number unless $overlap_number == 0;\n+ print $txt "$k\\t$num_per_overlap_size{$k}\\t"; printf $txt "%.2f\\n",$percentage;\n+ }\n+ close $txt;\n+ }\n+ }\n+\n+ foreach my $tabP ( @distri_overlap )\n+ {\n+ my $sum = sum($tabP);\n+ my $ten = $tabP->[9];\n+ my $mean = mean($tabP);\n+ my $std = standard_deviation($tabP, $mean);\n+ my $zsc = z_significance($ten, $mean, $std);\n+ my $name = shift @overlaps_names;\n+ my $prob = \'NA\';\n+ $prob = 1 - &Math::CDF::pnorm( $zsc ) if $zsc ne \'NA\';\n+ print $ppp_f (join ("\\t", $name, $sum, $ten, $mean, $std, $zsc, $prob ),"\\n" );\n+ }\n+ close $ppp_f;\n+}\n+\n+sub count_mapped\n+{\n+ my ( $fai, $in_file ) = @_;\n+ my ( %mapped, %dup, %has_ppp );\n+\n+ open my $f, \'<\', $fai || die "cannot open $fai $! \\n";\n+ while(<$f>)\n+ {\n+ if ($_ =~ /(.*)\\t(\\d+)\\n/)\n+ {\n+ $mapped{$1} = [];\n+ $mapped{$1}->[0] = []; $mapped{$1}->[1] = [];\n+ }\n+ }\n+ close $f;\n+\n+ open my $infile, "samtools view \'$in_file\' |"|| die "cannot open input file $! \\n";\n+ while(<$infile>)\n+ {\n+ unless ($_ =~ /^\\@[A-Za-z][A-Za-z](\\t[A-Za-z][A-Za-z0-9]:[ -~]+)+$/ || $_ =~ /^\\@CO\\t.*/ )\n+ {\n+ my @line = split (/\\t/,$_);\n+ if ($line[1] == 0)\n+ {\n+ unless ( exists ($dup{$line[3].$line[9].$line[1].$line[2]}) )\n+ {\n+ push @{$mapped{$line[2]}->[0]} , [$line[3], $line[9], $line[1], $line[2]];\n+ $has_ppp {$line[3].$line[9].$line[1].$line[2]} = 0;\n+ }\n+ $dup{$line[3].$line[9].$line[1].$line[2]}+=1;\n+ }\n+ elsif ($line[1] == 16)\n+ {\n+ unless ( exists ($dup{$line[3].$line[9].$line[1].$line[2]}) )\n+ {\n+ push @{$mapped{$line[2]}->[1]} , [$line[3], $line[9], $line[1], $line[2]];\n+ $has_ppp{$line[3].$line[9].$line[1].$line[2]} = 0;\n+ }\n+ $dup{$line[3].$line[9].$line[1].$line[2]}+=1\n+ }\n+ }\n+ }\n+ close $infile;\n+ return (\\%mapped, \\%dup, \\%has_ppp );\n+}\n+\n+sub sum\n+{\n+ my $arrayref = shift;\n+ my $result = 0;\n+ foreach (@$arrayref) {$result += $_}\n+ return $result;\n+}\n+\n+sub mean\n+{\n+ my $arrayref = shift;\n+ my $result;\n+ foreach (@$arrayref) {$result += $_}\n+ return $result / scalar(@$arrayref);\n+}\n+\n+sub standard_deviation\n+{\n+ my ($arrayref, $mean) = @_;\n+ return sqrt ( mean ( [map $_**2 , @$arrayref ]) - ($mean**2));\n+}\n+\n+sub z_significance\n+{\n+ my ($ten, $mean, $std) = @_;\n+ my $z = \'NA\';\n+ $z = (($ten - $mean) / $std) if $std != 0;\n+ return $z;\n+}\n+\n+1;\n+\n' |
| b |
| diff -r 9645d995fb3c -r 9185ca0a7b43 bin/resize.pm --- a/bin/resize.pm Wed Oct 24 07:40:20 2018 -0400 +++ b/bin/resize.pm Wed Jan 16 08:18:13 2019 -0500 |
| [ |
| @@ -1,101 +1,101 @@ -package resize; - -use strict; -use warnings; - -use FindBin; -use lib $FindBin::Bin; -use Rcall qw ( histogram ); - -use Exporter; -our @ISA = qw( Exporter ); -our @EXPORT_OK = qw( &size_distribution ); - -sub size_distribution -{ - my ( $fastq, $fastq_out, $dir, $min, $max ) = @_; - - my ( %fragments_size, %duplicates ) ; - my $num = size($min, $max, $fastq, $fastq_out, \%fragments_size, \%duplicates); - - my $png = $dir.'histogram.png'; - histogram(\%fragments_size, $png, $num); - - my $size = $dir.'reads_size.txt'; - - - my $pourcentage; - open my $o, '>', $size || die "cannot open $size $!\n"; - print $o "size\tnumber\tpercentage\n"; - foreach my $k (sort { $a <=> $b } keys %fragments_size ) - { - $pourcentage = $fragments_size{$k} / $num * 100; - - print $o "$k\t$fragments_size{$k}\t"; - printf $o "%.2f\n",$pourcentage; - } - close $o; - - my $dup = $dir.'duplicates.txt' ; - open $o, '>', $dup || die "cannot open $size $!\n"; - print $o "size\tnumber\n"; - foreach my $k (sort { $duplicates{$b} <=> $duplicates{$a} } keys %duplicates ) - { - print $o "$k\t$duplicates{$k}\n"; - } - close $o; -} - -sub size -{ - my ($min, $max, $in_file, $out_file, $sizeHashR, $duplicateHashR) = @_; - my ($numreads, $size, $cmp, $ok, $line) = (0, 0, 0, 0); - my @fastq; - open (my $in, $in_file) || die "cannot open $in_file $!\n"; - open (my $out, ">".$out_file) || die "cannot create $out_file $!\n"; - while(<$in>) - { - chomp $_; - $cmp++; $line++; - if ($cmp == 1) - { - die "file do not contain a @ at line $line\n" unless ($_ =~ /^\@/ ); - $ok = 0; @fastq = (); - push(@fastq,$_); - } - elsif ($cmp == 2) - { - #die "unrecognized symbol at line $line\n" unless ($_ =~ /[atcgATCGnN]+/ || $_ =~ /^$/ ); - push(@fastq,$_); - $size = length($_); - if ($size >= $min && $size <= $max) - { - $numreads++; - ${$sizeHashR}{$size}+=1; - ${$duplicateHashR}{$_}+=1 if (defined($duplicateHashR)); - $ok = 1; - } - } - elsif ($cmp == 3 ) - { - die "file do not contain a + at line $line\n" unless $_ =~ /^\+/; - push(@fastq,$_); - } - elsif ($cmp == 4 ) - { - push(@fastq,$_); - $cmp = 0; - if ($ok == 1) - { - foreach my $t (@fastq) - { - print $out $t."\n"; - } - } - } - } - close $in; close $out; - return $numreads; -} - -1; +package resize; + +use strict; +use warnings; + +use FindBin; +use lib $FindBin::Bin; +use Rcall qw ( histogram ); + +use Exporter; +our @ISA = qw( Exporter ); +our @EXPORT_OK = qw( &size_distribution ); + +sub size_distribution +{ + my ( $fastq, $fastq_out, $dir, $min, $max ) = @_; + + my ( %fragments_size, %duplicates ) ; + my $num = size($min, $max, $fastq, $fastq_out, \%fragments_size, \%duplicates); + + my $png = $dir.'histogram.png'; + histogram(\%fragments_size, $png, $num); + + my $size = $dir.'reads_size.txt'; + + + my $pourcentage; + open my $o, '>', $size || die "cannot open $size $!\n"; + print $o "size\tnumber\tpercentage\n"; + foreach my $k (sort { $a <=> $b } keys %fragments_size ) + { + $pourcentage = $fragments_size{$k} / $num * 100; + + print $o "$k\t$fragments_size{$k}\t"; + printf $o "%.2f\n",$pourcentage; + } + close $o; + + my $dup = $dir.'duplicates.txt' ; + open $o, '>', $dup || die "cannot open $size $!\n"; + print $o "size\tnumber\n"; + foreach my $k (sort { $duplicates{$b} <=> $duplicates{$a} } keys %duplicates ) + { + print $o "$k\t$duplicates{$k}\n"; + } + close $o; +} + +sub size +{ + my ($min, $max, $in_file, $out_file, $sizeHashR, $duplicateHashR) = @_; + my ($numreads, $size, $cmp, $ok, $line) = (0, 0, 0, 0); + my @fastq; + open (my $in, $in_file) || die "cannot open $in_file $!\n"; + open (my $out, ">".$out_file) || die "cannot create $out_file $!\n"; + while(<$in>) + { + chomp $_; + $cmp++; $line++; + if ($cmp == 1) + { + die "file do not contain a @ at line $line\n" unless ($_ =~ /^\@/ ); + $ok = 0; @fastq = (); + push(@fastq,$_); + } + elsif ($cmp == 2) + { + #die "unrecognized symbol at line $line\n" unless ($_ =~ /[atcgATCGnN]+/ || $_ =~ /^$/ ); + push(@fastq,$_); + $size = length($_); + if ($size >= $min && $size <= $max) + { + $numreads++; + ${$sizeHashR}{$size}+=1; + ${$duplicateHashR}{$_}+=1 if (defined($duplicateHashR)); + $ok = 1; + } + } + elsif ($cmp == 3 ) + { + die "file do not contain a + at line $line\n" unless $_ =~ /^\+/; + push(@fastq,$_); + } + elsif ($cmp == 4 ) + { + push(@fastq,$_); + $cmp = 0; + if ($ok == 1) + { + foreach my $t (@fastq) + { + print $out $t."\n"; + } + } + } + } + close $in; close $out; + return $numreads; +} + +1; |
| b |
| diff -r 9645d995fb3c -r 9185ca0a7b43 bin/sRNAPipe.pl --- a/bin/sRNAPipe.pl Wed Oct 24 07:40:20 2018 -0400 +++ b/bin/sRNAPipe.pl Wed Jan 16 08:18:13 2019 -0500 |
| [ |
| b'@@ -1,268 +1,277 @@\n-#!/usr/bin/perl\r\n-use strict;\r\n-use warnings;\r\n-use Getopt::Long;\r\n-use Parallel::ForkManager;\r\n-use File::Basename;\r\n-use File::Copy::Recursive qw( dircopy );\r\n-use POSIX;\r\n-use FindBin;\r\n-use lib $FindBin::Bin;\r\n-use resize qw ( size_distribution );\r\n-use subgroups qw (subgroups );\r\n-use ppp qw ( ping_pong_partners );\r\n-use Rcall qw (pie_chart bg_to_png );\r\n-use align qw ( to_build get_unique sam_count sam_count_mis sam_sorted_bam rpms_rpkm rpms_rpkm_te BWA_call get_fastq_seq extract_sam sam_to_bam_bg );\r\n-use html qw ( main_page details_pages menu_page ppp_page );\r\n-use File::Copy;\r\n-\r\n-my ( @fastq, @fastq_n, $dir, $min, $max, $mis, $misTE, $help, $Pcheck, $mapnumf, $html_out);\r\n-my ( $ref, $tRNAs, $rRNAs, $snRNAs, $miRNAs, $transcripts, $TE );\r\n-my ( $si_min, $si_max, $pi_min, $pi_max );\r\n-my ( $build_index, $build_tRNAs, $build_rRNAs, $build_snRNAs, $build_miRNAs, $build_transcripts, $build_TE );\r\n-my $max_procs = 8;\r\n-\r\n-( $build_index, $build_tRNAs, $build_rRNAs, $build_snRNAs, $build_miRNAs, $build_transcripts, $build_TE ) = (0,0,0,0,0,0,0);\r\n-( $min, $max, $mis, $misTE, $si_min, $si_max, $pi_min, $pi_max, $dir ) = ( 18, 29, 0, 3, 21, 21, 23, 29 );\r\n-$Pcheck =\'true\';\r\n-\r\n-GetOptions (\r\n-\t"fastq=s" => \\@fastq,\r\n-\t"fastq_n=s" => \\@fastq_n,\r\n-\t"dir=s" => \\$dir,\r\n-\t"min:i" => \\$min,\r\n-\t"max:i" => \\$max,\r\n-\t"si_min:i" => \\$si_min,\r\n-\t"si_max:i" => \\$si_max,\r\n-\t"pi_min:i" => \\$pi_min,\r\n-\t"pi_max:i" => \\$pi_max,\r\n-\t"mis:i" => \\$mis,\r\n-\t"misTE:i" => \\$misTE,\r\n-\t"html:s" => \\$html_out,\r\n-\t"PPPon:s" => \\$Pcheck,\r\n-\t"help" => \\$help,\r\n-\t"ref:s" => \\$ref,\r\n-\t"tRNAs:s" => \\$tRNAs,\r\n-\t"rRNAs:s" => \\$rRNAs,\r\n-\t"snRNAs:s" => \\$snRNAs,\r\n-\t"miRNAs:s" => \\$miRNAs,\r\n-\t"transcripts:s" => \\$transcripts,\r\n-\t"TE:s" => \\$TE,\r\n-\t"build_index" => \\$build_index,\r\n-\t"build_tRNAs" => \\$build_tRNAs,\r\n-\t"build_snRNAs" => \\$build_snRNAs,\r\n-\t"build_miRNAs" => \\$build_miRNAs,\r\n-\t"build_transcripts" => \\$build_transcripts,\r\n-\t"build_rRNAs" => \\$build_rRNAs,\r\n-\t"build_TE" => \\$build_TE\r\n-);\r\n-\r\n-my $fq_collection = \'fastq_dir/\';\r\n-mkdir $dir; mkdir $fq_collection;\r\n-$dir = $dir.\'/\' unless $dir =~ /\\/$/;\r\n-mkdir $dir.\'/css\';mkdir $dir.\'/js\';\r\n-dircopy( $FindBin::Bin.\'/css\', $dir.\'/css\' );\r\n-dircopy( $FindBin::Bin.\'/js\', $dir.\'/js\' );\r\n-\r\n-my $file = $dir.\'report.txt\';\r\n-open my $report, \'>\', $file or die "Cannot open $file $!\\n";\r\n-\r\n-my @toBuild = ( [$build_index, \\$ref], [$build_tRNAs, \\$tRNAs], [$build_rRNAs, \\$rRNAs], [$build_snRNAs, \\$snRNAs], [$build_miRNAs, \\$miRNAs], [$build_transcripts, \\$transcripts], [$build_TE, \\$TE] );\r\n-to_build ( \\@toBuild, $report, $dir );\r\n-\r\n-my $proc_child = ceil($max_procs / scalar(@fastq));\r\n-my $proc_grand_child = ceil($proc_child/4);\r\n-my $pm = Parallel::ForkManager->new($max_procs);\r\n-my $pm2 = Parallel::ForkManager->new($proc_grand_child);\r\n-\r\n-$pm->run_on_finish( sub {\r\n-\tmy ($pid, $exit_code, $ident) = @_;\r\n-\tprint $report "Fastq fork $ident just finished ".\r\n-\t"with PID $pid and exit code: $exit_code\\n";\r\n-\tdie "Something went wrong!\\n" if $exit_code != 0;\r\n-\t});\r\n-$pm->run_on_start( sub {\r\n-\tmy ($pid,$ident)=@_;\r\n-\tprint $report "Fastq fork : $ident started, pid: $pid\\n";\r\n-\t});\r\n-$pm2->run_on_finish( sub {\r\n-\tmy ($pid, $exit_code, $ident) = @_;\r\n-\tprint $report "** Subgroup fork $ident just finished ".\r\n-\t"with PID $pid and exit code: $exit_code\\n";\r\n-\tdie "Something went wrong!\\n" if $exit_code != 0;\r\n-\t});\r\n-$pm2->run_on_start( sub {\r\n-\tmy ($pid,$ident)=@_;\r\n-\tprint $report "** Subgroup fork $ident started, pid: $pid\\n";\r\n-\t});\r\n-\r\n-\r\n-foreach my $child ( 0 .. $#fastq )\r\n-{\r\n-\tmy @suffix = (\'.fastq\', \'.fastq.gz,\', \'.fq\', \'.fq.gz\', \'ref\', \'.dat\', \'.fa\',\'.fas\',\'.fasta\', \'.txt\');\r\n-\tmy ( $name, $path, $suffix ) = fileparse( $fastq[$child], @suffix );\r\n-\tmy ( $ref_name, $ref_path, $ref_suffix ) = fileparse( $ref, @suffix );\r\n-\tmy ( $TE_name, $TE_path, $TE_suffix ) = fileparse( $TE, @suffix );\r\n-\tmy ( $ex_name, $ex_path, $ex_suffix ) = fileparse( $transcripts, @suffix );\r\n-\r\n-\t$pm->start'..b'anscripts_fastq, $type_uni_transcripts_fastq );\n+ extract_sam ( $type_sequence_hashP, $sam_genome, $type_sam_genome, $type_sam_uni_genome, $type_genome_fastq, $type_uni_genome_fastq );\n+ }\n+ \n+ my $ex_count_file = $type_dir.$type_prefix.\'transcripts_reads_counts.txt\';\n+ my ( $ex_count, $ex_ref_size ) = sam_count_mis ( $type_sam_transcripts );\n+ rpms_rpkm_te( $ex_count, $ex_ref_size, $ma, $ex_count_file, $pi, $mi, $bo );\n+ \n+ my ( $TEs_count, $TEs_ref_size, $TEs_count_NoM, $TEs_count_M ) = sam_count_mis ( $type_sam_TEs );\n+ my $TEs_count_file = $type_dir.$type_prefix.\'TEs_reads_counts.txt\';\n+ my $TEs_count_file_M = $type_dir.$type_prefix.\'TEs_reads_counts_mismatches.txt\';\n+ my $TEs_count_file_noM = $type_dir.$type_prefix.\'TEs_reads_counts_nomismatches.txt\';\n+ rpms_rpkm_te( $TEs_count, $TEs_ref_size, $ma, $TEs_count_file, $pi, $mi, $bo );\n+ rpms_rpkm_te( $TEs_count_NoM, $TEs_ref_size, $ma, $TEs_count_file_noM, $pi, $mi, $bo );\n+ rpms_rpkm_te( $TEs_count_M, $TEs_ref_size, $ma, $TEs_count_file_M, $pi, $mi, $bo );\n+ \n+ sam_to_bam_bg ( $type_sam_TEs, $scale, $grand_child );\n+ sam_sorted_bam ( $type_sam_transcripts, $grand_child ); sam_sorted_bam ( $type_sam_uni_transcripts, $grand_child );\n+ sam_sorted_bam ( $type_sam_uni_TEs, $grand_child );\n+ \n+ my $Gviz_TEs = $type_dir.\'Gviz_TEs/\';\n+ mkdir $Gviz_TEs;\n+ bg_to_png ( $group_dir.\'TEs.fai\', $type_dir.$type_prefix.\'TEs_plus.bedgraph\', $type_dir.$type_prefix.\'TEs_minus.bedgraph\', $Gviz_TEs, \'Kb\' );\n+ \n+ my $Gviz_genome= $type_dir.\'Gviz_genome/\';\n+ my $Gviz_genome_rand = $Gviz_genome.\'rand/\';\n+ my $Gviz_genome_uni = $Gviz_genome.\'unique/\';\n+ mkdir $Gviz_genome; mkdir $Gviz_genome_uni; mkdir $Gviz_genome_rand;\n+ \n+ sam_to_bam_bg ( $type_sam_genome, $scale, $grand_child );\n+ sam_to_bam_bg ( $type_sam_uni_genome, $scale, $grand_child );\n+ \n+ bg_to_png ( $fai_file, $type_dir.$type_prefix.\'genome_unique_plus.bedgraph\', $type_dir.$type_prefix.\'genome_unique_minus.bedgraph\', $Gviz_genome_uni, \'Mb\' );\n+ bg_to_png ( $fai_file, $type_dir.$type_prefix.\'genome_plus.bedgraph\', $type_dir.$type_prefix.\'genome_minus.bedgraph\', $Gviz_genome_rand, \'Mb\' );\n+ \n+ #HTML Details\n+ my $prefix_details_pages = $dir.$fastq_n[$child].\'-\'.$types_names[$grand_child];\n+ details_pages ( $type_dir, $prefix_details_pages, \\@fastq_n, $fastq_n[$child], $misTE, $dir, $Pcheck );\n+ \n+ $pm2->finish();\n+ }\n+ $pm2->wait_all_children;\n+ \n+ if ( $Pcheck eq \'true\' )\n+ {\n+ my $ppp = $group_dir.\'PPPartners/\'; mkdir $ppp;\n+ print $report "ping_pong_partners $group_dir/piRNAs/TEs.sam $ppp\\n";\n+ ping_pong_partners ( $group_dir.\'TEs.fai\', $group_dir.\'piRNAs/piRNAs-TEs_sorted.bam\', $ppp, $pi_min );\n+ my $ppp_page = $dir.$fastq_n[$child].\'-piRNAs-PPP.html\';\n+ ppp_page ( $group_dir, $ppp_page, \\@fastq_n, $fastq_n[$child], $ppp, $dir );\n+ }\n+ \n+ #HTML Main Webpage\n+ my $index_page = $dir.$fastq_n[$child].\'.html\';\n+ main_page ( $gen_dir, $index_page, \\@fastq_n, $fastq_n[$child], $ma, $ma_uni, $dir );\n+ copy ($index_page, $html_out) if $child == 0;\n+ #HTML Menu\n+ my $menu_page = $dir.$fastq_n[$child].\'-sub.html\';\n+ menu_page ( $group_dir, $menu_page, \\@fastq_n, $fastq_n[$child], $min, $max, $si_min, $si_max, $pi_min, $pi_max, $dir );\n+ unlink glob "\'$group_dir\'*.sam"; unlink glob "\'$group_dir\'*.fastq";\n+ $pm->finish(); # pass an exit code to finish\n+ }\n+ $pm->wait_all_children;\n+ unlink glob "\'$dir\'"."dataset_*symlink.fa*";\n+ print $report "Job done!\\n";\n+ close $report;\n+} else {\n+ print "sRNAPipe v1.1\\n";\n+}\n' |
| b |
| diff -r 9645d995fb3c -r 9185ca0a7b43 bin/subgroups.pm --- a/bin/subgroups.pm Wed Oct 24 07:40:20 2018 -0400 +++ b/bin/subgroups.pm Wed Jan 16 08:18:13 2019 -0500 |
| [ |
| b'@@ -1,174 +1,174 @@\n-package subgroups;\r\n-\r\n-use strict;\r\n-use warnings;\r\n-use Exporter;\r\n-our @ISA = qw( Exporter );\r\n-our @EXPORT_OK = qw( &subgroups );\r\n-\r\n-use POSIX;\r\n-use File::Copy;\r\n-use FindBin;\r\n-use lib $FindBin::Bin;\r\n-use align qw ( get_hash_alignment );\r\n-\r\n-sub subgroups\r\n-{\r\n-\tmy ($fin, $dir, $mis, $mis_TE, $proc, $tRNAs, $rRNAs, $snRNAs, $miRNAs, $transcripts, $TE, $min_si, $max_si, $min_pi, $max_pi, $report ) = @_;\r\n-\tmy (@files, $sum, $pie, $repar, %ismapped, %isjunk, %repartition, @junk_ref, @all_ref );\r\n-\r\n-\tsrand();\r\n-\tprint $report "----------------------------\\n";\r\n-\tprint $report "Create subgroups:\\nfastq_in: $fin\\ndirectory_out: $dir\\nmismatches: $mis\\nmismatches TE: $mis_TE\\n";\r\n-\r\n-\tmkdir $dir;\r\n-\t$dir = $dir.\'/\' unless $dir =~ /(.*)\\/$/;\r\n-\r\n-\tmy $accept_miRNas = $dir.\'miRNAs.fastq\'; \r\n-\tmy $reject_miRNAs = $dir.\'miRNAs_rejected.fastq\';\r\n-\tmy $sam_miRNAs = $dir.\'miRNAs.sam\'; \r\n-\tmy @tmp = get_hash_alignment($miRNAs, $mis, 1, 1, $accept_miRNas, $reject_miRNAs, $fin, $proc, \'miRNAs\',$sam_miRNAs, $report);\r\n-\tmy $mi = $tmp[0]; my $sam = \'\';\r\n-\t$repartition{\'miRNAs\'} = $mi;\r\n-\r\n-\r\n-\tmy $reject_rRNAs = $dir.\'rRNAs_rejected.fastq\';\r\n-\tif ( $rRNAs eq \'None\')\r\n-\t{\r\n-\t\tmove($reject_miRNAs,$reject_rRNAs);\r\n-\t}\r\n-\telse\r\n-\t{\r\n-\t\t$sam = new String::Random;\r\n-\t\t$sam = $sam->randpattern("CCcccccc");\r\n-\t\t@tmp = get_hash_alignment($rRNAs, $mis, 0, 1, \'NA\', $reject_rRNAs, $reject_miRNAs, $proc, \'rRNAs\', $sam, $report);\r\n-\t\t$repartition{\'rRNAs\'} = $tmp[0];\r\n-\t\tunlink $sam, $sam.\'_aln.err\', $sam.\'_samse.err\';\r\n-\t}\r\n-\r\n-\tmy $reject_tRNAs = $dir.\'rRNAs_rejected.fastq\';\r\n-\tif ( $rRNAs eq \'None\')\r\n-\t{\r\n-\t\tmove($reject_rRNAs,$reject_tRNAs);\r\n-\t}\r\n-\telse\r\n-\t{\r\n-\t\t$sam = new String::Random;\r\n-\t\t$sam = $sam->randpattern("CCcccccc");\r\n-\t\t@tmp = get_hash_alignment($tRNAs, $mis, 0, 1, \'NA\', $reject_tRNAs, $reject_rRNAs, $proc, \'tRNAs\', $sam, $report);\r\n-\t\t$repartition{\'tRNAs\'} = $tmp[0];\r\n-\t\tunlink $sam, $sam.\'_aln.err\', $sam.\'_samse.err\';\r\n-\t}\r\n-\r\n-\r\n-\tmy $bonafide = $dir.\'bonafide_reads.fastq\';\r\n-\tif ( $rRNAs eq \'None\')\r\n-\t{\r\n-\t\tmove($reject_tRNAs,$bonafide);\r\n-\t}\r\n-\telse\r\n-\t{\r\n-\t\t$sam = new String::Random;\r\n-\t\t$sam = $sam->randpattern("CCcccccc");\r\n-\t\t@tmp = get_hash_alignment($snRNAs, $mis, 0, 1, \'NA\', $bonafide, $reject_tRNAs, $proc, \'snRNAs\', $sam, $report);\r\n-\t\t$repartition{\'snRNAs\'} = $tmp[0];\r\n-\r\n-\t\tunlink $sam, $sam.\'_aln.err\', $sam.\'_samse.err\';\r\n-\t}\r\n-\tmy $bo = $tmp[1];\r\n-\r\n-\tmy $sam_transcripts = $dir.\'transcripts.sam\'; \r\n-\tmy $reject_transcripts = $dir.\'rejected_transcripts.fastq\';\r\n-\t@tmp = get_hash_alignment($transcripts, $mis, 0, 1, \'NA\', $reject_transcripts, $bonafide, $proc, \'transcripts\', $sam_transcripts, $report, $dir.\'transcripts.fai\');\r\n-\t$repartition{\'transcripts\'} = $tmp[0];\r\n-\r\n-\t\r\n-\tmy $sam_TEs = $dir.\'TEs.sam\';\r\n-\tmy $reject_TEs = $dir.\'rejected.fastq\';\r\n-\t@tmp = get_hash_alignment($TE, $mis_TE, 0, 1, \'NA\', $reject_TEs, $reject_transcripts, $proc, \'TEs\', $sam_TEs, $report, $dir.\'TEs.fai\' );\r\n-\t$repartition{\'TEs\'} = $tmp[0] ; $repartition{\'others\'} = $tmp[1];\r\n-\tunlink $sam, $sam.\'_aln.err\', $sam.\'_samse.err\';\r\n-\tunlink $reject_transcripts;\r\n-\tunlink $reject_rRNAs;\r\n-\tunlink $reject_miRNAs;\r\n-\tunlink $reject_tRNAs;\r\n-\r\n-\t#create repartition\r\n-\tmy $pi = fastqSubgroups($bonafide, $dir, $min_si, $max_si, $min_pi, $max_pi );\r\n-\r\n-\topen (my $re, \'>\'.$dir.\'repartition.txt\') || die "cannot open $dir repartition.txt $!\\n";\r\n-\tprint $re "type\\tnumber\\tpercentage\\n";\r\n-\t$sum += $_ foreach values %repartition;\r\n-\tforeach my $k ( sort keys %repartition ) \r\n-\t{\r\n-\t\tmy $prct = 0;\r\n-\t\t$prct = $repartition{$k} / $sum * 100 if $sum != 0;\r\n-\t\tprint $re "$k\\t$repartition{$k}\\t"; printf $re "%.2f\\n",$prct;\r\n-\t}\r\n-\treturn ( $bo, $mi, $pi);\r\n-}\r\n-\r\n-sub fastqSubgroups\r\n-{\r\n- my ( $fastq, $output_directory, $min_si, $max_si, $min_pi, $max_pi ) = @_;\r\n- my $fastq_siRNA = $output_directory."siRNAs.fastq";\r\n- my $fastq_piRNA = $output_directory."piRNAs.fastq";\r\n-\r\n- open my $fic, \'<\', $fastq || die "cannot open input fi'..b'\n+ unlink $sam, $sam.\'_aln.err\', $sam.\'_samse.err\';\n+ }\n+\n+\n+ my $bonafide = $dir.\'bonafide_reads.fastq\';\n+ if ( $rRNAs eq \'None\')\n+ {\n+ move($reject_tRNAs,$bonafide);\n+ }\n+ else\n+ {\n+ $sam = new String::Random;\n+ $sam = $sam->randpattern("CCcccccc");\n+ @tmp = get_hash_alignment($snRNAs, $mis, 0, 1, \'NA\', $bonafide, $reject_tRNAs, $proc, \'snRNAs\', $sam, $report);\n+ $repartition{\'snRNAs\'} = $tmp[0];\n+\n+ unlink $sam, $sam.\'_aln.err\', $sam.\'_samse.err\';\n+ }\n+ my $bo = $tmp[1];\n+\n+ my $sam_transcripts = $dir.\'transcripts.sam\';\n+ my $reject_transcripts = $dir.\'rejected_transcripts.fastq\';\n+ @tmp = get_hash_alignment($transcripts, $mis, 0, 1, \'NA\', $reject_transcripts, $bonafide, $proc, \'transcripts\', $sam_transcripts, $report, $dir.\'transcripts.fai\');\n+ $repartition{\'transcripts\'} = $tmp[0];\n+\n+ \n+ my $sam_TEs = $dir.\'TEs.sam\';\n+ my $reject_TEs = $dir.\'rejected.fastq\';\n+ @tmp = get_hash_alignment($TE, $mis_TE, 0, 1, \'NA\', $reject_TEs, $reject_transcripts, $proc, \'TEs\', $sam_TEs, $report, $dir.\'TEs.fai\' );\n+ $repartition{\'TEs\'} = $tmp[0] ; $repartition{\'others\'} = $tmp[1];\n+ unlink $sam, $sam.\'_aln.err\', $sam.\'_samse.err\';\n+ unlink $reject_transcripts;\n+ unlink $reject_rRNAs;\n+ unlink $reject_miRNAs;\n+ unlink $reject_tRNAs;\n+\n+ #create repartition\n+ my $pi = fastqSubgroups($bonafide, $dir, $min_si, $max_si, $min_pi, $max_pi );\n+\n+ open (my $re, \'>\'.$dir.\'repartition.txt\') || die "cannot open $dir repartition.txt $!\\n";\n+ print $re "type\\tnumber\\tpercentage\\n";\n+ $sum += $_ foreach values %repartition;\n+ foreach my $k ( sort keys %repartition )\n+ {\n+ my $prct = 0;\n+ $prct = $repartition{$k} / $sum * 100 if $sum != 0;\n+ print $re "$k\\t$repartition{$k}\\t"; printf $re "%.2f\\n",$prct;\n+ }\n+ return ( $bo, $mi, $pi);\n+}\n+\n+sub fastqSubgroups\n+{\n+ my ( $fastq, $output_directory, $min_si, $max_si, $min_pi, $max_pi ) = @_;\n+ my $fastq_siRNA = $output_directory."siRNAs.fastq";\n+ my $fastq_piRNA = $output_directory."piRNAs.fastq";\n+\n+ open my $fic, \'<\', $fastq || die "cannot open input file $! \\n";\n+ open my $si, \'>\', $fastq_siRNA || die "cannot open siRNA.fastq $! \\n";\n+ open my $pi, \'>\', $fastq_piRNA || die "cannot open piRNA.fastq $! \\n";\n+ \n+ my ($length, $cmp, $type, $siRNA_number, $miRNA_h_number, $piRNA_number, $not_pi_number) = (0,0,0,0,0,0,0);\n+ my (@fastq) =(); my $seq_name;\n+ my $out;\n+ while(<$fic>)\n+ {\n+ chomp $_;\n+ $cmp++;\n+ if ($cmp == 1)\n+ {\n+ die "file do not contain a @ at line $cmp\\n" unless ($_ =~ /^\\@/ );\n+ $type = 0; @fastq = ();\n+ if ($_ =~ /^\\@(.*)\\s.*/) { $seq_name = $1;}\n+ elsif ($_ =~ /^\\@(.*)/) {$seq_name = $1;}\n+ push(@fastq,$_);\n+ }\n+ elsif ($cmp == 2)\n+ {\n+ #die "unrecognized symbol at line $cmp\\n" unless $_ =~ /[atcgATCGnN]+/;\n+ push(@fastq,$_);\n+ $length = length($_);\n+ $type = 0;\n+ if ( $length >= $min_si && $length <= $max_si )\n+ {\n+ $type = 2;\n+ $siRNA_number++;\n+ }\n+ if ($length >= $min_pi && $length <= $max_pi )\n+ {\n+ $type += 4;\n+ $piRNA_number++;\n+ }\n+ }\n+ elsif ($cmp == 3 )\n+ {\n+ die "file do not contain a + at line $cmp\\n" unless $_ =~ /^\\+/;\n+ push(@fastq,$_);\n+ }\n+ elsif ($cmp == 4 )\n+ {\n+ push(@fastq,$_);\n+ $cmp = 0;\n+ if ($type != 0)\n+ {\n+ if ($type & 4 ) { foreach my $t (@fastq) { print $pi $t."\\n";} }\n+ if ($type & 2 ) { foreach my $t (@fastq) { print $si $t."\\n";} }\n+ }\n+ }\n+ }\n+ close $fic;\n+ close $si; close $pi;\n+ return ($piRNA_number);\n+}\n+\n+1;\n' |
| b |
| diff -r 9645d995fb3c -r 9185ca0a7b43 sRNAPipe.xml --- a/sRNAPipe.xml Wed Oct 24 07:40:20 2018 -0400 +++ b/sRNAPipe.xml Wed Jan 16 08:18:13 2019 -0500 |
| [ |
| b'@@ -1,252 +1,271 @@\n-<tool id="sRNAPipe" name="sRNAPipe" version="1.0">\r\n- <description>In-depth study of small RNA</description>\r\n- <command><![CDATA[\r\n- perl \'$__tool_directory__/bin/sRNAPipe.pl\'\r\n-\r\n- --fastq \'${first_input}\'\r\n- --fastq_n \'${first_input.name}\'\r\n- #for $input_file in $input_files:\r\n- --fastq \'${input_file.additional_input}\'\r\n- --fastq_n \'${input_file.additional_input.name}\'\r\n- #end for\r\n-\r\n- #if $Genome.refGenomeSource == "history":\r\n- --ref \'${Genome.ownFile}\'\r\n- --build_index\r\n- #else:\r\n- --ref \'${Genome.indices.fields.path}\'\r\n- #end if\r\n-\r\n- #if $tRNAs.refGenomeSource == "history":\r\n- --tRNAs \'${tRNAs.ownFile}\'\r\n- --build_tRNAs\r\n- #elif $tRNAs.refGenomeSource == "none":\r\n- --tRNAs "None"\r\n- #else:\r\n- --tRNAs \'${tRNAs.indices.fields.path}\'\r\n- #end if\r\n-\r\n- #if $snRNAs.refGenomeSource == "history":\r\n- --snRNAs \'${snRNAs.ownFile}\'\r\n- --build_snRNAs\r\n- #elif $snRNAs.refGenomeSource == "none":\r\n- --snRNAs "None"\r\n- #else:\r\n- --snRNAs \'${snRNAs.indices.fields.path}\'\r\n- #end if\r\n-\r\n- #if $rRNAs.refGenomeSource == "history":\r\n- --rRNAs "${rRNAs.ownFile}"\r\n- --build_rRNAs\r\n- #elif $rRNAs.refGenomeSource == "none":\r\n- --rRNAs "None"\r\n- #else:\r\n- --rRNAs \'${rRNAs.indices.fields.path}\'\r\n- #end if\r\n-\r\n- #if $miRNAs.refGenomeSource == "history":\r\n- --miRNAs \'${miRNAs.ownFile}\'\r\n- --build_miRNAs\r\n- #else:\r\n- --miRNAs \'${miRNAs.indices.fields.path}\'\r\n- #end if\r\n-\r\n- #if $transcripts.refGenomeSource == "history":\r\n- --transcripts \'${transcripts.ownFile}\'\r\n- --build_transcripts\r\n- #else:\r\n- --transcripts \'${transcripts.indices.fields.path}\'\r\n- #end if\r\n-\r\n- #if $TE.refGenomeSource == "history":\r\n- --TE \'${TE.ownFile}\'\r\n- --build_TE\r\n- #else:\r\n- --TE \'${TE.indices.fields.path}\'\r\n- #end if\r\n-\r\n- --si_min $si_min\r\n- --si_max $si_max\r\n- --pi_min $pi_min\r\n- --pi_max $pi_max\r\n- --min $min\r\n- --max $max\r\n-\r\n- --mis $mis\r\n- --misTE $misTE\r\n- --dir $html_out.files_path\r\n- --html $html_out\r\n- --PPPon $PPPon\r\n- ]]>\r\n- </command>\r\n-\r\n- <requirements> \r\n- <requirement type="package" version="0.7.12">bwa</requirement>\r\n- <requirement type="package" version="2.24">bedtools</requirement>\r\n- <requirement type="package" version="1.5">samtools</requirement>\r\n- <requirement type="package" version="3.3.2">r-base</requirement>\r\n- <requirement type="package" version="5.22.0">perl</requirement>\r\n- <requirement type="package" version="2.50">perl-getopt-long</requirement>\r\n- <requirement type="package" version="1.17">perl-parallel-forkmanager</requirement>\r\n- <requirement type="package" version="0.34" >perl-statistics-r</requirement>\r\n- <requirement type="package" version="0.30">perl-string-random</requirement>\r\n- <requirement type="package" version="0.38" >perl-file-copy-recursive</requirement>\r\n- <requirement type="package" version="0.1" >perl-math-cdf</requirement>\r\n- <requirement type="package" version="3.6">r-plotrix</requirement>\r\n- <requirement type="package" version="1.14.0">bioconductor-sushi</requirement>\r\n- <requirement type="package" version="1.1_2">r-rcolorbrewer</requirement>\r\n- <requirement type="package" version="2.2.1">r-ggplot2</requirement>\r\n- </requirements> \r\n-\r\n- <inputs>\r\n- <param format="fastqsanger" name="first_input" type="data" label="fastqsanger (Q33)" help=""/>\r\n- <repeat name="input_files" title="Additional Fastq Files">\r\n- <param format="fastqsanger" name="additional_input" type="data" label="fastqsanger (Q33)" help=""/>\r\n- </repeat>\r\n- <conditional name="Genome">\r\n- <param name="refGenomeSource" type="select" label="Will you select a reference genome from your history or use a built-in index?">\r\n- <option value="indexed">Use a built-in index</option>\r\n- <option value="history">Use one from the history</option>\r\n- </param>\r\n- '..b'file="fastq_dir/reads-sample-small.fastq-bonafide_reads-transcripts_uni.fastq" />\n+ <element name="reads-sample-small.fastq-miRNAs-genome" file="fastq_dir/reads-sample-small.fastq-miRNAs-genome.fastq" />\n+ <element name="reads-sample-small.fastq-miRNAs-genome_uni" file="fastq_dir/reads-sample-small.fastq-miRNAs-genome_uni.fastq" />\n+ <element name="reads-sample-small.fastq-miRNAs-TEs_uni" file="fastq_dir/reads-sample-small.fastq-miRNAs-TEs_uni.fastq" />\n+ <element name="reads-sample-small.fastq-miRNAs-transcripts" file="fastq_dir/reads-sample-small.fastq-miRNAs-transcripts.fastq" />\n+ <element name="reads-sample-small.fastq-miRNAs-transcripts_uni" file="fastq_dir/reads-sample-small.fastq-miRNAs-transcripts_uni.fastq" />\n+ <element name="reads-sample-small.fastq-piRNAs-genome" file="fastq_dir/reads-sample-small.fastq-piRNAs-genome.fastq" />\n+ <element name="reads-sample-small.fastq-piRNAs-genome_uni" file="fastq_dir/reads-sample-small.fastq-piRNAs-genome_uni.fastq" />\n+ <element name="reads-sample-small.fastq-piRNAs-TEs" file="fastq_dir/reads-sample-small.fastq-piRNAs-TEs.fastq" />\n+ <element name="reads-sample-small.fastq-piRNAs-TEs_uni" file="fastq_dir/reads-sample-small.fastq-piRNAs-TEs_uni.fastq" />\n+ <element name="reads-sample-small.fastq-piRNAs-transcripts" file="fastq_dir/reads-sample-small.fastq-piRNAs-transcripts.fastq" />\n+ <element name="reads-sample-small.fastq-piRNAs-transcripts_uni" file="fastq_dir/reads-sample-small.fastq-piRNAs-transcripts_uni.fastq" />\n+ <element name="reads-sample-small.fastq-siRNAs-genome" file="fastq_dir/reads-sample-small.fastq-siRNAs-genome.fastq" />\n+ <element name="reads-sample-small.fastq-siRNAs-genome_uni" file="fastq_dir/reads-sample-small.fastq-siRNAs-genome_uni.fastq" />\n+ <element name="reads-sample-small.fastq-siRNAs-TEs" file="fastq_dir/reads-sample-small.fastq-siRNAs-TEs.fastq" />\n+ <element name="reads-sample-small.fastq-siRNAs-TEs_uni" file="fastq_dir/reads-sample-small.fastq-siRNAs-TEs_uni.fastq" />\n+ <element name="reads-sample-small.fastq-siRNAs-transcripts" file="fastq_dir/reads-sample-small.fastq-siRNAs-transcripts.fastq" />\n+ <element name="reads-sample-small.fastq-siRNAs-transcripts_uni" file="fastq_dir/reads-sample-small.fastq-siRNAs-transcripts_uni.fastq" />\n+ <element name="reads-sample-small.fastq_unique_mappers" file="fastq_dir/reads-sample-small.fastq_unique_mappers.fastq" />\n+ <element name="reads-sample-small.fastq_unmapped" file="fastq_dir/reads-sample-small.fastq_unmapped.fastq" />\n+ </output_collection>\n+ </test>\n+ </tests>\n+ <help>\n+ \t**User manual**\n+ \t"https://github.com/brassetjensen/sRNAPipe/blob/master/sRNAPipe_User_Manual.pdf"\n+ </help>\n+ <citations>\n+ <citation type="doi">10.1038/nature12962</citation>\n+ <citation type="doi">10.1038/nature11233</citation>\n+ <citation type="doi">10.1186/gb4172</citation>\n+ <citation type="doi">10.1038/nature04916</citation>\n+ <citation type="doi">10.1016/j.cell.2007.01.043</citation>\n+ <citation type="doi">10.1016/j.celrep.2015.02.062</citation>\n+ <citation type="doi">10.1093/bioinformatics/btp324</citation>\n+ <citation type="doi">10.1093/bioinformatics/btp352</citation>\n+ <citation type="doi">10.1002/0471250953.bi1112s47</citation>\n+ <citation type="doi">10.1093/bioinformatics/btu379</citation>\n+ <citation type="doi">10.1002/embr.201337898</citation>\n+ <citation type="doi">10.1038/ncomms13739</citation>\n+ <citation type="doi">10.1093/nar/gkt310</citation>\n+ <citation type="doi">10.1186/s13072-015-0041-5</citation>\n+ <citation type="doi">10.1093/bioinformatics/btu647</citation>\n+ </citations>\n+</tool>\n' |
| b |
| diff -r 9645d995fb3c -r 9185ca0a7b43 test-data/TE-file-small.fa --- a/test-data/TE-file-small.fa Wed Oct 24 07:40:20 2018 -0400 +++ b/test-data/TE-file-small.fa Wed Jan 16 08:18:13 2019 -0500 |
| b |
| b'@@ -1,34 +1,34 @@\n->BATUMI_I\tBEL\tDrosophila melanogaster\r\n-ttttggtccttcgagccggatcacctggattttcaagtttgtccaccagcgaacaaattataagataagtacgaaatttccattccttttaattgccggtctgcagcaaaaggttcgaaaatccaatttcgttcaatttgctgtaagatttattgtcaaatctaacggatttctccgacaaaaggcaattaaagaaaagtacttatccaatctcacgggcgccgcatattactcgccgttctccgttctcctttcaccctcattcgtgaaaatttctaaagtccaaatgggcgaatatatttaaatattaatccagtgcgataatgcaaaattccaaatgtgaaaaagtgaataatttgtgccaagttcagtgaaactttctaagtccaaagctctgccaaaattggcaaaaattctgttctcgtttcactgtgtcaaagcgaagccaaacttcttttcgcaacacatttttgctttaactccgcagtccacttaataccatttgctttgctatcgaagaataccacaacgaaacaaacaacaccataccctctggccattcaaataacatattaattaacatttccgcagttccatatctcttacatcaacatatacctactccatactcttgcatatattcacatcttacacaatatatcctcaccatatattacatatattacatcaacatataatatccacatatattaccgacatacattgcgcatattatcagcattcctttaacgtataccaaagtttaaattcgatcccgtcggcaaatccaaccacaaataaaatttattccaagtgccgacgcggaaaggcgttttcttttccatcaattttttccgtaaatttccaaattaatttccgagcaataaattaaaagcggttttttctttttttttaacaaataacttattgttgaaaacatttattaaattattaaaaattatataaataatacgaccgccaaatacaagtcgttcacccgacaaatattttttcctgtattgcttggatattaatttgtgtttgttttagaagtacttacaacgcggagaaaagactccaaatccaccattccattttctccgtttccagttataaacaaaaaaataaataaaattttcttccttctaataaacattttattttaccgtgttcacattccaagtgttccaaccgtaaataaggtggacctaattaccataaatcacaggtcatttatacaattcgctgttcactccgagtcacctgtccaattagtctaaactacggcgtttccacttcgcaaattcaacaccactttctcacccattacatcctatacggtccttttccgctgctttataccgttcacggcaggaagcttaaatttattaagtggaatctgtctactttttcaaaagtgtgaccgggctccaaaaacgcttcccttccatttcgtatttcttcgattatgcccatcggggacgataagaagaaattgtccgctgacaaacccaggtctattttttcaccacaagggcccaagagtccaagaatcccaagcatttcggtgaaaacgcctgcgcagatttccgacgactgtgccactccatccaaagccacagtacagcgcacagctaaaaatatggctgcttccgatctagcgctagccaaattcatttcggtttctgacgctcaagcgaatttgaggctcagatcaacactccggaatccgcagctccaaccgtcacgatgcttagcgtccgtcgcgaccaagtccgaagcctatgggacaaggttgaaaagaattcgacctctgctcagagtgccttgtgtcagcaggcgagcggcagcaagcggcatgcctattctcagggctagttacagttattgctattcagtctatgaaaggtgtgttgcccagctcgttgataaaatcgagcaggggcacttctcagtccatcccaagcgaacgctgcggcccaggcctacatttcctctggctgtcggttgcctccatgcgatacaggagttttcgcaggtgactatcttcgctggccgctttccggatcttttacacgccatttatattaataatccacggctgactccgttcgaaaagttattccacttaaatgccaaaacaagtggcgacgcgcatgccatagtttcgatttcgcctctcaccaaacgagggttttcctctgcgtgggaaaacctaatagagcgtttcgaaaataaacgattgttggtaaacagtcaattgaaaatactgtttaatgtgcagtcgataccacaggaatctggggcggccttgaaggtaatgcaaagtactgttcaaggttgcttgactgccttagaactgtcaggcatcaacactgagaactgggactgcctgctggaatatctgtgttcatccaagctcccgaagataactctctccttatgggagcagtctctacataagaaagccgacatcccgacatggggagaactgaacaccttcctcacagaacgtcatcgaaccctagaggccatcgatgatgtgagaccgtccgtaccaagtcagtcgcactccaaagcgatgaactcaagtgggccctctagagatggcaagctggcgtccgacttgtgcaacaaggaaaaccatcctgtccgtgtatgtcgcgttttctccaaatggtcggttgacgaccggtcagcctacattaaacggaagcagttatgcttaaactactttgcaaagggacatcagcttcgtgagtgcaaagatcgacaaagttttacttggtggccggcatcacacgttgttgcaccgaaacaacctcttttccagcaattcaagcccttcaaatcctgcaagcccaatttccgctactcaggccaatttcgttccaaacgagcaagccggtgttcaaaattattttgccacggctcaagagctatccttcttggcagtgccataatcaatagttcccatcttggcactaactttaaggcacgcgccctgatcgactccggatcagaggcgacattcataaccgagccactgttcaatctaattagattgccattccaggtggttcaagcccaagtctcgggcttaaaccaaacagtagctgctcagttcaagaacgctgcagtttcaccatccgatctccgactaggccgcgttgcagttggagacgacggcctatgtcctccctcaactagccggaaatctgccttcctacccaattccgcaaaatttcttcgggatcttcccgattttccactggcggatccaaaattctatgagagcgccccaatagatgtacttatccggagcccacatcctgcttcggtgcttctgagtggagcaaaaaccaacatctgtggctctctcttggggcaagagaccattttccgctgggtactaactgggccagtgtcagcctcagcccaaagcaggattcctctttttcgacacagatctcccacgcgtacgataattcactggacaaactcctcacaaaatttggggaggtggaggatataccaacaaagttgcaaaagaatccgattccatgtgcgagaacgggttggtaaatgcttacgacgacaccagtgcggcaaatatgtcgttactctgccttttcgcgacccagaacatatcggttgcgggctagggcattctaggtcttgggcgttggctcagttcttgaagaatgagcagcgtctaaaaaaagatgaggccttgaaagcgagatacgattcggtgatccaggaatatctcgacttaaagcacatgcgacaagttctgcctacccatgattgcaacgcctattatatgccacatcacgccgtcttaaaaccggagagtgtaactactaaactccgtgtagtattcaatgcctccagcccttcatcgaatggtaccagtttaaatgatatccttcatgct'..b'ggaagtttataagagactttgcacgaataacgaagcccatgactaaacaattgaaagggaaaagacaagttactacagacaaagactttgtagacgcattcgaacagtgcaaaactcttctgtccaatgacccaatactcatacacccagacttcgaaaaaccattcattcttactacggatgctagtaacttcgcgttaggagccgtactatctcaaggctccttacaaaacgatagacctgtatgttttgccagcaggaccctctccgacaccgaagtcaactattcaaccatagaaaaagaaatgttggcaataatatgggcagtaaaatacttcagaccatatatttatggcgtaaaatttactattgttacagatcacaagccactaatatggcttatgaatttcaaagaacccaactcaaaaataattcgttggagactccaactcatggaatacaattttgaaataattcacaagaaaggttcacaaaatgtaattgcagacgccttaagtagagcggacccaaatttaaactacaacgaaacactgactgttaagccttgccccacatccgaaaaacctattaacgaatttaacacgcaactcatactagaaatagatacaaatacgtcttaccaaactacaacaccatttaaacaaaagattaggaaaaaatattcacagccttgcttcgatttcgataatattgttaaaatcttgaaaggaaccctaaaacctaacaggatttgcgcattcttggcggacgataataattccgcattaatcgaaaaagcattctcaacgtattttgcacataaaaaacactttaaaattatcagatgcaaatcacttctccacgaaatcgtaggaaaccccgaacaaaacaaattcattcaggaatatcacactaacagcaaccacagaggcatagacgaaacattccttcacctcaaacgagaaacctacttccccaatatgaaaaacaaaatctctgaattaattaggaattgcgaaacctgtctaaaactcaaatacgacaggcaaccacaaaatatagtatttgaaaccccagaaaccccatcgaaacccctcgacataatacacatagacatctatactattaacaataattttaacctgacaatcatagacaaattctcaaaattcgcagctgtctaccccatcccaaatagaaacggcatcaattgcatcaaagcaatcaaaaattttttcagtcaattcggactacccaaaaaactaatacacgaccaaggagtagaattttgcaacgacatatttcgaaagttttgctctcaatataatatacttctccatgtcacatccttccagcaatcttcaagtaattctccagtagaacgtttacactcctctttgacagagatttacagaataatactagacacacggaaaaaacacaaattacctacagaccacgaagaaataatgtcagaaactgtaataacatataacaacgcaatccactccaccaccaaacacaccccttttgaactttttaatggtaggacccatttattcgagaaaacaataatacccaataatgagcatgactatttaaataaactaaatacgttccaagacaaactatactccgaaataaaagaaaaattgtccacaaacacccaacaaaggatagaaaagctaaacacaagcagagtagaaccaacaacagtacaacctaacagcacaattttcagaaaagaaaacaggagaaataaattaacaccacggttttccttacacagaacagcaaaagacaaaggaaaaactctagtaaccacaagaaatcaaaaaatccacaaatcaaaaattaggaaaatatccaaacctccaaatgacttaagcctttccacctgcattccagatcttgccatggggcataccaatctatcttcatccacaacttcaatagcaccaacctcctagcaaaagtgccggtagggaaaacactcgtgataggaaactataaaaaaattagccacataatcgatctgtccgaatacaccaactgtattgaaaaattataccacaccatcgataccctaagacaagatgaaacactcaccgattctatatcaatactaaatgctaaactggcccaaactcaaagtaaaatagacgcactaacacccttttcacgccacaaaagaggtcttattaacgggttaggtagtttagtcaaagtcgtcaccggcaacatggacgccaatgatgcaaagaatatagaaacagaaattaaccacttaaaaagccagtccaccactatctcagataacttcgaaatacagaactcgttcaatgatgaagttcaactacggttcaaaaacttaacaagacacattaacaatgaacagaatttgattaaaaacttcttcgaaaacactcaaaatacaatttacacaaaaatatacaacaacgaagaagaaataaagaaactacaatatataaataggcttaactacaatatagatttattagttagccacctaagcgacattatagaaagtacactgcttgccaaaattaatgttatcccaaaactcatcttagacaagacagaaataaccaaaatcaaacaaatttttaaaacacaaaactacacaataaaatccgagcaacacatttataacctcttaaaaatgaacgcactcaattaccaaaacaaaataatttttagtatcaaaattcctatttttttaagttgtaactacgaaatggcaagattaattccacttccaataaattccacacaatttgtaatagcacctaagtacttaatatataataacaaaagtaacagcatgttttcaactatgtataaatgtcctgtaatagaagaacaattcgtctgcgaaatcgactccatcaataatcttaaaaataatacttgcctgggacaccttatccaaaataagaccagctactgcgacataaaggaaacgggactcacgactgatgtgttcgaaccggaaaaaggcttcatacttgtatttaacgggaacaacctcccaatcatctcctccaaccagaccataactagtatcaatggatcagctataataaagtataacaattgcacattaaaaatcaatgaaataaactacgacaacagggcggtatcaacagaagagcaccccgacttcttcctaccaccaatgcggaaactaataaaaaatgccactatcaacatactcaccttggaaagacttcacctggatacactcacaacatccaataagctactggtcgtcgccgcaggaaactctcgacactcgacaaccttgtatatcctcttcaccgtatccctagtcgccgtaatactcacctggacacttcgaagggacacccacatcttccataccgggcccgaccacattcttccaatcgtcgctccaccaattcctccgtctatggccttcgctccaaactggggggggagg\n+>ZAM_LTR\tGypsy\tDrosophila melanogaster\n+agttaccgacccatcggtaccatacaccacccctccctctaagccaccacgcctacacaagtagaagacatcgaaccgggaagctttgcgatacaaagttgcagcataaacatcaacaacgggtcagacgccgacatccgcccaaaatgctgacaccacatccttttcgctcagacagaacaacgcatacaattccatatacatacgtataaacatactcatactttctgctgtgtcagatactttatttctaagaactttaacattgtaatacatacacacatattcactgttagcccatttaagacgaagaataaagacgaccacagtcgagtgcaagcagcaaacacttgtagacgtacataatctccgatcaaaattctcccaagacgaccgtggctacgttctggacccgcataactcctctatctttctgagtgataatacctccgcaagactccccggaggtaac\n' |
| b |
| diff -r 9645d995fb3c -r 9185ca0a7b43 test-data/dmel-all-rRNA-r6.03.fasta --- a/test-data/dmel-all-rRNA-r6.03.fasta Wed Oct 24 07:40:20 2018 -0400 +++ b/test-data/dmel-all-rRNA-r6.03.fasta Wed Jan 16 08:18:13 2019 -0500 |
| b |
| b'@@ -1,294 +1,294 @@\n->FBtr0086345 type=rRNA; loc=2R:complement(19766144..19766278); ID=FBtr0086345; name=5SrRNA:CR33353-RA; dbxref=FlyBase:FBtr0086345,FlyBase_Annotation_IDs:CR33353-RA,REFSEQ:NR_001892; score=0; score_text=Weakly Supported; MD5=9162f14f3b33b2210e2100cada0b7f92; length=135; parent=FBgn0053353; release=r6.03; species=Dmel; \r\n-GCCAACGACCATACCACGCTGAATACATCGGTTCTCGTCCGATCACCGAAATTAAGCAGCGTCGGGCGCGGTTAGTACTTAGATGAGGGACCGCTTGGGAACACCGCGTGTTGTTGGCCTCGTCCACAACTTTTT\r\n->FBtr0086346 type=rRNA; loc=2R:complement(19765775..19765909); ID=FBtr0086346; name=5SrRNA:CR33354-RA; dbxref=FlyBase:FBtr0086346,FlyBase_Annotation_IDs:CR33354-RA,REFSEQ:NR_001891; score=0; score_text=Weakly Supported; MD5=9162f14f3b33b2210e2100cada0b7f92; length=135; parent=FBgn0053354; release=r6.03; species=Dmel; \r\n-GCCAACGACCATACCACGCTGAATACATCGGTTCTCGTCCGATCACCGAAATTAAGCAGCGTCGGGCGCGGTTAGTACTTAGATGAGGGACCGCTTGGGAACACCGCGTGTTGTTGGCCTCGTCCACAACTTTTT\r\n->FBtr0086347 type=rRNA; loc=2R:complement(19765409..19765543); ID=FBtr0086347; name=5SrRNA:CR33355-RA; dbxref=FlyBase:FBtr0086347,FlyBase_Annotation_IDs:CR33355-RA,REFSEQ:NR_001890; score=0; score_text=Weakly Supported; MD5=9162f14f3b33b2210e2100cada0b7f92; length=135; parent=FBgn0053355; release=r6.03; species=Dmel; \r\n-GCCAACGACCATACCACGCTGAATACATCGGTTCTCGTCCGATCACCGAAATTAAGCAGCGTCGGGCGCGGTTAGTACTTAGATGAGGGACCGCTTGGGAACACCGCGTGTTGTTGGCCTCGTCCACAACTTTTT\r\n->FBtr0086349 type=rRNA; loc=2R:complement(19764648..19764782); ID=FBtr0086349; name=5SrRNA:CR33357-RA; dbxref=FlyBase:FBtr0086349,FlyBase_Annotation_IDs:CR33357-RA,REFSEQ:NR_001888; score=0; score_text=Weakly Supported; MD5=dacf3866c94cfe27156e359c01e8f212; length=135; parent=FBgn0053357; release=r6.03; species=Dmel; \r\n-GCCAACGACCATACCACGCTGAATACATCGGTTCTCGTCCGATCACCGAAATTAAGCAGCGTCGGGCGCGGTTAGTACTTAGATGGGGGACCGCTTGGGAACACCGCGTGTTGTTGGCCTCGTCCACAACTTTTT\r\n->FBtr0086350 type=rRNA; loc=2R:complement(19764289..19764423); ID=FBtr0086350; name=5SrRNA:CR33358-RA; dbxref=FlyBase:FBtr0086350,FlyBase_Annotation_IDs:CR33358-RA,REFSEQ:NR_001887; score=0; score_text=Weakly Supported; MD5=dacf3866c94cfe27156e359c01e8f212; length=135; parent=FBgn0053358; release=r6.03; species=Dmel; \r\n-GCCAACGACCATACCACGCTGAATACATCGGTTCTCGTCCGATCACCGAAATTAAGCAGCGTCGGGCGCGGTTAGTACTTAGATGGGGGACCGCTTGGGAACACCGCGTGTTGTTGGCCTCGTCCACAACTTTTT\r\n->FBtr0086351 type=rRNA; loc=2R:complement(19763913..19764047); ID=FBtr0086351; name=5SrRNA:CR33359-RA; dbxref=FlyBase:FBtr0086351,FlyBase_Annotation_IDs:CR33359-RA,REFSEQ:NR_001886; score=0; score_text=Weakly Supported; MD5=dacf3866c94cfe27156e359c01e8f212; length=135; parent=FBgn0053359; release=r6.03; species=Dmel; \r\n-GCCAACGACCATACCACGCTGAATACATCGGTTCTCGTCCGATCACCGAAATTAAGCAGCGTCGGGCGCGGTTAGTACTTAGATGGGGGACCGCTTGGGAACACCGCGTGTTGTTGGCCTCGTCCACAACTTTTT\r\n->FBtr0086352 type=rRNA; loc=2R:complement(19763544..19763678); ID=FBtr0086352; name=5SrRNA:CR33360-RA; dbxref=FlyBase:FBtr0086352,FlyBase_Annotation_IDs:CR33360-RA,REFSEQ:NR_001885; score=0; score_text=Weakly Supported; MD5=dacf3866c94cfe27156e359c01e8f212; length=135; parent=FBgn0053360; release=r6.03; species=Dmel; \r\n-GCCAACGACCATACCACGCTGAATACATCGGTTCTCGTCCGATCACCGAAATTAAGCAGCGTCGGGCGCGGTTAGTACTTAGATGGGGGACCGCTTGGGAACACCGCGTGTTGTTGGCCTCGTCCACAACTTTTT\r\n->FBtr0086353 type=rRNA; loc=2R:complement(19763175..19763309); ID=FBtr0086353; name=5SrRNA:CR33361-RA; dbxref=FlyBase:FBtr0086353,FlyBase_Annotation_IDs:CR33361-RA,REFSEQ:NR_001884; score=0; score_text=Weakly Supported; MD5=9162f14f3b33b2210e2100cada0b7f92; length=135; parent=FBgn0053361; release=r6.03; species=Dmel; \r\n-GCCAACGACCATACCACGCTGAATACATCGGTTCTCGTCCGATCACCGAAATTAAGCAGCGTCGGGCGCGGTTAGTACTTAGATGAGGGACCGCTTGGGAACACCGCGTGTTGTTGGCCTCGTCCACAACTTTTT\r\n->FBtr0086354 type=rRNA; loc=2R:complement(19762802..19762936); ID=FBtr0086354; name=5SrRNA:CR33362-RA; dbxref=FlyBase:FBtr0086354,FlyBase_Annotation_IDs:CR33362-RA,REFSEQ:NR_001883; score=0; score_text=Weakly Supported; MD5=dacf3866c94cfe27156e359c01e8f212; length=135; parent=FBgn0053362; release='..b'AATTATCATTGATTTTTGTGTTTATTATATGCACTTGTATGATTAACAATGCGAAAGATTCAGGATACCTTCGGGACCCGTCTTGAAACACGGACCAAGGAGTCTAACATATGTGCAAGTTATTGGGATATAAACCTAATAGCGTAATTAACTTGACTAATAATGGGATTAGTTTTTTAGCTATTTATAGCTAATTAACACAATCCCGGGGCGTTCTATATAGTTATGTATAATGTATATTTATATTATTTATGCCTCTAACTGGAACGTACCTTGAGCATATATGCTGTGACCCGAAAGATGGTGAACTATACTTGATCAGGTTGAAGTCAGGGGAAACCCTGATGGAAGACCGAAACAGTTCTGACGTGCAAATCGATTGTCAGAATTGAGTATAGGGGCGAAAGACCAATCGAACCATCTAGTAGCTGGTTCCTTCCGAAGTTTCCCTCAGGATAGCTGGTGCATTTTAATATTATATAAAATAATCTTATCTGGTAAAGCGAATGATTAGAGGCCTTAGGGTCGAAACGATCTTAACCTATTCTCAAACTTTAAATGGGTAAGAACCTTAACTTTCTTGATATGAAGTTCAAGGTTATGATATAATGTGCCCAGTGGGCCACTTTTGGTAAGCAGAACTGGCGCTGTGGGATGAACCAAACGTAATGTTACGGTGCCCAAATTAACAACTCATGCAGATACCATGAAAGGCGTTGGTTGCTTAAAACAGCAGGACGGTGATCATGGAAGTCGAAATCCGCTAAGGAGTGTGTAACAACTCACCTGCCGAAGCAACTAGCCCTTAAAATGGATGGCGCTTAAGTTGTATACCTATACATTACCGCTAAAGTAGATGATTTATATTACTTGTGATATAAATTTTGAAACTTTAGTGAGTAGGAAGGTACAATGGTATGCGTAGAAGTGTTTGGCGTAAGCCTGCATGGAGCTGCCATTGGTACAGATCTTGGTGGTAGTAGCAAATAATCGAATGAGACCTTGGAGGACTGAAGTGGAGAAGGGTTTCGTGTGAACAGTGGTTGATCACGAGTTAGTCGGTCCTAAGTTCAAGGCGAAAGCCGAAAATTTTCAAGTAAAACAAAAATGCCTAACTATATAAACAAAGCGAATTATAATACACTTGAATAATTTTGAACGAAAGGGAATACGGTTCCAATTCCGTAACCTGTTGAGTATCCGTTTGTTATTAAATATGGGCCTCGTGCTCATCCTGGCAACAGGAACGACCATAAAGAAGCCGTCGAGAGATATCGGAAGAGTTTTCTTTTCTGTTTTATAGCCGTACTACCATGGAAGTCTTTCGCAGAGAGATATGGTAGATGGGCTAGAAGAGCATGACATATACTGTTGTGTCGATATTTTCTCCTCGGACCTTGAAAATTTATGGTGGGGACACGCAAACTTCTCAACAGGCCGTACCAATATCCGCAGCTGGTCTCCAAGGTGAAGAGTCTCTAGTCGATAGAATAATGTAGGTAAGGGAAGTCGGCAAATTAGATCCGTAACTTCGGGATAAGGATTGGCTCTGAAGATTGAGATAGTCGGGCTTGATTGGGAAACAATAACATGGTTTATGTGCTCGTTCTGGGTAAATAGAGTTTCTAGCATTTATGTTAGTTACTTGTTCCCCGGATAGTTTAGTTACGTAGCCAATTGTGGAACTTTCTTGCTAAAATTTTTAAGAATACTATTTGGGTTAAACCAATTAGTTCTTATTAATTATAACGATTATCAATTAACAATCAATTCAGAACTGGCACGGACTTGGGGAATCCGACTGTCTAATTAAAACAAAGCATTGTGATGGCCCTAGCGGGTGTTGACACAATGTGATTTCTGCCCAGTGCTCTGAATGTCAAAGTGAAGAAATTCAAGTAAGCGCGGGTCAACGGCGGGAGTAACTATGACTCTCTTAAGGTAGCCAAATGCCTCGTCATCTAATTAGTGACGCGCATGAATGGATTAACGAGATTCCTACTTGTCCCTATCTACTATCTAGCGAAACCACAGCCAAGGGAACGGGCTTGGAATAATTAGCGGGGAAAGAAGACCCTTTTGAGCTTGACTCTAATCTGGCAGTGTAAGGAGACATAAGAGGTGTAGAATAAGTGGGAGATATTAGACCTCGGTTTGGTATCGTCAATGAAATACCACTACTCTTATTGTTTCCTTACTTACTTGATTAAATGGAACGTGTATCATTTCCTAGCCATTATACGGATATATTTATTATATCTTATGGTATTGGGTTTTGATGCAAGCTTCTTGATCAAAGTATCACGAGTTTGTTATATAATCGCAAACAAATTCTTTAATAAAACGATGCATTTATGTATTTTTGATTTGAAAATTTGGTATAACTCCAATTACTCAGGTATGATCCAATTCAAGGACATTGCCAGGTAGGGAGTTTGACTGGGGCGGTACATCTCTCAAATAATAACGGAGGTGTCCCAAGGCCAGCTCAGTGCGGACAGAAACCACACATAGAGCAAAAGGGCAAATGCTGACTTGATCTCGGTGTTCAGTACACACAGGGACAGCAAAAGCTCGGCCTATCGATCCTTTTGGTTTAAAGAGTTTTTAACAAGAGGTGTCAGAAAAGTTACCATAGGGATAACTGGCTTGTGGCGGCCAAGCGTTCATAGCGACGTCGCTTTTTGATCCTTCGATGTCGGCTCTTCCTATCATTGTGAAGCAAAATTCACCAAGCGTTGGATTGTTCACCCATGCAAGGGAACGTGAGCTGGGTTTAGACCGTCGTGAGACAGGTTAGTTTTACCCTACTAATGACAAAACGTTGTTGCGACAGCATTCCTGCGTAGTACGAGAGGAACCGCAGGTACGGACCAATGGCACAATACTTGTTCGAGCGAACAGTGGTATGACGCTACGTCCGTTGGATTATGCCTGAACGCCTCTAAGGTCGTATCCGTGCTGGACTGCAATGATAAATAAGGGGCAATTTGCATTGTATGGCTTCTAAACCATTTAAAGTTTATAATTTACTTTATAAACGACAATGGATGTGATGCCAATGTAATTTGTAACATAGTAAATTGGGAGGATCTTCGATCACCTGATGCCGCGCTAGTTACATATAAAAGCATTATTTAATACAATGACAAAGCCTAGAATCAATTGTAAACGACTTTTGTAACAGGCAAGGTGTTGTAAGTGGTTGAGCAGCTGCCATACTGCGATCCACTGAAGCTTATCCTTTGCTTGATGATTCGA\n+>FBtr0346887 type=rRNA; loc=rDNA:46205..46327; ID=FBtr0346887; name=5.8SrRNA:CR45852-RA; dbxref=FlyBase:FBtr0346887,FlyBase_Annotation_IDs:CR45852-RA; score=1; score_text=Weakly Supported; MD5=7f8e1dfdda0f9ae351c9e28c52e54e21; length=123; parent=FBgn0267512; release=r6.03; species=Dmel; \n+AACTCTAAGCGGTGGATCACTCGGCTCATGGGTCGATGAAGAACGCAGCAAACTGTGCGTCATCGTGTGAACTGCAGGACACATGAACATCGACATTTTGAACGCATATCGCAGTCCATGCTG\n+>FBtr0346898 type=rRNA; loc=X:23291700..23291729; ID=FBtr0346898; name=2SrRNA:CR45864-RA; dbxref=FlyBase:FBtr0346898,FlyBase_Annotation_IDs:CR45864-RA; score=1; score_text=Weakly Supported; MD5=79181b9131521cbf99fa2d8f99e7b410; length=30; parent=FBgn0267524; release=r6.03; species=Dmel; \n+TGCTTGGACTACATATGGTTGAGGGTTGTA\n' |
| b |
| diff -r 9645d995fb3c -r 9185ca0a7b43 test-data/dmel-all-sn-snoRNA-r6.03.fasta --- a/test-data/dmel-all-sn-snoRNA-r6.03.fasta Wed Oct 24 07:40:20 2018 -0400 +++ b/test-data/dmel-all-sn-snoRNA-r6.03.fasta Wed Jan 16 08:18:13 2019 -0500 |
| b |
| b'@@ -1,638 +1,638 @@\n->FBtr0081560 type=snoRNA; loc=3R:complement(7472907..7473222); ID=FBtr0081560; name=scaRNA:MeU5-C46-RA; dbxref=FlyBase:FBtr0081560,FlyBase_Annotation_IDs:CR32863-RA,REFSEQ:NR_001999; score=0; score_text=Weakly Supported; MD5=001dca55ff90bbedfc8b9a3593a2c84c; length=316; parent=FBgn0043853; release=r6.03; species=Dmel; \r\n-TGCCCATGATGAAATATTCGACATCGGAGTTTGCGCATTGGCGACAAGACCTAAGGCTCAGACTCTAGCAAATCTAGTTTCATCCGTTGTAATCTTTGCTGCTGCACTCCAGAATTTGCAGTGGCCGTAAGGCCAGCGGGACACCAACAGCCAGGGATCAAGACTATTATCTGTCATTGAGTCCTAGACAGATAGTTTAGTCTCTGGTTTACAGAACACCCAAATGGAAATGAAACACGCGCTTTTGTCGACCCAGGAGCCAGTTAGGTCTAAGCTGTTTGTCATGGTGACGACGTCTTTAGTAATCTGAGCGCAA\r\n->FBtr0070292 type=snoRNA; loc=X:complement(1482492..1482590); ID=FBtr0070292; name=snoRNA:M-RA; dbxref=FlyBase:FBtr0070292,FlyBase_Annotation_IDs:CR32807-RA,REFSEQ:NR_002093; score=0; score_text=Weakly Supported; MD5=81314d41b5db15222ab4c0daca9e3a65; length=99; parent=FBgn0044508; release=r6.03; species=Dmel; \r\n-AATTCAATGATTTCAACTTCACTGCTGACCAGCCACGCCTCAACGCCTCGGAGTGTTTGCCCCCAGTCTCTGATAGATACACCATATTCTAATACACAC\r\n->FBtr0076635 type=snoRNA; loc=3L:8601948..8602031; ID=FBtr0076635; name=snoRNA:U49:66Db-RA; dbxref=FlyBase:FBtr0076635,FlyBase_Annotation_IDs:CR32910-RA,REFSEQ:NR_001955; score=0; score_text=Weakly Supported; MD5=b2175b964d1d7e4cbe00bd8e55b73ca8; length=84; parent=FBgn0060291; release=r6.03; species=Dmel; \r\n-CTGCACATGATGATAATTGAAAGTTCTTGATAGGAATTGCCGGCTGACACATATATGAAGCTAATTCTAGTTTATCTGATTACA\r\n->FBtr0076634 type=snoRNA; loc=3L:8601473..8601552; ID=FBtr0076634; name=snoRNA:U49:66Da-RA; dbxref=FlyBase:FBtr0076634,FlyBase_Annotation_IDs:CR32911-RA,REFSEQ:NR_001954; score=0; score_text=Weakly Supported; MD5=9f94db9a46640f6af279661b83c98768; length=80; parent=FBgn0060292; release=r6.03; species=Dmel; \r\n-TGCACATGATGATAATTTGTCTTCTTGATAGGAAGTGCCAACTGACACATAAATGAAGCTAGTTTAACCCTCTGAAAGCA\r\n->FBtr0086857 type=snoRNA; loc=2R:17702873..17702949; ID=FBtr0086857; name=snoRNA:snR38:54Ec-RA; dbxref=FlyBase:FBtr0086857,FlyBase_Annotation_IDs:CR32901-RA,REFSEQ:NR_001769; score=1; score_text=Weakly Supported; MD5=b4b17beebede66cbd74a108e03863fa7; length=77; parent=FBgn0063373; release=r6.03; species=Dmel; \r\n-ATGATGTGATGAACACCTTATTTAAGCCAAACAGTTATCCCTGTCATAAGAATAATTGATGATATATTCAGCTGACA\r\n->FBtr0086852 type=snoRNA; loc=2R:17701689..17701764; ID=FBtr0086852; name=snoRNA:snR38:54Eb-RA; dbxref=FlyBase:FBtr0086852,FlyBase_Annotation_IDs:CR32896-RA,REFSEQ:NR_001764; score=0; score_text=Weakly Supported; MD5=8d40774ceb21d85153c649f6fc4db139; length=76; parent=FBgn0063374; release=r6.03; species=Dmel; \r\n-CCTTTGTGATGAGCATCCTTTTAAAGCCAAACAGTTATCCCTGTCATAAGAATAATTGATGATACAATAATCTGAC\r\n->FBtr0086851 type=snoRNA; loc=2R:17701447..17701523; ID=FBtr0086851; name=snoRNA:Me28S-G3277a-RA; dbxref=FlyBase:FBtr0086851,FlyBase_Annotation_IDs:CR32893-RA,REFSEQ:NR_001763; score=0; score_text=Weakly Supported; MD5=600b5d664ea787a79c37dee706e5f5c3; length=77; parent=FBgn0063375; release=r6.03; species=Dmel; \r\n-GGGCAATGATGAACACTTTATTTAAGCCAAACAGTTATCCCTGTCATAAGAATAATTGATGATAAAAGTTGCTGATT\r\n->FBtr0086848 type=snoRNA; loc=2R:17700741..17700813; ID=FBtr0086848; name=snoRNA:U76:54Eb-RA; dbxref=FlyBase:FBtr0086848,FlyBase_Annotation_IDs:CR32891-RA,REFSEQ:NR_001760; score=0; score_text=Weakly Supported; MD5=f3741fc5731e0cc5330b00315b4c69eb; length=73; parent=FBgn0063376; release=r6.03; species=Dmel; \r\n-TGAAAATGATGATTAATTATTATTTGCTACTCTTGAAGAGCTTTGATGAATACTTACACCTTAGAAACTGAGT\r\n->FBtr0086845 type=snoRNA; loc=2R:17699932..17700004; ID=FBtr0086845; name=snoRNA:Me28S-A1666a-RA; dbxref=FlyBase:FBtr0086845,FlyBase_Annotation_IDs:CR32889-RA,REFSEQ:NR_001757; score=1; score_text=Weakly Supported; MD5=31c77ac9f94d8024de98d0866f13ded1; length=73; parent=FBgn0063377; release=r6.03; species=Dmel; \r\n-TGTAAATGATGATTTATTATTATTTGCTACTCTTGAAGGTCATTGATGAATACTTTCACCTTAAAACCTGATG\r\n->FBtr0086855 type=snoRNA; loc=2R:17702411..17702477; ID=FBtr0086855; name=snoRNA:U31:54Ed-RA; dbxref=FlyBase:FBtr0086855,FlyBase_Annotation_IDs:CR32899-RA,REFSEQ:NR_00'..b'1f5; length=192; parent=FBgn0041720; release=r6.03; species=Dmel; \n+ATCGCTTCTCGGCCTTATGGCTAAGATCAAAGTGTAGTATCTGTTCTTATCAGCTTAACATCTGATAGTTCCTCCATTGGAGGACAACAAATGTTAAACTGATTTTTGGAATCAGACGGAGTGCTAGGAGCTTGCTCCACCTCTGTCGCGGGTTGGCCCGGTATTGCAGTACCGCCGGGATTTCGGCCCAAC\n+>FBtr0075315 type=snRNA; loc=3L:16653769..16654006; ID=FBtr0075315; name=snRNA:U12:73B-RA; dbxref=FlyBase:FBtr0075315,FlyBase_Annotation_IDs:CR32162-RA,REFSEQ:NR_001972; score=0; score_text=Weakly Supported; MD5=d1d774f1395d1eac2663f02d5417bf80; length=238; parent=FBgn0041721; release=r6.03; species=Dmel; \n+GTGCCTCAAACTAATGAGTAAGGAAAACCAATCAGCCTTGCTAATCGCTTGGCAGTATTGGCTTCTAGGCAGGGGGGCGTGTCCCGCGCCCCTTGAAGCTCAAATTTTTGCAAGGGCACAGGTCGTCCCCTCCTCCTCCGCGTGGGTGGCGTTCGGCCGAGCGAACCGGCGCCTACTTTGCGTCCGGCTAGCGAGGATCTCTGGGTGCCATCCCACGGCTGGGTGTTGCGATCTGCCC\n+>FBtr0081294 type=snRNA; loc=2L:19816414..19816540; ID=FBtr0081294; name=snRNA:U5:38ABb-RA; dbxref=FlyBase:FBtr0081294,FlyBase_Annotation_IDs:CR32880-RA,REFSEQ:NR_001674; score=0; score_text=Weakly Supported; MD5=a01600165b1bf498f3106a7b1d3e6994; length=127; parent=FBgn0043021; release=r6.03; species=Dmel; \n+ACTCTGGTTTCTCTTCAATTGTCGAATAAATCTTTCGCCTTTTACTAAAGATTTCCGTGGAGAGGAACACTCTAATGAGTCTAAACACAATTTTTATTGAGGCCTGATAACTTATGCTATCGGGCCA\n+>FBtr0081315 type=snRNA; loc=2L:complement(19811948..19812074); ID=FBtr0081315; name=snRNA:U5:38ABa-RA; dbxref=FlyBase:FBtr0081315,FlyBase_Annotation_IDs:CR32881-RA,REFSEQ:NR_001671; score=0; score_text=Weakly Supported; MD5=668f472d3ac9ab7cff94b99e52c1cd78; length=127; parent=FBgn0043022; release=r6.03; species=Dmel; \n+TACTCTGGTTTCTCTTCAATTGTCGAATAAATCTTTCGCCTTTTACTAAAGATTTCCGTGGAGAGGAACACTCTAATGAGTCTAAACTCAATTTTTGTATGACCTGGCTAAATATTTAGTTGGGCCA\n+>FBtr0100848 type=snRNA; loc=3L:3593823..3593893; ID=FBtr0100848; name=snRNA:U7-RA; dbxref=FlyBase_Annotation_IDs:CR33504-RA,FlyBase:FBtr0100848,REFSEQ:NR_002270; score=0; score_text=Weakly Supported; MD5=deb394a435f81cd75ed6b95c5a32647e; length=71; parent=FBgn0053504; release=r6.03; species=Dmel; \n+ATTGAAAATTTTTATTCTCTTTGAAATTTGTCTTGGTGGGACCCTTTGTCTAGGCATTGAGTGTTCCCGTT\n+>FBtr0091929 type=snRNA; loc=3R:complement(7474553..7474996); ID=FBtr0091929; name=snRNA:7SK-RA; dbxref=FlyBase:FBtr0091929,FlyBase_Annotation_IDs:CR33925-RA,REFSEQ:NR_002493,REFSEQ:NR_002493,REFSEQ:NR_002493; score=0; score_text=Weakly Supported; MD5=7cfa92ec944a572fe4ebf5510d257106; length=444; parent=FBgn0065099; release=r6.03; species=Dmel; \n+GGAAGTGTATTCTGTGATTGTTCTGTACATTGATCGATATTCAGGTAACTGCATCTGCTTATCAGATCTGTTCAGAGCCGACCCTCCGTCACACCTTTGTGTTTCCCAGTAATTCTGCCTGGCGTTGCCGTGGCTCCTCGTTCGGATCGGCTTTCCGCTGCCTTCCACTGGATGACGACGGGTTATCCGGCGGTCGACGCACGGTCATGCACCCCCGATCCGTCGCCCCCACCACCCCGCGGATTCTGGTCTCGACCGGAAGCCGTATTGGGCGGGGACGGGCGGCGGTCCGGTGCTGAAGCCGGCGACAGTTGCCCGAGTCAGCCACTTTCAAAATTTGTTGGTTAAGTAACTTAGTAGCTTAGCTTCGGATTTTCGTAACAAATTTGCTGTTCAGAACACTTCCATGTACGCGGCATTGCCGAGCAATTTGCCCATTCTTTT\n+>FBtr0111039 type=snRNA; loc=3L:complement(3893056..3893330); ID=FBtr0111039; name=snRNA:U11-RA; dbxref=FlyBase:FBtr0091696,FlyBase:FBtr0111039,FlyBase_Annotation_IDs:CR34151-RA,FlyBase_Annotation_IDs:CR33708-RA,REFSEQ:NR_003121; score=1; score_text=Weakly Supported; MD5=614c010295f08932d4b6d778d2e59eab; length=275; parent=FBgn0083987; release=r6.03; species=Dmel; \n+AAAAAGGGTGCTCGTCCTGGCACGTTTCCGATCACGAAACTCAAGTGCGGACGCATTGCGCCGCAGGAGCGTCTCCTTCGCTCCGCCCCTGGACTTCTCCGGGGATAGGCGGGGGCGAGCGTTCCATTGCCGCCTTCGACGCCTCCTTGCGCGCCCAGTGGGGTATGGCTTTGCATATCCAGTGCGTAATTTTTGTATTTGGGGCCGCGGCTGCACATTGTGGATTGCTCGGGGATTCCCGGATCTCCCTGCGTGCCAGTGCGCTGCGCCCCGCC\n+>FBtr0306791 type=snRNA; loc=3R:complement(5195004..5195163); ID=FBtr0306791; name=snRNA:U4atac:82E-RA; dbxref=REFSEQ:NR_048324,FlyBase:FBtr0306791,FlyBase_Annotation_IDs:CR43269-RA; score=0; score_text=Weakly Supported; MD5=e1ae4c911a264f805369d33185bc3304; length=160; parent=FBgn0263018; release=r6.03; species=Dmel; \n+ACCTTCCTTGTCTTGGGGAGCAGAAATGTTCAATGAACGTCTAGTGAGGACATTGCTGCTGACACCAATGATGACACCCCCGCTCGCCGATCGTTCGCGATTGGAGTTCGGAATTTTTGGACCAGGCTCCTTTACTTTACAGGGAGCCGCCTCTTGAATG\n' |
| b |
| diff -r 9645d995fb3c -r 9185ca0a7b43 test-data/dmel-all-tRNA-r6.03.fasta --- a/test-data/dmel-all-tRNA-r6.03.fasta Wed Oct 24 07:40:20 2018 -0400 +++ b/test-data/dmel-all-tRNA-r6.03.fasta Wed Jan 16 08:18:13 2019 -0500 |
| b |
| b'@@ -1,671 +1,671 @@\n->FBtr0086234 type=tRNA; loc=2R:20657891..20657962; ID=FBtr0086234; name=tRNA:CR30155-RA; dbxref=FlyBase:FBtr0086234,FlyBase_Annotation_IDs:CR30155-RA; score=0; score_text=Weakly Supported; MD5=243cf738b4d1a6d2ea2ee34d091c0d0a; length=72; parent=FBgn0050155; release=r6.03; species=Dmel; \r\n-GACTCCGTGGCGCAACGGTAGCGCGTCTGACTCCAGATCAGAAGGTTGCGTGTTCAAATCACGTCGGGGTCA\r\n->FBtr0072445 type=tRNA; loc=2R:25076005..25076076; ID=FBtr0072445; name=tRNA:CR30198-RA; dbxref=FlyBase:FBtr0072445,FlyBase_Annotation_IDs:CR30198-RA; score=0; score_text=Weakly Supported; MD5=0402c54abcbe0755c6f346504ea6eadc; length=72; parent=FBgn0050198; release=r6.03; species=Dmel; \r\n-GGGGACGTAGCTCAGTGGTAGAGCGCTCGCTTCGCATGTGAGAAGTCCCGGGTTCAAACCCCGGCGTCTCCA\r\n->FBtr0072446 type=tRNA; loc=2R:25076765..25076836; ID=FBtr0072446; name=tRNA:CR30199-RA; dbxref=FlyBase:FBtr0072446,FlyBase_Annotation_IDs:CR30199-RA; score=0; score_text=Weakly Supported; MD5=0402c54abcbe0755c6f346504ea6eadc; length=72; parent=FBgn0050199; release=r6.03; species=Dmel; \r\n-GGGGACGTAGCTCAGTGGTAGAGCGCTCGCTTCGCATGTGAGAAGTCCCGGGTTCAAACCCCGGCGTCTCCA\r\n->FBtr0072447 type=tRNA; loc=2R:25077048..25077119; ID=FBtr0072447; name=tRNA:CR30200-RA; dbxref=FlyBase:FBtr0072447,FlyBase_Annotation_IDs:CR30200-RA; score=0; score_text=Weakly Supported; MD5=0402c54abcbe0755c6f346504ea6eadc; length=72; parent=FBgn0050200; release=r6.03; species=Dmel; \r\n-GGGGACGTAGCTCAGTGGTAGAGCGCTCGCTTCGCATGTGAGAAGTCCCGGGTTCAAACCCCGGCGTCTCCA\r\n->FBtr0071983 type=tRNA; loc=2R:complement(23072019..23072100); ID=FBtr0071983; name=tRNA:CR30201-RA; dbxref=FlyBase:FBtr0071983,FlyBase_Annotation_IDs:CR30201-RA; score=0; score_text=Weakly Supported; MD5=b1d29cdc3617f5d88834dfcf6cb94669; length=82; parent=FBgn0050201; release=r6.03; species=Dmel; \r\n-GCTGCGGTGTCCGAGTGGTTAAGGAGATGGACTTGAAATCCATTGGGTTCTACCCGCACAGGTTCAAGTCCTGTCCGCA\r\n-GCG\r\n->FBtr0071962 type=tRNA; loc=2R:23072581..23072662; ID=FBtr0071962; name=tRNA:CR30202-RA; dbxref=FlyBase:FBtr0071962,FlyBase_Annotation_IDs:CR30202-RA; score=0; score_text=Weakly Supported; MD5=79b58dd799cb26435c738e215a4d9d46; length=82; parent=FBgn0050202; release=r6.03; species=Dmel; \r\n-GTTGCGGTGTCCGAGTGGTTAAGGAGATGGACTTGAAATCCATTGGGTTCTACCCGCGCAGGTTCGAATCCTGTCCGCA\r\n-GCG\r\n->FBtr0071631 type=tRNA; loc=2R:complement(21161063..21161134); ID=FBtr0071631; name=tRNA:CR30206-RA; dbxref=FlyBase:FBtr0071631,FlyBase_Annotation_IDs:CR30206-RA; score=0; score_text=Weakly Supported; MD5=9ff9c8260337fb111671830edb8e3824; length=72; parent=FBgn0050206; release=r6.03; species=Dmel; \r\n-GACTCCGTGGCGCAACGGTAGCGCGTCCGACTCCAGATCGGAAGGTTGCGTGTTCAAATCACGTCGGGGTCA\r\n->FBtr0071574 type=tRNA; loc=2R:21161526..21161597; ID=FBtr0071574; name=tRNA:CR30208-RA; dbxref=FlyBase:FBtr0071574,FlyBase_Annotation_IDs:CR30208-RA; score=0; score_text=Weakly Supported; MD5=9ff9c8260337fb111671830edb8e3824; length=72; parent=FBgn0050208; release=r6.03; species=Dmel; \r\n-GACTCCGTGGCGCAACGGTAGCGCGTCCGACTCCAGATCGGAAGGTTGCGTGTTCAAATCACGTCGGGGTCA\r\n->FBtr0071626 type=tRNA; loc=2R:complement(21182678..21182749); ID=FBtr0071626; name=tRNA:CR30209-RA; dbxref=FlyBase:FBtr0071626,FlyBase_Annotation_IDs:CR30209-RA; score=0; score_text=Weakly Supported; MD5=9ff9c8260337fb111671830edb8e3824; length=72; parent=FBgn0050209; release=r6.03; species=Dmel; \r\n-GACTCCGTGGCGCAACGGTAGCGCGTCCGACTCCAGATCGGAAGGTTGCGTGTTCAAATCACGTCGGGGTCA\r\n->FBtr0086247 type=tRNA; loc=2R:complement(20658104..20658175); ID=FBtr0086247; name=tRNA:CR30211-RA; dbxref=FlyBase:FBtr0086247,FlyBase_Annotation_IDs:CR30211-RA; score=0; score_text=Weakly Supported; MD5=243cf738b4d1a6d2ea2ee34d091c0d0a; length=72; parent=FBgn0050211; release=r6.03; species=Dmel; \r\n-GACTCCGTGGCGCAACGGTAGCGCGTCTGACTCCAGATCAGAAGGTTGCGTGTTCAAATCACGTCGGGGTCA\r\n->FBtr0086326 type=tRNA; loc=2R:complement(20000296..20000368); ID=FBtr0086326; name=tRNA:CR30212-RA; dbxref=FlyBase:FBtr0086326,FlyBase_Annotation_IDs:CR30212-RA; score=0; score_text=Weakly Supported; MD5=0567b432dd5034bd45ae2ceabd04c98a; length=73; pare'..b'Btr0070604; name=tRNA:P:3E-RA; dbxref=FlyBase:FBtr0070604,FlyBase_Annotation_IDs:CR32784-RA; score=0; score_text=Weakly Supported; MD5=6422ca8821a00d410403891c4f001230; length=72; parent=FBgn0025118; release=r6.03; species=Dmel; \n+GGCTCGTTGGTCTAGGGGTATGATTTTCGCTTCGGGTGCGAGAGGTCCCGGGTTCAATTCCCGGACGAGCCC\n+>FBtr0081622 type=tRNA; loc=3R:6819894..6819966; ID=FBtr0081622; name=tRNA:K5:84ABd-RA; dbxref=FlyBase:FBtr0081622,FlyBase_Annotation_IDs:CR31490-RA; score=0; score_text=Weakly Supported; MD5=4195a41533aa06bd1237285868c628ad; length=73; parent=FBgn0026162; release=r6.03; species=Dmel; \n+GCCCGGATAGCTCAGTCGGTAGAGCATTGGACTTTTAATCCAAGGGTCCAGGGTTCAAGTCCCTGTTCGGGCG\n+>FBtr0081661 type=tRNA; loc=3R:complement(6821068..6821140); ID=FBtr0081661; name=tRNA:K5:84ABc-RA; dbxref=FlyBase:FBtr0081661,FlyBase_Annotation_IDs:CR31487-RA; score=0; score_text=Weakly Supported; MD5=4195a41533aa06bd1237285868c628ad; length=73; parent=FBgn0026163; release=r6.03; species=Dmel; \n+GCCCGGATAGCTCAGTCGGTAGAGCATTGGACTTTTAATCCAAGGGTCCAGGGTTCAAGTCCCTGTTCGGGCG\n+>FBtr0081623 type=tRNA; loc=3R:6821789..6821861; ID=FBtr0081623; name=tRNA:K5:84ABb-RA; dbxref=FlyBase:FBtr0081623,FlyBase_Annotation_IDs:CR31489-RA; score=0; score_text=Weakly Supported; MD5=4195a41533aa06bd1237285868c628ad; length=73; parent=FBgn0026164; release=r6.03; species=Dmel; \n+GCCCGGATAGCTCAGTCGGTAGAGCATTGGACTTTTAATCCAAGGGTCCAGGGTTCAAGTCCCTGTTCGGGCG\n+>FBtr0080644 type=tRNA; loc=2L:14495878..14495949; ID=FBtr0080644; name=tRNA:P:35Bd-RA; dbxref=FlyBase:FBtr0080644,FlyBase_Annotation_IDs:CR31985-RA; score=0; score_text=Weakly Supported; MD5=c3cf92f97e1293f17ef34dd4a33c2dd2; length=72; parent=FBgn0028882; release=r6.03; species=Dmel; \n+GGCTCGTTGGTCTAGGGGTATGATTTCCGCTTAGGGTGCGGGAGGTCCCGGGTTCAAATCCCGGACGAGCCC\n+>FBtr0080717 type=tRNA; loc=2L:complement(15132306..15132389); ID=FBtr0080717; name=tRNA:L:35C-RA; dbxref=FlyBase:FBtr0080717,FlyBase_Annotation_IDs:CR31831-RA; score=1; score_text=Weakly Supported; MD5=250f163ecd83070ef11ff4724f417121; length=84; parent=FBgn0028889; release=r6.03; species=Dmel; \n+GCCAGGTTGGCCGAGCGGTCTAAGGCGCCAGATTTAAGCTCTGGTTCTCGAGAGAGAGCGTGGGTTCGAGTCCCACACC\n+TGGCA\n+>FBtr0080609 type=tRNA; loc=2L:complement(14010565..14010636); ID=FBtr0080609; name=tRNA:Q:34E-RA; dbxref=FlyBase:FBtr0080609,FlyBase_Annotation_IDs:CR31838-RA; score=0; score_text=Weakly Supported; MD5=ed31990a1414708ea663c4eb1a47f303; length=72; parent=FBgn0028909; release=r6.03; species=Dmel; \n+GGTTCTATGGTGTAATGGTTAGCACTTTGGACTCTGAATCCAGCGATCCGAGTTCAAATCTCGGTAGAACCT\n+>FBtr0080647 type=tRNA; loc=2L:14599674..14599745; ID=FBtr0080647; name=tRNA:P:35Bc-RA; dbxref=FlyBase:FBtr0080647,FlyBase_Annotation_IDs:CR31984-RA; score=0; score_text=Weakly Supported; MD5=c3cf92f97e1293f17ef34dd4a33c2dd2; length=72; parent=FBgn0028910; release=r6.03; species=Dmel; \n+GGCTCGTTGGTCTAGGGGTATGATTTCCGCTTAGGGTGCGGGAGGTCCCGGGTTCAAATCCCGGACGAGCCC\n+>FBtr0080660 type=tRNA; loc=2L:complement(14599396..14599467); ID=FBtr0080660; name=tRNA:P:35Bb-RA; dbxref=FlyBase:FBtr0080660,FlyBase_Annotation_IDs:CR31979-RA; score=0; score_text=Weakly Supported; MD5=c3cf92f97e1293f17ef34dd4a33c2dd2; length=72; parent=FBgn0028911; release=r6.03; species=Dmel; \n+GGCTCGTTGGTCTAGGGGTATGATTTCCGCTTAGGGTGCGGGAGGTCCCGGGTTCAAATCCCGGACGAGCCC\n+>FBtr0080646 type=tRNA; loc=2L:14598859..14598930; ID=FBtr0080646; name=tRNA:P:35Ba-RA; dbxref=FlyBase:FBtr0080646,FlyBase_Annotation_IDs:CR31983-RA; score=0; score_text=Weakly Supported; MD5=c3cf92f97e1293f17ef34dd4a33c2dd2; length=72; parent=FBgn0028912; release=r6.03; species=Dmel; \n+GGCTCGTTGGTCTAGGGGTATGATTTCCGCTTAGGGTGCGGGAGGTCCCGGGTTCAAATCCCGGACGAGCCC\n+>FBtr0086526 type=tRNA; loc=2R:19414598..19414679; ID=FBtr0086526; name=tRNA:S4:56D-RA; dbxref=FlyBase:FBtr0086526,FlyBase_Annotation_IDs:CR30224-RA; score=0; score_text=Weakly Supported; MD5=bda31e491947aa0e742dec30594b08f0; length=82; parent=FBgn0028981; release=r6.03; species=Dmel; \n+GCAGTCGTGGCCGAGTGGTTAAGGCGTCTGACTCGAAATCAGATTCCCTCTGGGAGCGTAGGTTCGAATCCTACCGGCT\n+GCG\n' |
| b |
| diff -r 9645d995fb3c -r 9185ca0a7b43 test-data/fastq_dir/reads-sample-small.fastq-bonafide_reads-TEs.fastq --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/fastq_dir/reads-sample-small.fastq-bonafide_reads-TEs.fastq Wed Jan 16 08:18:13 2019 -0500 |
| b |
| b'@@ -0,0 +1,105360 @@\n+@HWI-ST132:678:C1LFKACXX:6:1304:17199:58363\n+AAAAACACGACCGTTCGCTTTGAAA\n++\n+JJJIJJJJJJIHHHHFHFDDBFCC@\n+@HWI-ST132:678:C1LFKACXX:6:2106:15381:40802\n+TTCAAAGCGAACGGTCGTGTTTTT\n++\n+CCCFFFFFHHHHHJFEGEC?HHII\n+@HWI-ST132:678:C1LFKACXX:6:1114:10027:77795\n+AAGATTATTAAAAACCACTGCTG\n++\n+<<EFECE:?AA,FBADD;;D@@@\n+@HWI-ST132:678:C1LFKACXX:6:2103:3486:88354\n+CTTTAATTATCATATATTGTA\n++\n+BBBD;=ABFHHHHJJJJJDJI\n+@HWI-ST132:678:C1LFKACXX:6:1302:14522:72647\n+TTATTAAAGATCCGTTCGCTTCGCGAG\n++\n+CC@FFFFFHFHHHJHIJIJJJGGGIII\n+@HWI-ST132:678:C1LFKACXX:6:1103:11536:23013\n+TATTAAAGATCCGTTCGCTTCGCGAG\n++\n+B@@FBDDFHHHHHIIJIJJIJJJJIG\n+@HWI-ST132:678:C1LFKACXX:6:1206:10262:20669\n+TATTAAAGATCCGTTCGCTTCGCGAG\n++\n+@@@DDDDDH8FHHGDHII:CHHIIBF\n+@HWI-ST132:678:C1LFKACXX:6:1212:12068:74880\n+TTAAAGATCCGTTCGCTTCGCGAG\n++\n+CCCFDFDDHHHBBGC@FHFFDEGF\n+@HWI-ST132:678:C1LFKACXX:6:1213:19350:18162\n+TTAAAGATCCGTTCGCTTCGCGAG\n++\n+CCCFFFDFHHHHHIHIJIIJJHHI\n+@HWI-ST132:678:C1LFKACXX:6:1307:12279:8790\n+TTAAAGATCCGTTCGCTTCGCGAG\n++\n+???DDDBDDDDDDI1CEEIIII)C\n+@HWI-ST132:678:C1LFKACXX:6:1105:11371:76507\n+TTAAAGATCCGTTCGCTTCGCGAGTG\n++\n+BCCFFFFFHHFDFH)CGIJJIJIIDH\n+@HWI-ST132:678:C1LFKACXX:6:1101:3613:56171\n+TGATTTGTGCAGTAGTTTAAACAA\n++\n+BC@FFFFDHHHHHIJHHIJJJJJJ\n+@HWI-ST132:678:C1LFKACXX:6:1315:11705:87614\n+ACCGCACGAGAGCAGTCTGCACGCT\n++\n+IGGIIGHAIIFAHDDHHDD@4++::\n+@HWI-ST132:678:C1LFKACXX:6:1215:15419:77724\n+AACCGCACGAGAGCAGTCTGCACGCT\n++\n+IIIGFCIGGIJGHDCFDFDD?BB?@@\n+@HWI-ST132:678:C1LFKACXX:6:2102:3965:15607\n+TATCTGAACCACTGTGCACG\n++\n+CJHGEIHHHHDGDFFFFBCB\n+@HWI-ST132:678:C1LFKACXX:6:1309:1157:27805\n+TTCGGCCATTAAAACCAGCGCACT\n++\n+IIGGDIIHFFIHHHHHFFDDFB@@\n+@HWI-ST132:678:C1LFKACXX:6:1104:18136:49719\n+TCACTCGTTCGGCCATTAAAACCAGC\n++\n+IHJJIJIHJIIHFC6HHHFFFFFB@@\n+@HWI-ST132:678:C1LFKACXX:6:1206:4661:54441\n+TCATCACTCGTTCGGCCATTAAAAC\n++\n+JJJHGJIHHFC<HHHHHFFFFFCCC\n+@HWI-ST132:678:C1LFKACXX:6:1202:12284:43103\n+TTTAATGGCCGAACGAGTGATGACC\n++\n+B@BDFEFFHHCFHGIIJGHIIJJJJ\n+@HWI-ST132:678:C1LFKACXX:6:1105:18888:91816\n+TGCTAGGTCATCACTCGTTCGGCC\n++\n+JIIJJJJJJIIHDHHHDFFFFCCC\n+@HWI-ST132:678:C1LFKACXX:6:2104:13126:47993\n+TGCTAGGTCATCACTCGTTCGGCC\n++\n+JIHIIHJJJJJHHHHHDEDDFCCB\n+@HWI-ST132:678:C1LFKACXX:6:1310:10470:57499\n+TTAGATTTTTACCCTTTGCT\n++\n+JIGHGJJHHHGHFFEDF@@@\n+@HWI-ST132:678:C1LFKACXX:6:1208:10660:53352\n+GATGAAATCGTTTATGCGCCAAACT\n++\n+@@@DDDDDHHFHH=GHHIII@GCHI\n+@HWI-ST132:678:C1LFKACXX:6:2103:8188:10042\n+AGGTGGCTTGAAAGAACTGATCAACA\n++\n+@CCDDFFFHHHHHHGHIJHIJJCGHI\n+@HWI-ST132:678:C1LFKACXX:6:1116:8825:28862\n+GTTGATCAGTTCTTTCAAGCCACCT\n++\n+JIHCIEJIJJJJHHHDD;DDDA?@@\n+@HWI-ST132:678:C1LFKACXX:6:1109:17962:8377\n+TGGCTTGAAAGAACTGATCAACAGT\n++\n+CCCFFFFFHGHGHJJGCFHGIJIJJ\n+@HWI-ST132:678:C1LFKACXX:6:1202:14965:95853\n+TGGCTTGAAAGAACTGATCAACAGT\n++\n+CCCFFFFFHHHHHJJ<EHIJJJJJI\n+@HWI-ST132:678:C1LFKACXX:6:1209:11469:94001\n+TGGCTTGAAAGAACTGATCAACAGT\n++\n+CC@FFFFFGDFHGJJIIJIJJJ@HF\n+@HWI-ST132:678:C1LFKACXX:6:1213:13936:36177\n+TGGCTTGAAAGAACTGATCAACAGT\n++\n+CCCFFFFFGHHGFIIJJJJIIJIJH\n+@HWI-ST132:678:C1LFKACXX:6:1307:8164:25340\n+TCTCTAGCTATGCCAAAACTGT\n++\n+IJJJJJIJJHHDBHFFFFFB@B\n+@HWI-ST132:678:C1LFKACXX:6:1207:3316:75546\n+TCATCGGCTCGACGGAAACAATCTC\n++\n+GGEGIIIJHEFED@FHHFFFFFCC@\n+@HWI-ST132:678:C1LFKACXX:6:1306:3630:57103\n+TCATCGGCTCGACGGAAACAATCTC\n++\n+HHBGIHFGD1JGFAGHHFFFFFC@C\n+@HWI-ST132:678:C1LFKACXX:6:1106:13590:90955\n+TATCATCGGCTCGACGGAAACAATC\n++\n+GEIGEHGDC1<)HHDDDDBDDD@@@\n+@HWI-ST132:678:C1LFKACXX:6:2102:10526:18026\n+TATCATCGGCTCGACGGAAACAATC\n++\n+B<GD@?GEEDE>HAFHFDDB=A@@=\n+@HWI-ST132:678:C1LFKACXX:6:1301:18775:28385\n+TATCATCGGCTCGACGGAAA\n++\n+GHDHGGIGHHHHDDEDBC@@\n+@HWI-ST132:678:C1LFKACXX:6:1101:5698:75650\n+TAAACTGTGAATTAAGCGCGCACA\n++\n+JJIJJIGEAIJHHHFFDFFFFCBB\n+@HWI-ST132:678:C1LFKACXX:6:1113:19105:21652\n+TAAACTGTGAATTAAGCGCGCACA\n++\n+?C:?G:E<CF>F>FFC2D;B=+1=\n+@HWI-ST132:678:C1LFKACXX:6:1203:16184:49147\n+TTAAACTGTGAATTAAGCGCGCAC\n++\n+HGGHEGFA4IIHHHFBDDDDD@@@\n+@HWI-ST132:678:C1LFKACXX:6:1309:15681:14462\n+TTAAACTGTGAATTAAGCGCGCAC\n++\n+IHFIECJJJJJHGHHHFFFFFCCC\n+@HWI-ST132:678:C1LFKACXX:6:1304:3965:45774\n+TTAAACTGTGAATTAAGCGCG\n++'..b'+TGAATTGAGAGTCGGCGTTCGTC\n++\n+HEJJIJJGJHFFFFFDDDA4+:1\n+@HWI-ST132:678:C1LFKACXX:6:1316:16722:42018\n+TGAATTGAGAGTCGGCGTTCGTC\n++\n+HGJJJIJIJIHHHHHBEDA4+:1\n+@HWI-ST132:678:C1LFKACXX:6:2105:1246:21420\n+TGAATTGAGAGTCGGCGTTCGTC\n++\n+GCGEIJIIIGHHFDHEFDFD@@@\n+@HWI-ST132:678:C1LFKACXX:6:1101:8704:11437\n+TGAATTGAGAGTCGGCGTTCGTCA\n++\n+JIHIIHFGFE1FC<FHFFFFFCC@\n+@HWI-ST132:678:C1LFKACXX:6:1101:11649:25495\n+TGAATTGAGAGTCGGCGTTCGTCA\n++\n+JJJJJHGHIHGFAHDHFFFFFBCC\n+@HWI-ST132:678:C1LFKACXX:6:1103:18159:65506\n+TGAATTGAGAGTCGGCGTTCGTCA\n++\n+GGHJIHHHFECC<DDFFFFDD@@@\n+@HWI-ST132:678:C1LFKACXX:6:1105:19098:86110\n+TGAATTGAGAGTCGGCGTTCGTCA\n++\n+IHGJJIIJIHFA3CHHFFFFFCBB\n+@HWI-ST132:678:C1LFKACXX:6:1106:6923:42358\n+TGAATTGAGAGTCGGCGTTCGTCA\n++\n+GIHGG?CGFC222F;HFFDFF@@@\n+@HWI-ST132:678:C1LFKACXX:6:1110:4800:90404\n+TGAATTGAGAGTCGGCGTTCGTCA\n++\n+IHIJJIIHF:IHHHHHFFFFF@C@\n+@HWI-ST132:678:C1LFKACXX:6:1203:9910:19443\n+TGAATTGAGAGTCGGCGTTCGTCA\n++\n+JJIIIIGIGGFA<AHHFFFFFBB@\n+@HWI-ST132:678:C1LFKACXX:6:1204:6384:54699\n+TGAATTGAGAGTCGGCGTTCGTCA\n++\n+IHGIHGIIGGIHFHHHFFFFFCCC\n+@HWI-ST132:678:C1LFKACXX:6:1204:14453:87454\n+TGAATTGAGAGTCGGCGTTCGTCA\n++\n+IJIJIIHIGHGHHHHHFFFFFCCB\n+@HWI-ST132:678:C1LFKACXX:6:1204:12749:98529\n+TGAATTGAGAGTCGGCGTTCGTCA\n++\n+IJIJIHHHGGCD<<BHFFFFF@@@\n+@HWI-ST132:678:C1LFKACXX:6:1207:1627:36426\n+TGAATTGAGAGTCGGCGTTCGTCA\n++\n+JJIJIIJJIHGFBFDHFFFFF@C@\n+@HWI-ST132:678:C1LFKACXX:6:1208:12759:32103\n+TGAATTGAGAGTCGGCGTTCGTCA\n++\n+JIHJJHIIGGCFCHGHFFFFFCCC\n+@HWI-ST132:678:C1LFKACXX:6:1211:14889:36585\n+TGAATTGAGAGTCGGCGTTCGTCA\n++\n+JIHIIHGGCCCCAFHHFFFFFBB@\n+@HWI-ST132:678:C1LFKACXX:6:1212:12013:59978\n+TGAATTGAGAGTCGGCGTTCGTCA\n++\n+IJIJJJIGHFEHFHHHFFFFFBCB\n+@HWI-ST132:678:C1LFKACXX:6:1213:5120:11874\n+TGAATTGAGAGTCGGCGTTCGTCA\n++\n+IHHJIHBIFCGFCHHHFFFFF@CC\n+@HWI-ST132:678:C1LFKACXX:6:1213:2292:56427\n+TGAATTGAGAGTCGGCGTTCGTCA\n++\n+EEDIHECF@GEC:DHDFDBAD??@\n+@HWI-ST132:678:C1LFKACXX:6:1308:19681:44147\n+TGAATTGAGAGTCGGCGTTCGTCA\n++\n+JIHJJHHHE8GHDHGHFFFFFCCC\n+@HWI-ST132:678:C1LFKACXX:6:1308:8039:70634\n+TGAATTGAGAGTCGGCGTTCGTCA\n++\n+IJIJIHGIGHGFCHHHFFFFFBB@\n+@HWI-ST132:678:C1LFKACXX:6:1308:11417:88836\n+TGAATTGAGAGTCGGCGTTCGTCA\n++\n+IIIIIIIHFE@HF?A:DDDDD@@@\n+@HWI-ST132:678:C1LFKACXX:6:1312:15688:21389\n+TGAATTGAGAGTCGGCGTTCGTCA\n++\n+GFIHBGGAC@GDDF=HDDFDFC@@\n+@HWI-ST132:678:C1LFKACXX:6:1313:13049:80920\n+TGAATTGAGAGTCGGCGTTCGTCA\n++\n+HDCHGHGHIGEFAHFFFDDFF@@@\n+@HWI-ST132:678:C1LFKACXX:6:1314:12437:83452\n+TGAATTGAGAGTCGGCGTTCGTCA\n++\n+DBBIGGDAG?@?FF=FDDDDD@@@\n+@HWI-ST132:678:C1LFKACXX:6:1315:14028:76290\n+TGAATTGAGAGTCGGCGTTCGTCA\n++\n+EEIGGHEHDGEFDFDDDEDBD=?@\n+@HWI-ST132:678:C1LFKACXX:6:2102:9769:89923\n+TGAATTGAGAGTCGGCGTTCGTCA\n++\n+JHGJIHGGCC322<2AFFFFD?=:\n+@HWI-ST132:678:C1LFKACXX:6:2103:19515:10586\n+TGAATTGAGAGTCGGCGTTCGTCA\n++\n+IIHIGG@HEGHHFHGHFFFFFCCC\n+@HWI-ST132:678:C1LFKACXX:6:2104:17289:78956\n+TGAATTGAGAGTCGGCGTTCGTCA\n++\n+JIHJIHHJHFFFBHHHFFFFFCCB\n+@HWI-ST132:678:C1LFKACXX:6:2105:16331:25093\n+TGAATTGAGAGTCGGCGTTCGTCA\n++\n+IHEIJHHIHGEHFFHHFFFFFCCB\n+@HWI-ST132:678:C1LFKACXX:6:2105:9615:69542\n+TGAATTGAGAGTCGGCGTTCGTCA\n++\n+@FDFFE@F@F8DD<2+BBDDD??=\n+@HWI-ST132:678:C1LFKACXX:6:2106:17205:80780\n+TGAATTGAGAGTCGGCGTTCGTCA\n++\n+IJIJIHFE@2@HDHHHFFFFFCCC\n+@HWI-ST132:678:C1LFKACXX:6:2107:12087:100544\n+TGAATTGAGAGTCGGCGTTCGTCA\n++\n+JIHJIJIIGFFHFHGHFFFFFCCC\n+@HWI-ST132:678:C1LFKACXX:6:2108:15487:6127\n+TGAATTGAGAGTCGGCGTTCGTCA\n++\n+JIHIHGCFC<BHDHHHFFFFFCCC\n+@HWI-ST132:678:C1LFKACXX:6:2108:20167:16581\n+TGAATTGAGAGTCGGCGTTCGTCA\n++\n+IHGHCIIJIIHF<HGHFFFFFCCC\n+@HWI-ST132:678:C1LFKACXX:6:2108:7618:52633\n+TGAATTGAGAGTCGGCGTTCGTCA\n++\n+IIJIJJIGG@2<2<DAFFFFF@@=\n+@HWI-ST132:678:C1LFKACXX:6:2108:5338:71459\n+TGAATTGAGAGTCGGCGTTCGTCA\n++\n+JIIJIHGIJIHHHHHHFFFFFCCC\n+@HWI-ST132:678:C1LFKACXX:6:1212:8402:44665\n+TGAATTGAGAGTCGGCGTTCGTCAT\n++\n+HHD?JHGHHHFEDFHGHFFFFD@@@\n+@HWI-ST132:678:C1LFKACXX:6:1303:20279:89985\n+TTTTTAAAATCAAGCAGC\n++\n+CCCFFFFFHHHHHIJBHH\n+@HWI-ST132:678:C1LFKACXX:6:1108:17894:41355\n+GCTGACATTGCGAAAGTG\n++\n+CCCFFFFFHHHHH1EEHH\n+@HWI-ST132:678:C1LFKACXX:6:2106:6743:87840\n+GCTGACATTGCGAAAGTG\n++\n+B@BFDFFFHHHAFIJ1CF\n' |
| b |
| diff -r 9645d995fb3c -r 9185ca0a7b43 test-data/fastq_dir/reads-sample-small.fastq-bonafide_reads-TEs_uni.fastq --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/fastq_dir/reads-sample-small.fastq-bonafide_reads-TEs_uni.fastq Wed Jan 16 08:18:13 2019 -0500 |
| b |
| b'@@ -0,0 +1,105280 @@\n+@HWI-ST132:678:C1LFKACXX:6:1304:17199:58363\n+AAAAACACGACCGTTCGCTTTGAAA\n++\n+JJJIJJJJJJIHHHHFHFDDBFCC@\n+@HWI-ST132:678:C1LFKACXX:6:2106:15381:40802\n+TTCAAAGCGAACGGTCGTGTTTTT\n++\n+CCCFFFFFHHHHHJFEGEC?HHII\n+@HWI-ST132:678:C1LFKACXX:6:1114:10027:77795\n+AAGATTATTAAAAACCACTGCTG\n++\n+<<EFECE:?AA,FBADD;;D@@@\n+@HWI-ST132:678:C1LFKACXX:6:2103:3486:88354\n+CTTTAATTATCATATATTGTA\n++\n+BBBD;=ABFHHHHJJJJJDJI\n+@HWI-ST132:678:C1LFKACXX:6:1302:14522:72647\n+TTATTAAAGATCCGTTCGCTTCGCGAG\n++\n+CC@FFFFFHFHHHJHIJIJJJGGGIII\n+@HWI-ST132:678:C1LFKACXX:6:1103:11536:23013\n+TATTAAAGATCCGTTCGCTTCGCGAG\n++\n+B@@FBDDFHHHHHIIJIJJIJJJJIG\n+@HWI-ST132:678:C1LFKACXX:6:1206:10262:20669\n+TATTAAAGATCCGTTCGCTTCGCGAG\n++\n+@@@DDDDDH8FHHGDHII:CHHIIBF\n+@HWI-ST132:678:C1LFKACXX:6:1212:12068:74880\n+TTAAAGATCCGTTCGCTTCGCGAG\n++\n+CCCFDFDDHHHBBGC@FHFFDEGF\n+@HWI-ST132:678:C1LFKACXX:6:1213:19350:18162\n+TTAAAGATCCGTTCGCTTCGCGAG\n++\n+CCCFFFDFHHHHHIHIJIIJJHHI\n+@HWI-ST132:678:C1LFKACXX:6:1307:12279:8790\n+TTAAAGATCCGTTCGCTTCGCGAG\n++\n+???DDDBDDDDDDI1CEEIIII)C\n+@HWI-ST132:678:C1LFKACXX:6:1105:11371:76507\n+TTAAAGATCCGTTCGCTTCGCGAGTG\n++\n+BCCFFFFFHHFDFH)CGIJJIJIIDH\n+@HWI-ST132:678:C1LFKACXX:6:1101:3613:56171\n+TGATTTGTGCAGTAGTTTAAACAA\n++\n+BC@FFFFDHHHHHIJHHIJJJJJJ\n+@HWI-ST132:678:C1LFKACXX:6:1315:11705:87614\n+ACCGCACGAGAGCAGTCTGCACGCT\n++\n+IGGIIGHAIIFAHDDHHDD@4++::\n+@HWI-ST132:678:C1LFKACXX:6:1215:15419:77724\n+AACCGCACGAGAGCAGTCTGCACGCT\n++\n+IIIGFCIGGIJGHDCFDFDD?BB?@@\n+@HWI-ST132:678:C1LFKACXX:6:2102:3965:15607\n+TATCTGAACCACTGTGCACG\n++\n+CJHGEIHHHHDGDFFFFBCB\n+@HWI-ST132:678:C1LFKACXX:6:1309:1157:27805\n+TTCGGCCATTAAAACCAGCGCACT\n++\n+IIGGDIIHFFIHHHHHFFDDFB@@\n+@HWI-ST132:678:C1LFKACXX:6:1104:18136:49719\n+TCACTCGTTCGGCCATTAAAACCAGC\n++\n+IHJJIJIHJIIHFC6HHHFFFFFB@@\n+@HWI-ST132:678:C1LFKACXX:6:1206:4661:54441\n+TCATCACTCGTTCGGCCATTAAAAC\n++\n+JJJHGJIHHFC<HHHHHFFFFFCCC\n+@HWI-ST132:678:C1LFKACXX:6:1202:12284:43103\n+TTTAATGGCCGAACGAGTGATGACC\n++\n+B@BDFEFFHHCFHGIIJGHIIJJJJ\n+@HWI-ST132:678:C1LFKACXX:6:1105:18888:91816\n+TGCTAGGTCATCACTCGTTCGGCC\n++\n+JIIJJJJJJIIHDHHHDFFFFCCC\n+@HWI-ST132:678:C1LFKACXX:6:2104:13126:47993\n+TGCTAGGTCATCACTCGTTCGGCC\n++\n+JIHIIHJJJJJHHHHHDEDDFCCB\n+@HWI-ST132:678:C1LFKACXX:6:1310:10470:57499\n+TTAGATTTTTACCCTTTGCT\n++\n+JIGHGJJHHHGHFFEDF@@@\n+@HWI-ST132:678:C1LFKACXX:6:1208:10660:53352\n+GATGAAATCGTTTATGCGCCAAACT\n++\n+@@@DDDDDHHFHH=GHHIII@GCHI\n+@HWI-ST132:678:C1LFKACXX:6:2103:8188:10042\n+AGGTGGCTTGAAAGAACTGATCAACA\n++\n+@CCDDFFFHHHHHHGHIJHIJJCGHI\n+@HWI-ST132:678:C1LFKACXX:6:1116:8825:28862\n+GTTGATCAGTTCTTTCAAGCCACCT\n++\n+JIHCIEJIJJJJHHHDD;DDDA?@@\n+@HWI-ST132:678:C1LFKACXX:6:1109:17962:8377\n+TGGCTTGAAAGAACTGATCAACAGT\n++\n+CCCFFFFFHGHGHJJGCFHGIJIJJ\n+@HWI-ST132:678:C1LFKACXX:6:1202:14965:95853\n+TGGCTTGAAAGAACTGATCAACAGT\n++\n+CCCFFFFFHHHHHJJ<EHIJJJJJI\n+@HWI-ST132:678:C1LFKACXX:6:1209:11469:94001\n+TGGCTTGAAAGAACTGATCAACAGT\n++\n+CC@FFFFFGDFHGJJIIJIJJJ@HF\n+@HWI-ST132:678:C1LFKACXX:6:1213:13936:36177\n+TGGCTTGAAAGAACTGATCAACAGT\n++\n+CCCFFFFFGHHGFIIJJJJIIJIJH\n+@HWI-ST132:678:C1LFKACXX:6:1307:8164:25340\n+TCTCTAGCTATGCCAAAACTGT\n++\n+IJJJJJIJJHHDBHFFFFFB@B\n+@HWI-ST132:678:C1LFKACXX:6:1207:3316:75546\n+TCATCGGCTCGACGGAAACAATCTC\n++\n+GGEGIIIJHEFED@FHHFFFFFCC@\n+@HWI-ST132:678:C1LFKACXX:6:1306:3630:57103\n+TCATCGGCTCGACGGAAACAATCTC\n++\n+HHBGIHFGD1JGFAGHHFFFFFC@C\n+@HWI-ST132:678:C1LFKACXX:6:1106:13590:90955\n+TATCATCGGCTCGACGGAAACAATC\n++\n+GEIGEHGDC1<)HHDDDDBDDD@@@\n+@HWI-ST132:678:C1LFKACXX:6:2102:10526:18026\n+TATCATCGGCTCGACGGAAACAATC\n++\n+B<GD@?GEEDE>HAFHFDDB=A@@=\n+@HWI-ST132:678:C1LFKACXX:6:1301:18775:28385\n+TATCATCGGCTCGACGGAAA\n++\n+GHDHGGIGHHHHDDEDBC@@\n+@HWI-ST132:678:C1LFKACXX:6:1101:5698:75650\n+TAAACTGTGAATTAAGCGCGCACA\n++\n+JJIJJIGEAIJHHHFFDFFFFCBB\n+@HWI-ST132:678:C1LFKACXX:6:1113:19105:21652\n+TAAACTGTGAATTAAGCGCGCACA\n++\n+?C:?G:E<CF>F>FFC2D;B=+1=\n+@HWI-ST132:678:C1LFKACXX:6:1203:16184:49147\n+TTAAACTGTGAATTAAGCGCGCAC\n++\n+HGGHEGFA4IIHHHFBDDDDD@@@\n+@HWI-ST132:678:C1LFKACXX:6:1309:15681:14462\n+TTAAACTGTGAATTAAGCGCGCAC\n++\n+IHFIECJJJJJHGHHHFFFFFCCC\n+@HWI-ST132:678:C1LFKACXX:6:1304:3965:45774\n+TTAAACTGTGAATTAAGCGCG\n++'..b'+TGAATTGAGAGTCGGCGTTCGTC\n++\n+HEJJIJJGJHFFFFFDDDA4+:1\n+@HWI-ST132:678:C1LFKACXX:6:1316:16722:42018\n+TGAATTGAGAGTCGGCGTTCGTC\n++\n+HGJJJIJIJIHHHHHBEDA4+:1\n+@HWI-ST132:678:C1LFKACXX:6:2105:1246:21420\n+TGAATTGAGAGTCGGCGTTCGTC\n++\n+GCGEIJIIIGHHFDHEFDFD@@@\n+@HWI-ST132:678:C1LFKACXX:6:1101:8704:11437\n+TGAATTGAGAGTCGGCGTTCGTCA\n++\n+JIHIIHFGFE1FC<FHFFFFFCC@\n+@HWI-ST132:678:C1LFKACXX:6:1101:11649:25495\n+TGAATTGAGAGTCGGCGTTCGTCA\n++\n+JJJJJHGHIHGFAHDHFFFFFBCC\n+@HWI-ST132:678:C1LFKACXX:6:1103:18159:65506\n+TGAATTGAGAGTCGGCGTTCGTCA\n++\n+GGHJIHHHFECC<DDFFFFDD@@@\n+@HWI-ST132:678:C1LFKACXX:6:1105:19098:86110\n+TGAATTGAGAGTCGGCGTTCGTCA\n++\n+IHGJJIIJIHFA3CHHFFFFFCBB\n+@HWI-ST132:678:C1LFKACXX:6:1106:6923:42358\n+TGAATTGAGAGTCGGCGTTCGTCA\n++\n+GIHGG?CGFC222F;HFFDFF@@@\n+@HWI-ST132:678:C1LFKACXX:6:1110:4800:90404\n+TGAATTGAGAGTCGGCGTTCGTCA\n++\n+IHIJJIIHF:IHHHHHFFFFF@C@\n+@HWI-ST132:678:C1LFKACXX:6:1203:9910:19443\n+TGAATTGAGAGTCGGCGTTCGTCA\n++\n+JJIIIIGIGGFA<AHHFFFFFBB@\n+@HWI-ST132:678:C1LFKACXX:6:1204:6384:54699\n+TGAATTGAGAGTCGGCGTTCGTCA\n++\n+IHGIHGIIGGIHFHHHFFFFFCCC\n+@HWI-ST132:678:C1LFKACXX:6:1204:14453:87454\n+TGAATTGAGAGTCGGCGTTCGTCA\n++\n+IJIJIIHIGHGHHHHHFFFFFCCB\n+@HWI-ST132:678:C1LFKACXX:6:1204:12749:98529\n+TGAATTGAGAGTCGGCGTTCGTCA\n++\n+IJIJIHHHGGCD<<BHFFFFF@@@\n+@HWI-ST132:678:C1LFKACXX:6:1207:1627:36426\n+TGAATTGAGAGTCGGCGTTCGTCA\n++\n+JJIJIIJJIHGFBFDHFFFFF@C@\n+@HWI-ST132:678:C1LFKACXX:6:1208:12759:32103\n+TGAATTGAGAGTCGGCGTTCGTCA\n++\n+JIHJJHIIGGCFCHGHFFFFFCCC\n+@HWI-ST132:678:C1LFKACXX:6:1211:14889:36585\n+TGAATTGAGAGTCGGCGTTCGTCA\n++\n+JIHIIHGGCCCCAFHHFFFFFBB@\n+@HWI-ST132:678:C1LFKACXX:6:1212:12013:59978\n+TGAATTGAGAGTCGGCGTTCGTCA\n++\n+IJIJJJIGHFEHFHHHFFFFFBCB\n+@HWI-ST132:678:C1LFKACXX:6:1213:5120:11874\n+TGAATTGAGAGTCGGCGTTCGTCA\n++\n+IHHJIHBIFCGFCHHHFFFFF@CC\n+@HWI-ST132:678:C1LFKACXX:6:1213:2292:56427\n+TGAATTGAGAGTCGGCGTTCGTCA\n++\n+EEDIHECF@GEC:DHDFDBAD??@\n+@HWI-ST132:678:C1LFKACXX:6:1308:19681:44147\n+TGAATTGAGAGTCGGCGTTCGTCA\n++\n+JIHJJHHHE8GHDHGHFFFFFCCC\n+@HWI-ST132:678:C1LFKACXX:6:1308:8039:70634\n+TGAATTGAGAGTCGGCGTTCGTCA\n++\n+IJIJIHGIGHGFCHHHFFFFFBB@\n+@HWI-ST132:678:C1LFKACXX:6:1308:11417:88836\n+TGAATTGAGAGTCGGCGTTCGTCA\n++\n+IIIIIIIHFE@HF?A:DDDDD@@@\n+@HWI-ST132:678:C1LFKACXX:6:1312:15688:21389\n+TGAATTGAGAGTCGGCGTTCGTCA\n++\n+GFIHBGGAC@GDDF=HDDFDFC@@\n+@HWI-ST132:678:C1LFKACXX:6:1313:13049:80920\n+TGAATTGAGAGTCGGCGTTCGTCA\n++\n+HDCHGHGHIGEFAHFFFDDFF@@@\n+@HWI-ST132:678:C1LFKACXX:6:1314:12437:83452\n+TGAATTGAGAGTCGGCGTTCGTCA\n++\n+DBBIGGDAG?@?FF=FDDDDD@@@\n+@HWI-ST132:678:C1LFKACXX:6:1315:14028:76290\n+TGAATTGAGAGTCGGCGTTCGTCA\n++\n+EEIGGHEHDGEFDFDDDEDBD=?@\n+@HWI-ST132:678:C1LFKACXX:6:2102:9769:89923\n+TGAATTGAGAGTCGGCGTTCGTCA\n++\n+JHGJIHGGCC322<2AFFFFD?=:\n+@HWI-ST132:678:C1LFKACXX:6:2103:19515:10586\n+TGAATTGAGAGTCGGCGTTCGTCA\n++\n+IIHIGG@HEGHHFHGHFFFFFCCC\n+@HWI-ST132:678:C1LFKACXX:6:2104:17289:78956\n+TGAATTGAGAGTCGGCGTTCGTCA\n++\n+JIHJIHHJHFFFBHHHFFFFFCCB\n+@HWI-ST132:678:C1LFKACXX:6:2105:16331:25093\n+TGAATTGAGAGTCGGCGTTCGTCA\n++\n+IHEIJHHIHGEHFFHHFFFFFCCB\n+@HWI-ST132:678:C1LFKACXX:6:2105:9615:69542\n+TGAATTGAGAGTCGGCGTTCGTCA\n++\n+@FDFFE@F@F8DD<2+BBDDD??=\n+@HWI-ST132:678:C1LFKACXX:6:2106:17205:80780\n+TGAATTGAGAGTCGGCGTTCGTCA\n++\n+IJIJIHFE@2@HDHHHFFFFFCCC\n+@HWI-ST132:678:C1LFKACXX:6:2107:12087:100544\n+TGAATTGAGAGTCGGCGTTCGTCA\n++\n+JIHJIJIIGFFHFHGHFFFFFCCC\n+@HWI-ST132:678:C1LFKACXX:6:2108:15487:6127\n+TGAATTGAGAGTCGGCGTTCGTCA\n++\n+JIHIHGCFC<BHDHHHFFFFFCCC\n+@HWI-ST132:678:C1LFKACXX:6:2108:20167:16581\n+TGAATTGAGAGTCGGCGTTCGTCA\n++\n+IHGHCIIJIIHF<HGHFFFFFCCC\n+@HWI-ST132:678:C1LFKACXX:6:2108:7618:52633\n+TGAATTGAGAGTCGGCGTTCGTCA\n++\n+IIJIJJIGG@2<2<DAFFFFF@@=\n+@HWI-ST132:678:C1LFKACXX:6:2108:5338:71459\n+TGAATTGAGAGTCGGCGTTCGTCA\n++\n+JIIJIHGIJIHHHHHHFFFFFCCC\n+@HWI-ST132:678:C1LFKACXX:6:1212:8402:44665\n+TGAATTGAGAGTCGGCGTTCGTCAT\n++\n+HHD?JHGHHHFEDFHGHFFFFD@@@\n+@HWI-ST132:678:C1LFKACXX:6:1303:20279:89985\n+TTTTTAAAATCAAGCAGC\n++\n+CCCFFFFFHHHHHIJBHH\n+@HWI-ST132:678:C1LFKACXX:6:1108:17894:41355\n+GCTGACATTGCGAAAGTG\n++\n+CCCFFFFFHHHHH1EEHH\n+@HWI-ST132:678:C1LFKACXX:6:2106:6743:87840\n+GCTGACATTGCGAAAGTG\n++\n+B@BFDFFFHHHAFIJ1CF\n' |
| b |
| diff -r 9645d995fb3c -r 9185ca0a7b43 test-data/fastq_dir/reads-sample-small.fastq-bonafide_reads-genome.fastq --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/fastq_dir/reads-sample-small.fastq-bonafide_reads-genome.fastq Wed Jan 16 08:18:13 2019 -0500 |
| b |
| b'@@ -0,0 +1,122120 @@\n+@HWI-ST132:678:C1LFKACXX:6:2109:5620:9149\n+TTTTTAACGAATCTAGTATACCCT\n++\n+B@BDFFFFF?<ADFHHIJJJJJJJ\n+@HWI-ST132:678:C1LFKACXX:6:1213:14882:29587\n+TAATCGAATGCTAATTGTAATT\n++\n+=??AAD?B:<CD>,AFAGF9FA\n+@HWI-ST132:678:C1LFKACXX:6:1315:2668:98246\n+TTAACCGTTTTGAGCTCGGCGACCT\n++\n+1=14BDDDHHHFFIIIIFEA??@FH\n+@HWI-ST132:678:C1LFKACXX:6:1208:17824:38721\n+TCTTTATATTCGTTGGTATTTGGC\n++\n+CCCFFFFFHHH<2><C<CJJJJJJ\n+@HWI-ST132:678:C1LFKACXX:6:1203:15535:47028\n+CCGGGACTGCACAGACGAAGCGG\n++\n+@C@FFFFFHHHHHJJJIHIIIIJ\n+@HWI-ST132:678:C1LFKACXX:6:1213:1288:58514\n+AGATTCATGTTCGGATCGTCGATAC\n++\n+@C@FFFFFHHHHHIJBHIJJJJJIJ\n+@HWI-ST132:678:C1LFKACXX:6:2102:10820:38797\n+CGCTTCTTTTGAATGCGTCGTGGTG\n++\n+CCCFFFFFHHHHHJ,AGHI@<?HCG\n+@HWI-ST132:678:C1LFKACXX:6:1106:17295:99240\n+GCTGCCGCGATTCCCAAACCGTCCTG\n++\n+B@BDDFFFF?@DFEH<EGIGIJIJJJ\n+@HWI-ST132:678:C1LFKACXX:6:2101:14809:65434\n+TCCTGAGAGTCTGGTCACCGTAGAG\n++\n+CCCF?EFFHHHFHJHJJJJ3343<A\n+@HWI-ST132:678:C1LFKACXX:6:1103:14549:53735\n+ACCGTAGAGAATCTGAGCGTCAGAA\n++\n+@CCFDFFFGFHHHJGDGHGGHIJIJ\n+@HWI-ST132:678:C1LFKACXX:6:1301:3547:24519\n+CACCAGTCGGCAATATAGATCTCCT\n++\n+BCBFFFDFHHHHHJJJJJJJJJJJJ\n+@HWI-ST132:678:C1LFKACXX:6:1303:14743:8078\n+TCTATATTGCCGACTGGTGGCTCAGT\n++\n+BCBFDFFFHHHHHJJHFCFGGGHIJJ\n+@HWI-ST132:678:C1LFKACXX:6:1309:19811:76863\n+TCCTTGGCGGAGGTATCGTAGTGAG\n++\n+CCCFFFFFHHFHH?FHJJJJJHJIJ\n+@HWI-ST132:678:C1LFKACXX:6:2104:9716:27077\n+GTACTCGATCGCCTGAAGAAC\n++\n+@@CFFFFFHHCFHI+AEHHII\n+@HWI-ST132:678:C1LFKACXX:6:1310:11218:64506\n+TTCCGGATTGGCAATACCCGCCTC\n++\n+CCCFFFFFHHHHHGI<GHIJIIJJ\n+@HWI-ST132:678:C1LFKACXX:6:1306:4247:15664\n+TTACAAAGTCAGTGGGGATGC\n++\n+@@@FFFFFFFHFCGGE<F@A<\n+@HWI-ST132:678:C1LFKACXX:6:1308:7854:98971\n+TTTGGCAAGAGGCGGCTCCTCCTG\n++\n+@@BFFFFFHHDFHEHGIJIIIJII\n+@HWI-ST132:678:C1LFKACXX:6:2104:8198:11388\n+TCTGTTGGCAGCTAGATCAGGGGC\n++\n+BCCFDFFFHHFHHGIIJJJJJJJJ\n+@HWI-ST132:678:C1LFKACXX:6:1302:8323:14904\n+TCTGTTGGCAGCTAGATCAGGGG\n++\n+BBCFDEDFHA<DFHFFHIJJJJJ\n+@HWI-ST132:678:C1LFKACXX:6:2102:13088:36303\n+TACTTGAGGACATAGACAAACATTG\n++\n+BBCFFFFFD=CFHH+AEHIJJJJJJ\n+@HWI-ST132:678:C1LFKACXX:6:1107:9391:35335\n+TCCAGAACAGGTCTGTGGGACTGATC\n++\n+CCCFFFFFHHHDHI3<EGIIJJJJJJ\n+@HWI-ST132:678:C1LFKACXX:6:1209:13917:31506\n+TATCCAGAACAGGTCTGTGGGAC\n++\n+CCCFFFFFHHH?FFHJJIJJJJJ\n+@HWI-ST132:678:C1LFKACXX:6:1210:16851:33080\n+TCCATAATCCTGACCATCCGGGCAG\n++\n+CC@FFFFFHHHHGIJIJJJJIJJJJ\n+@HWI-ST132:678:C1LFKACXX:6:2104:16032:57923\n+CCCGGATGGTCAGGATTATGGAAGC\n++\n+CCCFFFFFHFHHHGHIIIIIJJJJJ\n+@HWI-ST132:678:C1LFKACXX:6:1109:16268:61514\n+TACGGTAGAACAACTACACCGAGTGGT\n++\n+@CCFFDDDGBHHHJIIIJJJJJJFHGI\n+@HWI-ST132:678:C1LFKACXX:6:1210:7403:36822\n+TTTGCTCGACCACTCGGTGTAGTTGT\n++\n+CCCFFFFFHHHHHJJEE<ACGIIIJI\n+@HWI-ST132:678:C1LFKACXX:6:1303:14362:59821\n+TTTGCTCGACCACTCGGTGTAGT\n++\n+@C@FFFFFHHHFHIJFEA+@CFH\n+@HWI-ST132:678:C1LFKACXX:6:1304:17199:58363\n+AAAAACACGACCGTTCGCTTTGAAA\n++\n+@CCFBDDFHFHHHHIJJJJJJIJJJ\n+@HWI-ST132:678:C1LFKACXX:6:2106:15381:40802\n+TTCAAAGCGAACGGTCGTGTTTTT\n++\n+CCCFFFFFHHHHHJFEGEC?HHII\n+@HWI-ST132:678:C1LFKACXX:6:1114:10027:77795\n+AAGATTATTAAAAACCACTGCTG\n++\n+@@@D;;DDABF,AA?:ECEFE<<\n+@HWI-ST132:678:C1LFKACXX:6:2103:3486:88354\n+CTTTAATTATCATATATTGTA\n++\n+BBBD;=ABFHHHHJJJJJDJI\n+@HWI-ST132:678:C1LFKACXX:6:1302:14522:72647\n+TTATTAAAGATCCGTTCGCTTCGCGAG\n++\n+CC@FFFFFHFHHHJHIJIJJJGGGIII\n+@HWI-ST132:678:C1LFKACXX:6:1103:11536:23013\n+TATTAAAGATCCGTTCGCTTCGCGAG\n++\n+B@@FBDDFHHHHHIIJIJJIJJJJIG\n+@HWI-ST132:678:C1LFKACXX:6:1206:10262:20669\n+TATTAAAGATCCGTTCGCTTCGCGAG\n++\n+@@@DDDDDH8FHHGDHII:CHHIIBF\n+@HWI-ST132:678:C1LFKACXX:6:1212:12068:74880\n+TTAAAGATCCGTTCGCTTCGCGAG\n++\n+CCCFDFDDHHHBBGC@FHFFDEGF\n+@HWI-ST132:678:C1LFKACXX:6:1213:19350:18162\n+TTAAAGATCCGTTCGCTTCGCGAG\n++\n+CCCFFFDFHHHHHIHIJIIJJHHI\n+@HWI-ST132:678:C1LFKACXX:6:1307:12279:8790\n+TTAAAGATCCGTTCGCTTCGCGAG\n++\n+???DDDBDDDDDDI1CEEIIII)C\n+@HWI-ST132:678:C1LFKACXX:6:1105:11371:76507\n+TTAAAGATCCGTTCGCTTCGCGAGTG\n++\n+BCCFFFFFHHFDFH)CGIJJIJIIDH\n+@HWI-ST132:678:C1LFKACXX:6:1101:3613:56171\n+TGATTTGTGCAGTAGTTTAAACAA\n++\n+BC@FFFFDHHHHHIJHHIJJJJJJ\n+@HWI-ST132:678:C1LFKACXX:6:1315:11705:87614\n+ACCGCACGAGAGCAGTCT'..b'TTTTTAAAATCAAGCAGC\n++\n+CCCFFFFFHHHHHIJBHH\n+@HWI-ST132:678:C1LFKACXX:6:2109:19607:31518\n+TCGTGGTGACTCGGTGCCGC\n++\n+@C@FFFDDHHHHHJCGGH@G\n+@HWI-ST132:678:C1LFKACXX:6:1305:17224:89111\n+CCGAGCCGACGAACCGTCCCTGGAA\n++\n+@@@FFF?DHHDHHJJJBHIICAHGI\n+@HWI-ST132:678:C1LFKACXX:6:1103:16749:88668\n+GCACCATAGACCAACTCTGCCATC\n++\n+BCCFFFFF+AFHHJJJJIHIJIJJ\n+@HWI-ST132:678:C1LFKACXX:6:1208:4638:88640\n+CTTTCGATGGCAGAGTTGGTC\n++\n+@BBFFFDDHHHHHJJGIIGHI\n+@HWI-ST132:678:C1LFKACXX:6:1108:5315:17099\n+CCACTGTGGAATTATGAGAGC\n++\n+B@BFFFDDFDHHH4CAEEGII\n+@HWI-ST132:678:C1LFKACXX:6:2105:9020:42698\n+AAGCAGCCAAAGCTCCAGGGC\n++\n+CCBFFFFFHHHDFIJJJJJJI\n+@HWI-ST132:678:C1LFKACXX:6:1111:18474:81416\n+GCAACCAGTTGATTGGGGACT\n++\n+@CCFFFFFFHHHHJIJEHIJJ\n+@HWI-ST132:678:C1LFKACXX:6:1310:16238:87083\n+ATCGTCGTCAACAACGTTGTCAGGAT\n++\n+CCCFFFFDHGHHHJHHFE+CHHIJII\n+@HWI-ST132:678:C1LFKACXX:6:1307:17701:69811\n+TCGGTTCGGTTCGGATCG\n++\n+BBCFDDFFHDFFHIHHII\n+@HWI-ST132:678:C1LFKACXX:6:2106:19244:87969\n+CCGAACCGAACCGAAACCAAACAAAA\n++\n+=B@D440@@FHHHJJJJJJIIJJJJJ\n+@HWI-ST132:678:C1LFKACXX:6:1107:2900:96158\n+TTCCAAAGTTGTGAGGCACTC\n++\n+@@@F?DDEDFHHHJIHIJJJJ\n+@HWI-ST132:678:C1LFKACXX:6:1302:12325:17230\n+TTAATTTCGCGTTTTTTCTCG\n++\n+:?BDDF?DFH@00BFHIIJJJ\n+@HWI-ST132:678:C1LFKACXX:6:1215:4582:40762\n+TCGTGTTCGCTCTCAAACTGAAAC\n++\n+@CCFFFFFGHHHHJJJGIJEIIJJ\n+@HWI-ST132:678:C1LFKACXX:6:1205:10933:11207\n+ACCGGACAGCACGGTCGTGTT\n++\n+@CCFFFFFFHHHGEEGIFGHG\n+@HWI-ST132:678:C1LFKACXX:6:1306:13426:31059\n+ACCGGACAGCACGGTCGT\n++\n+?@@DA@DDHHHHHIAEEC\n+@HWI-ST132:678:C1LFKACXX:6:1110:1636:70699\n+TTAACAATCAGTGCGGTGTAC\n++\n+CCCFFFFEHHHDFGIIIJJJJ\n+@HWI-ST132:678:C1LFKACXX:6:1309:7124:23190\n+CAAGCGACACGGACTGGAGCCA\n++\n+@BCFFFFFHHD<CGIFFHHIIJ\n+@HWI-ST132:678:C1LFKACXX:6:2104:19761:27328\n+CAAGCGACACGGACTGGAGCCA\n++\n+CCCFFFFFHHHHHIJCGHFGIJ\n+@HWI-ST132:678:C1LFKACXX:6:2105:13059:46395\n+AAACTCTAAGCGGTGGATC\n++\n+CCCFFFFFFHDFFCGHIIJ\n+@HWI-ST132:678:C1LFKACXX:6:1305:16206:81936\n+AAACTCTAAGCGGTGGATCA\n++\n+CCCFFFFFHHGHHHHIGIJJ\n+@HWI-ST132:678:C1LFKACXX:6:2107:10854:4790\n+AAACTCTAAGCGGTGGATCACTCG\n++\n+8?<BDDDDDC?88C@<GGDBEH9C\n+@HWI-ST132:678:C1LFKACXX:6:2106:17769:8524\n+GCATATCGCAGTCCATGCTGT\n++\n+CCCFFFFFHHHHHJJJJJJIH\n+@HWI-ST132:678:C1LFKACXX:6:1105:14942:89758\n+TACATATGGTTGAGGGTTGTAA\n++\n+B@BFFFFFHFHHHEEFCGHHIJ\n+@HWI-ST132:678:C1LFKACXX:6:1207:12907:27002\n+TACATATGGTTGAGGGTTGTAA\n++\n+BB@DFFFFHCDA<EHACGE>CH\n+@HWI-ST132:678:C1LFKACXX:6:2108:10584:25180\n+TACATATGGTTGAGGGTTGTAA\n++\n+B?@DFFFFHADCFACF2AF<CF\n+@HWI-ST132:678:C1LFKACXX:6:1104:5978:95171\n+TATGGTTGAGGGTTGTAA\n++\n+B@BFFDEFHHGH<EEBFG\n+@HWI-ST132:678:C1LFKACXX:6:1108:17894:41355\n+GCTGACATTGCGAAAGTG\n++\n+CCCFFFFFHHHHH1EEHH\n+@HWI-ST132:678:C1LFKACXX:6:2106:6743:87840\n+GCTGACATTGCGAAAGTG\n++\n+B@BFDFFFHHHAFIJ1CF\n+@HWI-ST132:678:C1LFKACXX:6:1104:16518:94276\n+GATCCCAGATCCGCTGTGTTT\n++\n+CCCFFFFFHHHHHIJFGHHIJ\n+@HWI-ST132:678:C1LFKACXX:6:1213:14045:90482\n+ATACTAGATTCGTTGAAAAGT\n++\n+@@@F7DDDFA<CC?;FAEBH?\n+@HWI-ST132:678:C1LFKACXX:6:1302:4633:32096\n+TGTTGCGGCAACTTCTTTAAGTTG\n++\n+CCCFFFFFHHHHHJJJJJJJJHIJ\n+@HWI-ST132:678:C1LFKACXX:6:2101:16974:2305\n+ACCGTTCTATGCTTTTTTTT\n++\n+:BBDDDDFHH<2<CFHIIJJ\n+@HWI-ST132:678:C1LFKACXX:6:1313:11404:80054\n+ACCGTTCTATGCTTTTTTTTA\n++\n+@@CFBDFF?FHHGIIIIGIIC\n+@HWI-ST132:678:C1LFKACXX:6:1116:12125:58757\n+AAGTAGCAGTCGTGGCCGAGTG\n++\n+??+4=B?DDHHF<EGHGGGIDG\n+@HWI-ST132:678:C1LFKACXX:6:1106:17247:63193\n+AATCCTACCGGCTGCGAATGA\n++\n+@BBFFDEFHFHHHFFFFHGHJ\n+@HWI-ST132:678:C1LFKACXX:6:1107:17291:97995\n+ATCCTACCGGCTGCGAATGA\n++\n+@CCFFFFFDFFHHJGEHGBG\n+@HWI-ST132:678:C1LFKACXX:6:2105:5531:13237\n+ACCGGCTGCGAATGAGAA\n++\n+B@BFFFFFGHDFCFHEGI\n+@HWI-ST132:678:C1LFKACXX:6:1111:11783:45506\n+ACCGGCTGCGAATGAGAATGT\n++\n+???DFFFFFHF:CCCGHHBG<\n+@HWI-ST132:678:C1LFKACXX:6:2105:11033:71535\n+CGGCTGCGAATGAGAATGTATATTT\n++\n+?BBDFFFF@<@ACAAEHHHGGIJJI\n+@HWI-ST132:678:C1LFKACXX:6:2103:20548:80488\n+AATGAGAATGTATATTTT\n++\n+BCBDDFFFHHFHHJJJJJ\n+@HWI-ST132:678:C1LFKACXX:6:2108:19159:27727\n+ATATAGCCTGAGCTTCGACC\n++\n+CCCFFFDFHHH?FHIJJJJJ\n+@HWI-ST132:678:C1LFKACXX:6:1303:5477:98042\n+GTAACTGACCGTGTGGCCCAATGGA\n++\n+??@DFFFFGHDHGG?GGIEH3<FGH\n' |
| b |
| diff -r 9645d995fb3c -r 9185ca0a7b43 test-data/fastq_dir/reads-sample-small.fastq-bonafide_reads-genome_uni.fastq --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/fastq_dir/reads-sample-small.fastq-bonafide_reads-genome_uni.fastq Wed Jan 16 08:18:13 2019 -0500 |
| b |
| b'@@ -0,0 +1,122036 @@\n+@HWI-ST132:678:C1LFKACXX:6:2109:5620:9149\n+TTTTTAACGAATCTAGTATACCCT\n++\n+B@BDFFFFF?<ADFHHIJJJJJJJ\n+@HWI-ST132:678:C1LFKACXX:6:1213:14882:29587\n+TAATCGAATGCTAATTGTAATT\n++\n+=??AAD?B:<CD>,AFAGF9FA\n+@HWI-ST132:678:C1LFKACXX:6:1315:2668:98246\n+TTAACCGTTTTGAGCTCGGCGACCT\n++\n+1=14BDDDHHHFFIIIIFEA??@FH\n+@HWI-ST132:678:C1LFKACXX:6:1208:17824:38721\n+TCTTTATATTCGTTGGTATTTGGC\n++\n+CCCFFFFFHHH<2><C<CJJJJJJ\n+@HWI-ST132:678:C1LFKACXX:6:1203:15535:47028\n+CCGGGACTGCACAGACGAAGCGG\n++\n+@C@FFFFFHHHHHJJJIHIIIIJ\n+@HWI-ST132:678:C1LFKACXX:6:1213:1288:58514\n+AGATTCATGTTCGGATCGTCGATAC\n++\n+@C@FFFFFHHHHHIJBHIJJJJJIJ\n+@HWI-ST132:678:C1LFKACXX:6:2102:10820:38797\n+CGCTTCTTTTGAATGCGTCGTGGTG\n++\n+CCCFFFFFHHHHHJ,AGHI@<?HCG\n+@HWI-ST132:678:C1LFKACXX:6:1106:17295:99240\n+GCTGCCGCGATTCCCAAACCGTCCTG\n++\n+B@BDDFFFF?@DFEH<EGIGIJIJJJ\n+@HWI-ST132:678:C1LFKACXX:6:2101:14809:65434\n+TCCTGAGAGTCTGGTCACCGTAGAG\n++\n+CCCF?EFFHHHFHJHJJJJ3343<A\n+@HWI-ST132:678:C1LFKACXX:6:1103:14549:53735\n+ACCGTAGAGAATCTGAGCGTCAGAA\n++\n+@CCFDFFFGFHHHJGDGHGGHIJIJ\n+@HWI-ST132:678:C1LFKACXX:6:1301:3547:24519\n+CACCAGTCGGCAATATAGATCTCCT\n++\n+BCBFFFDFHHHHHJJJJJJJJJJJJ\n+@HWI-ST132:678:C1LFKACXX:6:1303:14743:8078\n+TCTATATTGCCGACTGGTGGCTCAGT\n++\n+BCBFDFFFHHHHHJJHFCFGGGHIJJ\n+@HWI-ST132:678:C1LFKACXX:6:1309:19811:76863\n+TCCTTGGCGGAGGTATCGTAGTGAG\n++\n+CCCFFFFFHHFHH?FHJJJJJHJIJ\n+@HWI-ST132:678:C1LFKACXX:6:2104:9716:27077\n+GTACTCGATCGCCTGAAGAAC\n++\n+@@CFFFFFHHCFHI+AEHHII\n+@HWI-ST132:678:C1LFKACXX:6:1310:11218:64506\n+TTCCGGATTGGCAATACCCGCCTC\n++\n+CCCFFFFFHHHHHGI<GHIJIIJJ\n+@HWI-ST132:678:C1LFKACXX:6:1306:4247:15664\n+TTACAAAGTCAGTGGGGATGC\n++\n+@@@FFFFFFFHFCGGE<F@A<\n+@HWI-ST132:678:C1LFKACXX:6:1308:7854:98971\n+TTTGGCAAGAGGCGGCTCCTCCTG\n++\n+@@BFFFFFHHDFHEHGIJIIIJII\n+@HWI-ST132:678:C1LFKACXX:6:2104:8198:11388\n+TCTGTTGGCAGCTAGATCAGGGGC\n++\n+BCCFDFFFHHFHHGIIJJJJJJJJ\n+@HWI-ST132:678:C1LFKACXX:6:1302:8323:14904\n+TCTGTTGGCAGCTAGATCAGGGG\n++\n+BBCFDEDFHA<DFHFFHIJJJJJ\n+@HWI-ST132:678:C1LFKACXX:6:2102:13088:36303\n+TACTTGAGGACATAGACAAACATTG\n++\n+BBCFFFFFD=CFHH+AEHIJJJJJJ\n+@HWI-ST132:678:C1LFKACXX:6:1107:9391:35335\n+TCCAGAACAGGTCTGTGGGACTGATC\n++\n+CCCFFFFFHHHDHI3<EGIIJJJJJJ\n+@HWI-ST132:678:C1LFKACXX:6:1209:13917:31506\n+TATCCAGAACAGGTCTGTGGGAC\n++\n+CCCFFFFFHHH?FFHJJIJJJJJ\n+@HWI-ST132:678:C1LFKACXX:6:1210:16851:33080\n+TCCATAATCCTGACCATCCGGGCAG\n++\n+CC@FFFFFHHHHGIJIJJJJIJJJJ\n+@HWI-ST132:678:C1LFKACXX:6:2104:16032:57923\n+CCCGGATGGTCAGGATTATGGAAGC\n++\n+CCCFFFFFHFHHHGHIIIIIJJJJJ\n+@HWI-ST132:678:C1LFKACXX:6:1109:16268:61514\n+TACGGTAGAACAACTACACCGAGTGGT\n++\n+@CCFFDDDGBHHHJIIIJJJJJJFHGI\n+@HWI-ST132:678:C1LFKACXX:6:1210:7403:36822\n+TTTGCTCGACCACTCGGTGTAGTTGT\n++\n+CCCFFFFFHHHHHJJEE<ACGIIIJI\n+@HWI-ST132:678:C1LFKACXX:6:1303:14362:59821\n+TTTGCTCGACCACTCGGTGTAGT\n++\n+@C@FFFFFHHHFHIJFEA+@CFH\n+@HWI-ST132:678:C1LFKACXX:6:1304:17199:58363\n+AAAAACACGACCGTTCGCTTTGAAA\n++\n+@CCFBDDFHFHHHHIJJJJJJIJJJ\n+@HWI-ST132:678:C1LFKACXX:6:2106:15381:40802\n+TTCAAAGCGAACGGTCGTGTTTTT\n++\n+CCCFFFFFHHHHHJFEGEC?HHII\n+@HWI-ST132:678:C1LFKACXX:6:1114:10027:77795\n+AAGATTATTAAAAACCACTGCTG\n++\n+@@@D;;DDABF,AA?:ECEFE<<\n+@HWI-ST132:678:C1LFKACXX:6:2103:3486:88354\n+CTTTAATTATCATATATTGTA\n++\n+BBBD;=ABFHHHHJJJJJDJI\n+@HWI-ST132:678:C1LFKACXX:6:1302:14522:72647\n+TTATTAAAGATCCGTTCGCTTCGCGAG\n++\n+CC@FFFFFHFHHHJHIJIJJJGGGIII\n+@HWI-ST132:678:C1LFKACXX:6:1103:11536:23013\n+TATTAAAGATCCGTTCGCTTCGCGAG\n++\n+B@@FBDDFHHHHHIIJIJJIJJJJIG\n+@HWI-ST132:678:C1LFKACXX:6:1206:10262:20669\n+TATTAAAGATCCGTTCGCTTCGCGAG\n++\n+@@@DDDDDH8FHHGDHII:CHHIIBF\n+@HWI-ST132:678:C1LFKACXX:6:1212:12068:74880\n+TTAAAGATCCGTTCGCTTCGCGAG\n++\n+CCCFDFDDHHHBBGC@FHFFDEGF\n+@HWI-ST132:678:C1LFKACXX:6:1213:19350:18162\n+TTAAAGATCCGTTCGCTTCGCGAG\n++\n+CCCFFFDFHHHHHIHIJIIJJHHI\n+@HWI-ST132:678:C1LFKACXX:6:1307:12279:8790\n+TTAAAGATCCGTTCGCTTCGCGAG\n++\n+???DDDBDDDDDDI1CEEIIII)C\n+@HWI-ST132:678:C1LFKACXX:6:1105:11371:76507\n+TTAAAGATCCGTTCGCTTCGCGAGTG\n++\n+BCCFFFFFHHFDFH)CGIJJIJIIDH\n+@HWI-ST132:678:C1LFKACXX:6:1101:3613:56171\n+TGATTTGTGCAGTAGTTTAAACAA\n++\n+BC@FFFFDHHHHHIJHHIJJJJJJ\n+@HWI-ST132:678:C1LFKACXX:6:1315:11705:87614\n+ACCGCACGAGAGCAGTCT'..b':41000\n+TCTGCAGCGATTCCGAACTCC\n++\n+CC@FFFFFHGHHHI3<EHHHI\n+@HWI-ST132:678:C1LFKACXX:6:1212:5835:88214\n+TCTGCAGCGATTCCGAACTC\n++\n+@CCFFFFFGFHHHIIJJJIJ\n+@HWI-ST132:678:C1LFKACXX:6:1303:20279:89985\n+TTTTTAAAATCAAGCAGC\n++\n+CCCFFFFFHHHHHIJBHH\n+@HWI-ST132:678:C1LFKACXX:6:2109:19607:31518\n+TCGTGGTGACTCGGTGCCGC\n++\n+@C@FFFDDHHHHHJCGGH@G\n+@HWI-ST132:678:C1LFKACXX:6:1305:17224:89111\n+CCGAGCCGACGAACCGTCCCTGGAA\n++\n+@@@FFF?DHHDHHJJJBHIICAHGI\n+@HWI-ST132:678:C1LFKACXX:6:1103:16749:88668\n+GCACCATAGACCAACTCTGCCATC\n++\n+BCCFFFFF+AFHHJJJJIHIJIJJ\n+@HWI-ST132:678:C1LFKACXX:6:1208:4638:88640\n+CTTTCGATGGCAGAGTTGGTC\n++\n+@BBFFFDDHHHHHJJGIIGHI\n+@HWI-ST132:678:C1LFKACXX:6:1108:5315:17099\n+CCACTGTGGAATTATGAGAGC\n++\n+B@BFFFDDFDHHH4CAEEGII\n+@HWI-ST132:678:C1LFKACXX:6:2105:9020:42698\n+AAGCAGCCAAAGCTCCAGGGC\n++\n+CCBFFFFFHHHDFIJJJJJJI\n+@HWI-ST132:678:C1LFKACXX:6:1111:18474:81416\n+GCAACCAGTTGATTGGGGACT\n++\n+@CCFFFFFFHHHHJIJEHIJJ\n+@HWI-ST132:678:C1LFKACXX:6:1310:16238:87083\n+ATCGTCGTCAACAACGTTGTCAGGAT\n++\n+CCCFFFFDHGHHHJHHFE+CHHIJII\n+@HWI-ST132:678:C1LFKACXX:6:1307:17701:69811\n+TCGGTTCGGTTCGGATCG\n++\n+BBCFDDFFHDFFHIHHII\n+@HWI-ST132:678:C1LFKACXX:6:2106:19244:87969\n+CCGAACCGAACCGAAACCAAACAAAA\n++\n+=B@D440@@FHHHJJJJJJIIJJJJJ\n+@HWI-ST132:678:C1LFKACXX:6:1107:2900:96158\n+TTCCAAAGTTGTGAGGCACTC\n++\n+@@@F?DDEDFHHHJIHIJJJJ\n+@HWI-ST132:678:C1LFKACXX:6:1302:12325:17230\n+TTAATTTCGCGTTTTTTCTCG\n++\n+:?BDDF?DFH@00BFHIIJJJ\n+@HWI-ST132:678:C1LFKACXX:6:1215:4582:40762\n+TCGTGTTCGCTCTCAAACTGAAAC\n++\n+@CCFFFFFGHHHHJJJGIJEIIJJ\n+@HWI-ST132:678:C1LFKACXX:6:1205:10933:11207\n+ACCGGACAGCACGGTCGTGTT\n++\n+@CCFFFFFFHHHGEEGIFGHG\n+@HWI-ST132:678:C1LFKACXX:6:1306:13426:31059\n+ACCGGACAGCACGGTCGT\n++\n+?@@DA@DDHHHHHIAEEC\n+@HWI-ST132:678:C1LFKACXX:6:1110:1636:70699\n+TTAACAATCAGTGCGGTGTAC\n++\n+CCCFFFFEHHHDFGIIIJJJJ\n+@HWI-ST132:678:C1LFKACXX:6:1309:7124:23190\n+CAAGCGACACGGACTGGAGCCA\n++\n+@BCFFFFFHHD<CGIFFHHIIJ\n+@HWI-ST132:678:C1LFKACXX:6:2104:19761:27328\n+CAAGCGACACGGACTGGAGCCA\n++\n+CCCFFFFFHHHHHIJCGHFGIJ\n+@HWI-ST132:678:C1LFKACXX:6:2105:13059:46395\n+AAACTCTAAGCGGTGGATC\n++\n+CCCFFFFFFHDFFCGHIIJ\n+@HWI-ST132:678:C1LFKACXX:6:1305:16206:81936\n+AAACTCTAAGCGGTGGATCA\n++\n+CCCFFFFFHHGHHHHIGIJJ\n+@HWI-ST132:678:C1LFKACXX:6:2107:10854:4790\n+AAACTCTAAGCGGTGGATCACTCG\n++\n+8?<BDDDDDC?88C@<GGDBEH9C\n+@HWI-ST132:678:C1LFKACXX:6:2106:17769:8524\n+GCATATCGCAGTCCATGCTGT\n++\n+CCCFFFFFHHHHHJJJJJJIH\n+@HWI-ST132:678:C1LFKACXX:6:1105:14942:89758\n+TACATATGGTTGAGGGTTGTAA\n++\n+B@BFFFFFHFHHHEEFCGHHIJ\n+@HWI-ST132:678:C1LFKACXX:6:1207:12907:27002\n+TACATATGGTTGAGGGTTGTAA\n++\n+BB@DFFFFHCDA<EHACGE>CH\n+@HWI-ST132:678:C1LFKACXX:6:2108:10584:25180\n+TACATATGGTTGAGGGTTGTAA\n++\n+B?@DFFFFHADCFACF2AF<CF\n+@HWI-ST132:678:C1LFKACXX:6:1104:5978:95171\n+TATGGTTGAGGGTTGTAA\n++\n+B@BFFDEFHHGH<EEBFG\n+@HWI-ST132:678:C1LFKACXX:6:1108:17894:41355\n+GCTGACATTGCGAAAGTG\n++\n+CCCFFFFFHHHHH1EEHH\n+@HWI-ST132:678:C1LFKACXX:6:2106:6743:87840\n+GCTGACATTGCGAAAGTG\n++\n+B@BFDFFFHHHAFIJ1CF\n+@HWI-ST132:678:C1LFKACXX:6:1104:16518:94276\n+GATCCCAGATCCGCTGTGTTT\n++\n+CCCFFFFFHHHHHIJFGHHIJ\n+@HWI-ST132:678:C1LFKACXX:6:1213:14045:90482\n+ATACTAGATTCGTTGAAAAGT\n++\n+@@@F7DDDFA<CC?;FAEBH?\n+@HWI-ST132:678:C1LFKACXX:6:1302:4633:32096\n+TGTTGCGGCAACTTCTTTAAGTTG\n++\n+CCCFFFFFHHHHHJJJJJJJJHIJ\n+@HWI-ST132:678:C1LFKACXX:6:2101:16974:2305\n+ACCGTTCTATGCTTTTTTTT\n++\n+:BBDDDDFHH<2<CFHIIJJ\n+@HWI-ST132:678:C1LFKACXX:6:1313:11404:80054\n+ACCGTTCTATGCTTTTTTTTA\n++\n+@@CFBDFF?FHHGIIIIGIIC\n+@HWI-ST132:678:C1LFKACXX:6:1116:12125:58757\n+AAGTAGCAGTCGTGGCCGAGTG\n++\n+??+4=B?DDHHF<EGHGGGIDG\n+@HWI-ST132:678:C1LFKACXX:6:1106:17247:63193\n+AATCCTACCGGCTGCGAATGA\n++\n+@BBFFDEFHFHHHFFFFHGHJ\n+@HWI-ST132:678:C1LFKACXX:6:1107:17291:97995\n+ATCCTACCGGCTGCGAATGA\n++\n+@CCFFFFFDFFHHJGEHGBG\n+@HWI-ST132:678:C1LFKACXX:6:2105:5531:13237\n+ACCGGCTGCGAATGAGAA\n++\n+B@BFFFFFGHDFCFHEGI\n+@HWI-ST132:678:C1LFKACXX:6:1111:11783:45506\n+ACCGGCTGCGAATGAGAATGT\n++\n+???DFFFFFHF:CCCGHHBG<\n+@HWI-ST132:678:C1LFKACXX:6:2105:11033:71535\n+CGGCTGCGAATGAGAATGTATATTT\n++\n+?BBDFFFF@<@ACAAEHHHGGIJJI\n+@HWI-ST132:678:C1LFKACXX:6:2103:20548:80488\n+AATGAGAATGTATATTTT\n++\n+BCBDDFFFHHFHHJJJJJ\n' |
| b |
| diff -r 9645d995fb3c -r 9185ca0a7b43 test-data/fastq_dir/reads-sample-small.fastq-bonafide_reads-transcripts.fastq --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/fastq_dir/reads-sample-small.fastq-bonafide_reads-transcripts.fastq Wed Jan 16 08:18:13 2019 -0500 |
| b |
| b'@@ -0,0 +1,8984 @@\n+@HWI-ST132:678:C1LFKACXX:6:2105:17359:60231\n+TTTTTTGGCACACGATTTTT\n++\n+BCBFFFFFHHHHH@FHHIJI\n+@HWI-ST132:678:C1LFKACXX:6:1104:3361:38910\n+TTTTTTGGCACACGATTTTTTCG\n++\n+BCCFFFFFHHHGHF@EHIJJJJJ\n+@HWI-ST132:678:C1LFKACXX:6:1302:8271:27021\n+TGGCTCTAGAGGTGGCTCCAGGC\n++\n+C@CFFFFFHHG3<<ACHIIHGII\n+@HWI-ST132:678:C1LFKACXX:6:1306:9256:39375\n+TGGCTCTAGAGGTGGCTCCAGGC\n++\n+BBCFFFFFHFHA3+<<EGIIIJJ\n+@HWI-ST132:678:C1LFKACXX:6:1313:12263:15439\n+GCTCTAGAGGTGGCTCCAG\n++\n+@@@?DEFFHHACFGHJIIJ\n+@HWI-ST132:678:C1LFKACXX:6:2104:8543:80281\n+CTCTAGAGGTGGCTCCAGGCTCT\n++\n+BBCF=BBDHFHHHIJIIJGIJJJ\n+@HWI-ST132:678:C1LFKACXX:6:1102:13980:18156\n+TCTAGAGGTGGCTCCAGGC\n++\n+BBBDFFFFCFACDGIIIIJ\n+@HWI-ST132:678:C1LFKACXX:6:1103:10328:28844\n+TCTAGAGGTGGCTCCAGGCTC\n++\n+:BBDA2=A=CCFHIJJJJIJJ\n+@HWI-ST132:678:C1LFKACXX:6:1105:6326:49732\n+TCTAGAGGTGGCTCCAGGCTC\n++\n+?@BDD=BDADHHHHJ3CFGIJ\n+@HWI-ST132:678:C1LFKACXX:6:1105:11000:66079\n+TCTAGAGGTGGCTCCAGGCTC\n++\n+BBBDFFFFFHHHHJJIJJJJJ\n+@HWI-ST132:678:C1LFKACXX:6:1106:14064:43295\n+TCTAGAGGTGGCTCCAGGCTC\n++\n+B@BDDFFFHHHHFGIJJIIGI\n+@HWI-ST132:678:C1LFKACXX:6:1113:19938:48642\n+TCTAGAGGTGGCTCCAGGCTC\n++\n+JJJJJJJIHHHFFFFEDDB@@\n+@HWI-ST132:678:C1LFKACXX:6:1116:10596:49883\n+TCTAGAGGTGGCTCCAGGCTC\n++\n+B?BDFDFFCFHHHJJJJJJJJ\n+@HWI-ST132:678:C1LFKACXX:6:1201:7176:42559\n+TCTAGAGGTGGCTCCAGGCTC\n++\n+:?BDDDFFCF<<<<EGIIJJJ\n+@HWI-ST132:678:C1LFKACXX:6:1204:7366:53049\n+TCTAGAGGTGGCTCCAGGCTC\n++\n+JJJJJJJJHHHFCFDDDDBBB\n+@HWI-ST132:678:C1LFKACXX:6:1205:7458:21533\n+TCTAGAGGTGGCTCCAGGCTC\n++\n+B@BFFDFFDHFHHJJFIJJJJ\n+@HWI-ST132:678:C1LFKACXX:6:1207:18816:23955\n+TCTAGAGGTGGCTCCAGGCTC\n++\n+@BBDFDFFCFHHGHIJIJIJJ\n+@HWI-ST132:678:C1LFKACXX:6:1207:18521:50214\n+TCTAGAGGTGGCTCCAGGCTC\n++\n+JJJIJJJIHHHDAFDDDDBBB\n+@HWI-ST132:678:C1LFKACXX:6:1215:8094:48780\n+TCTAGAGGTGGCTCCAGGCTC\n++\n+?:?DADDD=?::DEEB:<+<:\n+@HWI-ST132:678:C1LFKACXX:6:1302:16933:22023\n+TCTAGAGGTGGCTCCAGGCTC\n++\n+BCBFFFFFFHHHHJJJJJJJJ\n+@HWI-ST132:678:C1LFKACXX:6:1308:15108:32948\n+TCTAGAGGTGGCTCCAGGCTC\n++\n+BCCFFFFFFHHHHJJJIJJJJ\n+@HWI-ST132:678:C1LFKACXX:6:1310:7792:7251\n+TCTAGAGGTGGCTCCAGGCTC\n++\n+BCCFFFFFFHHHHJJIJJJJJ\n+@HWI-ST132:678:C1LFKACXX:6:1310:5500:48225\n+TCTAGAGGTGGCTCCAGGCTC\n++\n+@@CFFFFFFHGHHJJIJJJJJ\n+@HWI-ST132:678:C1LFKACXX:6:1314:12694:59078\n+TCTAGAGGTGGCTCCAGGCTC\n++\n+@@@DFFFFF?FHGGIIEHEHG\n+@HWI-ST132:678:C1LFKACXX:6:1315:4806:7499\n+TCTAGAGGTGGCTCCAGGCTC\n++\n+BBCFFDDFA;DFHIJIIIGII\n+@HWI-ST132:678:C1LFKACXX:6:2101:15514:8580\n+TCTAGAGGTGGCTCCAGGCTC\n++\n+BBBDFDFFFFFHHJJJJJJJJ\n+@HWI-ST132:678:C1LFKACXX:6:2101:13883:37158\n+TCTAGAGGTGGCTCCAGGCTC\n++\n+JGJJJJJIHD;HHFFFFFBBB\n+@HWI-ST132:678:C1LFKACXX:6:2101:14995:100162\n+TCTAGAGGTGGCTCCAGGCTC\n++\n+IGIIGGIHDCA<44224AB:1\n+@HWI-ST132:678:C1LFKACXX:6:2103:10548:14756\n+TCTAGAGGTGGCTCCAGGCTC\n++\n+:B@DFDFFFH<<AEGHHIJIJ\n+@HWI-ST132:678:C1LFKACXX:6:2103:3737:60160\n+TCTAGAGGTGGCTCCAGGCTC\n++\n+B@BDDDEFDFHHHJJJJGIJJ\n+@HWI-ST132:678:C1LFKACXX:6:2104:8921:19194\n+TCTAGAGGTGGCTCCAGGCTC\n++\n+BBBDFFFFAFDFHIJJJJJJJ\n+@HWI-ST132:678:C1LFKACXX:6:2104:15981:63048\n+TCTAGAGGTGGCTCCAGGCTC\n++\n+B@BDDFFFFHHHHIJJJJJJJ\n+@HWI-ST132:678:C1LFKACXX:6:2104:11258:78941\n+TCTAGAGGTGGCTCCAGGCTC\n++\n+BBBFFFFFHH?FHHIJIJIJJ\n+@HWI-ST132:678:C1LFKACXX:6:2106:17344:88675\n+TCTAGAGGTGGCTCCAGGCTC\n++\n+BCCFFFFFFFFHHJJJJJJJJ\n+@HWI-ST132:678:C1LFKACXX:6:2107:1224:28968\n+TCTAGAGGTGGCTCCAGGCTC\n++\n+CGCFFGFEC<DAADA2A4=:=\n+@HWI-ST132:678:C1LFKACXX:6:2107:13563:38548\n+TCTAGAGGTGGCTCCAGGCTC\n++\n+@@@FF?DFHH?HHHIJJJJJJ\n+@HWI-ST132:678:C1LFKACXX:6:2108:9652:62249\n+TCTAGAGGTGGCTCCAGGCTC\n++\n+JJIIJIHGHHFHFFFFFDBB@\n+@HWI-ST132:678:C1LFKACXX:6:1212:17696:96425\n+TCTAGAGGTGGCTCCAGGCTCT\n++\n+B@@DDDFFCFDFHGGIIJIJJI\n+@HWI-ST132:678:C1LFKACXX:6:1302:11655:74544\n+TCTAGAGGTGGCTCCAGGCTCT\n++\n+:=@BD=+A4AAFFEG@EHIIIG\n+@HWI-ST132:678:C1LFKACXX:6:2103:15155:59922\n+TCTAGAGGTGGCTCCAGGCTCT\n++\n+BBBDDDFFFHACDHHIJJJJJJ\n+@HWI-ST132:678:C1LFKACXX:6:2106:12318:50696\n+TCTAGAGGTGGCTCCAGGCTCT\n++\n+BBBDFFFFFFHHHJJJJJJJJJ\n+@HWI-ST132:678:C1LFKACXX:6:2106:7049:81574\n+TCTAGAGGTGGCTCCAGGCTCT\n++\n+BBBDDDFFFHFHHIJJIJJIJJ\n+@HWI-ST132:678:C1LFKACXX:6:1206:10'..b'CGATCGCCGACGTGTGAAGACGT\n++\n+IJJJIIHFEIIIHHHHHFFFBFCCC\n+@HWI-ST132:678:C1LFKACXX:6:2105:8348:83371\n+TTCGATCGCCGACGTGTGAAGACGT\n++\n+DIGJIFD?1@@C<0@HHDFFDD??:\n+@HWI-ST132:678:C1LFKACXX:6:2105:19893:91541\n+TTCGATCGCCGACGTGTGAAGACGT\n++\n+?HEGHC4HFHG@HFDHHDDD=D@@@\n+@HWI-ST132:678:C1LFKACXX:6:2106:6481:37891\n+TTCGATCGCCGACGTGTGAAGACGT\n++\n+HJJJJJJHIIHIHFHHHFFFFF@CC\n+@HWI-ST132:678:C1LFKACXX:6:2106:15957:78129\n+TTCGATCGCCGACGTGTGAAGACGT\n++\n+HJJJJJJHIHIJHHHHHFFFFFBCC\n+@HWI-ST132:678:C1LFKACXX:6:2107:12188:11374\n+TTCGATCGCCGACGTGTGAAGACGT\n++\n+FJJIIIGD?FCGHHHHHDDB?FCBB\n+@HWI-ST132:678:C1LFKACXX:6:2108:18380:53781\n+TTCGATCGCCGACGTGTGAAGACGT\n++\n+JJJJIHF?114C@@CHHFFFFFBB=\n+@HWI-ST132:678:C1LFKACXX:6:1208:16812:100651\n+TTCGATCGCCGACGTGTGAAGACG\n++\n+IIIGC<HGGFGHHHHHFFEBFCCC\n+@HWI-ST132:678:C1LFKACXX:6:1103:13690:62133\n+ATTCGATCGCCGACGTGTGAAGACG\n++\n+JJIHGGCGIGJJGHHHHFFFFFCCB\n+@HWI-ST132:678:C1LFKACXX:6:1109:8695:89867\n+TTCGATCGCCGACGTGTGAAGAC\n++\n+JJHIGHEGFIHHHHHFFFFFCCC\n+@HWI-ST132:678:C1LFKACXX:6:1209:11040:19674\n+TCTTCACACGTCGGCGATCGA\n++\n+@@@DDFFFFHFFDHJGIDD@G\n+@HWI-ST132:678:C1LFKACXX:6:1210:17629:31055\n+TTCACACGTCGGCGATCGA\n++\n+CCCFFFFFHHHDC<EGHID\n+@HWI-ST132:678:C1LFKACXX:6:1203:18672:91263\n+AATTCGATCGCCGACGTGTGAA\n++\n+JIJJHHFJJHHHHHFFFFFCCC\n+@HWI-ST132:678:C1LFKACXX:6:1313:1560:43567\n+GCTTTTTCGTGGGGAGATC\n++\n+@BCDFFFFFDFFHIJJJIJ\n+@HWI-ST132:678:C1LFKACXX:6:1116:11668:16725\n+TAAGAATTCCGAAACGCCATC\n++\n+IHEGAG@ED8FDDBBDDD=+?\n+@HWI-ST132:678:C1LFKACXX:6:2103:4519:3225\n+TGCAAGCTAAGAATTCCGAAACGCC\n++\n+JJIJJJJJJIHFCAC:HDA==D?B:\n+@HWI-ST132:678:C1LFKACXX:6:1208:13565:65937\n+CGATGTGTTTGTTCGCCCGTC\n++\n+@@CFFBDBFHHDFHAFHI)@F\n+@HWI-ST132:678:C1LFKACXX:6:1209:11809:98806\n+AACCTCCTAGTCGCTGTGACT\n++\n+JJIJIJIGGHHHHFFFFFBCB\n+@HWI-ST132:678:C1LFKACXX:6:1206:18658:28841\n+CAGGTTAACCTCCTAGTCGCT\n++\n+JIJJJJJJHHHHHFFFDFCCB\n+@HWI-ST132:678:C1LFKACXX:6:1309:8277:38084\n+CAGGTTAACCTCCTAGTCGCT\n++\n+IIIJIJJIHHHHHFFFDFC@@\n+@HWI-ST132:678:C1LFKACXX:6:2103:17347:32864\n+TTCTTGAACTTGCGAGCACCG\n++\n+CCCFFFFFHHHAAFC3BEHIJ\n+@HWI-ST132:678:C1LFKACXX:6:2107:8602:93094\n+TTCTTGAACTTGCGAGCACCG\n++\n+CCCFFFFFHHHDHCCFFHIJJ\n+@HWI-ST132:678:C1LFKACXX:6:1215:11329:60877\n+GTAACACTTTGTAACGGATCGCAAA\n++\n+@@@DFFFFHHHGHIJJJEIIIIDII\n+@HWI-ST132:678:C1LFKACXX:6:1202:15474:8031\n+TGATGATCAAGTAGTTTCTC\n++\n+BBCFFFFFHFCAFCHHIIJJ\n+@HWI-ST132:678:C1LFKACXX:6:2106:14321:83705\n+TTGCATTAATCTGAAAGTTGC\n++\n+IHIGIJJJHHHHHFFFFFCCC\n+@HWI-ST132:678:C1LFKACXX:6:1306:11622:66870\n+CAAATTGGCTTTCCGTCGACT\n++\n+@@@DFFFFHHGHFHJJEIGHH\n+@HWI-ST132:678:C1LFKACXX:6:1315:14171:25693\n+TTTCCGTCGACTAACAATAAGCCGT\n++\n+B@CFFFDDFHHHHJJIJJDHIIIJG\n+@HWI-ST132:678:C1LFKACXX:6:1311:11389:80627\n+AAAATGTCAGTCACTCAGCCAAAGG\n++\n+BBCFFFDF?FHHHJJJJJJJJJJJJ\n+@HWI-ST132:678:C1LFKACXX:6:2101:11947:88765\n+TCCTTTGGCTGAGTGACTGACATTT\n++\n+HEHCFHFFHCA2<<CHFDBDDF@@?\n+@HWI-ST132:678:C1LFKACXX:6:1107:16523:27164\n+CCAAGGAGTCGGCAGCTGAAG\n++\n+@@@DDDDDCD?FF1)AEGGII\n+@HWI-ST132:678:C1LFKACXX:6:1208:6410:57476\n+CAAGGAGTCGGCAGCTGAAGTAGCA\n++\n+=@@DD?DDFF?)@FAH>FEFHHEHE\n+@HWI-ST132:678:C1LFKACXX:6:1206:20690:60805\n+AGTGGGGCCAGAGGGGCTGCT\n++\n+>?:C?:@BFFFCHDADDD@?<\n+@HWI-ST132:678:C1LFKACXX:6:1308:5462:60542\n+TTTGACAGAGAGTGGGGCC\n++\n+JHHFEFAHGHHFFFFFCCC\n+@HWI-ST132:678:C1LFKACXX:6:1309:15210:100042\n+CGGCTTTGTCACTGTTTGATC\n++\n+@CBFFFFFHHHHHIGHHIGJJ\n+@HWI-ST132:678:C1LFKACXX:6:1108:6289:74344\n+TTTGACAATTGGCGCCGGCG\n++\n+@C@FFFFFHHDCD8CFIJJJ\n+@HWI-ST132:678:C1LFKACXX:6:2108:11541:97204\n+TATTGAACTGAAGCCCCCGGC\n++\n+CCCFFFFFHHHHGJJJJJ@GG\n+@HWI-ST132:678:C1LFKACXX:6:2102:9712:32185\n+ATTGAACTGAAGCCCCCGGCC\n++\n+?@@BBDBDDFFADHIIIH)?F\n+@HWI-ST132:678:C1LFKACXX:6:1313:12783:74925\n+GAGCGGGTTTGGCCGGGGGCT\n++\n+JJJJJJJJHGHHHDFFFFCCB\n+@HWI-ST132:678:C1LFKACXX:6:2103:17748:30120\n+TGCACGATTCCAATAGTGCTG\n++\n+IJIGCJIJHHHHHFFFFFCCC\n+@HWI-ST132:678:C1LFKACXX:6:1206:15175:27778\n+AATTTGGCGGCTTGGGCTC\n++\n+C;?1)HHDF??DDDDD???\n+@HWI-ST132:678:C1LFKACXX:6:1105:9109:21614\n+TCGTACCGATCTAGACATCTCTTC\n++\n+GIJJJJJJIGJHHHGHD<FFD@@@\n+@HWI-ST132:678:C1LFKACXX:6:1107:17975:4570\n+GATCGGTACGACTCGTCGGAGT\n++\n+BCBFFFDFHHHHHJJIJGECFD\n' |
| b |
| diff -r 9645d995fb3c -r 9185ca0a7b43 test-data/fastq_dir/reads-sample-small.fastq-bonafide_reads-transcripts_uni.fastq --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/fastq_dir/reads-sample-small.fastq-bonafide_reads-transcripts_uni.fastq Wed Jan 16 08:18:13 2019 -0500 |
| b |
| b'@@ -0,0 +1,3304 @@\n+@HWI-ST132:678:C1LFKACXX:6:2107:14168:54674\n+TATCACTGTATGCGTAGAAAAGAG\n++\n+CCCFDFFFHHGDFFFHIJJJJJJJ\n+@HWI-ST132:678:C1LFKACXX:6:1210:20798:12533\n+TCTGCTATCACTGTATGCGTAGAAA\n++\n+@@@FDDDFHGHHGJIJIG@GCEFDB\n+@HWI-ST132:678:C1LFKACXX:6:2104:13786:79730\n+TCTGCTATCACTGTATGCGTAG\n++\n+BCCFFFFFHHHHHJHJJJJGIJ\n+@HWI-ST132:678:C1LFKACXX:6:2108:17764:96282\n+TCTGCTATCACTGTATGC\n++\n+BCBFFFFFHBHHHJJJJJ\n+@HWI-ST132:678:C1LFKACXX:6:1313:10358:95570\n+TAATATAGATTTAAAGTCTAAGAACT\n++\n+@@?B=DDDHHHHHJJJHIJIJJHIJJ\n+@HWI-ST132:678:C1LFKACXX:6:2108:18887:67124\n+TAATATAGATTTAAAGTCTAAGAACT\n++\n+BCCFFFFFGHHHH>GHFHJJJIGJJJ\n+@HWI-ST132:678:C1LFKACXX:6:1301:16563:56958\n+AAGGCAATGCAAAACAAGAATTT\n++\n+FAA3GHHBEIFHHFDDBDDB@@@\n+@HWI-ST132:678:C1LFKACXX:6:1115:14943:55336\n+TTCTTGTTTTGCATTGCC\n++\n+:B144ADDHHHHHJIIIG\n+@HWI-ST132:678:C1LFKACXX:6:1107:12070:23186\n+TAGTATATTTATTAAATCATTTGACT\n++\n+CCCDDEFFHHHHHJJJJJAJJJIJJJ\n+@HWI-ST132:678:C1LFKACXX:6:1110:20211:14418\n+TAGTATATTTATTAAATCATTTGACT\n++\n+CCCFFFFFHHHHHJJJJJIJJJJJJJ\n+@HWI-ST132:678:C1LFKACXX:6:1116:13578:65370\n+TAGTATATTTATTAAATCATTTGACT\n++\n+@8?D=BDFGHHFHIJJJJFGIJIJIJ\n+@HWI-ST132:678:C1LFKACXX:6:2101:7667:91449\n+TAGTATATTTATTAAATCATTTGACT\n++\n+CCCDDEFFHHHHHJJJJJJJJIJJJJ\n+@HWI-ST132:678:C1LFKACXX:6:2107:12382:29561\n+TAGTATATTTATTAAATCATTTGACT\n++\n+CCCFFFFFHHHHHJJJJJJJJJJJJJ\n+@HWI-ST132:678:C1LFKACXX:6:2107:9787:36481\n+TAGTATATTTATTAAATCATTTGACT\n++\n+BBBD:ADDHHHHH4HGHIJJJJJJJJ\n+@HWI-ST132:678:C1LFKACXX:6:2102:14356:68993\n+TAATGTTACATCATATTAAGTCAAATGA\n++\n+JIJJIHIHJJJJJJJHHHFHFFFFFCCC\n+@HWI-ST132:678:C1LFKACXX:6:1107:18073:46755\n+AAATATTTCGCTTTTAAAAAATTG\n++\n+@@CFFFFFHHHGHJIJJBDAGIII\n+@HWI-ST132:678:C1LFKACXX:6:1302:10066:99383\n+AATATTTCGCTTTTAAAAAATTG\n++\n+BBBDFFFFH@FHHJJJIJGIIIJ\n+@HWI-ST132:678:C1LFKACXX:6:1109:11961:47390\n+ATATTTCGCTTTTAAAAAATTG\n++\n+CCCFFFFFHHHHHIIHHJJIJJ\n+@HWI-ST132:678:C1LFKACXX:6:2103:9377:13404\n+TAAATTTGTTTGTTAAAATCGCCG\n++\n+CCCFFFFFHHHGHIJJJJJHIJJJ\n+@HWI-ST132:678:C1LFKACXX:6:1309:5142:10985\n+TTTAAATTTGTTTGTTAAAATCGCC\n++\n+BCCFDFFFHHHHHIJIJJJJIIIGH\n+@HWI-ST132:678:C1LFKACXX:6:1205:5640:63048\n+TAATAGTCAGGGCGCGAATTTT\n++\n+=;BD:2=BFHFDFEF6EHIJJJ\n+@HWI-ST132:678:C1LFKACXX:6:1211:3646:44689\n+TAATAGTCAGGGCGCGAATTTT\n++\n+@C@FFFDFHHHHGHHJJJIJJJ\n+@HWI-ST132:678:C1LFKACXX:6:1108:20386:47976\n+TAATAGTCAGGGCGCGAATTTTT\n++\n+?@?D;B=B?CAC:2<CFGHIIGI\n+@HWI-ST132:678:C1LFKACXX:6:1207:2583:92360\n+TAATAGTCAGGGCGCGAATTTTT\n++\n+B@CFFFDDHHDFFGFGHEGHIJI\n+@HWI-ST132:678:C1LFKACXX:6:1102:11267:71435\n+TAATAGTCAGGGCGCGAATTTTTA\n++\n+@@BFFDBDFHHDFIIHJBFFGIGG\n+@HWI-ST132:678:C1LFKACXX:6:1107:9710:51191\n+TAATAGTCAGGGCGCGAATTTTTA\n++\n+@@@FDF?DHHHDHFGHGGHGJJJJ\n+@HWI-ST132:678:C1LFKACXX:6:1108:5610:75509\n+TAATAGTCAGGGCGCGAATTTTTA\n++\n+BCCFFFFFFGHGG<DHGHGHIJJJ\n+@HWI-ST132:678:C1LFKACXX:6:1109:13565:15908\n+TAATAGTCAGGGCGCGAATTTTTA\n++\n+BCCFFFEFHHHCAFGHIIJJJJJJ\n+@HWI-ST132:678:C1LFKACXX:6:1109:11179:97926\n+TAATAGTCAGGGCGCGAATTTTTA\n++\n+@@@FDEBD<FH<DGGIIGGHGIII\n+@HWI-ST132:678:C1LFKACXX:6:1110:18682:30268\n+TAATAGTCAGGGCGCGAATTTTTA\n++\n+BCCFFFFFHHHFGIJJIHIIJJJJ\n+@HWI-ST132:678:C1LFKACXX:6:1114:13195:76362\n+TAATAGTCAGGGCGCGAATTTTTA\n++\n+?@?DDB=DFDDHGIIEBHD=FHIH\n+@HWI-ST132:678:C1LFKACXX:6:1201:9017:61055\n+TAATAGTCAGGGCGCGAATTTTTA\n++\n+BCCFDFFFHHFFH@BEEGIHJJJJ\n+@HWI-ST132:678:C1LFKACXX:6:1201:5418:63606\n+TAATAGTCAGGGCGCGAATTTTTA\n++\n+@@CFBDDEHHA<CFEFHIHIIIII\n+@HWI-ST132:678:C1LFKACXX:6:1213:8541:21411\n+TAATAGTCAGGGCGCGAATTTTTA\n++\n+@@CFFFDDHHFFFFGHIHIJJJII\n+@HWI-ST132:678:C1LFKACXX:6:1214:13791:80762\n+TAATAGTCAGGGCGCGAATTTTTA\n++\n+@@@FDDDDHFHDHIFII1DFHGGF\n+@HWI-ST132:678:C1LFKACXX:6:1309:8889:7362\n+TAATAGTCAGGGCGCGAATTTTTA\n++\n+@@CFFFFFDHHHHJIJJJHJJJJJ\n+@HWI-ST132:678:C1LFKACXX:6:1314:17898:28199\n+TAATAGTCAGGGCGCGAATTTTTA\n++\n+@??DFADDDHCHFFBGGEHIGJGI\n+@HWI-ST132:678:C1LFKACXX:6:2104:10515:36849\n+TAATAGTCAGGGCGCGAATTTTTA\n++\n+@CCFFFDFHHFHHJIJJJJJJJJJ\n+@HWI-ST132:678:C1LFKACXX:6:2105:6101:64627\n+TAATAGTCAGGGCGCGAATTTTTA\n++\n+@@@FFFFFHHD:C<@@@CGHIIII\n+@HWI-ST132:678:C1LFKACXX:6:2105:18687:69886\n+TAATAGTCAGGGCGCGAATTTTTA\n++\n+BCCFFFFEHHFFH@FHHIJJJJJJ'..b'CGATCGCCGACGTGTGAAGACGT\n++\n+IJJJIIHFEIIIHHHHHFFFBFCCC\n+@HWI-ST132:678:C1LFKACXX:6:2105:8348:83371\n+TTCGATCGCCGACGTGTGAAGACGT\n++\n+DIGJIFD?1@@C<0@HHDFFDD??:\n+@HWI-ST132:678:C1LFKACXX:6:2105:19893:91541\n+TTCGATCGCCGACGTGTGAAGACGT\n++\n+?HEGHC4HFHG@HFDHHDDD=D@@@\n+@HWI-ST132:678:C1LFKACXX:6:2106:6481:37891\n+TTCGATCGCCGACGTGTGAAGACGT\n++\n+HJJJJJJHIIHIHFHHHFFFFF@CC\n+@HWI-ST132:678:C1LFKACXX:6:2106:15957:78129\n+TTCGATCGCCGACGTGTGAAGACGT\n++\n+HJJJJJJHIHIJHHHHHFFFFFBCC\n+@HWI-ST132:678:C1LFKACXX:6:2107:12188:11374\n+TTCGATCGCCGACGTGTGAAGACGT\n++\n+FJJIIIGD?FCGHHHHHDDB?FCBB\n+@HWI-ST132:678:C1LFKACXX:6:2108:18380:53781\n+TTCGATCGCCGACGTGTGAAGACGT\n++\n+JJJJIHF?114C@@CHHFFFFFBB=\n+@HWI-ST132:678:C1LFKACXX:6:1208:16812:100651\n+TTCGATCGCCGACGTGTGAAGACG\n++\n+IIIGC<HGGFGHHHHHFFEBFCCC\n+@HWI-ST132:678:C1LFKACXX:6:1103:13690:62133\n+ATTCGATCGCCGACGTGTGAAGACG\n++\n+JJIHGGCGIGJJGHHHHFFFFFCCB\n+@HWI-ST132:678:C1LFKACXX:6:1109:8695:89867\n+TTCGATCGCCGACGTGTGAAGAC\n++\n+JJHIGHEGFIHHHHHFFFFFCCC\n+@HWI-ST132:678:C1LFKACXX:6:1209:11040:19674\n+TCTTCACACGTCGGCGATCGA\n++\n+@@@DDFFFFHFFDHJGIDD@G\n+@HWI-ST132:678:C1LFKACXX:6:1210:17629:31055\n+TTCACACGTCGGCGATCGA\n++\n+CCCFFFFFHHHDC<EGHID\n+@HWI-ST132:678:C1LFKACXX:6:1203:18672:91263\n+AATTCGATCGCCGACGTGTGAA\n++\n+JIJJHHFJJHHHHHFFFFFCCC\n+@HWI-ST132:678:C1LFKACXX:6:1313:1560:43567\n+GCTTTTTCGTGGGGAGATC\n++\n+@BCDFFFFFDFFHIJJJIJ\n+@HWI-ST132:678:C1LFKACXX:6:1116:11668:16725\n+TAAGAATTCCGAAACGCCATC\n++\n+IHEGAG@ED8FDDBBDDD=+?\n+@HWI-ST132:678:C1LFKACXX:6:2103:4519:3225\n+TGCAAGCTAAGAATTCCGAAACGCC\n++\n+JJIJJJJJJIHFCAC:HDA==D?B:\n+@HWI-ST132:678:C1LFKACXX:6:1208:13565:65937\n+CGATGTGTTTGTTCGCCCGTC\n++\n+@@CFFBDBFHHDFHAFHI)@F\n+@HWI-ST132:678:C1LFKACXX:6:1209:11809:98806\n+AACCTCCTAGTCGCTGTGACT\n++\n+JJIJIJIGGHHHHFFFFFBCB\n+@HWI-ST132:678:C1LFKACXX:6:1206:18658:28841\n+CAGGTTAACCTCCTAGTCGCT\n++\n+JIJJJJJJHHHHHFFFDFCCB\n+@HWI-ST132:678:C1LFKACXX:6:1309:8277:38084\n+CAGGTTAACCTCCTAGTCGCT\n++\n+IIIJIJJIHHHHHFFFDFC@@\n+@HWI-ST132:678:C1LFKACXX:6:2103:17347:32864\n+TTCTTGAACTTGCGAGCACCG\n++\n+CCCFFFFFHHHAAFC3BEHIJ\n+@HWI-ST132:678:C1LFKACXX:6:2107:8602:93094\n+TTCTTGAACTTGCGAGCACCG\n++\n+CCCFFFFFHHHDHCCFFHIJJ\n+@HWI-ST132:678:C1LFKACXX:6:1215:11329:60877\n+GTAACACTTTGTAACGGATCGCAAA\n++\n+@@@DFFFFHHHGHIJJJEIIIIDII\n+@HWI-ST132:678:C1LFKACXX:6:1202:15474:8031\n+TGATGATCAAGTAGTTTCTC\n++\n+BBCFFFFFHFCAFCHHIIJJ\n+@HWI-ST132:678:C1LFKACXX:6:2106:14321:83705\n+TTGCATTAATCTGAAAGTTGC\n++\n+IHIGIJJJHHHHHFFFFFCCC\n+@HWI-ST132:678:C1LFKACXX:6:1306:11622:66870\n+CAAATTGGCTTTCCGTCGACT\n++\n+@@@DFFFFHHGHFHJJEIGHH\n+@HWI-ST132:678:C1LFKACXX:6:1315:14171:25693\n+TTTCCGTCGACTAACAATAAGCCGT\n++\n+B@CFFFDDFHHHHJJIJJDHIIIJG\n+@HWI-ST132:678:C1LFKACXX:6:1311:11389:80627\n+AAAATGTCAGTCACTCAGCCAAAGG\n++\n+BBCFFFDF?FHHHJJJJJJJJJJJJ\n+@HWI-ST132:678:C1LFKACXX:6:2101:11947:88765\n+TCCTTTGGCTGAGTGACTGACATTT\n++\n+HEHCFHFFHCA2<<CHFDBDDF@@?\n+@HWI-ST132:678:C1LFKACXX:6:1107:16523:27164\n+CCAAGGAGTCGGCAGCTGAAG\n++\n+@@@DDDDDCD?FF1)AEGGII\n+@HWI-ST132:678:C1LFKACXX:6:1208:6410:57476\n+CAAGGAGTCGGCAGCTGAAGTAGCA\n++\n+=@@DD?DDFF?)@FAH>FEFHHEHE\n+@HWI-ST132:678:C1LFKACXX:6:1206:20690:60805\n+AGTGGGGCCAGAGGGGCTGCT\n++\n+>?:C?:@BFFFCHDADDD@?<\n+@HWI-ST132:678:C1LFKACXX:6:1308:5462:60542\n+TTTGACAGAGAGTGGGGCC\n++\n+JHHFEFAHGHHFFFFFCCC\n+@HWI-ST132:678:C1LFKACXX:6:1309:15210:100042\n+CGGCTTTGTCACTGTTTGATC\n++\n+@CBFFFFFHHHHHIGHHIGJJ\n+@HWI-ST132:678:C1LFKACXX:6:1108:6289:74344\n+TTTGACAATTGGCGCCGGCG\n++\n+@C@FFFFFHHDCD8CFIJJJ\n+@HWI-ST132:678:C1LFKACXX:6:2108:11541:97204\n+TATTGAACTGAAGCCCCCGGC\n++\n+CCCFFFFFHHHHGJJJJJ@GG\n+@HWI-ST132:678:C1LFKACXX:6:2102:9712:32185\n+ATTGAACTGAAGCCCCCGGCC\n++\n+?@@BBDBDDFFADHIIIH)?F\n+@HWI-ST132:678:C1LFKACXX:6:1313:12783:74925\n+GAGCGGGTTTGGCCGGGGGCT\n++\n+JJJJJJJJHGHHHDFFFFCCB\n+@HWI-ST132:678:C1LFKACXX:6:2103:17748:30120\n+TGCACGATTCCAATAGTGCTG\n++\n+IJIGCJIJHHHHHFFFFFCCC\n+@HWI-ST132:678:C1LFKACXX:6:1206:15175:27778\n+AATTTGGCGGCTTGGGCTC\n++\n+C;?1)HHDF??DDDDD???\n+@HWI-ST132:678:C1LFKACXX:6:1105:9109:21614\n+TCGTACCGATCTAGACATCTCTTC\n++\n+GIJJJJJJIGJHHHGHD<FFD@@@\n+@HWI-ST132:678:C1LFKACXX:6:1107:17975:4570\n+GATCGGTACGACTCGTCGGAGT\n++\n+BCBFFFDFHHHHHJJIJGECFD\n' |
| b |
| diff -r 9645d995fb3c -r 9185ca0a7b43 test-data/fastq_dir/reads-sample-small.fastq-miRNAs-genome.fastq --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/fastq_dir/reads-sample-small.fastq-miRNAs-genome.fastq Wed Jan 16 08:18:13 2019 -0500 |
| b |
| @@ -0,0 +1,252 @@ +@HWI-ST132:678:C1LFKACXX:6:1103:6450:33284 +AACCCGTAAATCCGAACTTG ++ +?@@DD<@DCCABFGF1@GHI +@HWI-ST132:678:C1LFKACXX:6:1104:7735:58473 +AACCCGTAAATCCGAACTTG ++ +:?@DDDDD@<2CAEFHGGIC +@HWI-ST132:678:C1LFKACXX:6:1111:8344:28118 +AACCCGTAAATCCGAACTTG ++ +?@@DDADD@B<ADCAEEGGI +@HWI-ST132:678:C1LFKACXX:6:1201:4901:28957 +AACCCGTAAATCCGAACTTG ++ +@@@FFFFFDAAFHFHGIIJH +@HWI-ST132:678:C1LFKACXX:6:1201:14858:55180 +AACCCGTAAATCCGAACTTG ++ +?B@FDFFFCAHAFGFHIJJJ +@HWI-ST132:678:C1LFKACXX:6:1208:10957:88261 +AACCCGTAAATCCGAACTTG ++ +@@@FFFDDFFFDFCE+CFHI +@HWI-ST132:678:C1LFKACXX:6:1211:4119:82063 +AACCCGTAAATCCGAACTTG ++ +B?@FFFDF@AACFFAEHHJI +@HWI-ST132:678:C1LFKACXX:6:1301:7756:37290 +AACCCGTAAATCCGAACTTG ++ +=BBDFFFF@<ADFHEGIJJI +@HWI-ST132:678:C1LFKACXX:6:1315:14080:19805 +AACCCGTAAATCCGAACTTG ++ +?@?DDDDFFDDHHJI;EGIE +@HWI-ST132:678:C1LFKACXX:6:2106:14523:50358 +AACCCGTAAATCCGAACTTG ++ +BBBFFFFFH:<ADHGIJJJJ +@HWI-ST132:678:C1LFKACXX:6:2107:6396:35457 +AACCCGTAAATCCGAACTTG ++ +:?BDFFFF<><ADFHIJJJJ +@HWI-ST132:678:C1LFKACXX:6:1106:15354:26782 +AACCCGTAAATCCGAACTTGTG ++ +BB@DFFDFCAADHGIGGHIII? +@HWI-ST132:678:C1LFKACXX:6:1206:3893:47334 +AACCCGTAAATCCGAACTTGTG ++ +?@@F@D@DDDDFHGIBCCHEAB +@HWI-ST132:678:C1LFKACXX:6:1212:8247:60863 +AACCCGTAAATCCGAACTTGTG ++ +?@@FFFDDCA?DFIIGEEHIGH +@HWI-ST132:678:C1LFKACXX:6:2103:20330:81235 +AACCCGTAAATCCGAACTTGTG ++ +=?BDFFFF<<<<D<CEHIJHAF +@HWI-ST132:678:C1LFKACXX:6:2105:18756:21094 +AACCCGTAAATCCGAACTTGTG ++ +CCCFFFFFHFHHHJJJJJJJII +@HWI-ST132:678:C1LFKACXX:6:2108:11590:68948 +AACCCGTAAATCCGAACTTGTG ++ +=?@;DDDD@<ACDGFHHEHAEE +@HWI-ST132:678:C1LFKACXX:6:2109:7213:21129 +AACCCGTAAATCCGAACTTGTG ++ +:B@DFFFF<<<ADBGEFFHIFH +@HWI-ST132:678:C1LFKACXX:6:1113:9515:60678 +CAAGACCGGCATTATGGGAGTC ++ +?@;DDFFFDFCFHJJGA8CGEH +@HWI-ST132:678:C1LFKACXX:6:1211:4033:43798 +CAAGACCGGCATTATGGGAGTC ++ +@CCFFFFFHHHHHJGHIJIJFH +@HWI-ST132:678:C1LFKACXX:6:2102:15781:17798 +CAAGACCGGCATTATGGGAGTC ++ +??@DDDDDFFDFFEH<CED:11 +@HWI-ST132:678:C1LFKACXX:6:2105:13568:17777 +CAAGACCGGCATTATGGGAGTC ++ +@BBFBDDD<CFHHHHAGHIJGH +@HWI-ST132:678:C1LFKACXX:6:1116:7415:45912 +TCCCTGAGACCCTAACTTGTG ++ +=?1=ABDDHHGHGICFCEIFF +@HWI-ST132:678:C1LFKACXX:6:1312:17503:22366 +TCCCTGAGACCCTAACTTGTG ++ +@@?DFFFFBHHGHIIIJIGHG +@HWI-ST132:678:C1LFKACXX:6:1101:13208:32198 +TCCCTGAGACCCTAACTTGTGA ++ +CCCFFFEFFHHHHIJJIIJHHI +@HWI-ST132:678:C1LFKACXX:6:1102:17974:5349 +TCCCTGAGACCCTAACTTGTGA ++ +CCCFFFDFHGHHHGIJJJJHGI +@HWI-ST132:678:C1LFKACXX:6:1105:10525:58469 +TCCCTGAGACCCTAACTTGTGA ++ +B@CFFFDDDHFHGHIIIGHHIJ +@HWI-ST132:678:C1LFKACXX:6:1106:11675:95913 +TCCCTGAGACCCTAACTTGTGA ++ +@@@DDDDDFHHHHAFH?G+AFH +@HWI-ST132:678:C1LFKACXX:6:1107:11700:11209 +TCCCTGAGACCCTAACTTGTGA ++ +?@@DD;==DHFDCGCFEDHHHE +@HWI-ST132:678:C1LFKACXX:6:1109:4618:19903 +TCCCTGAGACCCTAACTTGTGA ++ +CCCFFFFFHHHHHCGGHIJEHH +@HWI-ST132:678:C1LFKACXX:6:1111:16886:54124 +TCCCTGAGACCCTAACTTGTGA ++ +CCCFFFFFHHHHHEHIJJFHIJ +@HWI-ST132:678:C1LFKACXX:6:1113:14917:12939 +TCCCTGAGACCCTAACTTGTGA ++ +CCCFFFFFHHHHHJJJJJIAGH +@HWI-ST132:678:C1LFKACXX:6:1113:15286:60745 +TCCCTGAGACCCTAACTTGTGA ++ +@@@FFFDD2ADFFBHCGGAHHI +@HWI-ST132:678:C1LFKACXX:6:1116:10143:61594 +TCCCTGAGACCCTAACTTGTGA ++ +@B=DDFFFHHHHHIHIJJJHIH +@HWI-ST132:678:C1LFKACXX:6:1201:12358:31858 +TCCCTGAGACCCTAACTTGTGA ++ +:BBFFF24>ADHHIJJJJHAFH +@HWI-ST132:678:C1LFKACXX:6:1207:19763:6169 +TCCCTGAGACCCTAACTTGTGA ++ +CCCFFFFFHHHHHGIJIJEHHI +@HWI-ST132:678:C1LFKACXX:6:1208:17227:84730 +TCCCTGAGACCCTAACTTGTGA ++ +CCCFFFFFHHHGHGHIJIH<CH +@HWI-ST132:678:C1LFKACXX:6:1209:14006:3385 +TCCCTGAGACCCTAACTTGTGA ++ +CCCFFFFFFHHHHEHGHHIFGF +@HWI-ST132:678:C1LFKACXX:6:1212:19731:4329 +TCCCTGAGACCCTAACTTGTGA ++ +CCCFFFFFHHHHHJIHIIJHHI +@HWI-ST132:678:C1LFKACXX:6:1212:8981:55837 +TCCCTGAGACCCTAACTTGTGA ++ +@@@D?EFDFFHHHJJIBEGAFC +@HWI-ST132:678:C1LFKACXX:6:1214:16337:65541 +TCCCTGAGACCCTAACTTGTGA ++ +BC?DDFFFGHHHFIIJJIIFGG +@HWI-ST132:678:C1LFKACXX:6:1214:9263:76030 +TCCCTGAGACCCTAACTTGTGA ++ +@@@FFFFFHFHDHEEHIIHAFH +@HWI-ST132:678:C1LFKACXX:6:1215:7321:50488 +TCCCTGAGACCCTAACTTGTGA ++ +@C@DDFDDFFHBDHIIBE@FEH +@HWI-ST132:678:C1LFKACXX:6:1302:17139:90749 +TCCCTGAGACCCTAACTTGTGA ++ +CCCFFFFFHHHGHGIJHIIHHI +@HWI-ST132:678:C1LFKACXX:6:1302:8853:99407 +TCCCTGAGACCCTAACTTGTGA ++ +B@BFFFFFHFHHHBFHHIHAFH +@HWI-ST132:678:C1LFKACXX:6:1304:2649:24602 +TCCCTGAGACCCTAACTTGTGA ++ +CCCFFFFDHHHHHGHIJJJFGI +@HWI-ST132:678:C1LFKACXX:6:1304:17263:52290 +TCCCTGAGACCCTAACTTGTGA ++ +@CCFFFFFDHHHH@GIIIIHHI +@HWI-ST132:678:C1LFKACXX:6:1312:12615:9458 +TCCCTGAGACCCTAACTTGTGA ++ +CCCFFFFFGHHHH@FIJIF<CH +@HWI-ST132:678:C1LFKACXX:6:1314:17779:75206 +TCCCTGAGACCCTAACTTGTGA ++ +CCCFFFFFGHHHHEHJJJJFHJ +@HWI-ST132:678:C1LFKACXX:6:1315:9929:42151 +TCCCTGAGACCCTAACTTGTGA ++ +@@@DDF?D8FHHHGHHIIJEGI +@HWI-ST132:678:C1LFKACXX:6:2103:13958:97727 +TCCCTGAGACCCTAACTTGTGA ++ +@CCFFFFF<FHHHIIJJJJHHJ +@HWI-ST132:678:C1LFKACXX:6:2104:10613:2992 +TCCCTGAGACCCTAACTTGTGA ++ +CCCFFFFFHHHHHJJJJJJFHI +@HWI-ST132:678:C1LFKACXX:6:2106:15153:40613 +TCCCTGAGACCCTAACTTGTGA ++ +CCCFFFFFHHHHHJJIIIICGI +@HWI-ST132:678:C1LFKACXX:6:2106:15768:75632 +TCCCTGAGACCCTAACTTGTGA ++ +CCCFFFFFFHHHHJJJJJ4CFH +@HWI-ST132:678:C1LFKACXX:6:2109:16865:57940 +TCCCTGAGACCCTAACTTGTGA ++ +CCCFFFFFHHHHHIIIJJ<FHH +@HWI-ST132:678:C1LFKACXX:6:2109:18750:76156 +TCCCTGAGACCCTAACTTGTGA ++ +@@@DFFFDFFHHH>GHJHCHHG +@HWI-ST132:678:C1LFKACXX:6:1204:12959:93444 +TCCCTGAGACCCTAACTTGTGACT ++ +CCCFFFFFGHHHHJJJJI:AFHIJ +@HWI-ST132:678:C1LFKACXX:6:1113:14924:44339 +CCCTGAGACCCTAACTTGTGAC ++ +??@DD;B?DDFHBED?CHGHII +@HWI-ST132:678:C1LFKACXX:6:1107:1375:15117 +TCACAAGTTTTGATCTCCGGTAT ++ +=??D:2A2=?DDCEHBHIJICCG +@HWI-ST132:678:C1LFKACXX:6:2105:17358:56431 +CACAAGTTTTGATCTCCGGTAT ++ +@@@DADDDHH>FHGIGEB@<@F +@HWI-ST132:678:C1LFKACXX:6:1102:6534:83469 +ACAAGTTTTGATCTCCGGTAT ++ +@@CDDDDFHHHHHJJIJJHGI +@HWI-ST132:678:C1LFKACXX:6:1212:17825:83469 +ACAAGTTTTGATCTCCGGTAT ++ +@@@FFFFFHHDFHIJJJIFDH +@HWI-ST132:678:C1LFKACXX:6:1304:1702:48389 +ACAAGTTTTGATCTCCGGTAT ++ +@@@B?=DDHDGFFIIIGGF>E |
| b |
| diff -r 9645d995fb3c -r 9185ca0a7b43 test-data/fastq_dir/reads-sample-small.fastq-miRNAs-genome_uni.fastq --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/fastq_dir/reads-sample-small.fastq-miRNAs-genome_uni.fastq Wed Jan 16 08:18:13 2019 -0500 |
| b |
| @@ -0,0 +1,252 @@ +@HWI-ST132:678:C1LFKACXX:6:1103:6450:33284 +AACCCGTAAATCCGAACTTG ++ +?@@DD<@DCCABFGF1@GHI +@HWI-ST132:678:C1LFKACXX:6:1104:7735:58473 +AACCCGTAAATCCGAACTTG ++ +:?@DDDDD@<2CAEFHGGIC +@HWI-ST132:678:C1LFKACXX:6:1111:8344:28118 +AACCCGTAAATCCGAACTTG ++ +?@@DDADD@B<ADCAEEGGI +@HWI-ST132:678:C1LFKACXX:6:1201:4901:28957 +AACCCGTAAATCCGAACTTG ++ +@@@FFFFFDAAFHFHGIIJH +@HWI-ST132:678:C1LFKACXX:6:1201:14858:55180 +AACCCGTAAATCCGAACTTG ++ +?B@FDFFFCAHAFGFHIJJJ +@HWI-ST132:678:C1LFKACXX:6:1208:10957:88261 +AACCCGTAAATCCGAACTTG ++ +@@@FFFDDFFFDFCE+CFHI +@HWI-ST132:678:C1LFKACXX:6:1211:4119:82063 +AACCCGTAAATCCGAACTTG ++ +B?@FFFDF@AACFFAEHHJI +@HWI-ST132:678:C1LFKACXX:6:1301:7756:37290 +AACCCGTAAATCCGAACTTG ++ +=BBDFFFF@<ADFHEGIJJI +@HWI-ST132:678:C1LFKACXX:6:1315:14080:19805 +AACCCGTAAATCCGAACTTG ++ +?@?DDDDFFDDHHJI;EGIE +@HWI-ST132:678:C1LFKACXX:6:2106:14523:50358 +AACCCGTAAATCCGAACTTG ++ +BBBFFFFFH:<ADHGIJJJJ +@HWI-ST132:678:C1LFKACXX:6:2107:6396:35457 +AACCCGTAAATCCGAACTTG ++ +:?BDFFFF<><ADFHIJJJJ +@HWI-ST132:678:C1LFKACXX:6:1106:15354:26782 +AACCCGTAAATCCGAACTTGTG ++ +BB@DFFDFCAADHGIGGHIII? +@HWI-ST132:678:C1LFKACXX:6:1206:3893:47334 +AACCCGTAAATCCGAACTTGTG ++ +?@@F@D@DDDDFHGIBCCHEAB +@HWI-ST132:678:C1LFKACXX:6:1212:8247:60863 +AACCCGTAAATCCGAACTTGTG ++ +?@@FFFDDCA?DFIIGEEHIGH +@HWI-ST132:678:C1LFKACXX:6:2103:20330:81235 +AACCCGTAAATCCGAACTTGTG ++ +=?BDFFFF<<<<D<CEHIJHAF +@HWI-ST132:678:C1LFKACXX:6:2105:18756:21094 +AACCCGTAAATCCGAACTTGTG ++ +CCCFFFFFHFHHHJJJJJJJII +@HWI-ST132:678:C1LFKACXX:6:2108:11590:68948 +AACCCGTAAATCCGAACTTGTG ++ +=?@;DDDD@<ACDGFHHEHAEE +@HWI-ST132:678:C1LFKACXX:6:2109:7213:21129 +AACCCGTAAATCCGAACTTGTG ++ +:B@DFFFF<<<ADBGEFFHIFH +@HWI-ST132:678:C1LFKACXX:6:1113:9515:60678 +CAAGACCGGCATTATGGGAGTC ++ +?@;DDFFFDFCFHJJGA8CGEH +@HWI-ST132:678:C1LFKACXX:6:1211:4033:43798 +CAAGACCGGCATTATGGGAGTC ++ +@CCFFFFFHHHHHJGHIJIJFH +@HWI-ST132:678:C1LFKACXX:6:2102:15781:17798 +CAAGACCGGCATTATGGGAGTC ++ +??@DDDDDFFDFFEH<CED:11 +@HWI-ST132:678:C1LFKACXX:6:2105:13568:17777 +CAAGACCGGCATTATGGGAGTC ++ +@BBFBDDD<CFHHHHAGHIJGH +@HWI-ST132:678:C1LFKACXX:6:1116:7415:45912 +TCCCTGAGACCCTAACTTGTG ++ +=?1=ABDDHHGHGICFCEIFF +@HWI-ST132:678:C1LFKACXX:6:1312:17503:22366 +TCCCTGAGACCCTAACTTGTG ++ +@@?DFFFFBHHGHIIIJIGHG +@HWI-ST132:678:C1LFKACXX:6:1101:13208:32198 +TCCCTGAGACCCTAACTTGTGA ++ +CCCFFFEFFHHHHIJJIIJHHI +@HWI-ST132:678:C1LFKACXX:6:1102:17974:5349 +TCCCTGAGACCCTAACTTGTGA ++ +CCCFFFDFHGHHHGIJJJJHGI +@HWI-ST132:678:C1LFKACXX:6:1105:10525:58469 +TCCCTGAGACCCTAACTTGTGA ++ +B@CFFFDDDHFHGHIIIGHHIJ +@HWI-ST132:678:C1LFKACXX:6:1106:11675:95913 +TCCCTGAGACCCTAACTTGTGA ++ +@@@DDDDDFHHHHAFH?G+AFH +@HWI-ST132:678:C1LFKACXX:6:1107:11700:11209 +TCCCTGAGACCCTAACTTGTGA ++ +?@@DD;==DHFDCGCFEDHHHE +@HWI-ST132:678:C1LFKACXX:6:1109:4618:19903 +TCCCTGAGACCCTAACTTGTGA ++ +CCCFFFFFHHHHHCGGHIJEHH +@HWI-ST132:678:C1LFKACXX:6:1111:16886:54124 +TCCCTGAGACCCTAACTTGTGA ++ +CCCFFFFFHHHHHEHIJJFHIJ +@HWI-ST132:678:C1LFKACXX:6:1113:14917:12939 +TCCCTGAGACCCTAACTTGTGA ++ +CCCFFFFFHHHHHJJJJJIAGH +@HWI-ST132:678:C1LFKACXX:6:1113:15286:60745 +TCCCTGAGACCCTAACTTGTGA ++ +@@@FFFDD2ADFFBHCGGAHHI +@HWI-ST132:678:C1LFKACXX:6:1116:10143:61594 +TCCCTGAGACCCTAACTTGTGA ++ +@B=DDFFFHHHHHIHIJJJHIH +@HWI-ST132:678:C1LFKACXX:6:1201:12358:31858 +TCCCTGAGACCCTAACTTGTGA ++ +:BBFFF24>ADHHIJJJJHAFH +@HWI-ST132:678:C1LFKACXX:6:1207:19763:6169 +TCCCTGAGACCCTAACTTGTGA ++ +CCCFFFFFHHHHHGIJIJEHHI +@HWI-ST132:678:C1LFKACXX:6:1208:17227:84730 +TCCCTGAGACCCTAACTTGTGA ++ +CCCFFFFFHHHGHGHIJIH<CH +@HWI-ST132:678:C1LFKACXX:6:1209:14006:3385 +TCCCTGAGACCCTAACTTGTGA ++ +CCCFFFFFFHHHHEHGHHIFGF +@HWI-ST132:678:C1LFKACXX:6:1212:19731:4329 +TCCCTGAGACCCTAACTTGTGA ++ +CCCFFFFFHHHHHJIHIIJHHI +@HWI-ST132:678:C1LFKACXX:6:1212:8981:55837 +TCCCTGAGACCCTAACTTGTGA ++ +@@@D?EFDFFHHHJJIBEGAFC +@HWI-ST132:678:C1LFKACXX:6:1214:16337:65541 +TCCCTGAGACCCTAACTTGTGA ++ +BC?DDFFFGHHHFIIJJIIFGG +@HWI-ST132:678:C1LFKACXX:6:1214:9263:76030 +TCCCTGAGACCCTAACTTGTGA ++ +@@@FFFFFHFHDHEEHIIHAFH +@HWI-ST132:678:C1LFKACXX:6:1215:7321:50488 +TCCCTGAGACCCTAACTTGTGA ++ +@C@DDFDDFFHBDHIIBE@FEH +@HWI-ST132:678:C1LFKACXX:6:1302:17139:90749 +TCCCTGAGACCCTAACTTGTGA ++ +CCCFFFFFHHHGHGIJHIIHHI +@HWI-ST132:678:C1LFKACXX:6:1302:8853:99407 +TCCCTGAGACCCTAACTTGTGA ++ +B@BFFFFFHFHHHBFHHIHAFH +@HWI-ST132:678:C1LFKACXX:6:1304:2649:24602 +TCCCTGAGACCCTAACTTGTGA ++ +CCCFFFFDHHHHHGHIJJJFGI +@HWI-ST132:678:C1LFKACXX:6:1304:17263:52290 +TCCCTGAGACCCTAACTTGTGA ++ +@CCFFFFFDHHHH@GIIIIHHI +@HWI-ST132:678:C1LFKACXX:6:1312:12615:9458 +TCCCTGAGACCCTAACTTGTGA ++ +CCCFFFFFGHHHH@FIJIF<CH +@HWI-ST132:678:C1LFKACXX:6:1314:17779:75206 +TCCCTGAGACCCTAACTTGTGA ++ +CCCFFFFFGHHHHEHJJJJFHJ +@HWI-ST132:678:C1LFKACXX:6:1315:9929:42151 +TCCCTGAGACCCTAACTTGTGA ++ +@@@DDF?D8FHHHGHHIIJEGI +@HWI-ST132:678:C1LFKACXX:6:2103:13958:97727 +TCCCTGAGACCCTAACTTGTGA ++ +@CCFFFFF<FHHHIIJJJJHHJ +@HWI-ST132:678:C1LFKACXX:6:2104:10613:2992 +TCCCTGAGACCCTAACTTGTGA ++ +CCCFFFFFHHHHHJJJJJJFHI +@HWI-ST132:678:C1LFKACXX:6:2106:15153:40613 +TCCCTGAGACCCTAACTTGTGA ++ +CCCFFFFFHHHHHJJIIIICGI +@HWI-ST132:678:C1LFKACXX:6:2106:15768:75632 +TCCCTGAGACCCTAACTTGTGA ++ +CCCFFFFFFHHHHJJJJJ4CFH +@HWI-ST132:678:C1LFKACXX:6:2109:16865:57940 +TCCCTGAGACCCTAACTTGTGA ++ +CCCFFFFFHHHHHIIIJJ<FHH +@HWI-ST132:678:C1LFKACXX:6:2109:18750:76156 +TCCCTGAGACCCTAACTTGTGA ++ +@@@DFFFDFFHHH>GHJHCHHG +@HWI-ST132:678:C1LFKACXX:6:1204:12959:93444 +TCCCTGAGACCCTAACTTGTGACT ++ +CCCFFFFFGHHHHJJJJI:AFHIJ +@HWI-ST132:678:C1LFKACXX:6:1113:14924:44339 +CCCTGAGACCCTAACTTGTGAC ++ +??@DD;B?DDFHBED?CHGHII +@HWI-ST132:678:C1LFKACXX:6:1107:1375:15117 +TCACAAGTTTTGATCTCCGGTAT ++ +=??D:2A2=?DDCEHBHIJICCG +@HWI-ST132:678:C1LFKACXX:6:2105:17358:56431 +CACAAGTTTTGATCTCCGGTAT ++ +@@@DADDDHH>FHGIGEB@<@F +@HWI-ST132:678:C1LFKACXX:6:1102:6534:83469 +ACAAGTTTTGATCTCCGGTAT ++ +@@CDDDDFHHHHHJJIJJHGI +@HWI-ST132:678:C1LFKACXX:6:1212:17825:83469 +ACAAGTTTTGATCTCCGGTAT ++ +@@@FFFFFHHDFHIJJJIFDH +@HWI-ST132:678:C1LFKACXX:6:1304:1702:48389 +ACAAGTTTTGATCTCCGGTAT ++ +@@@B?=DDHDGFFIIIGGF>E |
| b |
| diff -r 9645d995fb3c -r 9185ca0a7b43 test-data/fastq_dir/reads-sample-small.fastq-piRNAs-TEs.fastq --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/fastq_dir/reads-sample-small.fastq-piRNAs-TEs.fastq Wed Jan 16 08:18:13 2019 -0500 |
| b |
| b'@@ -0,0 +1,80256 @@\n+@HWI-ST132:678:C1LFKACXX:6:1304:17199:58363\n+AAAAACACGACCGTTCGCTTTGAAA\n++\n+JJJIJJJJJJIHHHHFHFDDBFCC@\n+@HWI-ST132:678:C1LFKACXX:6:2106:15381:40802\n+TTCAAAGCGAACGGTCGTGTTTTT\n++\n+CCCFFFFFHHHHHJFEGEC?HHII\n+@HWI-ST132:678:C1LFKACXX:6:1114:10027:77795\n+AAGATTATTAAAAACCACTGCTG\n++\n+<<EFECE:?AA,FBADD;;D@@@\n+@HWI-ST132:678:C1LFKACXX:6:1302:14522:72647\n+TTATTAAAGATCCGTTCGCTTCGCGAG\n++\n+CC@FFFFFHFHHHJHIJIJJJGGGIII\n+@HWI-ST132:678:C1LFKACXX:6:1103:11536:23013\n+TATTAAAGATCCGTTCGCTTCGCGAG\n++\n+B@@FBDDFHHHHHIIJIJJIJJJJIG\n+@HWI-ST132:678:C1LFKACXX:6:1206:10262:20669\n+TATTAAAGATCCGTTCGCTTCGCGAG\n++\n+@@@DDDDDH8FHHGDHII:CHHIIBF\n+@HWI-ST132:678:C1LFKACXX:6:1212:12068:74880\n+TTAAAGATCCGTTCGCTTCGCGAG\n++\n+CCCFDFDDHHHBBGC@FHFFDEGF\n+@HWI-ST132:678:C1LFKACXX:6:1213:19350:18162\n+TTAAAGATCCGTTCGCTTCGCGAG\n++\n+CCCFFFDFHHHHHIHIJIIJJHHI\n+@HWI-ST132:678:C1LFKACXX:6:1307:12279:8790\n+TTAAAGATCCGTTCGCTTCGCGAG\n++\n+???DDDBDDDDDDI1CEEIIII)C\n+@HWI-ST132:678:C1LFKACXX:6:1105:11371:76507\n+TTAAAGATCCGTTCGCTTCGCGAGTG\n++\n+BCCFFFFFHHFDFH)CGIJJIJIIDH\n+@HWI-ST132:678:C1LFKACXX:6:1101:3613:56171\n+TGATTTGTGCAGTAGTTTAAACAA\n++\n+BC@FFFFDHHHHHIJHHIJJJJJJ\n+@HWI-ST132:678:C1LFKACXX:6:1315:11705:87614\n+ACCGCACGAGAGCAGTCTGCACGCT\n++\n+IGGIIGHAIIFAHDDHHDD@4++::\n+@HWI-ST132:678:C1LFKACXX:6:1215:15419:77724\n+AACCGCACGAGAGCAGTCTGCACGCT\n++\n+IIIGFCIGGIJGHDCFDFDD?BB?@@\n+@HWI-ST132:678:C1LFKACXX:6:1309:1157:27805\n+TTCGGCCATTAAAACCAGCGCACT\n++\n+IIGGDIIHFFIHHHHHFFDDFB@@\n+@HWI-ST132:678:C1LFKACXX:6:1104:18136:49719\n+TCACTCGTTCGGCCATTAAAACCAGC\n++\n+IHJJIJIHJIIHFC6HHHFFFFFB@@\n+@HWI-ST132:678:C1LFKACXX:6:1206:4661:54441\n+TCATCACTCGTTCGGCCATTAAAAC\n++\n+JJJHGJIHHFC<HHHHHFFFFFCCC\n+@HWI-ST132:678:C1LFKACXX:6:1202:12284:43103\n+TTTAATGGCCGAACGAGTGATGACC\n++\n+B@BDFEFFHHCFHGIIJGHIIJJJJ\n+@HWI-ST132:678:C1LFKACXX:6:1105:18888:91816\n+TGCTAGGTCATCACTCGTTCGGCC\n++\n+JIIJJJJJJIIHDHHHDFFFFCCC\n+@HWI-ST132:678:C1LFKACXX:6:2104:13126:47993\n+TGCTAGGTCATCACTCGTTCGGCC\n++\n+JIHIIHJJJJJHHHHHDEDDFCCB\n+@HWI-ST132:678:C1LFKACXX:6:1208:10660:53352\n+GATGAAATCGTTTATGCGCCAAACT\n++\n+@@@DDDDDHHFHH=GHHIII@GCHI\n+@HWI-ST132:678:C1LFKACXX:6:2103:8188:10042\n+AGGTGGCTTGAAAGAACTGATCAACA\n++\n+@CCDDFFFHHHHHHGHIJHIJJCGHI\n+@HWI-ST132:678:C1LFKACXX:6:1116:8825:28862\n+GTTGATCAGTTCTTTCAAGCCACCT\n++\n+JIHCIEJIJJJJHHHDD;DDDA?@@\n+@HWI-ST132:678:C1LFKACXX:6:1109:17962:8377\n+TGGCTTGAAAGAACTGATCAACAGT\n++\n+CCCFFFFFHGHGHJJGCFHGIJIJJ\n+@HWI-ST132:678:C1LFKACXX:6:1202:14965:95853\n+TGGCTTGAAAGAACTGATCAACAGT\n++\n+CCCFFFFFHHHHHJJ<EHIJJJJJI\n+@HWI-ST132:678:C1LFKACXX:6:1209:11469:94001\n+TGGCTTGAAAGAACTGATCAACAGT\n++\n+CC@FFFFFGDFHGJJIIJIJJJ@HF\n+@HWI-ST132:678:C1LFKACXX:6:1213:13936:36177\n+TGGCTTGAAAGAACTGATCAACAGT\n++\n+CCCFFFFFGHHGFIIJJJJIIJIJH\n+@HWI-ST132:678:C1LFKACXX:6:1207:3316:75546\n+TCATCGGCTCGACGGAAACAATCTC\n++\n+GGEGIIIJHEFED@FHHFFFFFCC@\n+@HWI-ST132:678:C1LFKACXX:6:1306:3630:57103\n+TCATCGGCTCGACGGAAACAATCTC\n++\n+HHBGIHFGD1JGFAGHHFFFFFC@C\n+@HWI-ST132:678:C1LFKACXX:6:1106:13590:90955\n+TATCATCGGCTCGACGGAAACAATC\n++\n+GEIGEHGDC1<)HHDDDDBDDD@@@\n+@HWI-ST132:678:C1LFKACXX:6:2102:10526:18026\n+TATCATCGGCTCGACGGAAACAATC\n++\n+B<GD@?GEEDE>HAFHFDDB=A@@=\n+@HWI-ST132:678:C1LFKACXX:6:1101:5698:75650\n+TAAACTGTGAATTAAGCGCGCACA\n++\n+JJIJJIGEAIJHHHFFDFFFFCBB\n+@HWI-ST132:678:C1LFKACXX:6:1113:19105:21652\n+TAAACTGTGAATTAAGCGCGCACA\n++\n+?C:?G:E<CF>F>FFC2D;B=+1=\n+@HWI-ST132:678:C1LFKACXX:6:1203:16184:49147\n+TTAAACTGTGAATTAAGCGCGCAC\n++\n+HGGHEGFA4IIHHHFBDDDDD@@@\n+@HWI-ST132:678:C1LFKACXX:6:1309:15681:14462\n+TTAAACTGTGAATTAAGCGCGCAC\n++\n+IHFIECJJJJJHGHHHFFFFFCCC\n+@HWI-ST132:678:C1LFKACXX:6:1106:6262:61387\n+TTTTTTGATCTTTGGAGATTTATC\n++\n+JJJJJIIIHIHHHHHHFFFFFCCC\n+@HWI-ST132:678:C1LFKACXX:6:1310:7732:65923\n+TCCTGTTGATCATTTGGCCGTGGT\n++\n+IJHGIJIIHJJHHHHHFFFFFCCC\n+@HWI-ST132:678:C1LFKACXX:6:1103:7321:66631\n+TCCTGTTGATCATTTGGCCGTGG\n++\n+HFCIHFC:IJHHHHHFFDFFCCC\n+@HWI-ST132:678:C1LFKACXX:6:1205:14661:3569\n+TCCTGTTGATCATTTGGCCGTGG\n++\n+HGGJJJJIJJHHHHHFEDFFCC@\n+@HWI-ST132:678:C1LFKACXX:6:1204:8331:100236\n+CAAATGATCAACAGGACTCCACAAC\n++\n+=@BFFF?=C:=>AFGCGGGIGHIII\n+@HWI-ST132:678:C1LFKACXX:6:1113:18652:'..b'JIIIIIHFE@HHFHHFFFFFBCB\n+@HWI-ST132:678:C1LFKACXX:6:1307:8460:50243\n+TGAATTGAGAGTCGGCGTTCGTC\n++\n+JIIIHIGC8GHFHHHFFFFFCCC\n+@HWI-ST132:678:C1LFKACXX:6:1308:10034:23861\n+TGAATTGAGAGTCGGCGTTCGTC\n++\n+IIIIEEE@)CC2DDDDDDDD???\n+@HWI-ST132:678:C1LFKACXX:6:1316:14693:8233\n+TGAATTGAGAGTCGGCGTTCGTC\n++\n+HEJJIJJGJHFFFFFDDDA4+:1\n+@HWI-ST132:678:C1LFKACXX:6:1316:16722:42018\n+TGAATTGAGAGTCGGCGTTCGTC\n++\n+HGJJJIJIJIHHHHHBEDA4+:1\n+@HWI-ST132:678:C1LFKACXX:6:2105:1246:21420\n+TGAATTGAGAGTCGGCGTTCGTC\n++\n+GCGEIJIIIGHHFDHEFDFD@@@\n+@HWI-ST132:678:C1LFKACXX:6:1101:8704:11437\n+TGAATTGAGAGTCGGCGTTCGTCA\n++\n+JIHIIHFGFE1FC<FHFFFFFCC@\n+@HWI-ST132:678:C1LFKACXX:6:1101:11649:25495\n+TGAATTGAGAGTCGGCGTTCGTCA\n++\n+JJJJJHGHIHGFAHDHFFFFFBCC\n+@HWI-ST132:678:C1LFKACXX:6:1103:18159:65506\n+TGAATTGAGAGTCGGCGTTCGTCA\n++\n+GGHJIHHHFECC<DDFFFFDD@@@\n+@HWI-ST132:678:C1LFKACXX:6:1105:19098:86110\n+TGAATTGAGAGTCGGCGTTCGTCA\n++\n+IHGJJIIJIHFA3CHHFFFFFCBB\n+@HWI-ST132:678:C1LFKACXX:6:1106:6923:42358\n+TGAATTGAGAGTCGGCGTTCGTCA\n++\n+GIHGG?CGFC222F;HFFDFF@@@\n+@HWI-ST132:678:C1LFKACXX:6:1110:4800:90404\n+TGAATTGAGAGTCGGCGTTCGTCA\n++\n+IHIJJIIHF:IHHHHHFFFFF@C@\n+@HWI-ST132:678:C1LFKACXX:6:1203:9910:19443\n+TGAATTGAGAGTCGGCGTTCGTCA\n++\n+JJIIIIGIGGFA<AHHFFFFFBB@\n+@HWI-ST132:678:C1LFKACXX:6:1204:6384:54699\n+TGAATTGAGAGTCGGCGTTCGTCA\n++\n+IHGIHGIIGGIHFHHHFFFFFCCC\n+@HWI-ST132:678:C1LFKACXX:6:1204:14453:87454\n+TGAATTGAGAGTCGGCGTTCGTCA\n++\n+IJIJIIHIGHGHHHHHFFFFFCCB\n+@HWI-ST132:678:C1LFKACXX:6:1204:12749:98529\n+TGAATTGAGAGTCGGCGTTCGTCA\n++\n+IJIJIHHHGGCD<<BHFFFFF@@@\n+@HWI-ST132:678:C1LFKACXX:6:1207:1627:36426\n+TGAATTGAGAGTCGGCGTTCGTCA\n++\n+JJIJIIJJIHGFBFDHFFFFF@C@\n+@HWI-ST132:678:C1LFKACXX:6:1208:12759:32103\n+TGAATTGAGAGTCGGCGTTCGTCA\n++\n+JIHJJHIIGGCFCHGHFFFFFCCC\n+@HWI-ST132:678:C1LFKACXX:6:1211:14889:36585\n+TGAATTGAGAGTCGGCGTTCGTCA\n++\n+JIHIIHGGCCCCAFHHFFFFFBB@\n+@HWI-ST132:678:C1LFKACXX:6:1212:12013:59978\n+TGAATTGAGAGTCGGCGTTCGTCA\n++\n+IJIJJJIGHFEHFHHHFFFFFBCB\n+@HWI-ST132:678:C1LFKACXX:6:1213:5120:11874\n+TGAATTGAGAGTCGGCGTTCGTCA\n++\n+IHHJIHBIFCGFCHHHFFFFF@CC\n+@HWI-ST132:678:C1LFKACXX:6:1213:2292:56427\n+TGAATTGAGAGTCGGCGTTCGTCA\n++\n+EEDIHECF@GEC:DHDFDBAD??@\n+@HWI-ST132:678:C1LFKACXX:6:1308:19681:44147\n+TGAATTGAGAGTCGGCGTTCGTCA\n++\n+JIHJJHHHE8GHDHGHFFFFFCCC\n+@HWI-ST132:678:C1LFKACXX:6:1308:8039:70634\n+TGAATTGAGAGTCGGCGTTCGTCA\n++\n+IJIJIHGIGHGFCHHHFFFFFBB@\n+@HWI-ST132:678:C1LFKACXX:6:1308:11417:88836\n+TGAATTGAGAGTCGGCGTTCGTCA\n++\n+IIIIIIIHFE@HF?A:DDDDD@@@\n+@HWI-ST132:678:C1LFKACXX:6:1312:15688:21389\n+TGAATTGAGAGTCGGCGTTCGTCA\n++\n+GFIHBGGAC@GDDF=HDDFDFC@@\n+@HWI-ST132:678:C1LFKACXX:6:1313:13049:80920\n+TGAATTGAGAGTCGGCGTTCGTCA\n++\n+HDCHGHGHIGEFAHFFFDDFF@@@\n+@HWI-ST132:678:C1LFKACXX:6:1314:12437:83452\n+TGAATTGAGAGTCGGCGTTCGTCA\n++\n+DBBIGGDAG?@?FF=FDDDDD@@@\n+@HWI-ST132:678:C1LFKACXX:6:1315:14028:76290\n+TGAATTGAGAGTCGGCGTTCGTCA\n++\n+EEIGGHEHDGEFDFDDDEDBD=?@\n+@HWI-ST132:678:C1LFKACXX:6:2102:9769:89923\n+TGAATTGAGAGTCGGCGTTCGTCA\n++\n+JHGJIHGGCC322<2AFFFFD?=:\n+@HWI-ST132:678:C1LFKACXX:6:2103:19515:10586\n+TGAATTGAGAGTCGGCGTTCGTCA\n++\n+IIHIGG@HEGHHFHGHFFFFFCCC\n+@HWI-ST132:678:C1LFKACXX:6:2104:17289:78956\n+TGAATTGAGAGTCGGCGTTCGTCA\n++\n+JIHJIHHJHFFFBHHHFFFFFCCB\n+@HWI-ST132:678:C1LFKACXX:6:2105:16331:25093\n+TGAATTGAGAGTCGGCGTTCGTCA\n++\n+IHEIJHHIHGEHFFHHFFFFFCCB\n+@HWI-ST132:678:C1LFKACXX:6:2105:9615:69542\n+TGAATTGAGAGTCGGCGTTCGTCA\n++\n+@FDFFE@F@F8DD<2+BBDDD??=\n+@HWI-ST132:678:C1LFKACXX:6:2106:17205:80780\n+TGAATTGAGAGTCGGCGTTCGTCA\n++\n+IJIJIHFE@2@HDHHHFFFFFCCC\n+@HWI-ST132:678:C1LFKACXX:6:2107:12087:100544\n+TGAATTGAGAGTCGGCGTTCGTCA\n++\n+JIHJIJIIGFFHFHGHFFFFFCCC\n+@HWI-ST132:678:C1LFKACXX:6:2108:15487:6127\n+TGAATTGAGAGTCGGCGTTCGTCA\n++\n+JIHIHGCFC<BHDHHHFFFFFCCC\n+@HWI-ST132:678:C1LFKACXX:6:2108:20167:16581\n+TGAATTGAGAGTCGGCGTTCGTCA\n++\n+IHGHCIIJIIHF<HGHFFFFFCCC\n+@HWI-ST132:678:C1LFKACXX:6:2108:7618:52633\n+TGAATTGAGAGTCGGCGTTCGTCA\n++\n+IIJIJJIGG@2<2<DAFFFFF@@=\n+@HWI-ST132:678:C1LFKACXX:6:2108:5338:71459\n+TGAATTGAGAGTCGGCGTTCGTCA\n++\n+JIIJIHGIJIHHHHHHFFFFFCCC\n+@HWI-ST132:678:C1LFKACXX:6:1212:8402:44665\n+TGAATTGAGAGTCGGCGTTCGTCAT\n++\n+HHD?JHGHHHFEDFHGHFFFFD@@@\n' |
| b |
| diff -r 9645d995fb3c -r 9185ca0a7b43 test-data/fastq_dir/reads-sample-small.fastq-piRNAs-TEs_uni.fastq --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/fastq_dir/reads-sample-small.fastq-piRNAs-TEs_uni.fastq Wed Jan 16 08:18:13 2019 -0500 |
| b |
| b'@@ -0,0 +1,80248 @@\n+@HWI-ST132:678:C1LFKACXX:6:1304:17199:58363\n+AAAAACACGACCGTTCGCTTTGAAA\n++\n+JJJIJJJJJJIHHHHFHFDDBFCC@\n+@HWI-ST132:678:C1LFKACXX:6:2106:15381:40802\n+TTCAAAGCGAACGGTCGTGTTTTT\n++\n+CCCFFFFFHHHHHJFEGEC?HHII\n+@HWI-ST132:678:C1LFKACXX:6:1114:10027:77795\n+AAGATTATTAAAAACCACTGCTG\n++\n+<<EFECE:?AA,FBADD;;D@@@\n+@HWI-ST132:678:C1LFKACXX:6:1302:14522:72647\n+TTATTAAAGATCCGTTCGCTTCGCGAG\n++\n+CC@FFFFFHFHHHJHIJIJJJGGGIII\n+@HWI-ST132:678:C1LFKACXX:6:1103:11536:23013\n+TATTAAAGATCCGTTCGCTTCGCGAG\n++\n+B@@FBDDFHHHHHIIJIJJIJJJJIG\n+@HWI-ST132:678:C1LFKACXX:6:1206:10262:20669\n+TATTAAAGATCCGTTCGCTTCGCGAG\n++\n+@@@DDDDDH8FHHGDHII:CHHIIBF\n+@HWI-ST132:678:C1LFKACXX:6:1212:12068:74880\n+TTAAAGATCCGTTCGCTTCGCGAG\n++\n+CCCFDFDDHHHBBGC@FHFFDEGF\n+@HWI-ST132:678:C1LFKACXX:6:1213:19350:18162\n+TTAAAGATCCGTTCGCTTCGCGAG\n++\n+CCCFFFDFHHHHHIHIJIIJJHHI\n+@HWI-ST132:678:C1LFKACXX:6:1307:12279:8790\n+TTAAAGATCCGTTCGCTTCGCGAG\n++\n+???DDDBDDDDDDI1CEEIIII)C\n+@HWI-ST132:678:C1LFKACXX:6:1105:11371:76507\n+TTAAAGATCCGTTCGCTTCGCGAGTG\n++\n+BCCFFFFFHHFDFH)CGIJJIJIIDH\n+@HWI-ST132:678:C1LFKACXX:6:1101:3613:56171\n+TGATTTGTGCAGTAGTTTAAACAA\n++\n+BC@FFFFDHHHHHIJHHIJJJJJJ\n+@HWI-ST132:678:C1LFKACXX:6:1315:11705:87614\n+ACCGCACGAGAGCAGTCTGCACGCT\n++\n+IGGIIGHAIIFAHDDHHDD@4++::\n+@HWI-ST132:678:C1LFKACXX:6:1215:15419:77724\n+AACCGCACGAGAGCAGTCTGCACGCT\n++\n+IIIGFCIGGIJGHDCFDFDD?BB?@@\n+@HWI-ST132:678:C1LFKACXX:6:1309:1157:27805\n+TTCGGCCATTAAAACCAGCGCACT\n++\n+IIGGDIIHFFIHHHHHFFDDFB@@\n+@HWI-ST132:678:C1LFKACXX:6:1104:18136:49719\n+TCACTCGTTCGGCCATTAAAACCAGC\n++\n+IHJJIJIHJIIHFC6HHHFFFFFB@@\n+@HWI-ST132:678:C1LFKACXX:6:1206:4661:54441\n+TCATCACTCGTTCGGCCATTAAAAC\n++\n+JJJHGJIHHFC<HHHHHFFFFFCCC\n+@HWI-ST132:678:C1LFKACXX:6:1202:12284:43103\n+TTTAATGGCCGAACGAGTGATGACC\n++\n+B@BDFEFFHHCFHGIIJGHIIJJJJ\n+@HWI-ST132:678:C1LFKACXX:6:1105:18888:91816\n+TGCTAGGTCATCACTCGTTCGGCC\n++\n+JIIJJJJJJIIHDHHHDFFFFCCC\n+@HWI-ST132:678:C1LFKACXX:6:2104:13126:47993\n+TGCTAGGTCATCACTCGTTCGGCC\n++\n+JIHIIHJJJJJHHHHHDEDDFCCB\n+@HWI-ST132:678:C1LFKACXX:6:1208:10660:53352\n+GATGAAATCGTTTATGCGCCAAACT\n++\n+@@@DDDDDHHFHH=GHHIII@GCHI\n+@HWI-ST132:678:C1LFKACXX:6:2103:8188:10042\n+AGGTGGCTTGAAAGAACTGATCAACA\n++\n+@CCDDFFFHHHHHHGHIJHIJJCGHI\n+@HWI-ST132:678:C1LFKACXX:6:1116:8825:28862\n+GTTGATCAGTTCTTTCAAGCCACCT\n++\n+JIHCIEJIJJJJHHHDD;DDDA?@@\n+@HWI-ST132:678:C1LFKACXX:6:1109:17962:8377\n+TGGCTTGAAAGAACTGATCAACAGT\n++\n+CCCFFFFFHGHGHJJGCFHGIJIJJ\n+@HWI-ST132:678:C1LFKACXX:6:1202:14965:95853\n+TGGCTTGAAAGAACTGATCAACAGT\n++\n+CCCFFFFFHHHHHJJ<EHIJJJJJI\n+@HWI-ST132:678:C1LFKACXX:6:1209:11469:94001\n+TGGCTTGAAAGAACTGATCAACAGT\n++\n+CC@FFFFFGDFHGJJIIJIJJJ@HF\n+@HWI-ST132:678:C1LFKACXX:6:1213:13936:36177\n+TGGCTTGAAAGAACTGATCAACAGT\n++\n+CCCFFFFFGHHGFIIJJJJIIJIJH\n+@HWI-ST132:678:C1LFKACXX:6:1207:3316:75546\n+TCATCGGCTCGACGGAAACAATCTC\n++\n+GGEGIIIJHEFED@FHHFFFFFCC@\n+@HWI-ST132:678:C1LFKACXX:6:1306:3630:57103\n+TCATCGGCTCGACGGAAACAATCTC\n++\n+HHBGIHFGD1JGFAGHHFFFFFC@C\n+@HWI-ST132:678:C1LFKACXX:6:1106:13590:90955\n+TATCATCGGCTCGACGGAAACAATC\n++\n+GEIGEHGDC1<)HHDDDDBDDD@@@\n+@HWI-ST132:678:C1LFKACXX:6:2102:10526:18026\n+TATCATCGGCTCGACGGAAACAATC\n++\n+B<GD@?GEEDE>HAFHFDDB=A@@=\n+@HWI-ST132:678:C1LFKACXX:6:1101:5698:75650\n+TAAACTGTGAATTAAGCGCGCACA\n++\n+JJIJJIGEAIJHHHFFDFFFFCBB\n+@HWI-ST132:678:C1LFKACXX:6:1113:19105:21652\n+TAAACTGTGAATTAAGCGCGCACA\n++\n+?C:?G:E<CF>F>FFC2D;B=+1=\n+@HWI-ST132:678:C1LFKACXX:6:1203:16184:49147\n+TTAAACTGTGAATTAAGCGCGCAC\n++\n+HGGHEGFA4IIHHHFBDDDDD@@@\n+@HWI-ST132:678:C1LFKACXX:6:1309:15681:14462\n+TTAAACTGTGAATTAAGCGCGCAC\n++\n+IHFIECJJJJJHGHHHFFFFFCCC\n+@HWI-ST132:678:C1LFKACXX:6:1106:6262:61387\n+TTTTTTGATCTTTGGAGATTTATC\n++\n+JJJJJIIIHIHHHHHHFFFFFCCC\n+@HWI-ST132:678:C1LFKACXX:6:1310:7732:65923\n+TCCTGTTGATCATTTGGCCGTGGT\n++\n+IJHGIJIIHJJHHHHHFFFFFCCC\n+@HWI-ST132:678:C1LFKACXX:6:1103:7321:66631\n+TCCTGTTGATCATTTGGCCGTGG\n++\n+HFCIHFC:IJHHHHHFFDFFCCC\n+@HWI-ST132:678:C1LFKACXX:6:1205:14661:3569\n+TCCTGTTGATCATTTGGCCGTGG\n++\n+HGGJJJJIJJHHHHHFEDFFCC@\n+@HWI-ST132:678:C1LFKACXX:6:1204:8331:100236\n+CAAATGATCAACAGGACTCCACAAC\n++\n+=@BFFF?=C:=>AFGCGGGIGHIII\n+@HWI-ST132:678:C1LFKACXX:6:1113:18652:'..b'JIIIIIHFE@HHFHHFFFFFBCB\n+@HWI-ST132:678:C1LFKACXX:6:1307:8460:50243\n+TGAATTGAGAGTCGGCGTTCGTC\n++\n+JIIIHIGC8GHFHHHFFFFFCCC\n+@HWI-ST132:678:C1LFKACXX:6:1308:10034:23861\n+TGAATTGAGAGTCGGCGTTCGTC\n++\n+IIIIEEE@)CC2DDDDDDDD???\n+@HWI-ST132:678:C1LFKACXX:6:1316:14693:8233\n+TGAATTGAGAGTCGGCGTTCGTC\n++\n+HEJJIJJGJHFFFFFDDDA4+:1\n+@HWI-ST132:678:C1LFKACXX:6:1316:16722:42018\n+TGAATTGAGAGTCGGCGTTCGTC\n++\n+HGJJJIJIJIHHHHHBEDA4+:1\n+@HWI-ST132:678:C1LFKACXX:6:2105:1246:21420\n+TGAATTGAGAGTCGGCGTTCGTC\n++\n+GCGEIJIIIGHHFDHEFDFD@@@\n+@HWI-ST132:678:C1LFKACXX:6:1101:8704:11437\n+TGAATTGAGAGTCGGCGTTCGTCA\n++\n+JIHIIHFGFE1FC<FHFFFFFCC@\n+@HWI-ST132:678:C1LFKACXX:6:1101:11649:25495\n+TGAATTGAGAGTCGGCGTTCGTCA\n++\n+JJJJJHGHIHGFAHDHFFFFFBCC\n+@HWI-ST132:678:C1LFKACXX:6:1103:18159:65506\n+TGAATTGAGAGTCGGCGTTCGTCA\n++\n+GGHJIHHHFECC<DDFFFFDD@@@\n+@HWI-ST132:678:C1LFKACXX:6:1105:19098:86110\n+TGAATTGAGAGTCGGCGTTCGTCA\n++\n+IHGJJIIJIHFA3CHHFFFFFCBB\n+@HWI-ST132:678:C1LFKACXX:6:1106:6923:42358\n+TGAATTGAGAGTCGGCGTTCGTCA\n++\n+GIHGG?CGFC222F;HFFDFF@@@\n+@HWI-ST132:678:C1LFKACXX:6:1110:4800:90404\n+TGAATTGAGAGTCGGCGTTCGTCA\n++\n+IHIJJIIHF:IHHHHHFFFFF@C@\n+@HWI-ST132:678:C1LFKACXX:6:1203:9910:19443\n+TGAATTGAGAGTCGGCGTTCGTCA\n++\n+JJIIIIGIGGFA<AHHFFFFFBB@\n+@HWI-ST132:678:C1LFKACXX:6:1204:6384:54699\n+TGAATTGAGAGTCGGCGTTCGTCA\n++\n+IHGIHGIIGGIHFHHHFFFFFCCC\n+@HWI-ST132:678:C1LFKACXX:6:1204:14453:87454\n+TGAATTGAGAGTCGGCGTTCGTCA\n++\n+IJIJIIHIGHGHHHHHFFFFFCCB\n+@HWI-ST132:678:C1LFKACXX:6:1204:12749:98529\n+TGAATTGAGAGTCGGCGTTCGTCA\n++\n+IJIJIHHHGGCD<<BHFFFFF@@@\n+@HWI-ST132:678:C1LFKACXX:6:1207:1627:36426\n+TGAATTGAGAGTCGGCGTTCGTCA\n++\n+JJIJIIJJIHGFBFDHFFFFF@C@\n+@HWI-ST132:678:C1LFKACXX:6:1208:12759:32103\n+TGAATTGAGAGTCGGCGTTCGTCA\n++\n+JIHJJHIIGGCFCHGHFFFFFCCC\n+@HWI-ST132:678:C1LFKACXX:6:1211:14889:36585\n+TGAATTGAGAGTCGGCGTTCGTCA\n++\n+JIHIIHGGCCCCAFHHFFFFFBB@\n+@HWI-ST132:678:C1LFKACXX:6:1212:12013:59978\n+TGAATTGAGAGTCGGCGTTCGTCA\n++\n+IJIJJJIGHFEHFHHHFFFFFBCB\n+@HWI-ST132:678:C1LFKACXX:6:1213:5120:11874\n+TGAATTGAGAGTCGGCGTTCGTCA\n++\n+IHHJIHBIFCGFCHHHFFFFF@CC\n+@HWI-ST132:678:C1LFKACXX:6:1213:2292:56427\n+TGAATTGAGAGTCGGCGTTCGTCA\n++\n+EEDIHECF@GEC:DHDFDBAD??@\n+@HWI-ST132:678:C1LFKACXX:6:1308:19681:44147\n+TGAATTGAGAGTCGGCGTTCGTCA\n++\n+JIHJJHHHE8GHDHGHFFFFFCCC\n+@HWI-ST132:678:C1LFKACXX:6:1308:8039:70634\n+TGAATTGAGAGTCGGCGTTCGTCA\n++\n+IJIJIHGIGHGFCHHHFFFFFBB@\n+@HWI-ST132:678:C1LFKACXX:6:1308:11417:88836\n+TGAATTGAGAGTCGGCGTTCGTCA\n++\n+IIIIIIIHFE@HF?A:DDDDD@@@\n+@HWI-ST132:678:C1LFKACXX:6:1312:15688:21389\n+TGAATTGAGAGTCGGCGTTCGTCA\n++\n+GFIHBGGAC@GDDF=HDDFDFC@@\n+@HWI-ST132:678:C1LFKACXX:6:1313:13049:80920\n+TGAATTGAGAGTCGGCGTTCGTCA\n++\n+HDCHGHGHIGEFAHFFFDDFF@@@\n+@HWI-ST132:678:C1LFKACXX:6:1314:12437:83452\n+TGAATTGAGAGTCGGCGTTCGTCA\n++\n+DBBIGGDAG?@?FF=FDDDDD@@@\n+@HWI-ST132:678:C1LFKACXX:6:1315:14028:76290\n+TGAATTGAGAGTCGGCGTTCGTCA\n++\n+EEIGGHEHDGEFDFDDDEDBD=?@\n+@HWI-ST132:678:C1LFKACXX:6:2102:9769:89923\n+TGAATTGAGAGTCGGCGTTCGTCA\n++\n+JHGJIHGGCC322<2AFFFFD?=:\n+@HWI-ST132:678:C1LFKACXX:6:2103:19515:10586\n+TGAATTGAGAGTCGGCGTTCGTCA\n++\n+IIHIGG@HEGHHFHGHFFFFFCCC\n+@HWI-ST132:678:C1LFKACXX:6:2104:17289:78956\n+TGAATTGAGAGTCGGCGTTCGTCA\n++\n+JIHJIHHJHFFFBHHHFFFFFCCB\n+@HWI-ST132:678:C1LFKACXX:6:2105:16331:25093\n+TGAATTGAGAGTCGGCGTTCGTCA\n++\n+IHEIJHHIHGEHFFHHFFFFFCCB\n+@HWI-ST132:678:C1LFKACXX:6:2105:9615:69542\n+TGAATTGAGAGTCGGCGTTCGTCA\n++\n+@FDFFE@F@F8DD<2+BBDDD??=\n+@HWI-ST132:678:C1LFKACXX:6:2106:17205:80780\n+TGAATTGAGAGTCGGCGTTCGTCA\n++\n+IJIJIHFE@2@HDHHHFFFFFCCC\n+@HWI-ST132:678:C1LFKACXX:6:2107:12087:100544\n+TGAATTGAGAGTCGGCGTTCGTCA\n++\n+JIHJIJIIGFFHFHGHFFFFFCCC\n+@HWI-ST132:678:C1LFKACXX:6:2108:15487:6127\n+TGAATTGAGAGTCGGCGTTCGTCA\n++\n+JIHIHGCFC<BHDHHHFFFFFCCC\n+@HWI-ST132:678:C1LFKACXX:6:2108:20167:16581\n+TGAATTGAGAGTCGGCGTTCGTCA\n++\n+IHGHCIIJIIHF<HGHFFFFFCCC\n+@HWI-ST132:678:C1LFKACXX:6:2108:7618:52633\n+TGAATTGAGAGTCGGCGTTCGTCA\n++\n+IIJIJJIGG@2<2<DAFFFFF@@=\n+@HWI-ST132:678:C1LFKACXX:6:2108:5338:71459\n+TGAATTGAGAGTCGGCGTTCGTCA\n++\n+JIIJIHGIJIHHHHHHFFFFFCCC\n+@HWI-ST132:678:C1LFKACXX:6:1212:8402:44665\n+TGAATTGAGAGTCGGCGTTCGTCAT\n++\n+HHD?JHGHHHFEDFHGHFFFFD@@@\n' |
| b |
| diff -r 9645d995fb3c -r 9185ca0a7b43 test-data/fastq_dir/reads-sample-small.fastq-piRNAs-genome.fastq --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/fastq_dir/reads-sample-small.fastq-piRNAs-genome.fastq Wed Jan 16 08:18:13 2019 -0500 |
| b |
| b'@@ -0,0 +1,92224 @@\n+@HWI-ST132:678:C1LFKACXX:6:2109:5620:9149\n+TTTTTAACGAATCTAGTATACCCT\n++\n+B@BDFFFFF?<ADFHHIJJJJJJJ\n+@HWI-ST132:678:C1LFKACXX:6:1315:2668:98246\n+TTAACCGTTTTGAGCTCGGCGACCT\n++\n+1=14BDDDHHHFFIIIIFEA??@FH\n+@HWI-ST132:678:C1LFKACXX:6:1208:17824:38721\n+TCTTTATATTCGTTGGTATTTGGC\n++\n+CCCFFFFFHHH<2><C<CJJJJJJ\n+@HWI-ST132:678:C1LFKACXX:6:1203:15535:47028\n+CCGGGACTGCACAGACGAAGCGG\n++\n+@C@FFFFFHHHHHJJJIHIIIIJ\n+@HWI-ST132:678:C1LFKACXX:6:1213:1288:58514\n+AGATTCATGTTCGGATCGTCGATAC\n++\n+@C@FFFFFHHHHHIJBHIJJJJJIJ\n+@HWI-ST132:678:C1LFKACXX:6:2102:10820:38797\n+CGCTTCTTTTGAATGCGTCGTGGTG\n++\n+CCCFFFFFHHHHHJ,AGHI@<?HCG\n+@HWI-ST132:678:C1LFKACXX:6:1106:17295:99240\n+GCTGCCGCGATTCCCAAACCGTCCTG\n++\n+B@BDDFFFF?@DFEH<EGIGIJIJJJ\n+@HWI-ST132:678:C1LFKACXX:6:2101:14809:65434\n+TCCTGAGAGTCTGGTCACCGTAGAG\n++\n+CCCF?EFFHHHFHJHJJJJ3343<A\n+@HWI-ST132:678:C1LFKACXX:6:1103:14549:53735\n+ACCGTAGAGAATCTGAGCGTCAGAA\n++\n+@CCFDFFFGFHHHJGDGHGGHIJIJ\n+@HWI-ST132:678:C1LFKACXX:6:1301:3547:24519\n+CACCAGTCGGCAATATAGATCTCCT\n++\n+BCBFFFDFHHHHHJJJJJJJJJJJJ\n+@HWI-ST132:678:C1LFKACXX:6:1303:14743:8078\n+TCTATATTGCCGACTGGTGGCTCAGT\n++\n+BCBFDFFFHHHHHJJHFCFGGGHIJJ\n+@HWI-ST132:678:C1LFKACXX:6:1309:19811:76863\n+TCCTTGGCGGAGGTATCGTAGTGAG\n++\n+CCCFFFFFHHFHH?FHJJJJJHJIJ\n+@HWI-ST132:678:C1LFKACXX:6:1310:11218:64506\n+TTCCGGATTGGCAATACCCGCCTC\n++\n+CCCFFFFFHHHHHGI<GHIJIIJJ\n+@HWI-ST132:678:C1LFKACXX:6:1308:7854:98971\n+TTTGGCAAGAGGCGGCTCCTCCTG\n++\n+@@BFFFFFHHDFHEHGIJIIIJII\n+@HWI-ST132:678:C1LFKACXX:6:2104:8198:11388\n+TCTGTTGGCAGCTAGATCAGGGGC\n++\n+BCCFDFFFHHFHHGIIJJJJJJJJ\n+@HWI-ST132:678:C1LFKACXX:6:1302:8323:14904\n+TCTGTTGGCAGCTAGATCAGGGG\n++\n+BBCFDEDFHA<DFHFFHIJJJJJ\n+@HWI-ST132:678:C1LFKACXX:6:2102:13088:36303\n+TACTTGAGGACATAGACAAACATTG\n++\n+BBCFFFFFD=CFHH+AEHIJJJJJJ\n+@HWI-ST132:678:C1LFKACXX:6:1107:9391:35335\n+TCCAGAACAGGTCTGTGGGACTGATC\n++\n+CCCFFFFFHHHDHI3<EGIIJJJJJJ\n+@HWI-ST132:678:C1LFKACXX:6:1209:13917:31506\n+TATCCAGAACAGGTCTGTGGGAC\n++\n+CCCFFFFFHHH?FFHJJIJJJJJ\n+@HWI-ST132:678:C1LFKACXX:6:1210:16851:33080\n+TCCATAATCCTGACCATCCGGGCAG\n++\n+CC@FFFFFHHHHGIJIJJJJIJJJJ\n+@HWI-ST132:678:C1LFKACXX:6:2104:16032:57923\n+CCCGGATGGTCAGGATTATGGAAGC\n++\n+CCCFFFFFHFHHHGHIIIIIJJJJJ\n+@HWI-ST132:678:C1LFKACXX:6:1109:16268:61514\n+TACGGTAGAACAACTACACCGAGTGGT\n++\n+@CCFFDDDGBHHHJIIIJJJJJJFHGI\n+@HWI-ST132:678:C1LFKACXX:6:1210:7403:36822\n+TTTGCTCGACCACTCGGTGTAGTTGT\n++\n+CCCFFFFFHHHHHJJEE<ACGIIIJI\n+@HWI-ST132:678:C1LFKACXX:6:1303:14362:59821\n+TTTGCTCGACCACTCGGTGTAGT\n++\n+@C@FFFFFHHHFHIJFEA+@CFH\n+@HWI-ST132:678:C1LFKACXX:6:1304:17199:58363\n+AAAAACACGACCGTTCGCTTTGAAA\n++\n+@CCFBDDFHFHHHHIJJJJJJIJJJ\n+@HWI-ST132:678:C1LFKACXX:6:2106:15381:40802\n+TTCAAAGCGAACGGTCGTGTTTTT\n++\n+CCCFFFFFHHHHHJFEGEC?HHII\n+@HWI-ST132:678:C1LFKACXX:6:1114:10027:77795\n+AAGATTATTAAAAACCACTGCTG\n++\n+@@@D;;DDABF,AA?:ECEFE<<\n+@HWI-ST132:678:C1LFKACXX:6:1302:14522:72647\n+TTATTAAAGATCCGTTCGCTTCGCGAG\n++\n+CC@FFFFFHFHHHJHIJIJJJGGGIII\n+@HWI-ST132:678:C1LFKACXX:6:1103:11536:23013\n+TATTAAAGATCCGTTCGCTTCGCGAG\n++\n+B@@FBDDFHHHHHIIJIJJIJJJJIG\n+@HWI-ST132:678:C1LFKACXX:6:1206:10262:20669\n+TATTAAAGATCCGTTCGCTTCGCGAG\n++\n+@@@DDDDDH8FHHGDHII:CHHIIBF\n+@HWI-ST132:678:C1LFKACXX:6:1212:12068:74880\n+TTAAAGATCCGTTCGCTTCGCGAG\n++\n+CCCFDFDDHHHBBGC@FHFFDEGF\n+@HWI-ST132:678:C1LFKACXX:6:1213:19350:18162\n+TTAAAGATCCGTTCGCTTCGCGAG\n++\n+CCCFFFDFHHHHHIHIJIIJJHHI\n+@HWI-ST132:678:C1LFKACXX:6:1307:12279:8790\n+TTAAAGATCCGTTCGCTTCGCGAG\n++\n+???DDDBDDDDDDI1CEEIIII)C\n+@HWI-ST132:678:C1LFKACXX:6:1105:11371:76507\n+TTAAAGATCCGTTCGCTTCGCGAGTG\n++\n+BCCFFFFFHHFDFH)CGIJJIJIIDH\n+@HWI-ST132:678:C1LFKACXX:6:1101:3613:56171\n+TGATTTGTGCAGTAGTTTAAACAA\n++\n+BC@FFFFDHHHHHIJHHIJJJJJJ\n+@HWI-ST132:678:C1LFKACXX:6:1315:11705:87614\n+ACCGCACGAGAGCAGTCTGCACGCT\n++\n+::++4@DDHHDDHAFIIAHGIIGGI\n+@HWI-ST132:678:C1LFKACXX:6:1215:15419:77724\n+AACCGCACGAGAGCAGTCTGCACGCT\n++\n+@@?BB?DDFDFCDHGJIGGICFGIII\n+@HWI-ST132:678:C1LFKACXX:6:1206:10939:52268\n+TAGCTGTTAAAACCGCACGAGAGC\n++\n+BCCFFFFFHHHFHJIIJJIIIJJJ\n+@HWI-ST132:678:C1LFKACXX:6:1206:12272:27806\n+ATGCTTATCTGAACCACTGTGCACG\n++\n+CC@FFFFFHHHHHIIEHH<IIIHII\n+@HWI-ST132:678:C1LFKACXX:6:1309'..b'678:C1LFKACXX:6:1311:5489:31007\n+ACATGGTCTTCGGGTAGCTCCAGT\n++\n+@@BDFFADFHHGHJGGGHIJJJJI\n+@HWI-ST132:678:C1LFKACXX:6:2108:4142:4308\n+TTACGAAATGGAACTAGTTTAGTCC\n++\n+@@CFFFFFHH?FDIJIJJJJJJJJJ\n+@HWI-ST132:678:C1LFKACXX:6:1307:5088:23177\n+TGCGGGTTAAACACTGCCTTGGTG\n++\n+=B@DB@0<CFHHHJJGEGIHIJGH\n+@HWI-ST132:678:C1LFKACXX:6:1111:13371:74417\n+TGTTTACTCAAGTCCGTGCACTCG\n++\n+B@BFFFFFH:=AAEHIHJIJJJJJ\n+@HWI-ST132:678:C1LFKACXX:6:2108:8994:56073\n+TCCAGGGGAGCGGACCAAGTCGATC\n++\n+CCCFFFFFHHH<02:CGHHHIIJJJ\n+@HWI-ST132:678:C1LFKACXX:6:1206:9820:97666\n+CAATTCGAGTGGGATTTCTGATCCA\n++\n+1:1=ADDEHF<ACAFHHIJIJJJJJ\n+@HWI-ST132:678:C1LFKACXX:6:1112:17211:43697\n+TCCAGGACAAGATGCAACGCCAAAT\n++\n+CCCFFFFFHHHHHIJGIIFHIJGIJ\n+@HWI-ST132:678:C1LFKACXX:6:1308:4977:37967\n+TCTGCAGATTCTTTTGGTGTGTCTG\n++\n+@C@FFFFFGHHHHJJJHGGGIGGHH\n+@HWI-ST132:678:C1LFKACXX:6:1211:6239:25199\n+CGCGCGGCTGCTTTTCACTTTCTGCA\n++\n+CCCFFFFFHHGHHJJJJJJJJJJJJJ\n+@HWI-ST132:678:C1LFKACXX:6:2104:18450:76819\n+TTGGTTAGCCTGGTACCTGCGAA\n++\n+CCCFDDEFHHHAA<<EFHICHII\n+@HWI-ST132:678:C1LFKACXX:6:2108:15223:32156\n+ATCGTGCAATCGTTCTCTGCCCGGA\n++\n+B@CFFFFFHHHHFIJJJJFFHIJJJ\n+@HWI-ST132:678:C1LFKACXX:6:2107:12241:76580\n+CTAGGCAAAAACTCAGAAGAAGG\n++\n+@CCFFFFF8DHHHIJHJJJJGIJ\n+@HWI-ST132:678:C1LFKACXX:6:1311:13842:17572\n+TAAATTACGGTGCGGGCAGCACT\n++\n+@@@DDDEF:DAFDGG@GGFHIIG\n+@HWI-ST132:678:C1LFKACXX:6:1311:3626:78835\n+TTGAATAAGTTATCAGTCGGCGC\n++\n+<@@DFFFFHFHFHJJIIIIJJIF\n+@HWI-ST132:678:C1LFKACXX:6:1108:16423:60929\n+CACCGCCGAATGCGCATAATTAAT\n++\n+CCBFFFFFHHHHH@FHHGHIJIJJ\n+@HWI-ST132:678:C1LFKACXX:6:2101:5257:5545\n+TGAGGAGTAGCGCTCCACCCCAACC\n++\n+BBCFDEFDDFHFFIIIJJIJJJJJJ\n+@HWI-ST132:678:C1LFKACXX:6:1314:17133:15596\n+TAGCCAGGAATCGGCAAGACAGGAAC\n++\n+CCCFFFFFHHHHHJJIJJIIIJJIIJ\n+@HWI-ST132:678:C1LFKACXX:6:1204:4415:33661\n+CAAAGTCGTCTGGCAGACGGACTT\n++\n+@@@FFBDDHHH+CGIGHI<FHIII\n+@HWI-ST132:678:C1LFKACXX:6:1302:1520:97310\n+CAAAGTCGTCTGGCAGACGGACTT\n++\n+B@CFFFFFHHHHGJJFFGFHIJII\n+@HWI-ST132:678:C1LFKACXX:6:1206:19361:50379\n+TGCTGATGGACGGCAGCTCCTCCTC\n++\n+BCCFFFFFGHH@HGHIIJJJJJJJI\n+@HWI-ST132:678:C1LFKACXX:6:1215:10959:84025\n+CTTTTGTGTTCGGGGCTAAAGTA\n++\n+B@BADEDDFHHDHJJJJHJJJCG\n+@HWI-ST132:678:C1LFKACXX:6:1112:17895:2328\n+TGTCGATGTTGGCGCGATTGTCT\n++\n+BCCFFDFFHHHGHHGIIJJJHIJ\n+@HWI-ST132:678:C1LFKACXX:6:1110:11426:42306\n+TGCGGCTGAGCTGCGACCCCCGAG\n++\n+@@@AFFFF3CFHHJIIJJJIJJGH\n+@HWI-ST132:678:C1LFKACXX:6:1109:4127:92377\n+TTTCGAGATGACGCTGGCTGACTG\n++\n+CCCFFFFFHHHHHIIJIHJIJJJJ\n+@HWI-ST132:678:C1LFKACXX:6:1301:3941:50559\n+TAAAACGAAGTCGAACTGAGAGGA\n++\n+B@BF?A@DFHDHHGIJJJJJJJJJ\n+@HWI-ST132:678:C1LFKACXX:6:1307:9525:53853\n+TTTGTGGGTCTAGACGCCAGCAAGG\n++\n+@@@DDDFFHHHHH4E@@C@FGIIII\n+@HWI-ST132:678:C1LFKACXX:6:1304:6688:77081\n+CGTAAACAGGAAAGGAGTCCGTGG\n++\n+@CCFDFFFHHHHGJIJIGHIJIJI\n+@HWI-ST132:678:C1LFKACXX:6:1304:15559:58628\n+TTTGCCTTTTTCTGCTTTCTTGCTG\n++\n+@CBF;DFFHHHHHJHIJJJJJJJJJ\n+@HWI-ST132:678:C1LFKACXX:6:2103:8015:68812\n+TCATGTCGTTTGAATCTATTTTCATT\n++\n+BC@FFDFFHHHHHIIJJIJJJJJJII\n+@HWI-ST132:678:C1LFKACXX:6:1107:10110:3863\n+CCGAGTGACTGAGTGCGGACGAGCGC\n++\n+B@@FFDDFHBFHHEHIGIIIHGHIJJ\n+@HWI-ST132:678:C1LFKACXX:6:1207:7295:27446\n+TCCAGTATCTGATGTCCGCTGTC\n++\n+@CCFFBDDHHHHHC<CHDHGIIG\n+@HWI-ST132:678:C1LFKACXX:6:1305:17224:89111\n+CCGAGCCGACGAACCGTCCCTGGAA\n++\n+@@@FFF?DHHDHHJJJBHIICAHGI\n+@HWI-ST132:678:C1LFKACXX:6:1103:16749:88668\n+GCACCATAGACCAACTCTGCCATC\n++\n+BCCFFFFF+AFHHJJJJIHIJIJJ\n+@HWI-ST132:678:C1LFKACXX:6:1310:16238:87083\n+ATCGTCGTCAACAACGTTGTCAGGAT\n++\n+CCCFFFFDHGHHHJHHFE+CHHIJII\n+@HWI-ST132:678:C1LFKACXX:6:2106:19244:87969\n+CCGAACCGAACCGAAACCAAACAAAA\n++\n+=B@D440@@FHHHJJJJJJIIJJJJJ\n+@HWI-ST132:678:C1LFKACXX:6:1215:4582:40762\n+TCGTGTTCGCTCTCAAACTGAAAC\n++\n+@CCFFFFFGHHHHJJJGIJEIIJJ\n+@HWI-ST132:678:C1LFKACXX:6:2107:10854:4790\n+AAACTCTAAGCGGTGGATCACTCG\n++\n+8?<BDDDDDC?88C@<GGDBEH9C\n+@HWI-ST132:678:C1LFKACXX:6:1302:4633:32096\n+TGTTGCGGCAACTTCTTTAAGTTG\n++\n+CCCFFFFFHHHHHJJJJJJJJHIJ\n+@HWI-ST132:678:C1LFKACXX:6:2105:11033:71535\n+CGGCTGCGAATGAGAATGTATATTT\n++\n+?BBDFFFF@<@ACAAEHHHGGIJJI\n+@HWI-ST132:678:C1LFKACXX:6:1303:5477:98042\n+GTAACTGACCGTGTGGCCCAATGGA\n++\n+??@DFFFFGHDHGG?GGIEH3<FGH\n' |
| b |
| diff -r 9645d995fb3c -r 9185ca0a7b43 test-data/fastq_dir/reads-sample-small.fastq-piRNAs-genome_uni.fastq --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/fastq_dir/reads-sample-small.fastq-piRNAs-genome_uni.fastq Wed Jan 16 08:18:13 2019 -0500 |
| b |
| b'@@ -0,0 +1,92212 @@\n+@HWI-ST132:678:C1LFKACXX:6:2109:5620:9149\n+TTTTTAACGAATCTAGTATACCCT\n++\n+B@BDFFFFF?<ADFHHIJJJJJJJ\n+@HWI-ST132:678:C1LFKACXX:6:1315:2668:98246\n+TTAACCGTTTTGAGCTCGGCGACCT\n++\n+1=14BDDDHHHFFIIIIFEA??@FH\n+@HWI-ST132:678:C1LFKACXX:6:1208:17824:38721\n+TCTTTATATTCGTTGGTATTTGGC\n++\n+CCCFFFFFHHH<2><C<CJJJJJJ\n+@HWI-ST132:678:C1LFKACXX:6:1203:15535:47028\n+CCGGGACTGCACAGACGAAGCGG\n++\n+@C@FFFFFHHHHHJJJIHIIIIJ\n+@HWI-ST132:678:C1LFKACXX:6:1213:1288:58514\n+AGATTCATGTTCGGATCGTCGATAC\n++\n+@C@FFFFFHHHHHIJBHIJJJJJIJ\n+@HWI-ST132:678:C1LFKACXX:6:2102:10820:38797\n+CGCTTCTTTTGAATGCGTCGTGGTG\n++\n+CCCFFFFFHHHHHJ,AGHI@<?HCG\n+@HWI-ST132:678:C1LFKACXX:6:1106:17295:99240\n+GCTGCCGCGATTCCCAAACCGTCCTG\n++\n+B@BDDFFFF?@DFEH<EGIGIJIJJJ\n+@HWI-ST132:678:C1LFKACXX:6:2101:14809:65434\n+TCCTGAGAGTCTGGTCACCGTAGAG\n++\n+CCCF?EFFHHHFHJHJJJJ3343<A\n+@HWI-ST132:678:C1LFKACXX:6:1103:14549:53735\n+ACCGTAGAGAATCTGAGCGTCAGAA\n++\n+@CCFDFFFGFHHHJGDGHGGHIJIJ\n+@HWI-ST132:678:C1LFKACXX:6:1301:3547:24519\n+CACCAGTCGGCAATATAGATCTCCT\n++\n+BCBFFFDFHHHHHJJJJJJJJJJJJ\n+@HWI-ST132:678:C1LFKACXX:6:1303:14743:8078\n+TCTATATTGCCGACTGGTGGCTCAGT\n++\n+BCBFDFFFHHHHHJJHFCFGGGHIJJ\n+@HWI-ST132:678:C1LFKACXX:6:1309:19811:76863\n+TCCTTGGCGGAGGTATCGTAGTGAG\n++\n+CCCFFFFFHHFHH?FHJJJJJHJIJ\n+@HWI-ST132:678:C1LFKACXX:6:1310:11218:64506\n+TTCCGGATTGGCAATACCCGCCTC\n++\n+CCCFFFFFHHHHHGI<GHIJIIJJ\n+@HWI-ST132:678:C1LFKACXX:6:1308:7854:98971\n+TTTGGCAAGAGGCGGCTCCTCCTG\n++\n+@@BFFFFFHHDFHEHGIJIIIJII\n+@HWI-ST132:678:C1LFKACXX:6:2104:8198:11388\n+TCTGTTGGCAGCTAGATCAGGGGC\n++\n+BCCFDFFFHHFHHGIIJJJJJJJJ\n+@HWI-ST132:678:C1LFKACXX:6:1302:8323:14904\n+TCTGTTGGCAGCTAGATCAGGGG\n++\n+BBCFDEDFHA<DFHFFHIJJJJJ\n+@HWI-ST132:678:C1LFKACXX:6:2102:13088:36303\n+TACTTGAGGACATAGACAAACATTG\n++\n+BBCFFFFFD=CFHH+AEHIJJJJJJ\n+@HWI-ST132:678:C1LFKACXX:6:1107:9391:35335\n+TCCAGAACAGGTCTGTGGGACTGATC\n++\n+CCCFFFFFHHHDHI3<EGIIJJJJJJ\n+@HWI-ST132:678:C1LFKACXX:6:1209:13917:31506\n+TATCCAGAACAGGTCTGTGGGAC\n++\n+CCCFFFFFHHH?FFHJJIJJJJJ\n+@HWI-ST132:678:C1LFKACXX:6:1210:16851:33080\n+TCCATAATCCTGACCATCCGGGCAG\n++\n+CC@FFFFFHHHHGIJIJJJJIJJJJ\n+@HWI-ST132:678:C1LFKACXX:6:2104:16032:57923\n+CCCGGATGGTCAGGATTATGGAAGC\n++\n+CCCFFFFFHFHHHGHIIIIIJJJJJ\n+@HWI-ST132:678:C1LFKACXX:6:1109:16268:61514\n+TACGGTAGAACAACTACACCGAGTGGT\n++\n+@CCFFDDDGBHHHJIIIJJJJJJFHGI\n+@HWI-ST132:678:C1LFKACXX:6:1210:7403:36822\n+TTTGCTCGACCACTCGGTGTAGTTGT\n++\n+CCCFFFFFHHHHHJJEE<ACGIIIJI\n+@HWI-ST132:678:C1LFKACXX:6:1303:14362:59821\n+TTTGCTCGACCACTCGGTGTAGT\n++\n+@C@FFFFFHHHFHIJFEA+@CFH\n+@HWI-ST132:678:C1LFKACXX:6:1304:17199:58363\n+AAAAACACGACCGTTCGCTTTGAAA\n++\n+@CCFBDDFHFHHHHIJJJJJJIJJJ\n+@HWI-ST132:678:C1LFKACXX:6:2106:15381:40802\n+TTCAAAGCGAACGGTCGTGTTTTT\n++\n+CCCFFFFFHHHHHJFEGEC?HHII\n+@HWI-ST132:678:C1LFKACXX:6:1114:10027:77795\n+AAGATTATTAAAAACCACTGCTG\n++\n+@@@D;;DDABF,AA?:ECEFE<<\n+@HWI-ST132:678:C1LFKACXX:6:1302:14522:72647\n+TTATTAAAGATCCGTTCGCTTCGCGAG\n++\n+CC@FFFFFHFHHHJHIJIJJJGGGIII\n+@HWI-ST132:678:C1LFKACXX:6:1103:11536:23013\n+TATTAAAGATCCGTTCGCTTCGCGAG\n++\n+B@@FBDDFHHHHHIIJIJJIJJJJIG\n+@HWI-ST132:678:C1LFKACXX:6:1206:10262:20669\n+TATTAAAGATCCGTTCGCTTCGCGAG\n++\n+@@@DDDDDH8FHHGDHII:CHHIIBF\n+@HWI-ST132:678:C1LFKACXX:6:1212:12068:74880\n+TTAAAGATCCGTTCGCTTCGCGAG\n++\n+CCCFDFDDHHHBBGC@FHFFDEGF\n+@HWI-ST132:678:C1LFKACXX:6:1213:19350:18162\n+TTAAAGATCCGTTCGCTTCGCGAG\n++\n+CCCFFFDFHHHHHIHIJIIJJHHI\n+@HWI-ST132:678:C1LFKACXX:6:1307:12279:8790\n+TTAAAGATCCGTTCGCTTCGCGAG\n++\n+???DDDBDDDDDDI1CEEIIII)C\n+@HWI-ST132:678:C1LFKACXX:6:1105:11371:76507\n+TTAAAGATCCGTTCGCTTCGCGAGTG\n++\n+BCCFFFFFHHFDFH)CGIJJIJIIDH\n+@HWI-ST132:678:C1LFKACXX:6:1101:3613:56171\n+TGATTTGTGCAGTAGTTTAAACAA\n++\n+BC@FFFFDHHHHHIJHHIJJJJJJ\n+@HWI-ST132:678:C1LFKACXX:6:1315:11705:87614\n+ACCGCACGAGAGCAGTCTGCACGCT\n++\n+::++4@DDHHDDHAFIIAHGIIGGI\n+@HWI-ST132:678:C1LFKACXX:6:1215:15419:77724\n+AACCGCACGAGAGCAGTCTGCACGCT\n++\n+@@?BB?DDFDFCDHGJIGGICFGIII\n+@HWI-ST132:678:C1LFKACXX:6:1206:10939:52268\n+TAGCTGTTAAAACCGCACGAGAGC\n++\n+BCCFFFFFHHHFHJIIJJIIIJJJ\n+@HWI-ST132:678:C1LFKACXX:6:1206:12272:27806\n+ATGCTTATCTGAACCACTGTGCACG\n++\n+CC@FFFFFHHHHHIIEHH<IIIHII\n+@HWI-ST132:678:C1LFKACXX:6:1309'..b'2:678:C1LFKACXX:6:1307:2988:76332\n+TCGAAAGTCCAACTGGAATGGCCC\n++\n+@CCFFFFDHHHHHJJIJGIJJJJJ\n+@HWI-ST132:678:C1LFKACXX:6:1311:5489:31007\n+ACATGGTCTTCGGGTAGCTCCAGT\n++\n+@@BDFFADFHHGHJGGGHIJJJJI\n+@HWI-ST132:678:C1LFKACXX:6:2108:4142:4308\n+TTACGAAATGGAACTAGTTTAGTCC\n++\n+@@CFFFFFHH?FDIJIJJJJJJJJJ\n+@HWI-ST132:678:C1LFKACXX:6:1307:5088:23177\n+TGCGGGTTAAACACTGCCTTGGTG\n++\n+=B@DB@0<CFHHHJJGEGIHIJGH\n+@HWI-ST132:678:C1LFKACXX:6:1111:13371:74417\n+TGTTTACTCAAGTCCGTGCACTCG\n++\n+B@BFFFFFH:=AAEHIHJIJJJJJ\n+@HWI-ST132:678:C1LFKACXX:6:2108:8994:56073\n+TCCAGGGGAGCGGACCAAGTCGATC\n++\n+CCCFFFFFHHH<02:CGHHHIIJJJ\n+@HWI-ST132:678:C1LFKACXX:6:1206:9820:97666\n+CAATTCGAGTGGGATTTCTGATCCA\n++\n+1:1=ADDEHF<ACAFHHIJIJJJJJ\n+@HWI-ST132:678:C1LFKACXX:6:1112:17211:43697\n+TCCAGGACAAGATGCAACGCCAAAT\n++\n+CCCFFFFFHHHHHIJGIIFHIJGIJ\n+@HWI-ST132:678:C1LFKACXX:6:1308:4977:37967\n+TCTGCAGATTCTTTTGGTGTGTCTG\n++\n+@C@FFFFFGHHHHJJJHGGGIGGHH\n+@HWI-ST132:678:C1LFKACXX:6:1211:6239:25199\n+CGCGCGGCTGCTTTTCACTTTCTGCA\n++\n+CCCFFFFFHHGHHJJJJJJJJJJJJJ\n+@HWI-ST132:678:C1LFKACXX:6:2104:18450:76819\n+TTGGTTAGCCTGGTACCTGCGAA\n++\n+CCCFDDEFHHHAA<<EFHICHII\n+@HWI-ST132:678:C1LFKACXX:6:2108:15223:32156\n+ATCGTGCAATCGTTCTCTGCCCGGA\n++\n+B@CFFFFFHHHHFIJJJJFFHIJJJ\n+@HWI-ST132:678:C1LFKACXX:6:2107:12241:76580\n+CTAGGCAAAAACTCAGAAGAAGG\n++\n+@CCFFFFF8DHHHIJHJJJJGIJ\n+@HWI-ST132:678:C1LFKACXX:6:1311:13842:17572\n+TAAATTACGGTGCGGGCAGCACT\n++\n+@@@DDDEF:DAFDGG@GGFHIIG\n+@HWI-ST132:678:C1LFKACXX:6:1311:3626:78835\n+TTGAATAAGTTATCAGTCGGCGC\n++\n+<@@DFFFFHFHFHJJIIIIJJIF\n+@HWI-ST132:678:C1LFKACXX:6:1108:16423:60929\n+CACCGCCGAATGCGCATAATTAAT\n++\n+CCBFFFFFHHHHH@FHHGHIJIJJ\n+@HWI-ST132:678:C1LFKACXX:6:2101:5257:5545\n+TGAGGAGTAGCGCTCCACCCCAACC\n++\n+BBCFDEFDDFHFFIIIJJIJJJJJJ\n+@HWI-ST132:678:C1LFKACXX:6:1314:17133:15596\n+TAGCCAGGAATCGGCAAGACAGGAAC\n++\n+CCCFFFFFHHHHHJJIJJIIIJJIIJ\n+@HWI-ST132:678:C1LFKACXX:6:1204:4415:33661\n+CAAAGTCGTCTGGCAGACGGACTT\n++\n+@@@FFBDDHHH+CGIGHI<FHIII\n+@HWI-ST132:678:C1LFKACXX:6:1302:1520:97310\n+CAAAGTCGTCTGGCAGACGGACTT\n++\n+B@CFFFFFHHHHGJJFFGFHIJII\n+@HWI-ST132:678:C1LFKACXX:6:1206:19361:50379\n+TGCTGATGGACGGCAGCTCCTCCTC\n++\n+BCCFFFFFGHH@HGHIIJJJJJJJI\n+@HWI-ST132:678:C1LFKACXX:6:1215:10959:84025\n+CTTTTGTGTTCGGGGCTAAAGTA\n++\n+B@BADEDDFHHDHJJJJHJJJCG\n+@HWI-ST132:678:C1LFKACXX:6:1112:17895:2328\n+TGTCGATGTTGGCGCGATTGTCT\n++\n+BCCFFDFFHHHGHHGIIJJJHIJ\n+@HWI-ST132:678:C1LFKACXX:6:1110:11426:42306\n+TGCGGCTGAGCTGCGACCCCCGAG\n++\n+@@@AFFFF3CFHHJIIJJJIJJGH\n+@HWI-ST132:678:C1LFKACXX:6:1109:4127:92377\n+TTTCGAGATGACGCTGGCTGACTG\n++\n+CCCFFFFFHHHHHIIJIHJIJJJJ\n+@HWI-ST132:678:C1LFKACXX:6:1301:3941:50559\n+TAAAACGAAGTCGAACTGAGAGGA\n++\n+B@BF?A@DFHDHHGIJJJJJJJJJ\n+@HWI-ST132:678:C1LFKACXX:6:1307:9525:53853\n+TTTGTGGGTCTAGACGCCAGCAAGG\n++\n+@@@DDDFFHHHHH4E@@C@FGIIII\n+@HWI-ST132:678:C1LFKACXX:6:1304:6688:77081\n+CGTAAACAGGAAAGGAGTCCGTGG\n++\n+@CCFDFFFHHHHGJIJIGHIJIJI\n+@HWI-ST132:678:C1LFKACXX:6:1304:15559:58628\n+TTTGCCTTTTTCTGCTTTCTTGCTG\n++\n+@CBF;DFFHHHHHJHIJJJJJJJJJ\n+@HWI-ST132:678:C1LFKACXX:6:2103:8015:68812\n+TCATGTCGTTTGAATCTATTTTCATT\n++\n+BC@FFDFFHHHHHIIJJIJJJJJJII\n+@HWI-ST132:678:C1LFKACXX:6:1107:10110:3863\n+CCGAGTGACTGAGTGCGGACGAGCGC\n++\n+B@@FFDDFHBFHHEHIGIIIHGHIJJ\n+@HWI-ST132:678:C1LFKACXX:6:1207:7295:27446\n+TCCAGTATCTGATGTCCGCTGTC\n++\n+@CCFFBDDHHHHHC<CHDHGIIG\n+@HWI-ST132:678:C1LFKACXX:6:1305:17224:89111\n+CCGAGCCGACGAACCGTCCCTGGAA\n++\n+@@@FFF?DHHDHHJJJBHIICAHGI\n+@HWI-ST132:678:C1LFKACXX:6:1103:16749:88668\n+GCACCATAGACCAACTCTGCCATC\n++\n+BCCFFFFF+AFHHJJJJIHIJIJJ\n+@HWI-ST132:678:C1LFKACXX:6:1310:16238:87083\n+ATCGTCGTCAACAACGTTGTCAGGAT\n++\n+CCCFFFFDHGHHHJHHFE+CHHIJII\n+@HWI-ST132:678:C1LFKACXX:6:2106:19244:87969\n+CCGAACCGAACCGAAACCAAACAAAA\n++\n+=B@D440@@FHHHJJJJJJIIJJJJJ\n+@HWI-ST132:678:C1LFKACXX:6:1215:4582:40762\n+TCGTGTTCGCTCTCAAACTGAAAC\n++\n+@CCFFFFFGHHHHJJJGIJEIIJJ\n+@HWI-ST132:678:C1LFKACXX:6:2107:10854:4790\n+AAACTCTAAGCGGTGGATCACTCG\n++\n+8?<BDDDDDC?88C@<GGDBEH9C\n+@HWI-ST132:678:C1LFKACXX:6:1302:4633:32096\n+TGTTGCGGCAACTTCTTTAAGTTG\n++\n+CCCFFFFFHHHHHJJJJJJJJHIJ\n+@HWI-ST132:678:C1LFKACXX:6:2105:11033:71535\n+CGGCTGCGAATGAGAATGTATATTT\n++\n+?BBDFFFF@<@ACAAEHHHGGIJJI\n' |
| b |
| diff -r 9645d995fb3c -r 9185ca0a7b43 test-data/fastq_dir/reads-sample-small.fastq-piRNAs-transcripts.fastq --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/fastq_dir/reads-sample-small.fastq-piRNAs-transcripts.fastq Wed Jan 16 08:18:13 2019 -0500 |
| b |
| b'@@ -0,0 +1,7136 @@\n+@HWI-ST132:678:C1LFKACXX:6:1104:3361:38910\n+TTTTTTGGCACACGATTTTTTCG\n++\n+BCCFFFFFHHHGHF@EHIJJJJJ\n+@HWI-ST132:678:C1LFKACXX:6:1302:8271:27021\n+TGGCTCTAGAGGTGGCTCCAGGC\n++\n+C@CFFFFFHHG3<<ACHIIHGII\n+@HWI-ST132:678:C1LFKACXX:6:1306:9256:39375\n+TGGCTCTAGAGGTGGCTCCAGGC\n++\n+BBCFFFFFHFHA3+<<EGIIIJJ\n+@HWI-ST132:678:C1LFKACXX:6:2104:8543:80281\n+CTCTAGAGGTGGCTCCAGGCTCT\n++\n+BBCF=BBDHFHHHIJIIJGIJJJ\n+@HWI-ST132:678:C1LFKACXX:6:1206:10520:35802\n+TCTAGAGGTGGCTCCAGGCTCTC\n++\n+BBBDFFFFFHAADGHIIIJJJJJ\n+@HWI-ST132:678:C1LFKACXX:6:1210:16796:70859\n+TCTAGAGGTGGCTCCAGGCTCTC\n++\n+BBBDFDFFFFHHDIJJJJJJJJJ\n+@HWI-ST132:678:C1LFKACXX:6:1312:8034:92577\n+TCTAGAGGTGGCTCCAGGCTCTC\n++\n+=?8ABBDDAFHHHIJIIIIJJII\n+@HWI-ST132:678:C1LFKACXX:6:2103:6868:77512\n+TCTAGAGGTGGCTCCAGGCTCTC\n++\n+BBBDDDFFCHHHHJJJJJJJJJJ\n+@HWI-ST132:678:C1LFKACXX:6:2105:8058:54317\n+TCTAGAGGTGGCTCCAGGCTCTC\n++\n+:BBDFDFFCF<<AAF?GHJJJJJ\n+@HWI-ST132:678:C1LFKACXX:6:2105:4030:77058\n+TCTAGAGGTGGCTCCAGGCTCTC\n++\n+BCBFDFFFDFHHHJJJIIIJJJI\n+@HWI-ST132:678:C1LFKACXX:6:2108:19158:37021\n+TCTAGAGGTGGCTCCAGGCTCTC\n++\n+BCBDFFFFFFHHHIJJIJJJJJI\n+@HWI-ST132:678:C1LFKACXX:6:2108:4761:89781\n+TCTAGAGGTGGCTCCAGGCTCTC\n++\n+@BBDFFFFADHFHEIIIJJIJJI\n+@HWI-ST132:678:C1LFKACXX:6:2109:17544:31829\n+TCTAGAGGTGGCTCCAGGCTCTC\n++\n+BCBFFFFFFHHHHJJIJIJJJJJ\n+@HWI-ST132:678:C1LFKACXX:6:1211:11818:23477\n+TCTAGAGGTGGCTCCAGGCTCTCT\n++\n+IHJIJIJIDGIFFDFFFFFFDBBB\n+@HWI-ST132:678:C1LFKACXX:6:1310:1057:72917\n+GAGAGCCTGGAGCCACCTCTAGA\n++\n+IHJJJJJIJJHHFFHFFFFF@@@\n+@HWI-ST132:678:C1LFKACXX:6:2107:14168:54674\n+TATCACTGTATGCGTAGAAAAGAG\n++\n+CCCFDFFFHHGDFFFHIJJJJJJJ\n+@HWI-ST132:678:C1LFKACXX:6:1210:20798:12533\n+TCTGCTATCACTGTATGCGTAGAAA\n++\n+@@@FDDDFHGHHGJIJIG@GCEFDB\n+@HWI-ST132:678:C1LFKACXX:6:1115:5746:10371\n+TATGCTCATGCATTGTAAATTTGACA\n++\n+=@B=BDEFGH>FHGGAFHEJIJIHJJ\n+@HWI-ST132:678:C1LFKACXX:6:1115:5725:10377\n+TATGCTCATGCATTGTAAATTTGACA\n++\n+=?1A4=BDADD<<AF<C:CIHAHJIB\n+@HWI-ST132:678:C1LFKACXX:6:1204:5988:3191\n+TTTTGTCAAATTTACAATGCATGAGC\n++\n+@CCFFDFFH4DHHIIGII<@IIIIII\n+@HWI-ST132:678:C1LFKACXX:6:1112:17845:55327\n+TTTTGTCAAATTTACAATGCATG\n++\n+JJJIGIHEEBHHHHDFFDFFCC@\n+@HWI-ST132:678:C1LFKACXX:6:1116:8060:21154\n+TTTTGTCAAATTTACAATGCATG\n++\n+GGIJIJJJJIHHHHGFFDDD@B@\n+@HWI-ST132:678:C1LFKACXX:6:1202:12362:65139\n+TTTTGTCAAATTTACAATGCATG\n++\n+BCCFFDFFHHHHHJJJJJIJJJJ\n+@HWI-ST132:678:C1LFKACXX:6:2101:10333:80069\n+TTTTGTCAAATTTACAATGCATG\n++\n+JJJJJJJJJJHHHHHFFDFFBCC\n+@HWI-ST132:678:C1LFKACXX:6:1115:14316:97559\n+TGCATTGTAAATTTGACAAAATATG\n++\n+GCGIDEJJIGIJHHHHFDFDDB:@?\n+@HWI-ST132:678:C1LFKACXX:6:1210:19160:87047\n+TGCATTGTAAATTTGACAAAATATG\n++\n+CCCFFFFDHHHHHJJHJIIJJJJJJ\n+@HWI-ST132:678:C1LFKACXX:6:1102:14990:61179\n+TTTGACAAAATATGCCCTTCACC\n++\n+@@@D+ADEHAHHHIIIIIIIGII\n+@HWI-ST132:678:C1LFKACXX:6:1103:12540:8868\n+TTTGACAAAATATGCCCTTCACC\n++\n+GHIGIIGFA,HF>FFB>DAF@@@\n+@HWI-ST132:678:C1LFKACXX:6:1103:6815:14215\n+TTTGACAAAATATGCCCTTCACC\n++\n+CIIIIIIIIIHHHFHEDB+F@@@\n+@HWI-ST132:678:C1LFKACXX:6:1107:5684:28828\n+TTTGACAAAATATGCCCTTCACC\n++\n+BCCFFFFFFCFHHEGHJIJJIIG\n+@HWI-ST132:678:C1LFKACXX:6:1108:15125:97763\n+TTTGACAAAATATGCCCTTCACC\n++\n+CCCFFFFFHHHHH<CGIJJJJII\n+@HWI-ST132:678:C1LFKACXX:6:1110:20123:8967\n+TTTGACAAAATATGCCCTTCACC\n++\n+JJJJJJJJIJHHHHGFFFFFCCC\n+@HWI-ST132:678:C1LFKACXX:6:1111:4327:25202\n+TTTGACAAAATATGCCCTTCACC\n++\n+@@@FFDFDHHA?FEBHF@HIGGG\n+@HWI-ST132:678:C1LFKACXX:6:1112:16367:41504\n+TTTGACAAAATATGCCCTTCACC\n++\n+@@CFDFFFHGFHHJIJIIJJIIE\n+@HWI-ST132:678:C1LFKACXX:6:1115:12597:83379\n+TTTGACAAAATATGCCCTTCACC\n++\n+IHIGGEGGGGCDFFHFFEADB;@\n+@HWI-ST132:678:C1LFKACXX:6:1202:11500:85997\n+TTTGACAAAATATGCCCTTCACC\n++\n+BBBF=DEFHHHHHIIJJJJJJJJ\n+@HWI-ST132:678:C1LFKACXX:6:1203:7440:86465\n+TTTGACAAAATATGCCCTTCACC\n++\n+JJJIIIIHFHHHDFHFDDAFCCB\n+@HWI-ST132:678:C1LFKACXX:6:1208:5601:13037\n+TTTGACAAAATATGCCCTTCACC\n++\n+CCCFFFFFHHHHHFFHIJJJIIJ\n+@HWI-ST132:678:C1LFKACXX:6:1208:3642:37562\n+TTTGACAAAATATGCCCTTCACC\n++\n+CCCFFFFFHGHHHGIJJJJIJJJ\n+@HWI-ST132:678:C1LFKACXX:6:1209:15199:72310\n+TTTGACAAAATATGCCCTTCACC\n++\n+CCCFFFFFHHHHHJJJJJJJJJJ\n+@HWI-ST132:678:C1LFKACXX:6:1210:10211:42145\n+TTT'..b'TGTGAAGACGT\n++\n+HJJJJIIGE?CGHHHHHFFFFFCCC\n+@HWI-ST132:678:C1LFKACXX:6:1305:13291:74216\n+TTCGATCGCCGACGTGTGAAGACGT\n++\n+HJJIHGC?1:E@HHHHGFFFFFCCC\n+@HWI-ST132:678:C1LFKACXX:6:1305:14099:91760\n+TTCGATCGCCGACGTGTGAAGACGT\n++\n+GIGIIIEHFC?EHGHHGFFFFFCCC\n+@HWI-ST132:678:C1LFKACXX:6:1306:4852:79972\n+TTCGATCGCCGACGTGTGAAGACGT\n++\n+IJIIIGFC:?FJHHHHHFFFFFCCC\n+@HWI-ST132:678:C1LFKACXX:6:1306:14526:93144\n+TTCGATCGCCGACGTGTGAAGACGT\n++\n+IIIIIIHFC8EHHF<HFFFFFF@@@\n+@HWI-ST132:678:C1LFKACXX:6:1306:12830:100458\n+TTCGATCGCCGACGTGTGAAGACGT\n++\n+JJIIGIGHEE:CHHHFHFFFFF@@@\n+@HWI-ST132:678:C1LFKACXX:6:1307:3341:79302\n+TTCGATCGCCGACGTGTGAAGACGT\n++\n+IIIIHG<HEGHIHFFHHDDD=D@@@\n+@HWI-ST132:678:C1LFKACXX:6:1309:20666:8951\n+TTCGATCGCCGACGTGTGAAGACGT\n++\n+IIHCBD?C:C?EDDHHGFFFDF@@@\n+@HWI-ST132:678:C1LFKACXX:6:1310:20517:19080\n+TTCGATCGCCGACGTGTGAAGACGT\n++\n+FHGGGF?GGFEHHHFHGFFFFFCCC\n+@HWI-ST132:678:C1LFKACXX:6:1310:19552:89269\n+TTCGATCGCCGACGTGTGAAGACGT\n++\n+HJJIJJIHFCCHHGHHGFFFFFCCC\n+@HWI-ST132:678:C1LFKACXX:6:1310:11672:92080\n+TTCGATCGCCGACGTGTGAAGACGT\n++\n+IIJIHFGHHGHJHHHHHFFFDFCCC\n+@HWI-ST132:678:C1LFKACXX:6:1312:14124:76448\n+TTCGATCGCCGACGTGTGAAGACGT\n++\n+JJJIHGDHEHHJHHHHGFFEFF@C@\n+@HWI-ST132:678:C1LFKACXX:6:1313:16741:57946\n+TTCGATCGCCGACGTGTGAAGACGT\n++\n+AIIJJJIHFFGDHHHHHFFFDFCC@\n+@HWI-ST132:678:C1LFKACXX:6:1315:9373:25299\n+TTCGATCGCCGACGTGTGAAGACGT\n++\n+G>FDCC4;;EEIFDFDFDD=+D?@@\n+@HWI-ST132:678:C1LFKACXX:6:1315:12968:32460\n+TTCGATCGCCGACGTGTGAAGACGT\n++\n+BD9FGFFBF?GGF<FFFDDDB=1@@\n+@HWI-ST132:678:C1LFKACXX:6:2101:18316:34316\n+TTCGATCGCCGACGTGTGAAGACGT\n++\n+JJJJJJJIHHEIHHFHHFFEDFCCB\n+@HWI-ST132:678:C1LFKACXX:6:2101:18438:36839\n+TTCGATCGCCGACGTGTGAAGACGT\n++\n+IJJJJJJHGG?HHHDHHFFDDFCCB\n+@HWI-ST132:678:C1LFKACXX:6:2101:14608:56807\n+TTCGATCGCCGACGTGTGAAGACGT\n++\n+JJJJJIHHHFIIHHHHHFFFDDBCB\n+@HWI-ST132:678:C1LFKACXX:6:2103:7602:64596\n+TTCGATCGCCGACGTGTGAAGACGT\n++\n+GHIIHFBC??:@FCCDF@+A;D??=\n+@HWI-ST132:678:C1LFKACXX:6:2103:17863:69050\n+TTCGATCGCCGACGTGTGAAGACGT\n++\n+GIJJJJIIHFGIHFHHHFFFFFCCB\n+@HWI-ST132:678:C1LFKACXX:6:2104:5137:4251\n+TTCGATCGCCGACGTGTGAAGACGT\n++\n+IJJIJJIHEHHJHHDHGFFEFFCCB\n+@HWI-ST132:678:C1LFKACXX:6:2104:20272:16658\n+TTCGATCGCCGACGTGTGAAGACGT\n++\n+HJJJJJJIHHJIHHHHHFFFFFCCC\n+@HWI-ST132:678:C1LFKACXX:6:2104:8336:35547\n+TTCGATCGCCGACGTGTGAAGACGT\n++\n+IJJJIHHDC?C@F@@HGFFFFD@B=\n+@HWI-ST132:678:C1LFKACXX:6:2104:17454:68818\n+TTCGATCGCCGACGTGTGAAGACGT\n++\n+IJJJIIHFEIIIHHHHHFFFBFCCC\n+@HWI-ST132:678:C1LFKACXX:6:2105:8348:83371\n+TTCGATCGCCGACGTGTGAAGACGT\n++\n+DIGJIFD?1@@C<0@HHDFFDD??:\n+@HWI-ST132:678:C1LFKACXX:6:2105:19893:91541\n+TTCGATCGCCGACGTGTGAAGACGT\n++\n+?HEGHC4HFHG@HFDHHDDD=D@@@\n+@HWI-ST132:678:C1LFKACXX:6:2106:6481:37891\n+TTCGATCGCCGACGTGTGAAGACGT\n++\n+HJJJJJJHIIHIHFHHHFFFFF@CC\n+@HWI-ST132:678:C1LFKACXX:6:2106:15957:78129\n+TTCGATCGCCGACGTGTGAAGACGT\n++\n+HJJJJJJHIHIJHHHHHFFFFFBCC\n+@HWI-ST132:678:C1LFKACXX:6:2107:12188:11374\n+TTCGATCGCCGACGTGTGAAGACGT\n++\n+FJJIIIGD?FCGHHHHHDDB?FCBB\n+@HWI-ST132:678:C1LFKACXX:6:2108:18380:53781\n+TTCGATCGCCGACGTGTGAAGACGT\n++\n+JJJJIHF?114C@@CHHFFFFFBB=\n+@HWI-ST132:678:C1LFKACXX:6:1208:16812:100651\n+TTCGATCGCCGACGTGTGAAGACG\n++\n+IIIGC<HGGFGHHHHHFFEBFCCC\n+@HWI-ST132:678:C1LFKACXX:6:1103:13690:62133\n+ATTCGATCGCCGACGTGTGAAGACG\n++\n+JJIHGGCGIGJJGHHHHFFFFFCCB\n+@HWI-ST132:678:C1LFKACXX:6:1109:8695:89867\n+TTCGATCGCCGACGTGTGAAGAC\n++\n+JJHIGHEGFIHHHHHFFFFFCCC\n+@HWI-ST132:678:C1LFKACXX:6:2103:4519:3225\n+TGCAAGCTAAGAATTCCGAAACGCC\n++\n+JJIJJJJJJIHFCAC:HDA==D?B:\n+@HWI-ST132:678:C1LFKACXX:6:1215:11329:60877\n+GTAACACTTTGTAACGGATCGCAAA\n++\n+@@@DFFFFHHHGHIJJJEIIIIDII\n+@HWI-ST132:678:C1LFKACXX:6:1315:14171:25693\n+TTTCCGTCGACTAACAATAAGCCGT\n++\n+B@CFFFDDFHHHHJJIJJDHIIIJG\n+@HWI-ST132:678:C1LFKACXX:6:1311:11389:80627\n+AAAATGTCAGTCACTCAGCCAAAGG\n++\n+BBCFFFDF?FHHHJJJJJJJJJJJJ\n+@HWI-ST132:678:C1LFKACXX:6:2101:11947:88765\n+TCCTTTGGCTGAGTGACTGACATTT\n++\n+HEHCFHFFHCA2<<CHFDBDDF@@?\n+@HWI-ST132:678:C1LFKACXX:6:1208:6410:57476\n+CAAGGAGTCGGCAGCTGAAGTAGCA\n++\n+=@@DD?DDFF?)@FAH>FEFHHEHE\n+@HWI-ST132:678:C1LFKACXX:6:1105:9109:21614\n+TCGTACCGATCTAGACATCTCTTC\n++\n+GIJJJJJJIGJHHHGHD<FFD@@@\n' |
| b |
| diff -r 9645d995fb3c -r 9185ca0a7b43 test-data/fastq_dir/reads-sample-small.fastq-piRNAs-transcripts_uni.fastq --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/fastq_dir/reads-sample-small.fastq-piRNAs-transcripts_uni.fastq Wed Jan 16 08:18:13 2019 -0500 |
| b |
| b'@@ -0,0 +1,2568 @@\n+@HWI-ST132:678:C1LFKACXX:6:2107:14168:54674\n+TATCACTGTATGCGTAGAAAAGAG\n++\n+CCCFDFFFHHGDFFFHIJJJJJJJ\n+@HWI-ST132:678:C1LFKACXX:6:1210:20798:12533\n+TCTGCTATCACTGTATGCGTAGAAA\n++\n+@@@FDDDFHGHHGJIJIG@GCEFDB\n+@HWI-ST132:678:C1LFKACXX:6:1313:10358:95570\n+TAATATAGATTTAAAGTCTAAGAACT\n++\n+@@?B=DDDHHHHHJJJHIJIJJHIJJ\n+@HWI-ST132:678:C1LFKACXX:6:2108:18887:67124\n+TAATATAGATTTAAAGTCTAAGAACT\n++\n+BCCFFFFFGHHHH>GHFHJJJIGJJJ\n+@HWI-ST132:678:C1LFKACXX:6:1301:16563:56958\n+AAGGCAATGCAAAACAAGAATTT\n++\n+FAA3GHHBEIFHHFDDBDDB@@@\n+@HWI-ST132:678:C1LFKACXX:6:1107:12070:23186\n+TAGTATATTTATTAAATCATTTGACT\n++\n+CCCDDEFFHHHHHJJJJJAJJJIJJJ\n+@HWI-ST132:678:C1LFKACXX:6:1110:20211:14418\n+TAGTATATTTATTAAATCATTTGACT\n++\n+CCCFFFFFHHHHHJJJJJIJJJJJJJ\n+@HWI-ST132:678:C1LFKACXX:6:1116:13578:65370\n+TAGTATATTTATTAAATCATTTGACT\n++\n+@8?D=BDFGHHFHIJJJJFGIJIJIJ\n+@HWI-ST132:678:C1LFKACXX:6:2101:7667:91449\n+TAGTATATTTATTAAATCATTTGACT\n++\n+CCCDDEFFHHHHHJJJJJJJJIJJJJ\n+@HWI-ST132:678:C1LFKACXX:6:2107:12382:29561\n+TAGTATATTTATTAAATCATTTGACT\n++\n+CCCFFFFFHHHHHJJJJJJJJJJJJJ\n+@HWI-ST132:678:C1LFKACXX:6:2107:9787:36481\n+TAGTATATTTATTAAATCATTTGACT\n++\n+BBBD:ADDHHHHH4HGHIJJJJJJJJ\n+@HWI-ST132:678:C1LFKACXX:6:2102:14356:68993\n+TAATGTTACATCATATTAAGTCAAATGA\n++\n+JIJJIHIHJJJJJJJHHHFHFFFFFCCC\n+@HWI-ST132:678:C1LFKACXX:6:1107:18073:46755\n+AAATATTTCGCTTTTAAAAAATTG\n++\n+@@CFFFFFHHHGHJIJJBDAGIII\n+@HWI-ST132:678:C1LFKACXX:6:1302:10066:99383\n+AATATTTCGCTTTTAAAAAATTG\n++\n+BBBDFFFFH@FHHJJJIJGIIIJ\n+@HWI-ST132:678:C1LFKACXX:6:2103:9377:13404\n+TAAATTTGTTTGTTAAAATCGCCG\n++\n+CCCFFFFFHHHGHIJJJJJHIJJJ\n+@HWI-ST132:678:C1LFKACXX:6:1309:5142:10985\n+TTTAAATTTGTTTGTTAAAATCGCC\n++\n+BCCFDFFFHHHHHIJIJJJJIIIGH\n+@HWI-ST132:678:C1LFKACXX:6:1108:20386:47976\n+TAATAGTCAGGGCGCGAATTTTT\n++\n+?@?D;B=B?CAC:2<CFGHIIGI\n+@HWI-ST132:678:C1LFKACXX:6:1207:2583:92360\n+TAATAGTCAGGGCGCGAATTTTT\n++\n+B@CFFFDDHHDFFGFGHEGHIJI\n+@HWI-ST132:678:C1LFKACXX:6:1102:11267:71435\n+TAATAGTCAGGGCGCGAATTTTTA\n++\n+@@BFFDBDFHHDFIIHJBFFGIGG\n+@HWI-ST132:678:C1LFKACXX:6:1107:9710:51191\n+TAATAGTCAGGGCGCGAATTTTTA\n++\n+@@@FDF?DHHHDHFGHGGHGJJJJ\n+@HWI-ST132:678:C1LFKACXX:6:1108:5610:75509\n+TAATAGTCAGGGCGCGAATTTTTA\n++\n+BCCFFFFFFGHGG<DHGHGHIJJJ\n+@HWI-ST132:678:C1LFKACXX:6:1109:13565:15908\n+TAATAGTCAGGGCGCGAATTTTTA\n++\n+BCCFFFEFHHHCAFGHIIJJJJJJ\n+@HWI-ST132:678:C1LFKACXX:6:1109:11179:97926\n+TAATAGTCAGGGCGCGAATTTTTA\n++\n+@@@FDEBD<FH<DGGIIGGHGIII\n+@HWI-ST132:678:C1LFKACXX:6:1110:18682:30268\n+TAATAGTCAGGGCGCGAATTTTTA\n++\n+BCCFFFFFHHHFGIJJIHIIJJJJ\n+@HWI-ST132:678:C1LFKACXX:6:1114:13195:76362\n+TAATAGTCAGGGCGCGAATTTTTA\n++\n+?@?DDB=DFDDHGIIEBHD=FHIH\n+@HWI-ST132:678:C1LFKACXX:6:1201:9017:61055\n+TAATAGTCAGGGCGCGAATTTTTA\n++\n+BCCFDFFFHHFFH@BEEGIHJJJJ\n+@HWI-ST132:678:C1LFKACXX:6:1201:5418:63606\n+TAATAGTCAGGGCGCGAATTTTTA\n++\n+@@CFBDDEHHA<CFEFHIHIIIII\n+@HWI-ST132:678:C1LFKACXX:6:1213:8541:21411\n+TAATAGTCAGGGCGCGAATTTTTA\n++\n+@@CFFFDDHHFFFFGHIHIJJJII\n+@HWI-ST132:678:C1LFKACXX:6:1214:13791:80762\n+TAATAGTCAGGGCGCGAATTTTTA\n++\n+@@@FDDDDHFHDHIFII1DFHGGF\n+@HWI-ST132:678:C1LFKACXX:6:1309:8889:7362\n+TAATAGTCAGGGCGCGAATTTTTA\n++\n+@@CFFFFFDHHHHJIJJJHJJJJJ\n+@HWI-ST132:678:C1LFKACXX:6:1314:17898:28199\n+TAATAGTCAGGGCGCGAATTTTTA\n++\n+@??DFADDDHCHFFBGGEHIGJGI\n+@HWI-ST132:678:C1LFKACXX:6:2104:10515:36849\n+TAATAGTCAGGGCGCGAATTTTTA\n++\n+@CCFFFDFHHFHHJIJJJJJJJJJ\n+@HWI-ST132:678:C1LFKACXX:6:2105:6101:64627\n+TAATAGTCAGGGCGCGAATTTTTA\n++\n+@@@FFFFFHHD:C<@@@CGHIIII\n+@HWI-ST132:678:C1LFKACXX:6:2105:18687:69886\n+TAATAGTCAGGGCGCGAATTTTTA\n++\n+BCCFFFFEHHFFH@FHHIJJJJJJ\n+@HWI-ST132:678:C1LFKACXX:6:2106:16747:90974\n+TAATAGTCAGGGCGCGAATTTTTA\n++\n+B@@F?DBDHHHCC<EGIJJJJJJI\n+@HWI-ST132:678:C1LFKACXX:6:2108:1476:22607\n+TAATAGTCAGGGCGCGAATTTTTA\n++\n+CCCFFFFFHHHHFGHJHHHIJJJJ\n+@HWI-ST132:678:C1LFKACXX:6:1101:4401:62600\n+TAATAGTCAGGGCGCGAATTTTTAA\n++\n+@@@FFFDEHHBCFGGIEHGHIJJGH\n+@HWI-ST132:678:C1LFKACXX:6:1103:11719:61615\n+TAATAGTCAGGGCGCGAATTTTTAA\n++\n+@CCFFFFFDHFFHIJFEGHIIJJJI\n+@HWI-ST132:678:C1LFKACXX:6:1104:5727:21771\n+TAATAGTCAGGGCGCGAATTTTTAA\n++\n+CCCFFFFFHHHDFIIFHIJJJJJJJ\n+@HWI-ST132:678:C1LFKACXX:6:1105:18599:5567\n+TAATAGTCA'..b'TGTGAAGACGT\n++\n+HJJJJIIGE?CGHHHHHFFFFFCCC\n+@HWI-ST132:678:C1LFKACXX:6:1305:13291:74216\n+TTCGATCGCCGACGTGTGAAGACGT\n++\n+HJJIHGC?1:E@HHHHGFFFFFCCC\n+@HWI-ST132:678:C1LFKACXX:6:1305:14099:91760\n+TTCGATCGCCGACGTGTGAAGACGT\n++\n+GIGIIIEHFC?EHGHHGFFFFFCCC\n+@HWI-ST132:678:C1LFKACXX:6:1306:4852:79972\n+TTCGATCGCCGACGTGTGAAGACGT\n++\n+IJIIIGFC:?FJHHHHHFFFFFCCC\n+@HWI-ST132:678:C1LFKACXX:6:1306:14526:93144\n+TTCGATCGCCGACGTGTGAAGACGT\n++\n+IIIIIIHFC8EHHF<HFFFFFF@@@\n+@HWI-ST132:678:C1LFKACXX:6:1306:12830:100458\n+TTCGATCGCCGACGTGTGAAGACGT\n++\n+JJIIGIGHEE:CHHHFHFFFFF@@@\n+@HWI-ST132:678:C1LFKACXX:6:1307:3341:79302\n+TTCGATCGCCGACGTGTGAAGACGT\n++\n+IIIIHG<HEGHIHFFHHDDD=D@@@\n+@HWI-ST132:678:C1LFKACXX:6:1309:20666:8951\n+TTCGATCGCCGACGTGTGAAGACGT\n++\n+IIHCBD?C:C?EDDHHGFFFDF@@@\n+@HWI-ST132:678:C1LFKACXX:6:1310:20517:19080\n+TTCGATCGCCGACGTGTGAAGACGT\n++\n+FHGGGF?GGFEHHHFHGFFFFFCCC\n+@HWI-ST132:678:C1LFKACXX:6:1310:19552:89269\n+TTCGATCGCCGACGTGTGAAGACGT\n++\n+HJJIJJIHFCCHHGHHGFFFFFCCC\n+@HWI-ST132:678:C1LFKACXX:6:1310:11672:92080\n+TTCGATCGCCGACGTGTGAAGACGT\n++\n+IIJIHFGHHGHJHHHHHFFFDFCCC\n+@HWI-ST132:678:C1LFKACXX:6:1312:14124:76448\n+TTCGATCGCCGACGTGTGAAGACGT\n++\n+JJJIHGDHEHHJHHHHGFFEFF@C@\n+@HWI-ST132:678:C1LFKACXX:6:1313:16741:57946\n+TTCGATCGCCGACGTGTGAAGACGT\n++\n+AIIJJJIHFFGDHHHHHFFFDFCC@\n+@HWI-ST132:678:C1LFKACXX:6:1315:9373:25299\n+TTCGATCGCCGACGTGTGAAGACGT\n++\n+G>FDCC4;;EEIFDFDFDD=+D?@@\n+@HWI-ST132:678:C1LFKACXX:6:1315:12968:32460\n+TTCGATCGCCGACGTGTGAAGACGT\n++\n+BD9FGFFBF?GGF<FFFDDDB=1@@\n+@HWI-ST132:678:C1LFKACXX:6:2101:18316:34316\n+TTCGATCGCCGACGTGTGAAGACGT\n++\n+JJJJJJJIHHEIHHFHHFFEDFCCB\n+@HWI-ST132:678:C1LFKACXX:6:2101:18438:36839\n+TTCGATCGCCGACGTGTGAAGACGT\n++\n+IJJJJJJHGG?HHHDHHFFDDFCCB\n+@HWI-ST132:678:C1LFKACXX:6:2101:14608:56807\n+TTCGATCGCCGACGTGTGAAGACGT\n++\n+JJJJJIHHHFIIHHHHHFFFDDBCB\n+@HWI-ST132:678:C1LFKACXX:6:2103:7602:64596\n+TTCGATCGCCGACGTGTGAAGACGT\n++\n+GHIIHFBC??:@FCCDF@+A;D??=\n+@HWI-ST132:678:C1LFKACXX:6:2103:17863:69050\n+TTCGATCGCCGACGTGTGAAGACGT\n++\n+GIJJJJIIHFGIHFHHHFFFFFCCB\n+@HWI-ST132:678:C1LFKACXX:6:2104:5137:4251\n+TTCGATCGCCGACGTGTGAAGACGT\n++\n+IJJIJJIHEHHJHHDHGFFEFFCCB\n+@HWI-ST132:678:C1LFKACXX:6:2104:20272:16658\n+TTCGATCGCCGACGTGTGAAGACGT\n++\n+HJJJJJJIHHJIHHHHHFFFFFCCC\n+@HWI-ST132:678:C1LFKACXX:6:2104:8336:35547\n+TTCGATCGCCGACGTGTGAAGACGT\n++\n+IJJJIHHDC?C@F@@HGFFFFD@B=\n+@HWI-ST132:678:C1LFKACXX:6:2104:17454:68818\n+TTCGATCGCCGACGTGTGAAGACGT\n++\n+IJJJIIHFEIIIHHHHHFFFBFCCC\n+@HWI-ST132:678:C1LFKACXX:6:2105:8348:83371\n+TTCGATCGCCGACGTGTGAAGACGT\n++\n+DIGJIFD?1@@C<0@HHDFFDD??:\n+@HWI-ST132:678:C1LFKACXX:6:2105:19893:91541\n+TTCGATCGCCGACGTGTGAAGACGT\n++\n+?HEGHC4HFHG@HFDHHDDD=D@@@\n+@HWI-ST132:678:C1LFKACXX:6:2106:6481:37891\n+TTCGATCGCCGACGTGTGAAGACGT\n++\n+HJJJJJJHIIHIHFHHHFFFFF@CC\n+@HWI-ST132:678:C1LFKACXX:6:2106:15957:78129\n+TTCGATCGCCGACGTGTGAAGACGT\n++\n+HJJJJJJHIHIJHHHHHFFFFFBCC\n+@HWI-ST132:678:C1LFKACXX:6:2107:12188:11374\n+TTCGATCGCCGACGTGTGAAGACGT\n++\n+FJJIIIGD?FCGHHHHHDDB?FCBB\n+@HWI-ST132:678:C1LFKACXX:6:2108:18380:53781\n+TTCGATCGCCGACGTGTGAAGACGT\n++\n+JJJJIHF?114C@@CHHFFFFFBB=\n+@HWI-ST132:678:C1LFKACXX:6:1208:16812:100651\n+TTCGATCGCCGACGTGTGAAGACG\n++\n+IIIGC<HGGFGHHHHHFFEBFCCC\n+@HWI-ST132:678:C1LFKACXX:6:1103:13690:62133\n+ATTCGATCGCCGACGTGTGAAGACG\n++\n+JJIHGGCGIGJJGHHHHFFFFFCCB\n+@HWI-ST132:678:C1LFKACXX:6:1109:8695:89867\n+TTCGATCGCCGACGTGTGAAGAC\n++\n+JJHIGHEGFIHHHHHFFFFFCCC\n+@HWI-ST132:678:C1LFKACXX:6:2103:4519:3225\n+TGCAAGCTAAGAATTCCGAAACGCC\n++\n+JJIJJJJJJIHFCAC:HDA==D?B:\n+@HWI-ST132:678:C1LFKACXX:6:1215:11329:60877\n+GTAACACTTTGTAACGGATCGCAAA\n++\n+@@@DFFFFHHHGHIJJJEIIIIDII\n+@HWI-ST132:678:C1LFKACXX:6:1315:14171:25693\n+TTTCCGTCGACTAACAATAAGCCGT\n++\n+B@CFFFDDFHHHHJJIJJDHIIIJG\n+@HWI-ST132:678:C1LFKACXX:6:1311:11389:80627\n+AAAATGTCAGTCACTCAGCCAAAGG\n++\n+BBCFFFDF?FHHHJJJJJJJJJJJJ\n+@HWI-ST132:678:C1LFKACXX:6:2101:11947:88765\n+TCCTTTGGCTGAGTGACTGACATTT\n++\n+HEHCFHFFHCA2<<CHFDBDDF@@?\n+@HWI-ST132:678:C1LFKACXX:6:1208:6410:57476\n+CAAGGAGTCGGCAGCTGAAGTAGCA\n++\n+=@@DD?DDFF?)@FAH>FEFHHEHE\n+@HWI-ST132:678:C1LFKACXX:6:1105:9109:21614\n+TCGTACCGATCTAGACATCTCTTC\n++\n+GIJJJJJJIGJHHHGHD<FFD@@@\n' |
| b |
| diff -r 9645d995fb3c -r 9185ca0a7b43 test-data/fastq_dir/reads-sample-small.fastq-siRNAs-TEs.fastq --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/fastq_dir/reads-sample-small.fastq-siRNAs-TEs.fastq Wed Jan 16 08:18:13 2019 -0500 |
| b |
| b'@@ -0,0 +1,9068 @@\n+@HWI-ST132:678:C1LFKACXX:6:2103:3486:88354\n+CTTTAATTATCATATATTGTA\n++\n+BBBD;=ABFHHHHJJJJJDJI\n+@HWI-ST132:678:C1LFKACXX:6:1304:3965:45774\n+TTAAACTGTGAATTAAGCGCG\n++\n+JGHJJJJJHHHFCFFFFF@CB\n+@HWI-ST132:678:C1LFKACXX:6:1112:13388:37433\n+TGTGGAGTCCTGTTGATCATT\n++\n+IJIJJJJIHDHHHDFFFF@C@\n+@HWI-ST132:678:C1LFKACXX:6:1103:5248:79079\n+ACAGCGAATTGATCGGATTGC\n++\n+CCIHIJJIHHHDHDDAFD@@@\n+@HWI-ST132:678:C1LFKACXX:6:1104:11153:32804\n+TTCCGAATTGTCTGCACTGGT\n++\n+CCCFFFFFHGHHHHFIIJJIH\n+@HWI-ST132:678:C1LFKACXX:6:1211:17694:10783\n+TTCCGAATTGTCTGCACTGGT\n++\n+CCCFFFFFHHFFHIJHHIJJH\n+@HWI-ST132:678:C1LFKACXX:6:1301:12823:86928\n+TTCCGAATTGTCTGCACTGGT\n++\n+:=?DDF:22<<DFGIBEGHIC\n+@HWI-ST132:678:C1LFKACXX:6:1315:17545:15989\n+CCCCTGATCAAACATCGTCTG\n++\n+B@BDFFDFHHHHHJJJJIIJJ\n+@HWI-ST132:678:C1LFKACXX:6:1216:10870:15777\n+TAATACAATACATCAGACGAT\n++\n+EEHFBIHIGHHDHDDB=4+??\n+@HWI-ST132:678:C1LFKACXX:6:2106:19483:23767\n+AAGACTTCGGAGTTAAGTATC\n++\n+IHHHJIHE>DHHHFFFFFCCC\n+@HWI-ST132:678:C1LFKACXX:6:1202:19924:85837\n+TACATACCTGGGAAGACTTCG\n++\n+JJIIIHEHHBFHHFFFFFCCC\n+@HWI-ST132:678:C1LFKACXX:6:2107:16400:98713\n+TTCTGGGAATTCCGAAGATGG\n++\n+JJJHHGEAHHHHHFFFFFCCC\n+@HWI-ST132:678:C1LFKACXX:6:1306:12648:89258\n+ATAAACTGTCTGACAGGGACC\n++\n+CCCFFFFFHHHBHIIGHIJJJ\n+@HWI-ST132:678:C1LFKACXX:6:1204:10596:80793\n+TACCTATGTCGATTGCCACCT\n++\n+GIIIHGHGF?A??DDDDD?@?\n+@HWI-ST132:678:C1LFKACXX:6:2106:14268:13093\n+AAGGCAATGATTGTTGAGGGC\n++\n+4==DBD+42>CFHHJGIJJJI\n+@HWI-ST132:678:C1LFKACXX:6:1205:15169:28150\n+TGACTTGGCCTCTGTGCGCAC\n++\n+CCCFFFEFHHHHHJHHHHIIJ\n+@HWI-ST132:678:C1LFKACXX:6:2109:6872:55506\n+CAATGACTTGGCCTCTGTGCG\n++\n+BB@DDEFFHHHGHJJJIGEHH\n+@HWI-ST132:678:C1LFKACXX:6:2108:12752:15836\n+CAGAGGCCAAGTCATTGAGCG\n++\n+FA+IIIIIHHHHHFDFFFC@@\n+@HWI-ST132:678:C1LFKACXX:6:1115:4388:39138\n+CGGCGCTCAATGACTTGGCCT\n++\n+@CCAFFFFHDHHHIIIIIIIH\n+@HWI-ST132:678:C1LFKACXX:6:2107:13841:82210\n+AGCGGCGCTCAATGACTTGGC\n++\n+CCCFDFFFHHHHHEGHJJCC?\n+@HWI-ST132:678:C1LFKACXX:6:2103:11417:67112\n+CAAGTCATTGAGCGCCGCTTC\n++\n+JJIIHFB2ACHHHFFFDFCCB\n+@HWI-ST132:678:C1LFKACXX:6:1205:15296:60784\n+GTCATTGAGCGCCGCTTCCAG\n++\n+JIIJIJIJHHFHHEBFFFB@B\n+@HWI-ST132:678:C1LFKACXX:6:2106:12781:78894\n+TCATTGAGCGCCGCTTCCAGG\n++\n+JJJJJJJIHHHHHFFFFFCCC\n+@HWI-ST132:678:C1LFKACXX:6:1213:6801:56774\n+TAAGAGCGACCTGGAAGCGGC\n++\n+CCCFFFFFDHHHHIIJJJJIH\n+@HWI-ST132:678:C1LFKACXX:6:2109:11200:65312\n+TCCAGGTCGCTCTTAAACTTG\n++\n+IIIGC,IIHHHD@DDDDD@@@\n+@HWI-ST132:678:C1LFKACXX:6:1201:10525:92672\n+GTCGCTCTTAAACTTGGGAAC\n++\n+HFJIHDHHHHFBHFFFFDBBB\n+@HWI-ST132:678:C1LFKACXX:6:1204:20435:17195\n+GGGGAAAGTTTCGGAAAGCGT\n++\n+BCCFFFFFFHHGHJIIJJJJG\n+@HWI-ST132:678:C1LFKACXX:6:2109:17802:67038\n+TAGAACTCAGCAAGGTGAGCT\n++\n+CCCFFFFFGHHHHFHCGIEHI\n+@HWI-ST132:678:C1LFKACXX:6:1301:15212:7880\n+TTTTGCGTACGTGGCTGCCCA\n++\n+JJJHGJIHDCFHHDFFFFCC@\n+@HWI-ST132:678:C1LFKACXX:6:1203:17614:29016\n+TTTGCGTACGTGGCTGCCCAG\n++\n+JIJJJJIHHFCHHDDFFDC@@\n+@HWI-ST132:678:C1LFKACXX:6:1312:6743:61160\n+GCTAAGATCGGACACGAGCCT\n++\n+@@BDDDFFFHHHHJIJJJIJJ\n+@HWI-ST132:678:C1LFKACXX:6:1306:10877:43166\n+CTCGTGTCCGATCTTAGCTTC\n++\n+IIHGGJJJHHFFHFDDDF@@@\n+@HWI-ST132:678:C1LFKACXX:6:1114:20246:58873\n+CAGATGCGTAGCTGCCTGGCT\n++\n+GIHEGIIIHGGHGFFDB=1<?\n+@HWI-ST132:678:C1LFKACXX:6:1210:1131:47701\n+CAGATGCGTAGCTGCCTGGCT\n++\n+BFAHEGH>HD>FHDDDDD@@@\n+@HWI-ST132:678:C1LFKACXX:6:1205:8301:45085\n+ACATTCGAGACTCAACGGCGC\n++\n+??@DFFFFH;CAC<FFHGB@F\n+@HWI-ST132:678:C1LFKACXX:6:1114:18437:39882\n+CTTTAGGTCCTCATTCTGGAG\n++\n+E?<CEFA4?FC=222244114\n+@HWI-ST132:678:C1LFKACXX:6:2103:20767:66007\n+TTCTGACTTGTCGCGGTGGTA\n++\n+E:C@2@FJHHDGHFFFFFCCC\n+@HWI-ST132:678:C1LFKACXX:6:2108:6048:16581\n+TTCTGACTTGTCGCGGTGGTA\n++\n+C:<<2<AGHHFHHFFFFFCCC\n+@HWI-ST132:678:C1LFKACXX:6:2109:18810:55523\n+TTGACTAGCGACTGCAGTGCT\n++\n+CCCFFFFFGFHHHJEGHHCHH\n+@HWI-ST132:678:C1LFKACXX:6:1212:19203:63197\n+CCTGAACGGGTCGTTGCGATC\n++\n+JJHGEEIHHFDHGFEDDF@@@\n+@HWI-ST132:678:C1LFKACXX:6:1311:7177:19732\n+CCCCTGATCGCAACGACCCGT\n++\n+@@@DDDD>FAFDDH1ACAGG:\n+@HWI-ST132:678:C1LFKACXX:6:1101:11100:95584\n+TCGAACGGTTGATCTGGCAAC\n++\n+JJJJJJJIHF?HFFFFFFCCB\n+@HWI-ST132:678:C1LFKACXX:6:1103:11021:88518'..b'CXX:6:2107:9456:8227\n+TGACGAGGCAGAGCGGGCTGC\n++\n+JIHIHF@IHHHHGFFFFFCCC\n+@HWI-ST132:678:C1LFKACXX:6:2108:6680:6448\n+TGACGAGGCAGAGCGGGCTGC\n++\n+IHGB:2@GHHHHHFFFFFCCC\n+@HWI-ST132:678:C1LFKACXX:6:2109:16435:34131\n+TGACGAGGCAGAGCGGGCTGC\n++\n+HGH@:@JIHHHHGFFFFFCCC\n+@HWI-ST132:678:C1LFKACXX:6:1307:1328:76760\n+GACGAGGCAGAGCGGGCTGCC\n++\n+GHF@<:IHHGGHHFFDDFC@@\n+@HWI-ST132:678:C1LFKACXX:6:2105:10714:3663\n+CAGAGCGGGCTGCCGGTCCCT\n++\n+JJJIIHJJHHHHHFFFFD@@B\n+@HWI-ST132:678:C1LFKACXX:6:2106:6452:10486\n+CAGAGCGGGCTGCCGGTCCCT\n++\n+IIIHHDIHHDD@)FFFFFC@@\n+@HWI-ST132:678:C1LFKACXX:6:2107:13837:84657\n+CAGAGCGGGCTGCCGGTCCCT\n++\n+JJIHFIHIHHHHHFFFFF@CB\n+@HWI-ST132:678:C1LFKACXX:6:1104:19315:94114\n+AGAGCGGGCTGCCGGTCCCTC\n++\n+JJJJIHGJGHHHGFFDBF@C@\n+@HWI-ST132:678:C1LFKACXX:6:1104:7430:21922\n+GCGGGCTGCCGGTCCCTCTCC\n++\n+JIJIIIHC<<DFHAFDFFC@@\n+@HWI-ST132:678:C1LFKACXX:6:1307:14679:35813\n+GCGGGCTGCCGGTCCCTCTCC\n++\n+JIJJJIHF@@FHHFFFFFC@B\n+@HWI-ST132:678:C1LFKACXX:6:1313:2242:53030\n+GCGGGCTGCCGGTCCCTCTCC\n++\n+HIHGGHHGCHDFGDDDFD@?=\n+@HWI-ST132:678:C1LFKACXX:6:2108:20023:78881\n+ACAACAGCTGGAGAGGGACCG\n++\n+BCCFFFFFHHDFFHGGCEGIJ\n+@HWI-ST132:678:C1LFKACXX:6:1116:19637:62229\n+CCTCTCCAGCTGTTGTTGTTG\n++\n+FHJIJJJIHGHHHFFDBA11+\n+@HWI-ST132:678:C1LFKACXX:6:1304:17194:95501\n+TACCTCCAACAACAACAGCTG\n++\n+BCCFFFFFFHHFHJFIJIIIJ\n+@HWI-ST132:678:C1LFKACXX:6:1205:5151:98200\n+TGTTGTTGTTGGAGGTAGCGG\n++\n+<<GFA<IGDFCHHFFFFFBBB\n+@HWI-ST132:678:C1LFKACXX:6:1209:9824:17749\n+TGTTGTTGTTGGAGGTAGCGG\n++\n+IHFE<3HFAFCHFFFFFFB@?\n+@HWI-ST132:678:C1LFKACXX:6:1111:15377:25850\n+TGTTGTTGGAGGTAGCGGGGC\n++\n+IIIGFA222FCFFFFEFF@@@\n+@HWI-ST132:678:C1LFKACXX:6:1215:3469:66547\n+TGTTGTTGGAGGTAGCGGGGC\n++\n+GGGIIIHE<GHHHFDD=D@C@\n+@HWI-ST132:678:C1LFKACXX:6:1215:3511:69906\n+TGTTGTTGGAGGTAGCGGGGC\n++\n+GGJGHGC?<FFFFDDDDD@@@\n+@HWI-ST132:678:C1LFKACXX:6:1302:9816:51867\n+TGTTGTTGGAGGTAGCGGGGC\n++\n+JJJIHGGACDHHHEDBDFCB@\n+@HWI-ST132:678:C1LFKACXX:6:1111:14307:12122\n+TAGCGGGGCTTCTGTCGGAGC\n++\n+IHGGHFBHFD?HHFDFFF@@@\n+@HWI-ST132:678:C1LFKACXX:6:1212:7672:92273\n+TAGCGGGGCTTCTGTCGGAGC\n++\n+GBIGHD?GFBFFAD?DDD@@@\n+@HWI-ST132:678:C1LFKACXX:6:1315:17800:56780\n+TCTGTCGGAGCCAATAGAGCG\n++\n+BEHCGEDFFDF?@==A4D8@?\n+@HWI-ST132:678:C1LFKACXX:6:1211:8820:25669\n+TCGGAGCCAATAGAGCGGGAG\n++\n+C?AIGC24FFCACDD@AB@@=\n+@HWI-ST132:678:C1LFKACXX:6:1107:4152:41817\n+CAACAAATCAAGAAAGAGCCC\n++\n+CCCFFFFFHHHHHHHIJIIIJ\n+@HWI-ST132:678:C1LFKACXX:6:1107:13749:41003\n+TGATTTGTTGGTAGAAGAAGG\n++\n+JJJIJJIGFFFHHFFFFFCCB\n+@HWI-ST132:678:C1LFKACXX:6:1112:7021:46842\n+TGATTTGTTGGTAGAAGAAGG\n++\n+JIGHHFGGHFHHFDFFFF@@B\n+@HWI-ST132:678:C1LFKACXX:6:2106:12928:28648\n+TGATTTGTTGGTAGAAGAAGG\n++\n+GGHEE<<+A3<DHDFFDD@?=\n+@HWI-ST132:678:C1LFKACXX:6:2107:17571:56192\n+TGATTTGTTGGTAGAAGAAGG\n++\n+JIHE<,A<23<HHFFFDD=:1\n+@HWI-ST132:678:C1LFKACXX:6:1104:18932:34578\n+GCTATGGGTTATTGACCGCTC\n++\n+JJJIHFE?GHFFFFFEDF@@@\n+@HWI-ST132:678:C1LFKACXX:6:1202:4878:86481\n+TGCGTTTGGGATTGTCGGTGA\n++\n+IHDJIHFHHGHHDFFFFFCCB\n+@HWI-ST132:678:C1LFKACXX:6:1115:14400:83897\n+TTTGGGATTGTCGGTGAGACG\n++\n+IHHFGGEGDFAFFBFDFD@?@\n+@HWI-ST132:678:C1LFKACXX:6:1213:16820:54984\n+TTGTCGGTGAGACGTAGGAGA\n++\n+IJIIGBFHFDFFFDFFFFCCB\n+@HWI-ST132:678:C1LFKACXX:6:1106:4136:80459\n+TAGGAGAAGTACGCGTTGTTG\n++\n+CDEE<<)EDDDDDD?A4D???\n+@HWI-ST132:678:C1LFKACXX:6:1108:12282:61422\n+TAGGAGAAGTACGCGTTGTTG\n++\n+JIIJJIJJHHFAFFDEDFCBB\n+@HWI-ST132:678:C1LFKACXX:6:1111:13707:90938\n+TAGGAGAAGTACGCGTTGTTG\n++\n+JJIHF@@JHFC<CFDDAF@@?\n+@HWI-ST132:678:C1LFKACXX:6:1314:12461:28557\n+TAGGAGAAGTACGCGTTGTTG\n++\n+JJHIHGHJGHFDHFDFFFC@B\n+@HWI-ST132:678:C1LFKACXX:6:2106:10137:48564\n+TAGGAGAAGTACGCGTTGTTG\n++\n+JJJJHHIIHHFFHFFFFFCCB\n+@HWI-ST132:678:C1LFKACXX:6:2109:19752:91497\n+TAGGAGAAGTACGCGTTGTTG\n++\n+GCHIIIEGHFFFHDDBD?@@@\n+@HWI-ST132:678:C1LFKACXX:6:1215:19556:9898\n+GAAGTACGCGTTGTTGCGCTG\n++\n+IIIIIIIIHFHHFDA2441+:\n+@HWI-ST132:678:C1LFKACXX:6:1208:16914:37703\n+TGTTGCGCTGAATTGAGAGTC\n++\n+HEGHFF<GFF6GHFFFFFC@@\n+@HWI-ST132:678:C1LFKACXX:6:2103:12622:49391\n+TGTTGCGCTGAATTGAGAGTC\n++\n+HAHJJJJJHHHHHFFFFFCCC\n+@HWI-ST132:678:C1LFKACXX:6:1104:12986:68120\n+TTGCGCTGAATTGAGAGTCGG\n++\n+IGHEGC2+FFF<FDDDDD@@@\n' |
| b |
| diff -r 9645d995fb3c -r 9185ca0a7b43 test-data/fastq_dir/reads-sample-small.fastq-siRNAs-TEs_uni.fastq --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/fastq_dir/reads-sample-small.fastq-siRNAs-TEs_uni.fastq Wed Jan 16 08:18:13 2019 -0500 |
| b |
| b'@@ -0,0 +1,9068 @@\n+@HWI-ST132:678:C1LFKACXX:6:2103:3486:88354\n+CTTTAATTATCATATATTGTA\n++\n+BBBD;=ABFHHHHJJJJJDJI\n+@HWI-ST132:678:C1LFKACXX:6:1304:3965:45774\n+TTAAACTGTGAATTAAGCGCG\n++\n+JGHJJJJJHHHFCFFFFF@CB\n+@HWI-ST132:678:C1LFKACXX:6:1112:13388:37433\n+TGTGGAGTCCTGTTGATCATT\n++\n+IJIJJJJIHDHHHDFFFF@C@\n+@HWI-ST132:678:C1LFKACXX:6:1103:5248:79079\n+ACAGCGAATTGATCGGATTGC\n++\n+CCIHIJJIHHHDHDDAFD@@@\n+@HWI-ST132:678:C1LFKACXX:6:1104:11153:32804\n+TTCCGAATTGTCTGCACTGGT\n++\n+CCCFFFFFHGHHHHFIIJJIH\n+@HWI-ST132:678:C1LFKACXX:6:1211:17694:10783\n+TTCCGAATTGTCTGCACTGGT\n++\n+CCCFFFFFHHFFHIJHHIJJH\n+@HWI-ST132:678:C1LFKACXX:6:1301:12823:86928\n+TTCCGAATTGTCTGCACTGGT\n++\n+:=?DDF:22<<DFGIBEGHIC\n+@HWI-ST132:678:C1LFKACXX:6:1315:17545:15989\n+CCCCTGATCAAACATCGTCTG\n++\n+B@BDFFDFHHHHHJJJJIIJJ\n+@HWI-ST132:678:C1LFKACXX:6:1216:10870:15777\n+TAATACAATACATCAGACGAT\n++\n+EEHFBIHIGHHDHDDB=4+??\n+@HWI-ST132:678:C1LFKACXX:6:2106:19483:23767\n+AAGACTTCGGAGTTAAGTATC\n++\n+IHHHJIHE>DHHHFFFFFCCC\n+@HWI-ST132:678:C1LFKACXX:6:1202:19924:85837\n+TACATACCTGGGAAGACTTCG\n++\n+JJIIIHEHHBFHHFFFFFCCC\n+@HWI-ST132:678:C1LFKACXX:6:2107:16400:98713\n+TTCTGGGAATTCCGAAGATGG\n++\n+JJJHHGEAHHHHHFFFFFCCC\n+@HWI-ST132:678:C1LFKACXX:6:1306:12648:89258\n+ATAAACTGTCTGACAGGGACC\n++\n+CCCFFFFFHHHBHIIGHIJJJ\n+@HWI-ST132:678:C1LFKACXX:6:1204:10596:80793\n+TACCTATGTCGATTGCCACCT\n++\n+GIIIHGHGF?A??DDDDD?@?\n+@HWI-ST132:678:C1LFKACXX:6:2106:14268:13093\n+AAGGCAATGATTGTTGAGGGC\n++\n+4==DBD+42>CFHHJGIJJJI\n+@HWI-ST132:678:C1LFKACXX:6:1205:15169:28150\n+TGACTTGGCCTCTGTGCGCAC\n++\n+CCCFFFEFHHHHHJHHHHIIJ\n+@HWI-ST132:678:C1LFKACXX:6:2109:6872:55506\n+CAATGACTTGGCCTCTGTGCG\n++\n+BB@DDEFFHHHGHJJJIGEHH\n+@HWI-ST132:678:C1LFKACXX:6:2108:12752:15836\n+CAGAGGCCAAGTCATTGAGCG\n++\n+FA+IIIIIHHHHHFDFFFC@@\n+@HWI-ST132:678:C1LFKACXX:6:1115:4388:39138\n+CGGCGCTCAATGACTTGGCCT\n++\n+@CCAFFFFHDHHHIIIIIIIH\n+@HWI-ST132:678:C1LFKACXX:6:2107:13841:82210\n+AGCGGCGCTCAATGACTTGGC\n++\n+CCCFDFFFHHHHHEGHJJCC?\n+@HWI-ST132:678:C1LFKACXX:6:2103:11417:67112\n+CAAGTCATTGAGCGCCGCTTC\n++\n+JJIIHFB2ACHHHFFFDFCCB\n+@HWI-ST132:678:C1LFKACXX:6:1205:15296:60784\n+GTCATTGAGCGCCGCTTCCAG\n++\n+JIIJIJIJHHFHHEBFFFB@B\n+@HWI-ST132:678:C1LFKACXX:6:2106:12781:78894\n+TCATTGAGCGCCGCTTCCAGG\n++\n+JJJJJJJIHHHHHFFFFFCCC\n+@HWI-ST132:678:C1LFKACXX:6:1213:6801:56774\n+TAAGAGCGACCTGGAAGCGGC\n++\n+CCCFFFFFDHHHHIIJJJJIH\n+@HWI-ST132:678:C1LFKACXX:6:2109:11200:65312\n+TCCAGGTCGCTCTTAAACTTG\n++\n+IIIGC,IIHHHD@DDDDD@@@\n+@HWI-ST132:678:C1LFKACXX:6:1201:10525:92672\n+GTCGCTCTTAAACTTGGGAAC\n++\n+HFJIHDHHHHFBHFFFFDBBB\n+@HWI-ST132:678:C1LFKACXX:6:1204:20435:17195\n+GGGGAAAGTTTCGGAAAGCGT\n++\n+BCCFFFFFFHHGHJIIJJJJG\n+@HWI-ST132:678:C1LFKACXX:6:2109:17802:67038\n+TAGAACTCAGCAAGGTGAGCT\n++\n+CCCFFFFFGHHHHFHCGIEHI\n+@HWI-ST132:678:C1LFKACXX:6:1301:15212:7880\n+TTTTGCGTACGTGGCTGCCCA\n++\n+JJJHGJIHDCFHHDFFFFCC@\n+@HWI-ST132:678:C1LFKACXX:6:1203:17614:29016\n+TTTGCGTACGTGGCTGCCCAG\n++\n+JIJJJJIHHFCHHDDFFDC@@\n+@HWI-ST132:678:C1LFKACXX:6:1312:6743:61160\n+GCTAAGATCGGACACGAGCCT\n++\n+@@BDDDFFFHHHHJIJJJIJJ\n+@HWI-ST132:678:C1LFKACXX:6:1306:10877:43166\n+CTCGTGTCCGATCTTAGCTTC\n++\n+IIHGGJJJHHFFHFDDDF@@@\n+@HWI-ST132:678:C1LFKACXX:6:1114:20246:58873\n+CAGATGCGTAGCTGCCTGGCT\n++\n+GIHEGIIIHGGHGFFDB=1<?\n+@HWI-ST132:678:C1LFKACXX:6:1210:1131:47701\n+CAGATGCGTAGCTGCCTGGCT\n++\n+BFAHEGH>HD>FHDDDDD@@@\n+@HWI-ST132:678:C1LFKACXX:6:1205:8301:45085\n+ACATTCGAGACTCAACGGCGC\n++\n+??@DFFFFH;CAC<FFHGB@F\n+@HWI-ST132:678:C1LFKACXX:6:1114:18437:39882\n+CTTTAGGTCCTCATTCTGGAG\n++\n+E?<CEFA4?FC=222244114\n+@HWI-ST132:678:C1LFKACXX:6:2103:20767:66007\n+TTCTGACTTGTCGCGGTGGTA\n++\n+E:C@2@FJHHDGHFFFFFCCC\n+@HWI-ST132:678:C1LFKACXX:6:2108:6048:16581\n+TTCTGACTTGTCGCGGTGGTA\n++\n+C:<<2<AGHHFHHFFFFFCCC\n+@HWI-ST132:678:C1LFKACXX:6:2109:18810:55523\n+TTGACTAGCGACTGCAGTGCT\n++\n+CCCFFFFFGFHHHJEGHHCHH\n+@HWI-ST132:678:C1LFKACXX:6:1212:19203:63197\n+CCTGAACGGGTCGTTGCGATC\n++\n+JJHGEEIHHFDHGFEDDF@@@\n+@HWI-ST132:678:C1LFKACXX:6:1311:7177:19732\n+CCCCTGATCGCAACGACCCGT\n++\n+@@@DDDD>FAFDDH1ACAGG:\n+@HWI-ST132:678:C1LFKACXX:6:1101:11100:95584\n+TCGAACGGTTGATCTGGCAAC\n++\n+JJJJJJJIHF?HFFFFFFCCB\n+@HWI-ST132:678:C1LFKACXX:6:1103:11021:88518'..b'CXX:6:2107:9456:8227\n+TGACGAGGCAGAGCGGGCTGC\n++\n+JIHIHF@IHHHHGFFFFFCCC\n+@HWI-ST132:678:C1LFKACXX:6:2108:6680:6448\n+TGACGAGGCAGAGCGGGCTGC\n++\n+IHGB:2@GHHHHHFFFFFCCC\n+@HWI-ST132:678:C1LFKACXX:6:2109:16435:34131\n+TGACGAGGCAGAGCGGGCTGC\n++\n+HGH@:@JIHHHHGFFFFFCCC\n+@HWI-ST132:678:C1LFKACXX:6:1307:1328:76760\n+GACGAGGCAGAGCGGGCTGCC\n++\n+GHF@<:IHHGGHHFFDDFC@@\n+@HWI-ST132:678:C1LFKACXX:6:2105:10714:3663\n+CAGAGCGGGCTGCCGGTCCCT\n++\n+JJJIIHJJHHHHHFFFFD@@B\n+@HWI-ST132:678:C1LFKACXX:6:2106:6452:10486\n+CAGAGCGGGCTGCCGGTCCCT\n++\n+IIIHHDIHHDD@)FFFFFC@@\n+@HWI-ST132:678:C1LFKACXX:6:2107:13837:84657\n+CAGAGCGGGCTGCCGGTCCCT\n++\n+JJIHFIHIHHHHHFFFFF@CB\n+@HWI-ST132:678:C1LFKACXX:6:1104:19315:94114\n+AGAGCGGGCTGCCGGTCCCTC\n++\n+JJJJIHGJGHHHGFFDBF@C@\n+@HWI-ST132:678:C1LFKACXX:6:1104:7430:21922\n+GCGGGCTGCCGGTCCCTCTCC\n++\n+JIJIIIHC<<DFHAFDFFC@@\n+@HWI-ST132:678:C1LFKACXX:6:1307:14679:35813\n+GCGGGCTGCCGGTCCCTCTCC\n++\n+JIJJJIHF@@FHHFFFFFC@B\n+@HWI-ST132:678:C1LFKACXX:6:1313:2242:53030\n+GCGGGCTGCCGGTCCCTCTCC\n++\n+HIHGGHHGCHDFGDDDFD@?=\n+@HWI-ST132:678:C1LFKACXX:6:2108:20023:78881\n+ACAACAGCTGGAGAGGGACCG\n++\n+BCCFFFFFHHDFFHGGCEGIJ\n+@HWI-ST132:678:C1LFKACXX:6:1116:19637:62229\n+CCTCTCCAGCTGTTGTTGTTG\n++\n+FHJIJJJIHGHHHFFDBA11+\n+@HWI-ST132:678:C1LFKACXX:6:1304:17194:95501\n+TACCTCCAACAACAACAGCTG\n++\n+BCCFFFFFFHHFHJFIJIIIJ\n+@HWI-ST132:678:C1LFKACXX:6:1205:5151:98200\n+TGTTGTTGTTGGAGGTAGCGG\n++\n+<<GFA<IGDFCHHFFFFFBBB\n+@HWI-ST132:678:C1LFKACXX:6:1209:9824:17749\n+TGTTGTTGTTGGAGGTAGCGG\n++\n+IHFE<3HFAFCHFFFFFFB@?\n+@HWI-ST132:678:C1LFKACXX:6:1111:15377:25850\n+TGTTGTTGGAGGTAGCGGGGC\n++\n+IIIGFA222FCFFFFEFF@@@\n+@HWI-ST132:678:C1LFKACXX:6:1215:3469:66547\n+TGTTGTTGGAGGTAGCGGGGC\n++\n+GGGIIIHE<GHHHFDD=D@C@\n+@HWI-ST132:678:C1LFKACXX:6:1215:3511:69906\n+TGTTGTTGGAGGTAGCGGGGC\n++\n+GGJGHGC?<FFFFDDDDD@@@\n+@HWI-ST132:678:C1LFKACXX:6:1302:9816:51867\n+TGTTGTTGGAGGTAGCGGGGC\n++\n+JJJIHGGACDHHHEDBDFCB@\n+@HWI-ST132:678:C1LFKACXX:6:1111:14307:12122\n+TAGCGGGGCTTCTGTCGGAGC\n++\n+IHGGHFBHFD?HHFDFFF@@@\n+@HWI-ST132:678:C1LFKACXX:6:1212:7672:92273\n+TAGCGGGGCTTCTGTCGGAGC\n++\n+GBIGHD?GFBFFAD?DDD@@@\n+@HWI-ST132:678:C1LFKACXX:6:1315:17800:56780\n+TCTGTCGGAGCCAATAGAGCG\n++\n+BEHCGEDFFDF?@==A4D8@?\n+@HWI-ST132:678:C1LFKACXX:6:1211:8820:25669\n+TCGGAGCCAATAGAGCGGGAG\n++\n+C?AIGC24FFCACDD@AB@@=\n+@HWI-ST132:678:C1LFKACXX:6:1107:4152:41817\n+CAACAAATCAAGAAAGAGCCC\n++\n+CCCFFFFFHHHHHHHIJIIIJ\n+@HWI-ST132:678:C1LFKACXX:6:1107:13749:41003\n+TGATTTGTTGGTAGAAGAAGG\n++\n+JJJIJJIGFFFHHFFFFFCCB\n+@HWI-ST132:678:C1LFKACXX:6:1112:7021:46842\n+TGATTTGTTGGTAGAAGAAGG\n++\n+JIGHHFGGHFHHFDFFFF@@B\n+@HWI-ST132:678:C1LFKACXX:6:2106:12928:28648\n+TGATTTGTTGGTAGAAGAAGG\n++\n+GGHEE<<+A3<DHDFFDD@?=\n+@HWI-ST132:678:C1LFKACXX:6:2107:17571:56192\n+TGATTTGTTGGTAGAAGAAGG\n++\n+JIHE<,A<23<HHFFFDD=:1\n+@HWI-ST132:678:C1LFKACXX:6:1104:18932:34578\n+GCTATGGGTTATTGACCGCTC\n++\n+JJJIHFE?GHFFFFFEDF@@@\n+@HWI-ST132:678:C1LFKACXX:6:1202:4878:86481\n+TGCGTTTGGGATTGTCGGTGA\n++\n+IHDJIHFHHGHHDFFFFFCCB\n+@HWI-ST132:678:C1LFKACXX:6:1115:14400:83897\n+TTTGGGATTGTCGGTGAGACG\n++\n+IHHFGGEGDFAFFBFDFD@?@\n+@HWI-ST132:678:C1LFKACXX:6:1213:16820:54984\n+TTGTCGGTGAGACGTAGGAGA\n++\n+IJIIGBFHFDFFFDFFFFCCB\n+@HWI-ST132:678:C1LFKACXX:6:1106:4136:80459\n+TAGGAGAAGTACGCGTTGTTG\n++\n+CDEE<<)EDDDDDD?A4D???\n+@HWI-ST132:678:C1LFKACXX:6:1108:12282:61422\n+TAGGAGAAGTACGCGTTGTTG\n++\n+JIIJJIJJHHFAFFDEDFCBB\n+@HWI-ST132:678:C1LFKACXX:6:1111:13707:90938\n+TAGGAGAAGTACGCGTTGTTG\n++\n+JJIHF@@JHFC<CFDDAF@@?\n+@HWI-ST132:678:C1LFKACXX:6:1314:12461:28557\n+TAGGAGAAGTACGCGTTGTTG\n++\n+JJHIHGHJGHFDHFDFFFC@B\n+@HWI-ST132:678:C1LFKACXX:6:2106:10137:48564\n+TAGGAGAAGTACGCGTTGTTG\n++\n+JJJJHHIIHHFFHFFFFFCCB\n+@HWI-ST132:678:C1LFKACXX:6:2109:19752:91497\n+TAGGAGAAGTACGCGTTGTTG\n++\n+GCHIIIEGHFFFHDDBD?@@@\n+@HWI-ST132:678:C1LFKACXX:6:1215:19556:9898\n+GAAGTACGCGTTGTTGCGCTG\n++\n+IIIIIIIIHFHHFDA2441+:\n+@HWI-ST132:678:C1LFKACXX:6:1208:16914:37703\n+TGTTGCGCTGAATTGAGAGTC\n++\n+HEGHFF<GFF6GHFFFFFC@@\n+@HWI-ST132:678:C1LFKACXX:6:2103:12622:49391\n+TGTTGCGCTGAATTGAGAGTC\n++\n+HAHJJJJJHHHHHFFFFFCCC\n+@HWI-ST132:678:C1LFKACXX:6:1104:12986:68120\n+TTGCGCTGAATTGAGAGTCGG\n++\n+IGHEGC2+FFF<FDDDDD@@@\n' |
| b |
| diff -r 9645d995fb3c -r 9185ca0a7b43 test-data/fastq_dir/reads-sample-small.fastq-siRNAs-genome.fastq --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/fastq_dir/reads-sample-small.fastq-siRNAs-genome.fastq Wed Jan 16 08:18:13 2019 -0500 |
| b |
| b'@@ -0,0 +1,11656 @@\n+@HWI-ST132:678:C1LFKACXX:6:2104:9716:27077\n+GTACTCGATCGCCTGAAGAAC\n++\n+@@CFFFFFHHCFHI+AEHHII\n+@HWI-ST132:678:C1LFKACXX:6:1306:4247:15664\n+TTACAAAGTCAGTGGGGATGC\n++\n+@@@FFFFFFFHFCGGE<F@A<\n+@HWI-ST132:678:C1LFKACXX:6:2103:3486:88354\n+CTTTAATTATCATATATTGTA\n++\n+BBBD;=ABFHHHHJJJJJDJI\n+@HWI-ST132:678:C1LFKACXX:6:1304:3965:45774\n+TTAAACTGTGAATTAAGCGCG\n++\n+BC@FFFFFCFHHHJJJJJHGJ\n+@HWI-ST132:678:C1LFKACXX:6:1112:13388:37433\n+TGTGGAGTCCTGTTGATCATT\n++\n+@C@FFFFDHHHDHIJJJJIJI\n+@HWI-ST132:678:C1LFKACXX:6:1103:5248:79079\n+ACAGCGAATTGATCGGATTGC\n++\n+@@@DFADDHDHHHIJJIHICC\n+@HWI-ST132:678:C1LFKACXX:6:1104:11153:32804\n+TTCCGAATTGTCTGCACTGGT\n++\n+CCCFFFFFHGHHHHFIIJJIH\n+@HWI-ST132:678:C1LFKACXX:6:1211:17694:10783\n+TTCCGAATTGTCTGCACTGGT\n++\n+CCCFFFFFHHFFHIJHHIJJH\n+@HWI-ST132:678:C1LFKACXX:6:1301:12823:86928\n+TTCCGAATTGTCTGCACTGGT\n++\n+:=?DDF:22<<DFGIBEGHIC\n+@HWI-ST132:678:C1LFKACXX:6:1315:17545:15989\n+CCCCTGATCAAACATCGTCTG\n++\n+B@BDFFDFHHHHHJJJJIIJJ\n+@HWI-ST132:678:C1LFKACXX:6:1216:10870:15777\n+TAATACAATACATCAGACGAT\n++\n+??+4=BDDHDHHGIHIBFHEE\n+@HWI-ST132:678:C1LFKACXX:6:2106:19483:23767\n+AAGACTTCGGAGTTAAGTATC\n++\n+CCCFFFFFHHHD>EHIJHHHI\n+@HWI-ST132:678:C1LFKACXX:6:1202:19924:85837\n+TACATACCTGGGAAGACTTCG\n++\n+CCCFFFFFHHFBHHEHIIIJJ\n+@HWI-ST132:678:C1LFKACXX:6:2107:16400:98713\n+TTCTGGGAATTCCGAAGATGG\n++\n+CCCFFFFFHHHHHAEGHHJJJ\n+@HWI-ST132:678:C1LFKACXX:6:1306:12648:89258\n+ATAAACTGTCTGACAGGGACC\n++\n+CCCFFFFFHHHBHIIGHIJJJ\n+@HWI-ST132:678:C1LFKACXX:6:1204:10596:80793\n+TACCTATGTCGATTGCCACCT\n++\n+?@?DDDDD??A?FGHGHIIIG\n+@HWI-ST132:678:C1LFKACXX:6:2105:13825:18518\n+TGTCCAGTCTGACGATATCAG\n++\n+CCCFFFFFGHHHH:FHIJJJJ\n+@HWI-ST132:678:C1LFKACXX:6:1111:12949:86137\n+TGATGCCAGACCGGGCTTCAG\n++\n+CCCFFFFFHHHHHHIJJJJJJ\n+@HWI-ST132:678:C1LFKACXX:6:1109:14660:78489\n+CCGGGCTTCAGTCTGGGCGCC\n++\n+B@@FFFFFHGDAFGEGGHJGJ\n+@HWI-ST132:678:C1LFKACXX:6:1301:9997:96604\n+CCGGGCTTCAGTCTGGGCGCC\n++\n+@CCFFFFDHHHHHGHIHH<?G\n+@HWI-ST132:678:C1LFKACXX:6:2103:4365:12003\n+CGGGCTTCAGTCTGGGCGCCA\n++\n+BCCFFFFFHHFHHIGDABCGI\n+@HWI-ST132:678:C1LFKACXX:6:1315:14025:50396\n+TAGAGTCTGGACTGTGGCGCC\n++\n+@@@DFDFDFH?DBH<EFGGBE\n+@HWI-ST132:678:C1LFKACXX:6:1103:10328:28844\n+TCTAGAGGTGGCTCCAGGCTC\n++\n+:BBDA2=A=CCFHIJJJJIJJ\n+@HWI-ST132:678:C1LFKACXX:6:1105:6326:49732\n+TCTAGAGGTGGCTCCAGGCTC\n++\n+?@BDD=BDADHHHHJ3CFGIJ\n+@HWI-ST132:678:C1LFKACXX:6:1105:11000:66079\n+TCTAGAGGTGGCTCCAGGCTC\n++\n+BBBDFFFFFHHHHJJIJJJJJ\n+@HWI-ST132:678:C1LFKACXX:6:1106:14064:43295\n+TCTAGAGGTGGCTCCAGGCTC\n++\n+B@BDDFFFHHHHFGIJJIIGI\n+@HWI-ST132:678:C1LFKACXX:6:1113:19938:48642\n+TCTAGAGGTGGCTCCAGGCTC\n++\n+@@BDDEFFFFHHHIJJJJJJJ\n+@HWI-ST132:678:C1LFKACXX:6:1116:10596:49883\n+TCTAGAGGTGGCTCCAGGCTC\n++\n+B?BDFDFFCFHHHJJJJJJJJ\n+@HWI-ST132:678:C1LFKACXX:6:1201:7176:42559\n+TCTAGAGGTGGCTCCAGGCTC\n++\n+:?BDDDFFCF<<<<EGIIJJJ\n+@HWI-ST132:678:C1LFKACXX:6:1204:7366:53049\n+TCTAGAGGTGGCTCCAGGCTC\n++\n+BBBDDDDFCFHHHJJJJJJJJ\n+@HWI-ST132:678:C1LFKACXX:6:1205:7458:21533\n+TCTAGAGGTGGCTCCAGGCTC\n++\n+B@BFFDFFDHFHHJJFIJJJJ\n+@HWI-ST132:678:C1LFKACXX:6:1207:18816:23955\n+TCTAGAGGTGGCTCCAGGCTC\n++\n+@BBDFDFFCFHHGHIJIJIJJ\n+@HWI-ST132:678:C1LFKACXX:6:1207:18521:50214\n+TCTAGAGGTGGCTCCAGGCTC\n++\n+BBBDDDDFADHHHIJJJIJJJ\n+@HWI-ST132:678:C1LFKACXX:6:1215:8094:48780\n+TCTAGAGGTGGCTCCAGGCTC\n++\n+?:?DADDD=?::DEEB:<+<:\n+@HWI-ST132:678:C1LFKACXX:6:1302:16933:22023\n+TCTAGAGGTGGCTCCAGGCTC\n++\n+BCBFFFFFFHHHHJJJJJJJJ\n+@HWI-ST132:678:C1LFKACXX:6:1308:15108:32948\n+TCTAGAGGTGGCTCCAGGCTC\n++\n+BCCFFFFFFHHHHJJJIJJJJ\n+@HWI-ST132:678:C1LFKACXX:6:1310:7792:7251\n+TCTAGAGGTGGCTCCAGGCTC\n++\n+BCCFFFFFFHHHHJJIJJJJJ\n+@HWI-ST132:678:C1LFKACXX:6:1310:5500:48225\n+TCTAGAGGTGGCTCCAGGCTC\n++\n+@@CFFFFFFHGHHJJIJJJJJ\n+@HWI-ST132:678:C1LFKACXX:6:1314:12694:59078\n+TCTAGAGGTGGCTCCAGGCTC\n++\n+@@@DFFFFF?FHGGIIEHEHG\n+@HWI-ST132:678:C1LFKACXX:6:1315:4806:7499\n+TCTAGAGGTGGCTCCAGGCTC\n++\n+BBCFFDDFA;DFHIJIIIGII\n+@HWI-ST132:678:C1LFKACXX:6:2101:15514:8580\n+TCTAGAGGTGGCTCCAGGCTC\n++\n+BBBDFDFFFFFHHJJJJJJJJ\n+@HWI-ST132:678:C1LFKACXX:6:2101:13883:37158\n+TCTAGAGGTGGCTCCAGGCTC\n++\n+BBBFFFFFHH;DHIJJJJJGJ\n+@HWI-ST132:678:C1LFKACXX:6:2101:14995:100162\n+TC'..b'ACXX:6:1204:8915:42482\n+ACACCCACTTCATGTCGACAG\n++\n+@@@FBDDDHHFGHH<EGFHGG\n+@HWI-ST132:678:C1LFKACXX:6:1109:5525:6504\n+TAATTTATTGTCGACTCCTGA\n++\n+C@CFFFDFHHHHH3EHIIJJJ\n+@HWI-ST132:678:C1LFKACXX:6:1109:16003:74425\n+GAGGACAACCACTCCGGCAGC\n++\n+CC@FDFDFHHGHHJJJJJJII\n+@HWI-ST132:678:C1LFKACXX:6:1103:16164:28590\n+ATTGCGGCTGCACACAGAGAA\n++\n+BCBDDFFFHHHHHJIJJJJJJ\n+@HWI-ST132:678:C1LFKACXX:6:2101:17496:94074\n+ATACGACAAATGATACTGAGT\n++\n+CCCFFFFFHHHDHIJJJIFA<\n+@HWI-ST132:678:C1LFKACXX:6:1310:11295:14789\n+CCAGACGACTTTGTCCGCCTC\n++\n+CCCFFFFFHHHHHJJJJJJJJ\n+@HWI-ST132:678:C1LFKACXX:6:2107:16743:60430\n+TGCAGGATCAGAACTCAGAAT\n++\n+CCCFFFFFHHHHHIJJJJIJJ\n+@HWI-ST132:678:C1LFKACXX:6:1108:9976:99924\n+GTTCCTCTTCTTTATCGGGTG\n++\n+C@@FFFFFHHHHHGHIII<AF\n+@HWI-ST132:678:C1LFKACXX:6:1311:17281:3877\n+CCACGACGTTCAACATTGACT\n++\n+@@BFFDDFHDHFH@EHIIHIG\n+@HWI-ST132:678:C1LFKACXX:6:1209:13387:2204\n+ACTTCATATCCTTTTCGGGTG\n++\n+@BBDFFFFHHHHHJJJJJJFG\n+@HWI-ST132:678:C1LFKACXX:6:1201:10388:40542\n+GCAACTCTGCCACTTGAACCC\n++\n+CCCFFFFFHHHHHJJGIJJJJ\n+@HWI-ST132:678:C1LFKACXX:6:1207:6411:98409\n+GCAACTCTGCCACTTGAACCC\n++\n+@@@FFFED8CFHDGIHIIIIJ\n+@HWI-ST132:678:C1LFKACXX:6:1205:6060:56314\n+CGAGATGACGCTGGCTGACTG\n++\n+@C@DDFFFGHHFHHGIIIJIJ\n+@HWI-ST132:678:C1LFKACXX:6:1110:13887:78568\n+CAACTGCGCTCTGGAATAAAC\n++\n+CCCFFFFFHHHHHIJJIIJIJ\n+@HWI-ST132:678:C1LFKACXX:6:1303:1449:44316\n+CGCTGTTCAGCTCCTCTCAGT\n++\n+B@CFDDDDHHHHHJJJJJIIH\n+@HWI-ST132:678:C1LFKACXX:6:2103:8728:29903\n+TAGACGCCAGCAAGGATTGCT\n++\n+CCCFFFFFHHFHG2AGFHIJJ\n+@HWI-ST132:678:C1LFKACXX:6:2105:10389:44836\n+TCTCCAGCTGTAAATACAACT\n++\n+BBBFFFFFHHCFH<FHIIJJJ\n+@HWI-ST132:678:C1LFKACXX:6:1208:2325:6974\n+AAAACAAAATTCGGCGGCATC\n++\n+CCCFFFFFDHHHHIIJJIJJJ\n+@HWI-ST132:678:C1LFKACXX:6:1312:11197:31549\n+AAAACAAAATTCGGCGGCATC\n++\n+@@@FFDFF@FFFHCFFHHIGG\n+@HWI-ST132:678:C1LFKACXX:6:1314:11236:21715\n+ATCAGGGGCTTTGCTGACGCC\n++\n+CCBFFFFFHHHHHIJIIJJIJ\n+@HWI-ST132:678:C1LFKACXX:6:2108:7857:86148\n+AACATACTTGTGGCCTGGCCT\n++\n+C@CFFFFFHHHBFIJJJJJJJ\n+@HWI-ST132:678:C1LFKACXX:6:1315:17527:21097\n+AGATGTTGACATTGAATGGCC\n++\n+BC@DFFFFFHHGHIIIJIJIJ\n+@HWI-ST132:678:C1LFKACXX:6:1210:8227:45651\n+CGCACTCAGTCACTCGGTTTG\n++\n+@CCFFFFFDFHFHHIJJIJJJ\n+@HWI-ST132:678:C1LFKACXX:6:1112:16767:67452\n+GCAGCTCTAGTTGGTCGCGGC\n++\n+@C@FFFFF>FCFHEGGGIGHI\n+@HWI-ST132:678:C1LFKACXX:6:1114:13156:95650\n+AATTATTTACAAGCGGCGAGC\n++\n+@@@=BDFFHDFHFIFH<GIJJ\n+@HWI-ST132:678:C1LFKACXX:6:1303:18254:36868\n+GTCGATCGATCGAACGGGCGT\n++\n+BBCDFFFFHHHHHGIGHIJIH\n+@HWI-ST132:678:C1LFKACXX:6:1101:2206:66004\n+AACCAGCGGACATCGGACATC\n++\n+:?@D?DBDH@@CCFHIIJJIJ\n+@HWI-ST132:678:C1LFKACXX:6:2108:3454:76338\n+TTTACACATAACTCTTCGCAT\n++\n+@@@D?DDDHFHBFBGHIIIIG\n+@HWI-ST132:678:C1LFKACXX:6:2108:18053:41000\n+TCTGCAGCGATTCCGAACTCC\n++\n+CC@FFFFFHGHHHI3<EHHHI\n+@HWI-ST132:678:C1LFKACXX:6:1208:4638:88640\n+CTTTCGATGGCAGAGTTGGTC\n++\n+@BBFFFDDHHHHHJJGIIGHI\n+@HWI-ST132:678:C1LFKACXX:6:1108:5315:17099\n+CCACTGTGGAATTATGAGAGC\n++\n+B@BFFFDDFDHHH4CAEEGII\n+@HWI-ST132:678:C1LFKACXX:6:2105:9020:42698\n+AAGCAGCCAAAGCTCCAGGGC\n++\n+CCBFFFFFHHHDFIJJJJJJI\n+@HWI-ST132:678:C1LFKACXX:6:1111:18474:81416\n+GCAACCAGTTGATTGGGGACT\n++\n+@CCFFFFFFHHHHJIJEHIJJ\n+@HWI-ST132:678:C1LFKACXX:6:1107:2900:96158\n+TTCCAAAGTTGTGAGGCACTC\n++\n+@@@F?DDEDFHHHJIHIJJJJ\n+@HWI-ST132:678:C1LFKACXX:6:1302:12325:17230\n+TTAATTTCGCGTTTTTTCTCG\n++\n+:?BDDF?DFH@00BFHIIJJJ\n+@HWI-ST132:678:C1LFKACXX:6:1205:10933:11207\n+ACCGGACAGCACGGTCGTGTT\n++\n+@CCFFFFFFHHHGEEGIFGHG\n+@HWI-ST132:678:C1LFKACXX:6:1110:1636:70699\n+TTAACAATCAGTGCGGTGTAC\n++\n+CCCFFFFEHHHDFGIIIJJJJ\n+@HWI-ST132:678:C1LFKACXX:6:2106:17769:8524\n+GCATATCGCAGTCCATGCTGT\n++\n+CCCFFFFFHHHHHJJJJJJIH\n+@HWI-ST132:678:C1LFKACXX:6:1104:16518:94276\n+GATCCCAGATCCGCTGTGTTT\n++\n+CCCFFFFFHHHHHIJFGHHIJ\n+@HWI-ST132:678:C1LFKACXX:6:1213:14045:90482\n+ATACTAGATTCGTTGAAAAGT\n++\n+@@@F7DDDFA<CC?;FAEBH?\n+@HWI-ST132:678:C1LFKACXX:6:1313:11404:80054\n+ACCGTTCTATGCTTTTTTTTA\n++\n+@@CFBDFF?FHHGIIIIGIIC\n+@HWI-ST132:678:C1LFKACXX:6:1106:17247:63193\n+AATCCTACCGGCTGCGAATGA\n++\n+@BBFFDEFHFHHHFFFFHGHJ\n+@HWI-ST132:678:C1LFKACXX:6:1111:11783:45506\n+ACCGGCTGCGAATGAGAATGT\n++\n+???DFFFFFHF:CCCGHHBG<\n' |
| b |
| diff -r 9645d995fb3c -r 9185ca0a7b43 test-data/fastq_dir/reads-sample-small.fastq-siRNAs-genome_uni.fastq --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/fastq_dir/reads-sample-small.fastq-siRNAs-genome_uni.fastq Wed Jan 16 08:18:13 2019 -0500 |
| b |
| b'@@ -0,0 +1,11652 @@\n+@HWI-ST132:678:C1LFKACXX:6:2104:9716:27077\n+GTACTCGATCGCCTGAAGAAC\n++\n+@@CFFFFFHHCFHI+AEHHII\n+@HWI-ST132:678:C1LFKACXX:6:1306:4247:15664\n+TTACAAAGTCAGTGGGGATGC\n++\n+@@@FFFFFFFHFCGGE<F@A<\n+@HWI-ST132:678:C1LFKACXX:6:2103:3486:88354\n+CTTTAATTATCATATATTGTA\n++\n+BBBD;=ABFHHHHJJJJJDJI\n+@HWI-ST132:678:C1LFKACXX:6:1304:3965:45774\n+TTAAACTGTGAATTAAGCGCG\n++\n+BC@FFFFFCFHHHJJJJJHGJ\n+@HWI-ST132:678:C1LFKACXX:6:1112:13388:37433\n+TGTGGAGTCCTGTTGATCATT\n++\n+@C@FFFFDHHHDHIJJJJIJI\n+@HWI-ST132:678:C1LFKACXX:6:1103:5248:79079\n+ACAGCGAATTGATCGGATTGC\n++\n+@@@DFADDHDHHHIJJIHICC\n+@HWI-ST132:678:C1LFKACXX:6:1104:11153:32804\n+TTCCGAATTGTCTGCACTGGT\n++\n+CCCFFFFFHGHHHHFIIJJIH\n+@HWI-ST132:678:C1LFKACXX:6:1211:17694:10783\n+TTCCGAATTGTCTGCACTGGT\n++\n+CCCFFFFFHHFFHIJHHIJJH\n+@HWI-ST132:678:C1LFKACXX:6:1301:12823:86928\n+TTCCGAATTGTCTGCACTGGT\n++\n+:=?DDF:22<<DFGIBEGHIC\n+@HWI-ST132:678:C1LFKACXX:6:1315:17545:15989\n+CCCCTGATCAAACATCGTCTG\n++\n+B@BDFFDFHHHHHJJJJIIJJ\n+@HWI-ST132:678:C1LFKACXX:6:1216:10870:15777\n+TAATACAATACATCAGACGAT\n++\n+??+4=BDDHDHHGIHIBFHEE\n+@HWI-ST132:678:C1LFKACXX:6:2106:19483:23767\n+AAGACTTCGGAGTTAAGTATC\n++\n+CCCFFFFFHHHD>EHIJHHHI\n+@HWI-ST132:678:C1LFKACXX:6:1202:19924:85837\n+TACATACCTGGGAAGACTTCG\n++\n+CCCFFFFFHHFBHHEHIIIJJ\n+@HWI-ST132:678:C1LFKACXX:6:2107:16400:98713\n+TTCTGGGAATTCCGAAGATGG\n++\n+CCCFFFFFHHHHHAEGHHJJJ\n+@HWI-ST132:678:C1LFKACXX:6:1306:12648:89258\n+ATAAACTGTCTGACAGGGACC\n++\n+CCCFFFFFHHHBHIIGHIJJJ\n+@HWI-ST132:678:C1LFKACXX:6:1204:10596:80793\n+TACCTATGTCGATTGCCACCT\n++\n+?@?DDDDD??A?FGHGHIIIG\n+@HWI-ST132:678:C1LFKACXX:6:2105:13825:18518\n+TGTCCAGTCTGACGATATCAG\n++\n+CCCFFFFFGHHHH:FHIJJJJ\n+@HWI-ST132:678:C1LFKACXX:6:1111:12949:86137\n+TGATGCCAGACCGGGCTTCAG\n++\n+CCCFFFFFHHHHHHIJJJJJJ\n+@HWI-ST132:678:C1LFKACXX:6:1109:14660:78489\n+CCGGGCTTCAGTCTGGGCGCC\n++\n+B@@FFFFFHGDAFGEGGHJGJ\n+@HWI-ST132:678:C1LFKACXX:6:1301:9997:96604\n+CCGGGCTTCAGTCTGGGCGCC\n++\n+@CCFFFFDHHHHHGHIHH<?G\n+@HWI-ST132:678:C1LFKACXX:6:2103:4365:12003\n+CGGGCTTCAGTCTGGGCGCCA\n++\n+BCCFFFFFHHFHHIGDABCGI\n+@HWI-ST132:678:C1LFKACXX:6:1315:14025:50396\n+TAGAGTCTGGACTGTGGCGCC\n++\n+@@@DFDFDFH?DBH<EFGGBE\n+@HWI-ST132:678:C1LFKACXX:6:1103:10328:28844\n+TCTAGAGGTGGCTCCAGGCTC\n++\n+:BBDA2=A=CCFHIJJJJIJJ\n+@HWI-ST132:678:C1LFKACXX:6:1105:6326:49732\n+TCTAGAGGTGGCTCCAGGCTC\n++\n+?@BDD=BDADHHHHJ3CFGIJ\n+@HWI-ST132:678:C1LFKACXX:6:1105:11000:66079\n+TCTAGAGGTGGCTCCAGGCTC\n++\n+BBBDFFFFFHHHHJJIJJJJJ\n+@HWI-ST132:678:C1LFKACXX:6:1106:14064:43295\n+TCTAGAGGTGGCTCCAGGCTC\n++\n+B@BDDFFFHHHHFGIJJIIGI\n+@HWI-ST132:678:C1LFKACXX:6:1113:19938:48642\n+TCTAGAGGTGGCTCCAGGCTC\n++\n+@@BDDEFFFFHHHIJJJJJJJ\n+@HWI-ST132:678:C1LFKACXX:6:1116:10596:49883\n+TCTAGAGGTGGCTCCAGGCTC\n++\n+B?BDFDFFCFHHHJJJJJJJJ\n+@HWI-ST132:678:C1LFKACXX:6:1201:7176:42559\n+TCTAGAGGTGGCTCCAGGCTC\n++\n+:?BDDDFFCF<<<<EGIIJJJ\n+@HWI-ST132:678:C1LFKACXX:6:1204:7366:53049\n+TCTAGAGGTGGCTCCAGGCTC\n++\n+BBBDDDDFCFHHHJJJJJJJJ\n+@HWI-ST132:678:C1LFKACXX:6:1205:7458:21533\n+TCTAGAGGTGGCTCCAGGCTC\n++\n+B@BFFDFFDHFHHJJFIJJJJ\n+@HWI-ST132:678:C1LFKACXX:6:1207:18816:23955\n+TCTAGAGGTGGCTCCAGGCTC\n++\n+@BBDFDFFCFHHGHIJIJIJJ\n+@HWI-ST132:678:C1LFKACXX:6:1207:18521:50214\n+TCTAGAGGTGGCTCCAGGCTC\n++\n+BBBDDDDFADHHHIJJJIJJJ\n+@HWI-ST132:678:C1LFKACXX:6:1215:8094:48780\n+TCTAGAGGTGGCTCCAGGCTC\n++\n+?:?DADDD=?::DEEB:<+<:\n+@HWI-ST132:678:C1LFKACXX:6:1302:16933:22023\n+TCTAGAGGTGGCTCCAGGCTC\n++\n+BCBFFFFFFHHHHJJJJJJJJ\n+@HWI-ST132:678:C1LFKACXX:6:1308:15108:32948\n+TCTAGAGGTGGCTCCAGGCTC\n++\n+BCCFFFFFFHHHHJJJIJJJJ\n+@HWI-ST132:678:C1LFKACXX:6:1310:7792:7251\n+TCTAGAGGTGGCTCCAGGCTC\n++\n+BCCFFFFFFHHHHJJIJJJJJ\n+@HWI-ST132:678:C1LFKACXX:6:1310:5500:48225\n+TCTAGAGGTGGCTCCAGGCTC\n++\n+@@CFFFFFFHGHHJJIJJJJJ\n+@HWI-ST132:678:C1LFKACXX:6:1314:12694:59078\n+TCTAGAGGTGGCTCCAGGCTC\n++\n+@@@DFFFFF?FHGGIIEHEHG\n+@HWI-ST132:678:C1LFKACXX:6:1315:4806:7499\n+TCTAGAGGTGGCTCCAGGCTC\n++\n+BBCFFDDFA;DFHIJIIIGII\n+@HWI-ST132:678:C1LFKACXX:6:2101:15514:8580\n+TCTAGAGGTGGCTCCAGGCTC\n++\n+BBBDFDFFFFFHHJJJJJJJJ\n+@HWI-ST132:678:C1LFKACXX:6:2101:13883:37158\n+TCTAGAGGTGGCTCCAGGCTC\n++\n+BBBFFFFFHH;DHIJJJJJGJ\n+@HWI-ST132:678:C1LFKACXX:6:2101:14995:100162\n+TC'..b'ACXX:6:1204:8915:42482\n+ACACCCACTTCATGTCGACAG\n++\n+@@@FBDDDHHFGHH<EGFHGG\n+@HWI-ST132:678:C1LFKACXX:6:1109:5525:6504\n+TAATTTATTGTCGACTCCTGA\n++\n+C@CFFFDFHHHHH3EHIIJJJ\n+@HWI-ST132:678:C1LFKACXX:6:1109:16003:74425\n+GAGGACAACCACTCCGGCAGC\n++\n+CC@FDFDFHHGHHJJJJJJII\n+@HWI-ST132:678:C1LFKACXX:6:1103:16164:28590\n+ATTGCGGCTGCACACAGAGAA\n++\n+BCBDDFFFHHHHHJIJJJJJJ\n+@HWI-ST132:678:C1LFKACXX:6:2101:17496:94074\n+ATACGACAAATGATACTGAGT\n++\n+CCCFFFFFHHHDHIJJJIFA<\n+@HWI-ST132:678:C1LFKACXX:6:1310:11295:14789\n+CCAGACGACTTTGTCCGCCTC\n++\n+CCCFFFFFHHHHHJJJJJJJJ\n+@HWI-ST132:678:C1LFKACXX:6:2107:16743:60430\n+TGCAGGATCAGAACTCAGAAT\n++\n+CCCFFFFFHHHHHIJJJJIJJ\n+@HWI-ST132:678:C1LFKACXX:6:1108:9976:99924\n+GTTCCTCTTCTTTATCGGGTG\n++\n+C@@FFFFFHHHHHGHIII<AF\n+@HWI-ST132:678:C1LFKACXX:6:1311:17281:3877\n+CCACGACGTTCAACATTGACT\n++\n+@@BFFDDFHDHFH@EHIIHIG\n+@HWI-ST132:678:C1LFKACXX:6:1209:13387:2204\n+ACTTCATATCCTTTTCGGGTG\n++\n+@BBDFFFFHHHHHJJJJJJFG\n+@HWI-ST132:678:C1LFKACXX:6:1201:10388:40542\n+GCAACTCTGCCACTTGAACCC\n++\n+CCCFFFFFHHHHHJJGIJJJJ\n+@HWI-ST132:678:C1LFKACXX:6:1207:6411:98409\n+GCAACTCTGCCACTTGAACCC\n++\n+@@@FFFED8CFHDGIHIIIIJ\n+@HWI-ST132:678:C1LFKACXX:6:1205:6060:56314\n+CGAGATGACGCTGGCTGACTG\n++\n+@C@DDFFFGHHFHHGIIIJIJ\n+@HWI-ST132:678:C1LFKACXX:6:1110:13887:78568\n+CAACTGCGCTCTGGAATAAAC\n++\n+CCCFFFFFHHHHHIJJIIJIJ\n+@HWI-ST132:678:C1LFKACXX:6:1303:1449:44316\n+CGCTGTTCAGCTCCTCTCAGT\n++\n+B@CFDDDDHHHHHJJJJJIIH\n+@HWI-ST132:678:C1LFKACXX:6:2103:8728:29903\n+TAGACGCCAGCAAGGATTGCT\n++\n+CCCFFFFFHHFHG2AGFHIJJ\n+@HWI-ST132:678:C1LFKACXX:6:2105:10389:44836\n+TCTCCAGCTGTAAATACAACT\n++\n+BBBFFFFFHHCFH<FHIIJJJ\n+@HWI-ST132:678:C1LFKACXX:6:1208:2325:6974\n+AAAACAAAATTCGGCGGCATC\n++\n+CCCFFFFFDHHHHIIJJIJJJ\n+@HWI-ST132:678:C1LFKACXX:6:1312:11197:31549\n+AAAACAAAATTCGGCGGCATC\n++\n+@@@FFDFF@FFFHCFFHHIGG\n+@HWI-ST132:678:C1LFKACXX:6:1314:11236:21715\n+ATCAGGGGCTTTGCTGACGCC\n++\n+CCBFFFFFHHHHHIJIIJJIJ\n+@HWI-ST132:678:C1LFKACXX:6:2108:7857:86148\n+AACATACTTGTGGCCTGGCCT\n++\n+C@CFFFFFHHHBFIJJJJJJJ\n+@HWI-ST132:678:C1LFKACXX:6:1315:17527:21097\n+AGATGTTGACATTGAATGGCC\n++\n+BC@DFFFFFHHGHIIIJIJIJ\n+@HWI-ST132:678:C1LFKACXX:6:1210:8227:45651\n+CGCACTCAGTCACTCGGTTTG\n++\n+@CCFFFFFDFHFHHIJJIJJJ\n+@HWI-ST132:678:C1LFKACXX:6:1112:16767:67452\n+GCAGCTCTAGTTGGTCGCGGC\n++\n+@C@FFFFF>FCFHEGGGIGHI\n+@HWI-ST132:678:C1LFKACXX:6:1114:13156:95650\n+AATTATTTACAAGCGGCGAGC\n++\n+@@@=BDFFHDFHFIFH<GIJJ\n+@HWI-ST132:678:C1LFKACXX:6:1303:18254:36868\n+GTCGATCGATCGAACGGGCGT\n++\n+BBCDFFFFHHHHHGIGHIJIH\n+@HWI-ST132:678:C1LFKACXX:6:1101:2206:66004\n+AACCAGCGGACATCGGACATC\n++\n+:?@D?DBDH@@CCFHIIJJIJ\n+@HWI-ST132:678:C1LFKACXX:6:2108:3454:76338\n+TTTACACATAACTCTTCGCAT\n++\n+@@@D?DDDHFHBFBGHIIIIG\n+@HWI-ST132:678:C1LFKACXX:6:2108:18053:41000\n+TCTGCAGCGATTCCGAACTCC\n++\n+CC@FFFFFHGHHHI3<EHHHI\n+@HWI-ST132:678:C1LFKACXX:6:1208:4638:88640\n+CTTTCGATGGCAGAGTTGGTC\n++\n+@BBFFFDDHHHHHJJGIIGHI\n+@HWI-ST132:678:C1LFKACXX:6:1108:5315:17099\n+CCACTGTGGAATTATGAGAGC\n++\n+B@BFFFDDFDHHH4CAEEGII\n+@HWI-ST132:678:C1LFKACXX:6:2105:9020:42698\n+AAGCAGCCAAAGCTCCAGGGC\n++\n+CCBFFFFFHHHDFIJJJJJJI\n+@HWI-ST132:678:C1LFKACXX:6:1111:18474:81416\n+GCAACCAGTTGATTGGGGACT\n++\n+@CCFFFFFFHHHHJIJEHIJJ\n+@HWI-ST132:678:C1LFKACXX:6:1107:2900:96158\n+TTCCAAAGTTGTGAGGCACTC\n++\n+@@@F?DDEDFHHHJIHIJJJJ\n+@HWI-ST132:678:C1LFKACXX:6:1302:12325:17230\n+TTAATTTCGCGTTTTTTCTCG\n++\n+:?BDDF?DFH@00BFHIIJJJ\n+@HWI-ST132:678:C1LFKACXX:6:1205:10933:11207\n+ACCGGACAGCACGGTCGTGTT\n++\n+@CCFFFFFFHHHGEEGIFGHG\n+@HWI-ST132:678:C1LFKACXX:6:1110:1636:70699\n+TTAACAATCAGTGCGGTGTAC\n++\n+CCCFFFFEHHHDFGIIIJJJJ\n+@HWI-ST132:678:C1LFKACXX:6:2106:17769:8524\n+GCATATCGCAGTCCATGCTGT\n++\n+CCCFFFFFHHHHHJJJJJJIH\n+@HWI-ST132:678:C1LFKACXX:6:1104:16518:94276\n+GATCCCAGATCCGCTGTGTTT\n++\n+CCCFFFFFHHHHHIJFGHHIJ\n+@HWI-ST132:678:C1LFKACXX:6:1213:14045:90482\n+ATACTAGATTCGTTGAAAAGT\n++\n+@@@F7DDDFA<CC?;FAEBH?\n+@HWI-ST132:678:C1LFKACXX:6:1313:11404:80054\n+ACCGTTCTATGCTTTTTTTTA\n++\n+@@CFBDFF?FHHGIIIIGIIC\n+@HWI-ST132:678:C1LFKACXX:6:1106:17247:63193\n+AATCCTACCGGCTGCGAATGA\n++\n+@BBFFDEFHFHHHFFFFHGHJ\n+@HWI-ST132:678:C1LFKACXX:6:1111:11783:45506\n+ACCGGCTGCGAATGAGAATGT\n++\n+???DFFFFFHF:CCCGHHBG<\n' |
| b |
| diff -r 9645d995fb3c -r 9185ca0a7b43 test-data/fastq_dir/reads-sample-small.fastq-siRNAs-transcripts.fastq --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/fastq_dir/reads-sample-small.fastq-siRNAs-transcripts.fastq Wed Jan 16 08:18:13 2019 -0500 |
| b |
| b'@@ -0,0 +1,628 @@\n+@HWI-ST132:678:C1LFKACXX:6:1103:10328:28844\n+TCTAGAGGTGGCTCCAGGCTC\n++\n+:BBDA2=A=CCFHIJJJJIJJ\n+@HWI-ST132:678:C1LFKACXX:6:1105:6326:49732\n+TCTAGAGGTGGCTCCAGGCTC\n++\n+?@BDD=BDADHHHHJ3CFGIJ\n+@HWI-ST132:678:C1LFKACXX:6:1105:11000:66079\n+TCTAGAGGTGGCTCCAGGCTC\n++\n+BBBDFFFFFHHHHJJIJJJJJ\n+@HWI-ST132:678:C1LFKACXX:6:1106:14064:43295\n+TCTAGAGGTGGCTCCAGGCTC\n++\n+B@BDDFFFHHHHFGIJJIIGI\n+@HWI-ST132:678:C1LFKACXX:6:1113:19938:48642\n+TCTAGAGGTGGCTCCAGGCTC\n++\n+JJJJJJJIHHHFFFFEDDB@@\n+@HWI-ST132:678:C1LFKACXX:6:1116:10596:49883\n+TCTAGAGGTGGCTCCAGGCTC\n++\n+B?BDFDFFCFHHHJJJJJJJJ\n+@HWI-ST132:678:C1LFKACXX:6:1201:7176:42559\n+TCTAGAGGTGGCTCCAGGCTC\n++\n+:?BDDDFFCF<<<<EGIIJJJ\n+@HWI-ST132:678:C1LFKACXX:6:1204:7366:53049\n+TCTAGAGGTGGCTCCAGGCTC\n++\n+JJJJJJJJHHHFCFDDDDBBB\n+@HWI-ST132:678:C1LFKACXX:6:1205:7458:21533\n+TCTAGAGGTGGCTCCAGGCTC\n++\n+B@BFFDFFDHFHHJJFIJJJJ\n+@HWI-ST132:678:C1LFKACXX:6:1207:18816:23955\n+TCTAGAGGTGGCTCCAGGCTC\n++\n+@BBDFDFFCFHHGHIJIJIJJ\n+@HWI-ST132:678:C1LFKACXX:6:1207:18521:50214\n+TCTAGAGGTGGCTCCAGGCTC\n++\n+JJJIJJJIHHHDAFDDDDBBB\n+@HWI-ST132:678:C1LFKACXX:6:1215:8094:48780\n+TCTAGAGGTGGCTCCAGGCTC\n++\n+?:?DADDD=?::DEEB:<+<:\n+@HWI-ST132:678:C1LFKACXX:6:1302:16933:22023\n+TCTAGAGGTGGCTCCAGGCTC\n++\n+BCBFFFFFFHHHHJJJJJJJJ\n+@HWI-ST132:678:C1LFKACXX:6:1308:15108:32948\n+TCTAGAGGTGGCTCCAGGCTC\n++\n+BCCFFFFFFHHHHJJJIJJJJ\n+@HWI-ST132:678:C1LFKACXX:6:1310:7792:7251\n+TCTAGAGGTGGCTCCAGGCTC\n++\n+BCCFFFFFFHHHHJJIJJJJJ\n+@HWI-ST132:678:C1LFKACXX:6:1310:5500:48225\n+TCTAGAGGTGGCTCCAGGCTC\n++\n+@@CFFFFFFHGHHJJIJJJJJ\n+@HWI-ST132:678:C1LFKACXX:6:1314:12694:59078\n+TCTAGAGGTGGCTCCAGGCTC\n++\n+@@@DFFFFF?FHGGIIEHEHG\n+@HWI-ST132:678:C1LFKACXX:6:1315:4806:7499\n+TCTAGAGGTGGCTCCAGGCTC\n++\n+BBCFFDDFA;DFHIJIIIGII\n+@HWI-ST132:678:C1LFKACXX:6:2101:15514:8580\n+TCTAGAGGTGGCTCCAGGCTC\n++\n+BBBDFDFFFFFHHJJJJJJJJ\n+@HWI-ST132:678:C1LFKACXX:6:2101:13883:37158\n+TCTAGAGGTGGCTCCAGGCTC\n++\n+JGJJJJJIHD;HHFFFFFBBB\n+@HWI-ST132:678:C1LFKACXX:6:2101:14995:100162\n+TCTAGAGGTGGCTCCAGGCTC\n++\n+IGIIGGIHDCA<44224AB:1\n+@HWI-ST132:678:C1LFKACXX:6:2103:10548:14756\n+TCTAGAGGTGGCTCCAGGCTC\n++\n+:B@DFDFFFH<<AEGHHIJIJ\n+@HWI-ST132:678:C1LFKACXX:6:2103:3737:60160\n+TCTAGAGGTGGCTCCAGGCTC\n++\n+B@BDDDEFDFHHHJJJJGIJJ\n+@HWI-ST132:678:C1LFKACXX:6:2104:8921:19194\n+TCTAGAGGTGGCTCCAGGCTC\n++\n+BBBDFFFFAFDFHIJJJJJJJ\n+@HWI-ST132:678:C1LFKACXX:6:2104:15981:63048\n+TCTAGAGGTGGCTCCAGGCTC\n++\n+B@BDDFFFFHHHHIJJJJJJJ\n+@HWI-ST132:678:C1LFKACXX:6:2104:11258:78941\n+TCTAGAGGTGGCTCCAGGCTC\n++\n+BBBFFFFFHH?FHHIJIJIJJ\n+@HWI-ST132:678:C1LFKACXX:6:2106:17344:88675\n+TCTAGAGGTGGCTCCAGGCTC\n++\n+BCCFFFFFFFFHHJJJJJJJJ\n+@HWI-ST132:678:C1LFKACXX:6:2107:1224:28968\n+TCTAGAGGTGGCTCCAGGCTC\n++\n+CGCFFGFEC<DAADA2A4=:=\n+@HWI-ST132:678:C1LFKACXX:6:2107:13563:38548\n+TCTAGAGGTGGCTCCAGGCTC\n++\n+@@@FF?DFHH?HHHIJJJJJJ\n+@HWI-ST132:678:C1LFKACXX:6:2108:9652:62249\n+TCTAGAGGTGGCTCCAGGCTC\n++\n+JJIIJIHGHHFHFFFFFDBB@\n+@HWI-ST132:678:C1LFKACXX:6:2103:10593:14771\n+CTAGAGGTGGCTCCAGGCTCT\n++\n+@BCFDFFAFFHHHJJJGIIJG\n+@HWI-ST132:678:C1LFKACXX:6:1303:18356:53287\n+TAGAGGTGGCTCCAGGCTCTC\n++\n+@@@AA?DDDDDD?F<+AAF??\n+@HWI-ST132:678:C1LFKACXX:6:1116:9986:43842\n+TTTTGTCAAATTTACAATGCA\n++\n+:;?4A+2A:2=CDEE4E@FC4\n+@HWI-ST132:678:C1LFKACXX:6:1204:5313:61167\n+TATTATTTTTGATCAATTGGC\n++\n+GC<GIGEA22<HHFDD7D@==\n+@HWI-ST132:678:C1LFKACXX:6:1303:7540:74272\n+TTTTTGATCAATTGGCACCAT\n++\n+<GGEBEE<CC<>HDD@DD@@@\n+@HWI-ST132:678:C1LFKACXX:6:1306:18477:89522\n+TTTTTGATCAATTGGCACCAT\n++\n+HFBIIIHFHHHDHFDABFC@@\n+@HWI-ST132:678:C1LFKACXX:6:1105:15526:35511\n+TTTTGATCAATTGGCACCATG\n++\n+JJIJIHC:HHHFHFFFFFBCB\n+@HWI-ST132:678:C1LFKACXX:6:1209:1090:70698\n+TTTTGATCAATTGGCACCATG\n++\n+H<?EA<A+HHFFFB?D7D@@@\n+@HWI-ST132:678:C1LFKACXX:6:1313:1351:74638\n+TTTTGATCAATTGGCACCATG\n++\n+IIIJIIIJGHFDFFDDDBB@@\n+@HWI-ST132:678:C1LFKACXX:6:1104:10085:14672\n+TGATCAATTGGCACCATGCGA\n++\n+CCCFFFFFHHHHHJJJJJJJJ\n+@HWI-ST132:678:C1LFKACXX:6:1105:15364:57523\n+TGATCAATTGGCACCATGCGA\n++\n+JIHIJJIGDABHHFED?D@@B\n+@HWI-ST132:678:C1LFKACXX:6:1308:14142:6756\n+TGATCAATTGGCACCATGCGA\n++\n+JJJIJJJIHHHHHFFFFFCCC\n+@HWI-ST132:678:C1LFKACXX:6:2101:15343:9804\n+TAGAGTAT'..b'465:39807\n+TTTATTTCTTCGTTGTCGGCT\n++\n+GC)JIJJJHHHHHFFFFFCCC\n+@HWI-ST132:678:C1LFKACXX:6:1305:18383:99803\n+TTTATTTCTTCGTTGTCGGCT\n++\n+JJIGC>2>3AHHHFFFFFCCC\n+@HWI-ST132:678:C1LFKACXX:6:2102:14700:71462\n+TTTATTTCTTCGTTGTCGGCT\n++\n+FGGHE<+IHHHHHFFFFFBCB\n+@HWI-ST132:678:C1LFKACXX:6:2105:13617:68367\n+TTTATTTCTTCGTTGTCGGCT\n++\n+GC1HE<+IHHHHHDDDDD@@@\n+@HWI-ST132:678:C1LFKACXX:6:2105:19074:82706\n+TTTATTTCTTCGTTGTCGGCT\n++\n+HE1IIIIGF?HHHDDDDD@@@\n+@HWI-ST132:678:C1LFKACXX:6:2105:12588:90115\n+TTTATTTCTTCGTTGTCGGCT\n++\n+JJJJJHJIHFHHHFFFFFCCC\n+@HWI-ST132:678:C1LFKACXX:6:2107:6251:60107\n+TTTATTTCTTCGTTGTCGGCT\n++\n+HB@JJHJIHHHHHFFFFFCCC\n+@HWI-ST132:678:C1LFKACXX:6:2109:11439:45695\n+TTTATTTCTTCGTTGTCGGCT\n++\n+JJJIHGHIFHHHHFFFFFCCC\n+@HWI-ST132:678:C1LFKACXX:6:1211:17814:64440\n+CTTTATTTCTTCGTTGTCGGC\n++\n+IIIIIIIHHHHHHFDB=4?@@\n+@HWI-ST132:678:C1LFKACXX:6:1307:19394:48868\n+CTTTATTTCTTCGTTGTCGGC\n++\n+GF<IHHIJHHHHHFFDDF@@@\n+@HWI-ST132:678:C1LFKACXX:6:1316:17264:85131\n+CTTTATTTCTTCGTTGTCGGC\n++\n+IIIIIIIIHHHHHFDD=4?::\n+@HWI-ST132:678:C1LFKACXX:6:1115:13122:92533\n+GATCTTTATTTCTTCGTTGTC\n++\n+JIIJJJJJHHGHHAFFFD@@;\n+@HWI-ST132:678:C1LFKACXX:6:1116:15851:89973\n+GATCTTTATTTCTTCGTTGTC\n++\n+HFGHFEGGHDHFDFFFFFC@@\n+@HWI-ST132:678:C1LFKACXX:6:1303:3205:5702\n+CTTTTATTTATTGAATCTTCT\n++\n+BCCFFFFFHHHHHHEHIJJJJ\n+@HWI-ST132:678:C1LFKACXX:6:1311:7780:75331\n+TATTATTTTTCCAACTGTTCT\n++\n+@@@FFFEAHHDHHHBGH<IHH\n+@HWI-ST132:678:C1LFKACXX:6:1312:5511:15085\n+TATTATTTTTCCAACTGTTCT\n++\n+@CCFFFFFHHHHH@GIJIIJJ\n+@HWI-ST132:678:C1LFKACXX:6:2107:17724:13368\n+ATTGAGAGTCGGCGTTCGTCA\n++\n+B@BFFFDFFHH:DHIJJJJJJ\n+@HWI-ST132:678:C1LFKACXX:6:1307:8604:58747\n+TTGAGAGTCGGCGTTCGTCAT\n++\n+BBCFDDFDFHFHHGIJJFHIJ\n+@HWI-ST132:678:C1LFKACXX:6:1215:11848:43824\n+TGAGAGTCGGCGTTCGTCATG\n++\n+CCCFFFFFHHHHFHJHGHGII\n+@HWI-ST132:678:C1LFKACXX:6:2109:18960:100005\n+TGAGAGTCGGCGTTCGTCATG\n++\n+=BBF:=2AFCF@0BE?FGHJJ\n+@HWI-ST132:678:C1LFKACXX:6:1209:18683:51205\n+GTCGGCGTTCGTCATGCTCGC\n++\n+BBBFFFFFHFHFHHHHIIJJJ\n+@HWI-ST132:678:C1LFKACXX:6:1213:4432:47194\n+GTCGGCGTTCGTCATGCTCGC\n++\n+@??DDD:DHHDACEAGIEH;G\n+@HWI-ST132:678:C1LFKACXX:6:1309:20184:93600\n+GTCGGCGTTCGTCATGCTCGC\n++\n+@@@D?DDDHHHBAH;FFGGG<\n+@HWI-ST132:678:C1LFKACXX:6:1314:14515:11013\n+AGCGCGAGCATGACGAACGCC\n++\n+JIJIGIHGHDHHGFFFFF@B@\n+@HWI-ST132:678:C1LFKACXX:6:1310:19583:64029\n+CAGCGCGAGCATGACGAACGC\n++\n+JJIHHECBHGHHHFFFFFCCC\n+@HWI-ST132:678:C1LFKACXX:6:2108:10695:38989\n+ACCGATTTTGTGCGGAGCACG\n++\n+@CCFFFFFHHFHHCF@EGIGJ\n+@HWI-ST132:678:C1LFKACXX:6:1209:11040:19674\n+TCTTCACACGTCGGCGATCGA\n++\n+@@@DDFFFFHFFDHJGIDD@G\n+@HWI-ST132:678:C1LFKACXX:6:1116:11668:16725\n+TAAGAATTCCGAAACGCCATC\n++\n+IHEGAG@ED8FDDBBDDD=+?\n+@HWI-ST132:678:C1LFKACXX:6:1208:13565:65937\n+CGATGTGTTTGTTCGCCCGTC\n++\n+@@CFFBDBFHHDFHAFHI)@F\n+@HWI-ST132:678:C1LFKACXX:6:1209:11809:98806\n+AACCTCCTAGTCGCTGTGACT\n++\n+JJIJIJIGGHHHHFFFFFBCB\n+@HWI-ST132:678:C1LFKACXX:6:1206:18658:28841\n+CAGGTTAACCTCCTAGTCGCT\n++\n+JIJJJJJJHHHHHFFFDFCCB\n+@HWI-ST132:678:C1LFKACXX:6:1309:8277:38084\n+CAGGTTAACCTCCTAGTCGCT\n++\n+IIIJIJJIHHHHHFFFDFC@@\n+@HWI-ST132:678:C1LFKACXX:6:2103:17347:32864\n+TTCTTGAACTTGCGAGCACCG\n++\n+CCCFFFFFHHHAAFC3BEHIJ\n+@HWI-ST132:678:C1LFKACXX:6:2107:8602:93094\n+TTCTTGAACTTGCGAGCACCG\n++\n+CCCFFFFFHHHDHCCFFHIJJ\n+@HWI-ST132:678:C1LFKACXX:6:2106:14321:83705\n+TTGCATTAATCTGAAAGTTGC\n++\n+IHIGIJJJHHHHHFFFFFCCC\n+@HWI-ST132:678:C1LFKACXX:6:1306:11622:66870\n+CAAATTGGCTTTCCGTCGACT\n++\n+@@@DFFFFHHGHFHJJEIGHH\n+@HWI-ST132:678:C1LFKACXX:6:1107:16523:27164\n+CCAAGGAGTCGGCAGCTGAAG\n++\n+@@@DDDDDCD?FF1)AEGGII\n+@HWI-ST132:678:C1LFKACXX:6:1206:20690:60805\n+AGTGGGGCCAGAGGGGCTGCT\n++\n+>?:C?:@BFFFCHDADDD@?<\n+@HWI-ST132:678:C1LFKACXX:6:1309:15210:100042\n+CGGCTTTGTCACTGTTTGATC\n++\n+@CBFFFFFHHHHHIGHHIGJJ\n+@HWI-ST132:678:C1LFKACXX:6:2108:11541:97204\n+TATTGAACTGAAGCCCCCGGC\n++\n+CCCFFFFFHHHHGJJJJJ@GG\n+@HWI-ST132:678:C1LFKACXX:6:2102:9712:32185\n+ATTGAACTGAAGCCCCCGGCC\n++\n+?@@BBDBDDFFADHIIIH)?F\n+@HWI-ST132:678:C1LFKACXX:6:1313:12783:74925\n+GAGCGGGTTTGGCCGGGGGCT\n++\n+JJJJJJJJHGHHHDFFFFCCB\n+@HWI-ST132:678:C1LFKACXX:6:2103:17748:30120\n+TGCACGATTCCAATAGTGCTG\n++\n+IJIGCJIJHHHHHFFFFFCCC\n' |
| b |
| diff -r 9645d995fb3c -r 9185ca0a7b43 test-data/fastq_dir/reads-sample-small.fastq-siRNAs-transcripts_uni.fastq --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/fastq_dir/reads-sample-small.fastq-siRNAs-transcripts_uni.fastq Wed Jan 16 08:18:13 2019 -0500 |
| b |
| @@ -0,0 +1,316 @@ +@HWI-ST132:678:C1LFKACXX:6:1215:7425:70721 +TTTAAAAATTCGCGCCCTGAC ++ +GGGBGIIHADHHHFDDFFCC@ +@HWI-ST132:678:C1LFKACXX:6:1107:4740:59863 +CATGTCGTGGCTATACAGGCA ++ +@CCFFFFDDFFHHJJJJJGIJ +@HWI-ST132:678:C1LFKACXX:6:1110:13407:81154 +TATACAGGCAGTAGAGCAGGG ++ +@CCFFFFFGHHHHGIHIJHII +@HWI-ST132:678:C1LFKACXX:6:1208:19446:35829 +TATACAGGCAGTAGAGCAGGG ++ +BCCDDFDFHHHFFHGEFFGIJ +@HWI-ST132:678:C1LFKACXX:6:1311:4516:46469 +TATACAGGCAGTAGAGCAGGG ++ +@@@DFDFF@FHBHIGGGBBGH +@HWI-ST132:678:C1LFKACXX:6:2102:18209:60973 +GTAGTGTCCTCGGCCCCCTGC ++ +IGJJJIHGF@HHFFFFDDBCB +@HWI-ST132:678:C1LFKACXX:6:2107:16133:23528 +CAAGGTAGTGTCCTCGGCCCC ++ +JJIJJIJJHHFFFFFEFFCC@ +@HWI-ST132:678:C1LFKACXX:6:1105:9134:90339 +CCACAAGGTAGTGTCCTCGGC ++ +3<JJJJJHHFFDADDB?FB@@ +@HWI-ST132:678:C1LFKACXX:6:1214:4589:21667 +CCACAAGGTAGTGTCCTCGGC ++ +IGIIHEHGHFFFAFFFFFC@B +@HWI-ST132:678:C1LFKACXX:6:1113:8038:50061 +ATTGTAAGGATTATGGAAGCC ++ +JIIJJJJJHHHHHEDDDDBBB +@HWI-ST132:678:C1LFKACXX:6:1313:3092:45831 +ATTGTAAGGATTATGGAAGCC ++ +JGJHGGGEBFHFHDFDDFC@@ +@HWI-ST132:678:C1LFKACXX:6:1315:9832:44147 +ATTGTAAGGATTATGGAAGCC ++ +IFIGF>E<3FDADDB==A?=1 +@HWI-ST132:678:C1LFKACXX:6:2107:18504:90825 +ATTGTAAGGATTATGGAAGCC ++ +HFFA>2<JHHHFFFFFDFBBB +@HWI-ST132:678:C1LFKACXX:6:1305:2494:20888 +CTTCGTTGTCGGCTTAAGACT ++ +HF9IHDGBHFCFFFEDFFC@@ +@HWI-ST132:678:C1LFKACXX:6:1308:7696:86834 +CTTCGTTGTCGGCTTAAGACT ++ +HJJIIIIHF@DHHFDBFFB@@ +@HWI-ST132:678:C1LFKACXX:6:2103:15073:18548 +CTTCGTTGTCGGCTTAAGACT ++ +JIGGEA<20@0A32224B=14 +@HWI-ST132:678:C1LFKACXX:6:2105:19555:27066 +CTTCGTTGTCGGCTTAAGACT ++ +JJIJJIJIHAHHHFFDFFBCB +@HWI-ST132:678:C1LFKACXX:6:2108:8901:73378 +CTTCGTTGTCGGCTTAAGACT ++ +JJJJJJJJHGHHHFFFFFCBB +@HWI-ST132:678:C1LFKACXX:6:1313:16120:41247 +TCTTCGTTGTCGGCTTAAGAC ++ +F??DE@A@1FFFFDDDDD?8@ +@HWI-ST132:678:C1LFKACXX:6:1314:16626:18588 +TCTTCGTTGTCGGCTTAAGAC ++ +C9FIHHGGAFHHFDBADD@@? +@HWI-ST132:678:C1LFKACXX:6:2108:9483:4135 +TCTTCGTTGTCGGCTTAAGAC ++ +HF9JJJJIHHHHHFFFFFBCB +@HWI-ST132:678:C1LFKACXX:6:1110:13753:56378 +TTTCTTCGTTGTCGGCTTAAG ++ +IIGHE@1IHHHHDFDEFF@@@ +@HWI-ST132:678:C1LFKACXX:6:2108:8693:52625 +TTTCTTCGTTGTCGGCTTAAG ++ +HGIIHIHGHHHHHFFFFFBCB +@HWI-ST132:678:C1LFKACXX:6:1102:14940:58653 +TTATTTCTTCGTTGTCGGCTT ++ +JJJJIHGHDCFHHFFFFFCCB +@HWI-ST132:678:C1LFKACXX:6:1205:17717:14363 +TTATTTCTTCGTTGTCGGCTT ++ +JJJJHGCFHHHHHFFFFFCCC +@HWI-ST132:678:C1LFKACXX:6:1209:4476:91514 +TTATTTCTTCGTTGTCGGCTT ++ +JIJJJIJJHHHHHFFFFFCCC +@HWI-ST132:678:C1LFKACXX:6:2105:20298:47029 +TTATTTCTTCGTTGTCGGCTT ++ +JJJJIGFAHGHHHFFFFFCCC +@HWI-ST132:678:C1LFKACXX:6:1108:9462:85509 +TTTATTTCTTCGTTGTCGGCT ++ +IGFIIFIJHGHHHEFFFFCC@ +@HWI-ST132:678:C1LFKACXX:6:1110:11726:92535 +TTTATTTCTTCGTTGTCGGCT ++ +JIGIHG@IHGHHHFFFFFCCC +@HWI-ST132:678:C1LFKACXX:6:1115:13091:61553 +TTTATTTCTTCGTTGTCGGCT ++ +FFE:FECA?DFFFDDB4+=@? +@HWI-ST132:678:C1LFKACXX:6:1205:13792:13310 +TTTATTTCTTCGTTGTCGGCT ++ +GGHGHGHFAFHHHFFFFFCC@ +@HWI-ST132:678:C1LFKACXX:6:1206:8454:66983 +TTTATTTCTTCGTTGTCGGCT ++ +JJIHGC:IHBHHHFFFFFCCC +@HWI-ST132:678:C1LFKACXX:6:1207:14397:31782 +TTTATTTCTTCGTTGTCGGCT ++ +IG@IHGHIHGHHHFFFFFCCC +@HWI-ST132:678:C1LFKACXX:6:1212:12155:21211 +TTTATTTCTTCGTTGTCGGCT ++ +HGFHHEHHFHHHHFFFFDCCB +@HWI-ST132:678:C1LFKACXX:6:1215:9718:26126 +TTTATTTCTTCGTTGTCGGCT ++ +EHAD@HGGDDDHHDDFFD@@@ +@HWI-ST132:678:C1LFKACXX:6:1303:16630:18638 +TTTATTTCTTCGTTGTCGGCT ++ +HHJJJHIIFHHHHFFFFFCCC +@HWI-ST132:678:C1LFKACXX:6:1305:4465:39807 +TTTATTTCTTCGTTGTCGGCT ++ +GC)JIJJJHHHHHFFFFFCCC +@HWI-ST132:678:C1LFKACXX:6:1305:18383:99803 +TTTATTTCTTCGTTGTCGGCT ++ +JJIGC>2>3AHHHFFFFFCCC +@HWI-ST132:678:C1LFKACXX:6:2102:14700:71462 +TTTATTTCTTCGTTGTCGGCT ++ +FGGHE<+IHHHHHFFFFFBCB +@HWI-ST132:678:C1LFKACXX:6:2105:13617:68367 +TTTATTTCTTCGTTGTCGGCT ++ +GC1HE<+IHHHHHDDDDD@@@ +@HWI-ST132:678:C1LFKACXX:6:2105:19074:82706 +TTTATTTCTTCGTTGTCGGCT ++ +HE1IIIIGF?HHHDDDDD@@@ +@HWI-ST132:678:C1LFKACXX:6:2105:12588:90115 +TTTATTTCTTCGTTGTCGGCT ++ +JJJJJHJIHFHHHFFFFFCCC +@HWI-ST132:678:C1LFKACXX:6:2107:6251:60107 +TTTATTTCTTCGTTGTCGGCT ++ +HB@JJHJIHHHHHFFFFFCCC +@HWI-ST132:678:C1LFKACXX:6:2109:11439:45695 +TTTATTTCTTCGTTGTCGGCT ++ +JJJIHGHIFHHHHFFFFFCCC +@HWI-ST132:678:C1LFKACXX:6:1211:17814:64440 +CTTTATTTCTTCGTTGTCGGC ++ +IIIIIIIHHHHHHFDB=4?@@ +@HWI-ST132:678:C1LFKACXX:6:1307:19394:48868 +CTTTATTTCTTCGTTGTCGGC ++ +GF<IHHIJHHHHHFFDDF@@@ +@HWI-ST132:678:C1LFKACXX:6:1316:17264:85131 +CTTTATTTCTTCGTTGTCGGC ++ +IIIIIIIIHHHHHFDD=4?:: +@HWI-ST132:678:C1LFKACXX:6:1115:13122:92533 +GATCTTTATTTCTTCGTTGTC ++ +JIIJJJJJHHGHHAFFFD@@; +@HWI-ST132:678:C1LFKACXX:6:1116:15851:89973 +GATCTTTATTTCTTCGTTGTC ++ +HFGHFEGGHDHFDFFFFFC@@ +@HWI-ST132:678:C1LFKACXX:6:1303:3205:5702 +CTTTTATTTATTGAATCTTCT ++ +BCCFFFFFHHHHHHEHIJJJJ +@HWI-ST132:678:C1LFKACXX:6:1311:7780:75331 +TATTATTTTTCCAACTGTTCT ++ +@@@FFFEAHHDHHHBGH<IHH +@HWI-ST132:678:C1LFKACXX:6:1312:5511:15085 +TATTATTTTTCCAACTGTTCT ++ +@CCFFFFFHHHHH@GIJIIJJ +@HWI-ST132:678:C1LFKACXX:6:2107:17724:13368 +ATTGAGAGTCGGCGTTCGTCA ++ +B@BFFFDFFHH:DHIJJJJJJ +@HWI-ST132:678:C1LFKACXX:6:1307:8604:58747 +TTGAGAGTCGGCGTTCGTCAT ++ +BBCFDDFDFHFHHGIJJFHIJ +@HWI-ST132:678:C1LFKACXX:6:1215:11848:43824 +TGAGAGTCGGCGTTCGTCATG ++ +CCCFFFFFHHHHFHJHGHGII +@HWI-ST132:678:C1LFKACXX:6:2109:18960:100005 +TGAGAGTCGGCGTTCGTCATG ++ +=BBF:=2AFCF@0BE?FGHJJ +@HWI-ST132:678:C1LFKACXX:6:1209:18683:51205 +GTCGGCGTTCGTCATGCTCGC ++ +BBBFFFFFHFHFHHHHIIJJJ +@HWI-ST132:678:C1LFKACXX:6:1213:4432:47194 +GTCGGCGTTCGTCATGCTCGC ++ +@??DDD:DHHDACEAGIEH;G +@HWI-ST132:678:C1LFKACXX:6:1309:20184:93600 +GTCGGCGTTCGTCATGCTCGC ++ +@@@D?DDDHHHBAH;FFGGG< +@HWI-ST132:678:C1LFKACXX:6:1314:14515:11013 +AGCGCGAGCATGACGAACGCC ++ +JIJIGIHGHDHHGFFFFF@B@ +@HWI-ST132:678:C1LFKACXX:6:1310:19583:64029 +CAGCGCGAGCATGACGAACGC ++ +JJIHHECBHGHHHFFFFFCCC +@HWI-ST132:678:C1LFKACXX:6:2108:10695:38989 +ACCGATTTTGTGCGGAGCACG ++ +@CCFFFFFHHFHHCF@EGIGJ +@HWI-ST132:678:C1LFKACXX:6:1209:11040:19674 +TCTTCACACGTCGGCGATCGA ++ +@@@DDFFFFHFFDHJGIDD@G +@HWI-ST132:678:C1LFKACXX:6:1116:11668:16725 +TAAGAATTCCGAAACGCCATC ++ +IHEGAG@ED8FDDBBDDD=+? +@HWI-ST132:678:C1LFKACXX:6:1208:13565:65937 +CGATGTGTTTGTTCGCCCGTC ++ +@@CFFBDBFHHDFHAFHI)@F +@HWI-ST132:678:C1LFKACXX:6:1209:11809:98806 +AACCTCCTAGTCGCTGTGACT ++ +JJIJIJIGGHHHHFFFFFBCB +@HWI-ST132:678:C1LFKACXX:6:1206:18658:28841 +CAGGTTAACCTCCTAGTCGCT ++ +JIJJJJJJHHHHHFFFDFCCB +@HWI-ST132:678:C1LFKACXX:6:1309:8277:38084 +CAGGTTAACCTCCTAGTCGCT ++ +IIIJIJJIHHHHHFFFDFC@@ +@HWI-ST132:678:C1LFKACXX:6:2103:17347:32864 +TTCTTGAACTTGCGAGCACCG ++ +CCCFFFFFHHHAAFC3BEHIJ +@HWI-ST132:678:C1LFKACXX:6:2107:8602:93094 +TTCTTGAACTTGCGAGCACCG ++ +CCCFFFFFHHHDHCCFFHIJJ +@HWI-ST132:678:C1LFKACXX:6:2106:14321:83705 +TTGCATTAATCTGAAAGTTGC ++ +IHIGIJJJHHHHHFFFFFCCC +@HWI-ST132:678:C1LFKACXX:6:1306:11622:66870 +CAAATTGGCTTTCCGTCGACT ++ +@@@DFFFFHHGHFHJJEIGHH +@HWI-ST132:678:C1LFKACXX:6:1107:16523:27164 +CCAAGGAGTCGGCAGCTGAAG ++ +@@@DDDDDCD?FF1)AEGGII +@HWI-ST132:678:C1LFKACXX:6:1206:20690:60805 +AGTGGGGCCAGAGGGGCTGCT ++ +>?:C?:@BFFFCHDADDD@?< +@HWI-ST132:678:C1LFKACXX:6:1309:15210:100042 +CGGCTTTGTCACTGTTTGATC ++ +@CBFFFFFHHHHHIGHHIGJJ +@HWI-ST132:678:C1LFKACXX:6:2108:11541:97204 +TATTGAACTGAAGCCCCCGGC ++ +CCCFFFFFHHHHGJJJJJ@GG +@HWI-ST132:678:C1LFKACXX:6:2102:9712:32185 +ATTGAACTGAAGCCCCCGGCC ++ +?@@BBDBDDFFADHIIIH)?F +@HWI-ST132:678:C1LFKACXX:6:1313:12783:74925 +GAGCGGGTTTGGCCGGGGGCT ++ +JJJJJJJJHGHHHDFFFFCCB +@HWI-ST132:678:C1LFKACXX:6:2103:17748:30120 +TGCACGATTCCAATAGTGCTG ++ +IJIGCJIJHHHHHFFFFFCCC |
| b |
| diff -r 9645d995fb3c -r 9185ca0a7b43 test-data/fastq_dir/reads-sample-small.fastq_all_mappers.fastq --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/fastq_dir/reads-sample-small.fastq_all_mappers.fastq Wed Jan 16 08:18:13 2019 -0500 |
| b |
| b'@@ -0,0 +1,156160 @@\n+@HWI-ST132:678:C1LFKACXX:6:2109:5620:9149\n+TTTTTAACGAATCTAGTATACCCT\n++\n+B@BDFFFFF?<ADFHHIJJJJJJJ\n+@HWI-ST132:678:C1LFKACXX:6:1213:14882:29587\n+TAATCGAATGCTAATTGTAATT\n++\n+=??AAD?B:<CD>,AFAGF9FA\n+@HWI-ST132:678:C1LFKACXX:6:1315:2668:98246\n+TTAACCGTTTTGAGCTCGGCGACCT\n++\n+1=14BDDDHHHFFIIIIFEA??@FH\n+@HWI-ST132:678:C1LFKACXX:6:1208:17824:38721\n+TCTTTATATTCGTTGGTATTTGGC\n++\n+CCCFFFFFHHH<2><C<CJJJJJJ\n+@HWI-ST132:678:C1LFKACXX:6:1203:15535:47028\n+CCGGGACTGCACAGACGAAGCGG\n++\n+@C@FFFFFHHHHHJJJIHIIIIJ\n+@HWI-ST132:678:C1LFKACXX:6:1213:1288:58514\n+AGATTCATGTTCGGATCGTCGATAC\n++\n+@C@FFFFFHHHHHIJBHIJJJJJIJ\n+@HWI-ST132:678:C1LFKACXX:6:2102:10820:38797\n+CGCTTCTTTTGAATGCGTCGTGGTG\n++\n+CCCFFFFFHHHHHJ,AGHI@<?HCG\n+@HWI-ST132:678:C1LFKACXX:6:1106:17295:99240\n+GCTGCCGCGATTCCCAAACCGTCCTG\n++\n+B@BDDFFFF?@DFEH<EGIGIJIJJJ\n+@HWI-ST132:678:C1LFKACXX:6:2101:14809:65434\n+TCCTGAGAGTCTGGTCACCGTAGAG\n++\n+CCCF?EFFHHHFHJHJJJJ3343<A\n+@HWI-ST132:678:C1LFKACXX:6:1103:14549:53735\n+ACCGTAGAGAATCTGAGCGTCAGAA\n++\n+@CCFDFFFGFHHHJGDGHGGHIJIJ\n+@HWI-ST132:678:C1LFKACXX:6:1301:3547:24519\n+CACCAGTCGGCAATATAGATCTCCT\n++\n+BCBFFFDFHHHHHJJJJJJJJJJJJ\n+@HWI-ST132:678:C1LFKACXX:6:1303:14743:8078\n+TCTATATTGCCGACTGGTGGCTCAGT\n++\n+BCBFDFFFHHHHHJJHFCFGGGHIJJ\n+@HWI-ST132:678:C1LFKACXX:6:1309:19811:76863\n+TCCTTGGCGGAGGTATCGTAGTGAG\n++\n+CCCFFFFFHHFHH?FHJJJJJHJIJ\n+@HWI-ST132:678:C1LFKACXX:6:2104:9716:27077\n+GTACTCGATCGCCTGAAGAAC\n++\n+@@CFFFFFHHCFHI+AEHHII\n+@HWI-ST132:678:C1LFKACXX:6:1310:11218:64506\n+TTCCGGATTGGCAATACCCGCCTC\n++\n+CCCFFFFFHHHHHGI<GHIJIIJJ\n+@HWI-ST132:678:C1LFKACXX:6:1306:4247:15664\n+TTACAAAGTCAGTGGGGATGC\n++\n+@@@FFFFFFFHFCGGE<F@A<\n+@HWI-ST132:678:C1LFKACXX:6:1308:7854:98971\n+TTTGGCAAGAGGCGGCTCCTCCTG\n++\n+@@BFFFFFHHDFHEHGIJIIIJII\n+@HWI-ST132:678:C1LFKACXX:6:2104:8198:11388\n+TCTGTTGGCAGCTAGATCAGGGGC\n++\n+BCCFDFFFHHFHHGIIJJJJJJJJ\n+@HWI-ST132:678:C1LFKACXX:6:1302:8323:14904\n+TCTGTTGGCAGCTAGATCAGGGG\n++\n+BBCFDEDFHA<DFHFFHIJJJJJ\n+@HWI-ST132:678:C1LFKACXX:6:2102:13088:36303\n+TACTTGAGGACATAGACAAACATTG\n++\n+BBCFFFFFD=CFHH+AEHIJJJJJJ\n+@HWI-ST132:678:C1LFKACXX:6:1107:9391:35335\n+TCCAGAACAGGTCTGTGGGACTGATC\n++\n+CCCFFFFFHHHDHI3<EGIIJJJJJJ\n+@HWI-ST132:678:C1LFKACXX:6:1209:13917:31506\n+TATCCAGAACAGGTCTGTGGGAC\n++\n+CCCFFFFFHHH?FFHJJIJJJJJ\n+@HWI-ST132:678:C1LFKACXX:6:1210:16851:33080\n+TCCATAATCCTGACCATCCGGGCAG\n++\n+CC@FFFFFHHHHGIJIJJJJIJJJJ\n+@HWI-ST132:678:C1LFKACXX:6:2104:16032:57923\n+CCCGGATGGTCAGGATTATGGAAGC\n++\n+CCCFFFFFHFHHHGHIIIIIJJJJJ\n+@HWI-ST132:678:C1LFKACXX:6:1109:16268:61514\n+TACGGTAGAACAACTACACCGAGTGGT\n++\n+@CCFFDDDGBHHHJIIIJJJJJJFHGI\n+@HWI-ST132:678:C1LFKACXX:6:1210:7403:36822\n+TTTGCTCGACCACTCGGTGTAGTTGT\n++\n+CCCFFFFFHHHHHJJEE<ACGIIIJI\n+@HWI-ST132:678:C1LFKACXX:6:1303:14362:59821\n+TTTGCTCGACCACTCGGTGTAGT\n++\n+@C@FFFFFHHHFHIJFEA+@CFH\n+@HWI-ST132:678:C1LFKACXX:6:1304:17199:58363\n+AAAAACACGACCGTTCGCTTTGAAA\n++\n+@CCFBDDFHFHHHHIJJJJJJIJJJ\n+@HWI-ST132:678:C1LFKACXX:6:2106:15381:40802\n+TTCAAAGCGAACGGTCGTGTTTTT\n++\n+CCCFFFFFHHHHHJFEGEC?HHII\n+@HWI-ST132:678:C1LFKACXX:6:1114:10027:77795\n+AAGATTATTAAAAACCACTGCTG\n++\n+@@@D;;DDABF,AA?:ECEFE<<\n+@HWI-ST132:678:C1LFKACXX:6:2103:3486:88354\n+CTTTAATTATCATATATTGTA\n++\n+BBBD;=ABFHHHHJJJJJDJI\n+@HWI-ST132:678:C1LFKACXX:6:1302:14522:72647\n+TTATTAAAGATCCGTTCGCTTCGCGAG\n++\n+CC@FFFFFHFHHHJHIJIJJJGGGIII\n+@HWI-ST132:678:C1LFKACXX:6:1103:11536:23013\n+TATTAAAGATCCGTTCGCTTCGCGAG\n++\n+B@@FBDDFHHHHHIIJIJJIJJJJIG\n+@HWI-ST132:678:C1LFKACXX:6:1206:10262:20669\n+TATTAAAGATCCGTTCGCTTCGCGAG\n++\n+@@@DDDDDH8FHHGDHII:CHHIIBF\n+@HWI-ST132:678:C1LFKACXX:6:1212:12068:74880\n+TTAAAGATCCGTTCGCTTCGCGAG\n++\n+CCCFDFDDHHHBBGC@FHFFDEGF\n+@HWI-ST132:678:C1LFKACXX:6:1213:19350:18162\n+TTAAAGATCCGTTCGCTTCGCGAG\n++\n+CCCFFFDFHHHHHIHIJIIJJHHI\n+@HWI-ST132:678:C1LFKACXX:6:1307:12279:8790\n+TTAAAGATCCGTTCGCTTCGCGAG\n++\n+???DDDBDDDDDDI1CEEIIII)C\n+@HWI-ST132:678:C1LFKACXX:6:1105:11371:76507\n+TTAAAGATCCGTTCGCTTCGCGAGTG\n++\n+BCCFFFFFHHFDFH)CGIJJIJIIDH\n+@HWI-ST132:678:C1LFKACXX:6:1101:3613:56171\n+TGATTTGTGCAGTAGTTTAAACAA\n++\n+BC@FFFFDHHHHHIJHHIJJJJJJ\n+@HWI-ST132:678:C1LFKACXX:6:1315:11705:87614\n+ACCGCACGAGAGCAGTCT'..b'276\n+GATCCCAGATCCGCTGTGTTT\n++\n+CCCFFFFFHHHHHIJFGHHIJ\n+@HWI-ST132:678:C1LFKACXX:6:1213:14045:90482\n+ATACTAGATTCGTTGAAAAGT\n++\n+@@@F7DDDFA<CC?;FAEBH?\n+@HWI-ST132:678:C1LFKACXX:6:1302:4633:32096\n+TGTTGCGGCAACTTCTTTAAGTTG\n++\n+CCCFFFFFHHHHHJJJJJJJJHIJ\n+@HWI-ST132:678:C1LFKACXX:6:2107:6041:64276\n+TGGCCTAATGGATAAGGCGTCGGACT\n++\n+@CCFFFDFHHHHHIJJJJ<FHIJJJJ\n+@HWI-ST132:678:C1LFKACXX:6:1112:9014:81599\n+TTCGGATCCGAAGATTGCAGG\n++\n+@CCFFDFFHGGGGDCEGIJJJ\n+@HWI-ST132:678:C1LFKACXX:6:2105:11875:25254\n+CGAAGATTGCAGGTTCGAGTC\n++\n+CC@FFFFFHHHFCAFHIJ+AH\n+@HWI-ST132:678:C1LFKACXX:6:2101:16974:2305\n+ACCGTTCTATGCTTTTTTTT\n++\n+:BBDDDDFHH<2<CFHIIJJ\n+@HWI-ST132:678:C1LFKACXX:6:1313:11404:80054\n+ACCGTTCTATGCTTTTTTTTA\n++\n+@@CFBDFF?FHHGIIIIGIIC\n+@HWI-ST132:678:C1LFKACXX:6:1116:12125:58757\n+AAGTAGCAGTCGTGGCCGAGTG\n++\n+??+4=B?DDHHF<EGHGGGIDG\n+@HWI-ST132:678:C1LFKACXX:6:1205:9493:45438\n+GCAGTCGTGGCCGAGTGG\n++\n+BCCFDFFFHHHHHIDCFH\n+@HWI-ST132:678:C1LFKACXX:6:1207:2720:86231\n+GCAGTCGTGGCCGAGTGG\n++\n+@@@FFFFDHHHGFIG2AF\n+@HWI-ST132:678:C1LFKACXX:6:1214:18091:41339\n+GCAGTCGTGGCCGAGTGGTTAAGG\n++\n+?@:4ABDDHHFHFDGCGDFHFGIG\n+@HWI-ST132:678:C1LFKACXX:6:1309:18921:24185\n+GCAGTCGTGGCCGAGTGGTTAAGG\n++\n+@CCFDFFFHHHHHI@ACGFHIIIJ\n+@HWI-ST132:678:C1LFKACXX:6:1106:1391:88663\n+GCAGTCGTGGCCGAGTGGTTAAGGC\n++\n+@@@FDEDDAFHHHJH+AFFHIJEHG\n+@HWI-ST132:678:C1LFKACXX:6:1310:15410:68712\n+GCAGTCGTGGCCGAGTGGTTAAGGC\n++\n+@@@DDFFFHHHHH?EEGHIJHIEEH\n+@HWI-ST132:678:C1LFKACXX:6:1202:15769:84946\n+AGCGTAGGTTCGAATCCT\n++\n+?@@D=ADDHHFDHFGGIG\n+@HWI-ST132:678:C1LFKACXX:6:2105:13686:25294\n+AGCGTAGGTTCGAATCCT\n++\n+BCCFFFFFFHHDDHHIJJ\n+@HWI-ST132:678:C1LFKACXX:6:1106:17247:63193\n+AATCCTACCGGCTGCGAATGA\n++\n+@BBFFDEFHFHHHFFFFHGHJ\n+@HWI-ST132:678:C1LFKACXX:6:1107:17291:97995\n+ATCCTACCGGCTGCGAATGA\n++\n+@CCFFFFFDFFHHJGEHGBG\n+@HWI-ST132:678:C1LFKACXX:6:2105:5531:13237\n+ACCGGCTGCGAATGAGAA\n++\n+B@BFFFFFGHDFCFHEGI\n+@HWI-ST132:678:C1LFKACXX:6:1111:11783:45506\n+ACCGGCTGCGAATGAGAATGT\n++\n+???DFFFFFHF:CCCGHHBG<\n+@HWI-ST132:678:C1LFKACXX:6:2105:11033:71535\n+CGGCTGCGAATGAGAATGTATATTT\n++\n+?BBDFFFF@<@ACAAEHHHGGIJJI\n+@HWI-ST132:678:C1LFKACXX:6:2103:20548:80488\n+AATGAGAATGTATATTTT\n++\n+BCBDDFFFHHFHHJJJJJ\n+@HWI-ST132:678:C1LFKACXX:6:1213:10954:88904\n+GCAGTCGTGGCCGAGTGG\n++\n+B@CFFFFFFHGFHGIFHI\n+@HWI-ST132:678:C1LFKACXX:6:1301:8478:85932\n+GCAGTCGTGGCCGAGTGG\n++\n+@CCFDFFDFHHHHGHAFG\n+@HWI-ST132:678:C1LFKACXX:6:2101:5467:98324\n+GCAGTCGTGGCCGAGTGG\n++\n+@@CFFDFFHHGHH>GAGH\n+@HWI-ST132:678:C1LFKACXX:6:2107:20194:63182\n+GCAGTCGTGGCCGAGTGG\n++\n+BCCFFFFFHGHHHBH<EH\n+@HWI-ST132:678:C1LFKACXX:6:1116:13015:74545\n+GCAGTCGTGGCCGAGTGGTTAAGGC\n++\n+B@:BDDFDFHFFFBG2CDHGGGFHI\n+@HWI-ST132:678:C1LFKACXX:6:1209:1463:48119\n+GCAGTCGTGGCCGAGTGGTTAAGGC\n++\n+BCCFDFDDHHHHHJJFHIIJJJIJJ\n+@HWI-ST132:678:C1LFKACXX:6:1313:4928:7411\n+GCAGTCGTGGCCGAGTGGTTAAGGC\n++\n+@C@FFDFFHHFHHJJAEGGHGIIJI\n+@HWI-ST132:678:C1LFKACXX:6:1113:20573:45425\n+AGTCGTGGCCGAGTGGTTAAGGC\n++\n+CCCFFFFFFHHHH?EHHHIIJJJ\n+@HWI-ST132:678:C1LFKACXX:6:2109:6492:70002\n+GTCGTGGCCGAGTGGTTAAGGC\n++\n+CCCFFFFFGHG@2<EAFHGGJI\n+@HWI-ST132:678:C1LFKACXX:6:1104:13333:89311\n+TTAAGGCGTCTGACTCGAAATCAGA\n++\n+CCCFFFFFHHHHHIIJJGGIJJJJJ\n+@HWI-ST132:678:C1LFKACXX:6:1306:7606:88539\n+TGACTCGAAATCAGATTCCCTCTG\n++\n+CCCFFFFFHHHHHJJJIJGIJJJJ\n+@HWI-ST132:678:C1LFKACXX:6:2108:19159:27727\n+ATATAGCCTGAGCTTCGACC\n++\n+CCCFFFDFHHH?FHIJJJJJ\n+@HWI-ST132:678:C1LFKACXX:6:1211:6213:41030\n+TCGGATCCGAAGATTGCAGG\n++\n+@@CFFFFFDHHGHEHEFFHI\n+@HWI-ST132:678:C1LFKACXX:6:1203:8956:45599\n+AGATTGCAGGTTCGAGTCCT\n++\n+@@@DFFFFHHFHH<A<AEHH\n+@HWI-ST132:678:C1LFKACXX:6:1303:5477:98042\n+GTAACTGACCGTGTGGCCCAATGGA\n++\n+??@DFFFFGHDHGG?GGIEH3<FGH\n+@HWI-ST132:678:C1LFKACXX:6:1315:9507:45115\n+AAGATTGCAGGTTCGAGTC\n++\n+@@@:BDDDAFHHFIIGHFA\n+@HWI-ST132:678:C1LFKACXX:6:1306:9972:7484\n+AAGATTGCAGGTTCGAGTCCT\n++\n+@@CFFFFAFFHHHG@GEBGHH\n+@HWI-ST132:678:C1LFKACXX:6:1303:16006:44426\n+AGATTGCAGGTTCGAGTCCT\n++\n+@@@FFFFFDHDFHCE<AEHI\n+@HWI-ST132:678:C1LFKACXX:6:1214:13442:64117\n+AATGGATAAGGCGTCGGA\n++\n+818A:3ADHHFBFC1@FB\n+@HWI-ST132:678:C1LFKACXX:6:1214:1663:16969\n+ATTGCAGGTTCGAGTCCTG\n++\n+@@@FDFFFCFFHHIGHIIJ\n' |
| b |
| diff -r 9645d995fb3c -r 9185ca0a7b43 test-data/fastq_dir/reads-sample-small.fastq_unique_mappers.fastq --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/fastq_dir/reads-sample-small.fastq_unique_mappers.fastq Wed Jan 16 08:18:13 2019 -0500 |
| b |
| b'@@ -0,0 +1,155964 @@\n+@HWI-ST132:678:C1LFKACXX:6:2109:5620:9149\n+TTTTTAACGAATCTAGTATACCCT\n++\n+B@BDFFFFF?<ADFHHIJJJJJJJ\n+@HWI-ST132:678:C1LFKACXX:6:1213:14882:29587\n+TAATCGAATGCTAATTGTAATT\n++\n+=??AAD?B:<CD>,AFAGF9FA\n+@HWI-ST132:678:C1LFKACXX:6:1315:2668:98246\n+TTAACCGTTTTGAGCTCGGCGACCT\n++\n+1=14BDDDHHHFFIIIIFEA??@FH\n+@HWI-ST132:678:C1LFKACXX:6:1208:17824:38721\n+TCTTTATATTCGTTGGTATTTGGC\n++\n+CCCFFFFFHHH<2><C<CJJJJJJ\n+@HWI-ST132:678:C1LFKACXX:6:1203:15535:47028\n+CCGGGACTGCACAGACGAAGCGG\n++\n+@C@FFFFFHHHHHJJJIHIIIIJ\n+@HWI-ST132:678:C1LFKACXX:6:1213:1288:58514\n+AGATTCATGTTCGGATCGTCGATAC\n++\n+@C@FFFFFHHHHHIJBHIJJJJJIJ\n+@HWI-ST132:678:C1LFKACXX:6:2102:10820:38797\n+CGCTTCTTTTGAATGCGTCGTGGTG\n++\n+CCCFFFFFHHHHHJ,AGHI@<?HCG\n+@HWI-ST132:678:C1LFKACXX:6:1106:17295:99240\n+GCTGCCGCGATTCCCAAACCGTCCTG\n++\n+B@BDDFFFF?@DFEH<EGIGIJIJJJ\n+@HWI-ST132:678:C1LFKACXX:6:2101:14809:65434\n+TCCTGAGAGTCTGGTCACCGTAGAG\n++\n+CCCF?EFFHHHFHJHJJJJ3343<A\n+@HWI-ST132:678:C1LFKACXX:6:1103:14549:53735\n+ACCGTAGAGAATCTGAGCGTCAGAA\n++\n+@CCFDFFFGFHHHJGDGHGGHIJIJ\n+@HWI-ST132:678:C1LFKACXX:6:1301:3547:24519\n+CACCAGTCGGCAATATAGATCTCCT\n++\n+BCBFFFDFHHHHHJJJJJJJJJJJJ\n+@HWI-ST132:678:C1LFKACXX:6:1303:14743:8078\n+TCTATATTGCCGACTGGTGGCTCAGT\n++\n+BCBFDFFFHHHHHJJHFCFGGGHIJJ\n+@HWI-ST132:678:C1LFKACXX:6:1309:19811:76863\n+TCCTTGGCGGAGGTATCGTAGTGAG\n++\n+CCCFFFFFHHFHH?FHJJJJJHJIJ\n+@HWI-ST132:678:C1LFKACXX:6:2104:9716:27077\n+GTACTCGATCGCCTGAAGAAC\n++\n+@@CFFFFFHHCFHI+AEHHII\n+@HWI-ST132:678:C1LFKACXX:6:1310:11218:64506\n+TTCCGGATTGGCAATACCCGCCTC\n++\n+CCCFFFFFHHHHHGI<GHIJIIJJ\n+@HWI-ST132:678:C1LFKACXX:6:1306:4247:15664\n+TTACAAAGTCAGTGGGGATGC\n++\n+@@@FFFFFFFHFCGGE<F@A<\n+@HWI-ST132:678:C1LFKACXX:6:1308:7854:98971\n+TTTGGCAAGAGGCGGCTCCTCCTG\n++\n+@@BFFFFFHHDFHEHGIJIIIJII\n+@HWI-ST132:678:C1LFKACXX:6:2104:8198:11388\n+TCTGTTGGCAGCTAGATCAGGGGC\n++\n+BCCFDFFFHHFHHGIIJJJJJJJJ\n+@HWI-ST132:678:C1LFKACXX:6:1302:8323:14904\n+TCTGTTGGCAGCTAGATCAGGGG\n++\n+BBCFDEDFHA<DFHFFHIJJJJJ\n+@HWI-ST132:678:C1LFKACXX:6:2102:13088:36303\n+TACTTGAGGACATAGACAAACATTG\n++\n+BBCFFFFFD=CFHH+AEHIJJJJJJ\n+@HWI-ST132:678:C1LFKACXX:6:1107:9391:35335\n+TCCAGAACAGGTCTGTGGGACTGATC\n++\n+CCCFFFFFHHHDHI3<EGIIJJJJJJ\n+@HWI-ST132:678:C1LFKACXX:6:1209:13917:31506\n+TATCCAGAACAGGTCTGTGGGAC\n++\n+CCCFFFFFHHH?FFHJJIJJJJJ\n+@HWI-ST132:678:C1LFKACXX:6:1210:16851:33080\n+TCCATAATCCTGACCATCCGGGCAG\n++\n+CC@FFFFFHHHHGIJIJJJJIJJJJ\n+@HWI-ST132:678:C1LFKACXX:6:2104:16032:57923\n+CCCGGATGGTCAGGATTATGGAAGC\n++\n+CCCFFFFFHFHHHGHIIIIIJJJJJ\n+@HWI-ST132:678:C1LFKACXX:6:1109:16268:61514\n+TACGGTAGAACAACTACACCGAGTGGT\n++\n+@CCFFDDDGBHHHJIIIJJJJJJFHGI\n+@HWI-ST132:678:C1LFKACXX:6:1210:7403:36822\n+TTTGCTCGACCACTCGGTGTAGTTGT\n++\n+CCCFFFFFHHHHHJJEE<ACGIIIJI\n+@HWI-ST132:678:C1LFKACXX:6:1303:14362:59821\n+TTTGCTCGACCACTCGGTGTAGT\n++\n+@C@FFFFFHHHFHIJFEA+@CFH\n+@HWI-ST132:678:C1LFKACXX:6:1304:17199:58363\n+AAAAACACGACCGTTCGCTTTGAAA\n++\n+@CCFBDDFHFHHHHIJJJJJJIJJJ\n+@HWI-ST132:678:C1LFKACXX:6:2106:15381:40802\n+TTCAAAGCGAACGGTCGTGTTTTT\n++\n+CCCFFFFFHHHHHJFEGEC?HHII\n+@HWI-ST132:678:C1LFKACXX:6:1114:10027:77795\n+AAGATTATTAAAAACCACTGCTG\n++\n+@@@D;;DDABF,AA?:ECEFE<<\n+@HWI-ST132:678:C1LFKACXX:6:2103:3486:88354\n+CTTTAATTATCATATATTGTA\n++\n+BBBD;=ABFHHHHJJJJJDJI\n+@HWI-ST132:678:C1LFKACXX:6:1302:14522:72647\n+TTATTAAAGATCCGTTCGCTTCGCGAG\n++\n+CC@FFFFFHFHHHJHIJIJJJGGGIII\n+@HWI-ST132:678:C1LFKACXX:6:1103:11536:23013\n+TATTAAAGATCCGTTCGCTTCGCGAG\n++\n+B@@FBDDFHHHHHIIJIJJIJJJJIG\n+@HWI-ST132:678:C1LFKACXX:6:1206:10262:20669\n+TATTAAAGATCCGTTCGCTTCGCGAG\n++\n+@@@DDDDDH8FHHGDHII:CHHIIBF\n+@HWI-ST132:678:C1LFKACXX:6:1212:12068:74880\n+TTAAAGATCCGTTCGCTTCGCGAG\n++\n+CCCFDFDDHHHBBGC@FHFFDEGF\n+@HWI-ST132:678:C1LFKACXX:6:1213:19350:18162\n+TTAAAGATCCGTTCGCTTCGCGAG\n++\n+CCCFFFDFHHHHHIHIJIIJJHHI\n+@HWI-ST132:678:C1LFKACXX:6:1307:12279:8790\n+TTAAAGATCCGTTCGCTTCGCGAG\n++\n+???DDDBDDDDDDI1CEEIIII)C\n+@HWI-ST132:678:C1LFKACXX:6:1105:11371:76507\n+TTAAAGATCCGTTCGCTTCGCGAGTG\n++\n+BCCFFFFFHHFDFH)CGIJJIJIIDH\n+@HWI-ST132:678:C1LFKACXX:6:1101:3613:56171\n+TGATTTGTGCAGTAGTTTAAACAA\n++\n+BC@FFFFDHHHHHIJHHIJJJJJJ\n+@HWI-ST132:678:C1LFKACXX:6:1315:11705:87614\n+ACCGCACGAGAGCAGTCT'..b'TAGTATCT\n++\n+???>B,ADAADDDAB4<4AFB\n+@HWI-ST132:678:C1LFKACXX:6:2109:9914:52085\n+TACTACACTTTGATCTTAGCC\n++\n+@C@FBDDFHHHCFIJJIIIII\n+@HWI-ST132:678:C1LFKACXX:6:2102:1701:35741\n+GGCTAAGATCAAAGTGTAGTA\n++\n+BB?DDDEBFDFHFHIIJHIJG\n+@HWI-ST132:678:C1LFKACXX:6:1202:8828:29937\n+ATCGCTTCTCGGCCTTATGGC\n++\n+@@@DDDDDFF:+<@EGEI4AE\n+@HWI-ST132:678:C1LFKACXX:6:2104:17481:85616\n+ATCGCTTCTCGGCCTTATGGC\n++\n+CCCFFFFFHHHAFHJJJJHGG\n+@HWI-ST132:678:C1LFKACXX:6:1212:17759:93921\n+TCTGGTTTCTCTTCAATTGTCGAA\n++\n+CCCFFDFFHHHHHJIIJJJJJIIH\n+@HWI-ST132:678:C1LFKACXX:6:2104:8345:10717\n+TCTGGTTTCTCTTCAATTGTCGAA\n++\n+BCBFFDFFHHHHHJHGGIHJJIJJ\n+@HWI-ST132:678:C1LFKACXX:6:2101:6634:31854\n+TCTGGTTTCTCTTCAATTGTCGAATA\n++\n+B@BDDBDFHHHHHIIJJJJHHIIJJI\n+@HWI-ST132:678:C1LFKACXX:6:1209:12786:26644\n+TTCAATTGTCGAATAAATC\n++\n+=?BDDDFFHH<>ACDHIIH\n+@HWI-ST132:678:C1LFKACXX:6:1209:18048:62736\n+TCAATTGTCGAATAAATCTTTCGCCT\n++\n+BBCFFFFDHCFFHGHDGEHIGIIIII\n+@HWI-ST132:678:C1LFKACXX:6:1105:18208:78501\n+TACTAAAGATTTCCGTGGAGA\n++\n+CC@FFFFFHHHHGIIIBEGGI\n+@HWI-ST132:678:C1LFKACXX:6:1304:17498:41952\n+TAAAGATTTCCGTGGAGAGGAACAC\n++\n+@CCFFFFFH?HA2AFFEBGGIJIGI\n+@HWI-ST132:678:C1LFKACXX:6:1111:20383:95318\n+ATTTCCGTGGAGAGGAACACTCTAA\n++\n+?BBFFFFDF@BFBHGHJJIJJJJJJ\n+@HWI-ST132:678:C1LFKACXX:6:1308:3875:44175\n+TTTCCGTGGAGAGGAACACTCTAAT\n++\n+?@@=DD;D>CAADB9GGBHGHHEHH\n+@HWI-ST132:678:C1LFKACXX:6:1106:2389:76347\n+TCCGTGGAGAGGAACACTCTAATGAGTC\n++\n+@@@D??DDHF?=FGB?FGE4CHHBC<CE\n+@HWI-ST132:678:C1LFKACXX:6:1115:16622:79776\n+TTTTATTGAGGCCTGATAAC\n++\n+??B=BDFADCFHHJJGIJJJ\n+@HWI-ST132:678:C1LFKACXX:6:1116:4776:14732\n+TTTTATTGAGGCCTGATAAC\n++\n+:=?BBAD?FCFF1CF9F@FH\n+@HWI-ST132:678:C1LFKACXX:6:1309:10904:34703\n+TTTTATTGAGGCCTGATAAC\n++\n+@@@DDDDDF?FFBGGECFHF\n+@HWI-ST132:678:C1LFKACXX:6:2104:17165:61168\n+TTTTATTGAGGCCTGATAACTTA\n++\n+B@CFDFFFHHFHHJGHHJJJIH@\n+@HWI-ST132:678:C1LFKACXX:6:1110:7504:42025\n+TTTTATTGAGGCCTGATAACTTATG\n++\n+@CCFFDFEHDHHGJJIFHJJJJJJJ\n+@HWI-ST132:678:C1LFKACXX:6:1105:3736:74280\n+TTTATTGAGGCCTGATAAC\n++\n+?;@BDD4B+=CF<ECEC<F\n+@HWI-ST132:678:C1LFKACXX:6:1114:8935:54596\n+TTTATTGAGGCCTGATAAC\n++\n+?@@DD?DBFF7FHIIIIGI\n+@HWI-ST132:678:C1LFKACXX:6:1208:18583:40303\n+TTTATTGAGGCCTGATAAC\n++\n+BCBDFFFFHHHHHHIIIIJ\n+@HWI-ST132:678:C1LFKACXX:6:1209:18835:53497\n+TTTATTGAGGCCTGATAAC\n++\n+@BCDFFDEFHFHHJIJJIJ\n+@HWI-ST132:678:C1LFKACXX:6:1306:9714:54959\n+TTTATTGAGGCCTGATAAC\n++\n+BBBDDFFFFFHHHJJJJJJ\n+@HWI-ST132:678:C1LFKACXX:6:1315:9439:5750\n+TTTATTGAGGCCTGATAAC\n++\n+BCBDDFEFHHHHHJIJJIJ\n+@HWI-ST132:678:C1LFKACXX:6:2108:7718:72736\n+TTTATTGAGGCCTGATAAC\n++\n+B@BDDFDDFDFHHFGHIJJ\n+@HWI-ST132:678:C1LFKACXX:6:1304:3050:15239\n+TTATTGAGGCCTGATAAC\n++\n+@@@FFF<DFHHHH3CGHI\n+@HWI-ST132:678:C1LFKACXX:6:1305:10473:68713\n+TTATTGAGGCCTGATAAC\n++\n+@CCFFFDAFHHHHJJFIJ\n+@HWI-ST132:678:C1LFKACXX:6:1314:14439:63568\n+TTATTGAGGCCTGATAAC\n++\n+@@@FFFFFGHGGHGI4CF\n+@HWI-ST132:678:C1LFKACXX:6:1104:16518:94276\n+GATCCCAGATCCGCTGTGTTT\n++\n+CCCFFFFFHHHHHIJFGHHIJ\n+@HWI-ST132:678:C1LFKACXX:6:1213:14045:90482\n+ATACTAGATTCGTTGAAAAGT\n++\n+@@@F7DDDFA<CC?;FAEBH?\n+@HWI-ST132:678:C1LFKACXX:6:1302:4633:32096\n+TGTTGCGGCAACTTCTTTAAGTTG\n++\n+CCCFFFFFHHHHHJJJJJJJJHIJ\n+@HWI-ST132:678:C1LFKACXX:6:2107:6041:64276\n+TGGCCTAATGGATAAGGCGTCGGACT\n++\n+@CCFFFDFHHHHHIJJJJ<FHIJJJJ\n+@HWI-ST132:678:C1LFKACXX:6:2101:16974:2305\n+ACCGTTCTATGCTTTTTTTT\n++\n+:BBDDDDFHH<2<CFHIIJJ\n+@HWI-ST132:678:C1LFKACXX:6:1313:11404:80054\n+ACCGTTCTATGCTTTTTTTTA\n++\n+@@CFBDFF?FHHGIIIIGIIC\n+@HWI-ST132:678:C1LFKACXX:6:1116:12125:58757\n+AAGTAGCAGTCGTGGCCGAGTG\n++\n+??+4=B?DDHHF<EGHGGGIDG\n+@HWI-ST132:678:C1LFKACXX:6:1106:17247:63193\n+AATCCTACCGGCTGCGAATGA\n++\n+@BBFFDEFHFHHHFFFFHGHJ\n+@HWI-ST132:678:C1LFKACXX:6:1107:17291:97995\n+ATCCTACCGGCTGCGAATGA\n++\n+@CCFFFFFDFFHHJGEHGBG\n+@HWI-ST132:678:C1LFKACXX:6:2105:5531:13237\n+ACCGGCTGCGAATGAGAA\n++\n+B@BFFFFFGHDFCFHEGI\n+@HWI-ST132:678:C1LFKACXX:6:1111:11783:45506\n+ACCGGCTGCGAATGAGAATGT\n++\n+???DFFFFFHF:CCCGHHBG<\n+@HWI-ST132:678:C1LFKACXX:6:2105:11033:71535\n+CGGCTGCGAATGAGAATGTATATTT\n++\n+?BBDFFFF@<@ACAAEHHHGGIJJI\n+@HWI-ST132:678:C1LFKACXX:6:2103:20548:80488\n+AATGAGAATGTATATTTT\n++\n+BCBDDFFFHHFHHJJJJJ\n' |
| b |
| diff -r 9645d995fb3c -r 9185ca0a7b43 test-data/fastq_dir/reads-sample-small.fastq_unmapped.fastq --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/fastq_dir/reads-sample-small.fastq_unmapped.fastq Wed Jan 16 08:18:13 2019 -0500 |
| b |
| b'@@ -0,0 +1,26120 @@\n+@HWI-ST132:678:C1LFKACXX:6:1103:5043:24327\n+TCTGTCGTGCATTGTCGG\n++\n+IHFC<HHHHHDFFFFCCB\n+@HWI-ST132:678:C1LFKACXX:6:1101:19372:1918\n+AGAATTGTGACCTGAATC\n++\n+BCCFFFFDFFHHHFHIJJ\n+@HWI-ST132:678:C1LFKACXX:6:1101:18439:2762\n+CGCGCGCTACACTGACGG\n++\n+@@@D?DD@FFFDDEEFGI\n+@HWI-ST132:678:C1LFKACXX:6:1101:10715:4477\n+TAACTGAGTACCTGGCTC\n++\n+:??DDD2222ADDE<CGG\n+@HWI-ST132:678:C1LFKACXX:6:1101:20172:4409\n+TTCTACAGTCCGACGATC\n++\n+=@BF:====DFFHBGGIJ\n+@HWI-ST132:678:C1LFKACXX:6:1101:11143:4891\n+TTCGAGACAGTAACCACA\n++\n+=@@D;D?D>C<DFIIHGG\n+@HWI-ST132:678:C1LFKACXX:6:1101:9335:5110\n+AAGTAACGAAAGGATTAC\n++\n+:?@B4=2=CFHHHJIJJJ\n+@HWI-ST132:678:C1LFKACXX:6:1101:16012:5749\n+AGATTTACAATTTTGGGC\n++\n+BC@DFFFFHDFFHJIJJJ\n+@HWI-ST132:678:C1LFKACXX:6:1101:4811:6756\n+TGTACTACTCTACTTGTT\n++\n+CCCFFFADHHHHHJJCGI\n+@HWI-ST132:678:C1LFKACXX:6:1101:7299:9245\n+CATTGGAACTAAATGACC\n++\n+=BBDA4=BFHHHHJIIHJ\n+@HWI-ST132:678:C1LFKACXX:6:1101:13600:10898\n+ATCCCGGACGAGCCCCCA\n++\n+@CCFFFFFHHH@FHIJJI\n+@HWI-ST132:678:C1LFKACXX:6:1101:9047:12024\n+ACGACAACCGTCATCCCG\n++\n+@CCFFFFFHHHHFJJIJI\n+@HWI-ST132:678:C1LFKACXX:6:1101:7548:13223\n+ATAGACCTGACAGCGTGC\n++\n+?@@FDDFFH:ADAFHCGI\n+@HWI-ST132:678:C1LFKACXX:6:1101:7552:14739\n+GGAGGAAGTAGCTTTTTT\n++\n+BBBDDDFFH2AADFHIJI\n+@HWI-ST132:678:C1LFKACXX:6:1101:19574:14871\n+TTCCCCGTCGGGGAGCCA\n++\n+BBBFFFFDF?FHF:??FH\n+@HWI-ST132:678:C1LFKACXX:6:1101:9689:16020\n+TGCTGGTCGACTATACTC\n++\n+B?@DAAADFFHHHJJ@FG\n+@HWI-ST132:678:C1LFKACXX:6:1101:10332:16559\n+GCCCGGCTAGCTCAACCC\n++\n+=B@FA=@DHFHHHIJIIJ\n+@HWI-ST132:678:C1LFKACXX:6:1101:16598:17271\n+TCCACCACGTTCCCGTGG\n++\n+BBBFFF:AA<CFHIHCGH\n+@HWI-ST132:678:C1LFKACXX:6:1101:16473:17908\n+TTCTACAGTCCGACGATC\n++\n+BBBFFF>AADHFHGHHHI\n+@HWI-ST132:678:C1LFKACXX:6:1101:17076:19365\n+TCCCCGGCATCTCCACCA\n++\n+CC@FFFFFHHHHHJIJJJ\n+@HWI-ST132:678:C1LFKACXX:6:1101:2970:20077\n+TCCCGGATGGAACCACCA\n++\n+B@BFDBAD@DFHHHHIJI\n+@HWI-ST132:678:C1LFKACXX:6:1101:19292:22029\n+TACAGAGGGCTGCGAGAC\n++\n+CCCFFFFFHHHHG@FDHH\n+@HWI-ST132:678:C1LFKACXX:6:1101:7403:22551\n+GCAGTCGTGGCCGCGCGG\n++\n+@@@DDDDDHDHHF12?FH\n+@HWI-ST132:678:C1LFKACXX:6:1101:6550:24420\n+TCTTTGGTATTCTCGCTG\n++\n+@@@DDDDAFHHHF<+AEG\n+@HWI-ST132:678:C1LFKACXX:6:1101:15312:25043\n+ATGACACCGTTGGAAGAA\n++\n+@BCFFFFFHHHHFGHEEF\n+@HWI-ST132:678:C1LFKACXX:6:1101:10841:25468\n+TCTTTGGTATTCTCGCTG\n++\n+BCCFFFFBFHHHHEIJJJ\n+@HWI-ST132:678:C1LFKACXX:6:1101:6460:26533\n+TCCCGGGTTTCGGCACCA\n++\n+CCCFFFFDHHH<DGHIJJ\n+@HWI-ST132:678:C1LFKACXX:6:1101:8169:26973\n+ATCCTGGTCACGGCACCA\n++\n+@CCFFFFEHBH@FHIJJJ\n+@HWI-ST132:678:C1LFKACXX:6:1101:17561:28189\n+TCCCGGATGGAACCACCA\n++\n+BBCFFFDD?FDFHJIJJJ\n+@HWI-ST132:678:C1LFKACXX:6:1101:11670:30039\n+TTCTACAGTCCGACGATC\n++\n+CCCFFFFFHHHHGJJIIJ\n+@HWI-ST132:678:C1LFKACXX:6:1101:5395:30961\n+TACGGACCAATGGCAAAA\n++\n+@B@FDDDDH=FHDHIGIG\n+@HWI-ST132:678:C1LFKACXX:6:1101:8747:33935\n+CGCATGAATGGATTAAAA\n++\n+@@@DDF<DHH>FHGGBHG\n+@HWI-ST132:678:C1LFKACXX:6:1101:9941:34387\n+ATCCCATCCTCGTCGCCA\n++\n+BCBDFFFFHHHHHH@FHI\n+@HWI-ST132:678:C1LFKACXX:6:1101:14543:34442\n+TCCACCACGTTCCCGTGG\n++\n+@C@FFFADFFHGHJJEHI\n+@HWI-ST132:678:C1LFKACXX:6:1101:5887:34986\n+AAACTTTCAACAACGGAT\n++\n+@@@DFFFFH<FHHIICGI\n+@HWI-ST132:678:C1LFKACXX:6:1101:9891:35111\n+AAGAGTCTTGTCTGGTAC\n++\n+BCCFFBDFHHHHHJFHHI\n+@HWI-ST132:678:C1LFKACXX:6:1101:10051:35463\n+TCTTGATCGAAGCCCCGG\n++\n+B@BFFFFFHFFHGJJJJJ\n+@HWI-ST132:678:C1LFKACXX:6:1101:4680:35647\n+CGGGATGTAGCGCAGCTT\n++\n+BB@FADFDFHGFHEIIJJ\n+@HWI-ST132:678:C1LFKACXX:6:1101:14569:35583\n+AAGATAGAGTAGTTTTTT\n++\n+BBCDFFFFHCHHHHIJJJ\n+@HWI-ST132:678:C1LFKACXX:6:1101:13960:37817\n+AAAGTTCGGAAAACTGGC\n++\n+@CCFDFDFHHHHHBGFGI\n+@HWI-ST132:678:C1LFKACXX:6:1101:16007:38099\n+GATGACTGGGGTGAAGTC\n++\n+B@BDDFFFHG?CFBGIEG\n+@HWI-ST132:678:C1LFKACXX:6:1101:8213:39438\n+TAATGATTCCTGTACTGA\n++\n+BBBFFFFFHHHHFHIJIJ\n+@HWI-ST132:678:C1LFKACXX:6:1101:15318:43042\n+CCGCTGCTGATCACACTG\n++\n+CCCFFFFFHDHHHJJJJJ\n+@HWI-ST132:678:C1LFKACXX:6:1101:16708:44453\n+TGCTAGAGGGTCTCGGTA\n++\n+?BBF;A=DFH<DHIE<<C\n+@HWI-ST132:678:C1LFKACXX:6:1101:8544:45645\n+TGCGGCTGGATCACCTCC\n++\n+@CCFFFFF:FHHHIJJJI\n+@HWI-ST132:678:C1LFKACXX:6:1101:16382:46217\n+ATC'..b'+\n+@CCFFFFFBFHGHJJIIJ<@FHIJFII\n+@HWI-ST132:678:C1LFKACXX:6:1103:4015:38357\n+CCAACGCTGGACGCATTGACCAAAGCT\n++\n+CCCFFFFFHHHHH)CGHIFHJJGHIJI\n+@HWI-ST132:678:C1LFKACXX:6:1103:10731:44106\n+TCCCGTGACATATTATCGATCGTTCGC\n++\n+BBBFFDDF+AFHHJJJJJJJJIIJJJI\n+@HWI-ST132:678:C1LFKACXX:6:1103:13696:44351\n+AAGGATAGCTCTTGAGCCCGTGGCGTT\n++\n+@BCFFFDDFHHHHCF2CGHJHIJJJHJ\n+@HWI-ST132:678:C1LFKACXX:6:1103:20448:46278\n+CTTATCTGGTTCTGTCGCCCTATGGCC\n++\n+=:=:BB4?4ACDD+2,CDED@FBFFIC\n+@HWI-ST132:678:C1LFKACXX:6:1103:13957:53937\n+TTCCCGAACTCAGAATTGAAACCTCTT\n++\n+CCCFFFFFHHHHHJIJJIJIJJJJJJJ\n+@HWI-ST132:678:C1LFKACXX:6:1103:13988:55183\n+AATTGGCCAACATTAATTCGGACGGCC\n++\n+@CCFFFFFHHHHHJJJJJJJJJJJJIJ\n+@HWI-ST132:678:C1LFKACXX:6:1103:10971:57682\n+GAGGACTGGATGCACATTTTGTGCGAA\n++\n+@@@DDDDD?FFHHIIGHIGIGHI@@GF\n+@HWI-ST132:678:C1LFKACXX:6:1103:4202:58320\n+TTTAACGGACTAGCATACCATTTGCCC\n++\n+BCCFFFFFHHGGHJIJJJHHIJJJJJJ\n+@HWI-ST132:678:C1LFKACXX:6:1103:19968:60340\n+TTCAATTAGGGACCCCGACAAAACACC\n++\n+@@@DDDDDFFFFF;F?FGIIIIAGGII\n+@HWI-ST132:678:C1LFKACXX:6:1103:10844:68056\n+TCATAGACTTCGGCTTCTCGGCCGCGT\n++\n+CCCFFFFFHHHHHJIJJJIJIIJJDHG\n+@HWI-ST132:678:C1LFKACXX:6:1101:5856:40000\n+TGTAGCGGCGGCGCTTATATAGTGGCCG\n++\n+@@CFFFFFHHFFDGHIIJJJHFEHHFFD\n+@HWI-ST132:678:C1LFKACXX:6:1101:13547:49997\n+CCCGAAAGATGGTGAACTATGCCTGAAT\n++\n+@CCDDFDFHHHHAFHHIIJIJJJJJJII\n+@HWI-ST132:678:C1LFKACXX:6:1101:20671:76457\n+TGTTGGGACAGCTACCTCTCGATGGCAC\n++\n+@@CFFFFDD?C?FGGIIJJIJGGIBCHI\n+@HWI-ST132:678:C1LFKACXX:6:1101:16663:80406\n+TTTGACCAGTCGGTCAGCCTCTTGACCC\n++\n+@@BFBDFFHFHHHHIGIJJJIJJGHHIJ\n+@HWI-ST132:678:C1LFKACXX:6:1101:8314:83490\n+TGTTAAGTTGGATGTGAAAGCCCCGGGC\n++\n+CCCFFFFFHHGDHHEEFGIGGIJJJJJJ\n+@HWI-ST132:678:C1LFKACXX:6:1102:20297:6808\n+TTCTAAGGTGAGCGAGCGAACTCTCGTT\n++\n+BCBFFFFFFHHAFHIHIJHGIJJJJJIJ\n+@HWI-ST132:678:C1LFKACXX:6:1102:9536:12163\n+ATGAGGATTGACAGATTGAGAGCTCTTT\n++\n+11144=+222AF>B@FBF?IDF3A:FEB\n+@HWI-ST132:678:C1LFKACXX:6:1102:15554:36142\n+TGACCTCGTGTGGCCATACTCTTGGCAT\n++\n+BCCFFFFFHHH3DGHJJJJJJJJJJJJJ\n+@HWI-ST132:678:C1LFKACXX:6:1102:4674:57784\n+CGTGTCTCTCCCTGAACCTTGGCCACCC\n++\n+CCCFFFFFHHHHHJJJJJJJHIJIHHIJ\n+@HWI-ST132:678:C1LFKACXX:6:1102:5627:63941\n+AACCTAAACCTGAACCAATTCGAACTTA\n++\n+@C@FFFFDBHHHGJIJEEGHHIIIIJII\n+@HWI-ST132:678:C1LFKACXX:6:1102:4255:84044\n+TACTGATATCGACGTGACAATCGTCAAT\n++\n+@CCFFFFFHHCDHIHCAFHJIJJGIJJJ\n+@HWI-ST132:678:C1LFKACXX:6:1102:9732:91789\n+TCTGCTTCGGCGCCTGGACTTTGGCACC\n++\n+@BBDDFFFHFF)@CGHGFHGIEIJFHJJ\n+@HWI-ST132:678:C1LFKACXX:6:1102:6869:95396\n+TGGTGGGGCAACCCCCTTAGCGAGGGAC\n++\n+BC@DDFFFHHHHH)CGIJGGIGIIIIJI\n+@HWI-ST132:678:C1LFKACXX:6:1103:9280:32811\n+CGGCCCGCGTCTGATTAGCTAGTTGGTG\n++\n+BCCFFFFFHFHHHGIJIJJJJJIJJJFH\n+@HWI-ST132:678:C1LFKACXX:6:1103:10425:50137\n+CGCAACCGGAACTAAAAATTCAATTAAT\n++\n+CCCFFFFFHHHHHIIJJJJJJJJJJJJJ\n+@HWI-ST132:678:C1LFKACXX:6:1103:7067:58224\n+TAAGTCAGAATCCGGGCCAGAAGCGACG\n++\n+:BBFDD22=:=AFHEGHIIIIJJIJIJJ\n+@HWI-ST132:678:C1LFKACXX:6:1103:8620:61880\n+TGACATCGATCGTTCTTTGGAAGATGCC\n++\n+CCCFFFFFHHHHHIJJJJEFHIGIIHIJ\n+@HWI-ST132:678:C1LFKACXX:6:1103:13352:72268\n+CGTCAGCTTGACGTCGCCGTCGCGGCAC\n++\n+?@@FBDDD+2CFHGIJJIGGIIJJJIII\n+@HWI-ST132:678:C1LFKACXX:6:1103:20658:95716\n+TGCGGGATCGTCTAATGGTAGGACGCTC\n++\n+BB@FFDDDH8DHHJIJJJHHIIIJJIIJ\n+@HWI-ST132:678:C1LFKACXX:6:1104:9884:16062\n+TCAACCGCGGTCTGGGCCAGGAGGCTCT\n++\n+@@@D?DDFFHCCFGB?EHIGHIHIIIII\n+@HWI-ST132:678:C1LFKACXX:6:1104:15610:16782\n+TACGGACTCCAACCTTGTTTTGAAGCGA\n++\n+@@@DFDDDFDHDH>EHIFHIGGDBF?C?\n+@HWI-ST132:678:C1LFKACXX:6:1102:3401:22303\n+AAACCAAGGCAAACTCCGAATACCGAAGA\n++\n+@@@FFFAEFFHHHJJJJJJJIJIIJIJJI\n+@HWI-ST132:678:C1LFKACXX:6:1102:10848:27205\n+GCGGGCGGCCCGGGTTCGTTTCCCGGCCG\n++\n+@@@FDDDDDHHFFI7C@<EHIEHH=??A8\n+@HWI-ST132:678:C1LFKACXX:6:1102:7363:42223\n+TCCCGTGGTCAGTATGTCCCAGATAAATG\n++\n+:@BFA=@@AFFHDEHAAEJHJJJJJJJJJ\n+@HWI-ST132:678:C1LFKACXX:6:1102:7577:49564\n+TAGGTAGTGCCTCAAGTATCACCATCGGG\n++\n+@CCFDDFDHHGGHJJJHJHIJJIJIJJJI\n+@HWI-ST132:678:C1LFKACXX:6:1102:16100:98436\n+AAGAGCTCAAGGAGTTCCTTAAGAGGGAC\n++\n+=?@FFFFFHF<CCEAEHHJJJJIJJIIHI\n+@HWI-ST132:678:C1LFKACXX:6:1104:6554:5377\n+ACCTTATCGGATTGGTTGTGCTTTGAAGA\n++\n+@C@FFFFFHHDHHF?2CFGIIJJJJJJJI\n' |
| b |
| diff -r 9645d995fb3c -r 9185ca0a7b43 test-data/genome-small.fa --- a/test-data/genome-small.fa Wed Oct 24 07:40:20 2018 -0400 +++ b/test-data/genome-small.fa Wed Jan 16 08:18:13 2019 -0500 |
| b |
| b'@@ -1,13 +1,13 @@\n->chrom_1 2R_6242001-6272000_and_2R_6490001-6550000\r\n-TCAGTTTGGTCAGTCAAGTGCGTTTTGCTAGGCGTGGAGTAAGATGAACGCGAACAGAAACTTTTGAATTTTGAAGTAAAATTTAAATTTAAGTGAAAGGTTCGAAGTAATTGTTAATTGAAAAATAAATCAAATGCAGTTTAGCCTGATCTGAGGAAAGAAAGAACGAGTGCTAAGCTCAATGAACTTTCACTCTCCGCTCTCTCCCTATACATCGCGCTTCCAGCGAGAAATCTCTGCTGATCGTTCTCATTTCCACGTTCGCTTGGCGTTTTGATCAGTTTCGAATTTGACTTATAGCGACGCTGGTCGGAGCTCTCTCGGCAAACAAAAACCGTGACAAGCAAAGATTTGAGCAAAGATTTGCCCAGAAGGGGTCTTGCTCGACACCAATAATAAAAATGCCGCGATAGAAGTGTGTGTGCCATTGACCAACATTTTAATATTTTTAAATTGTTTCTTGTGTGCTCACGAAACGTGTTCATGTGGCGCCTCAATTGATTTGATCTTATTTCACCAATTATCAAAGTGTTAAGTCTGCCATACGAAAGCATTTAAATGAAGTAATACATATGTATAAATGTACATATATACACTTAACCCACTGCTGAGGTCTCCAGCTTTCAGTGCCAGTTTGGAGTCCACGACGGAGAAGTTAAGCCACAACTTCTGGCATCAGATTAAGAGCTAAACCTATTTCAGCAGTAGCCGCAAGCATGTGAGTGCTTTAAATTCATAAAAACACATTAAAGTGCGTATTTTTAACTTTATTTAAATTGATAAATTTTATACCATTGATTGATTTATTTTATACCAATATTTATAAAATAGTTGGCCTGCTTTGGAAAAAAGAAGATGGATAAAAGTTGCACAAATAAAATGTGTGAAACGTGGTAAAAACTTGTGAATTTTGTGTCCAAAAATGGTTTAACATATATTATTACAATATCATTTAAACAAATTGTGGGTTCAGGCAGTTTAAAATTTCAATATATGGCAAAAGGCAAGTTAAAATTTTTCCCCAAATCATCAGACACAAGGACACTAAAATAAGTTTTTACTTTAGAAGTCACCCAGAACCATGTGCTGGAAAATGTTCTCCAACGAAGCTTCGGATTTTAATAATCATTAGGTACCAGTTGCTAATCAATTTTAGATTAAATATGCTTTTAGATAAGGATGTTGTCAGGTGATATTATGGATACGTATGAACATATGTTGCTACTTATTCTTGTTTAGTCCCACATCCCTAGATCAGTTAAAGGGTATACTAGATTCTTTTAAAAGTATCCAACATGTAAAACAAAGTCTTTTCGACCAAGGAAAGTATATAAATTCTTGATCAAGATTATTAATTGAGTCGATTATGTCCGTTCGTATATCCATTTGAACTTCGGGATCTCTGTACCTATAAAGGATTCAGCATACAGATCCTAAAGACTTTCCACACGTATGCTTATTTCCAAACGTAGCCACACCCAATGTAACGTCGACACACTGCAAACCATTTTTGGCCCTGATTTTAATTTCTTGGAATATGAACCTCTAAACCAATACTCTGTCTTTAATGACAGGAGCGGATTATAGAAGCACATTTCTTATCTTATCACTATTTATGTATATTTCACAAGTGTGACCAAGCTAATAGTGATATTAGTAAAATCTAATAGGCAACGCATAGACCTAAAGAATTAGAATGTGGTTTCCCACAACGATCAAAAAAAAAAATATTAAAACATTTTCAAAAGGTGTGTCAGTTTTGGGCGGTTGTGGGCGTGCCTCTAGAATCGTTTTATCTAATCTCAACTCTCTAGCTATAATGGTTCCTGAGATGGTGGTGTTCATACGGACAGACTGACATGGCCAGATCAACTCGGCTATTGGTTCTGATCAAGAATATATATACTTTATAATAATAAATAAATAATATACTTTATATGGTCGAAAACGTTTTGTCTGTTACATACTTTTTAACGAATCTAGTATACCCTTTTACTCTACGAGTAACGGGTACAACAAAAATGCTATATTCGACTTATGTTCTGACAGTCAGATACCCGTTACTCAGTTAGTGGAAATGGTGAATTGATTGAGAAAATATTTAAACAAATTTGAAAGTATGGGCGTGGCAAAAAGTTTTTTGGTAAATCGATAAAAATTTACAAGTGTAATAAAAATATAAAAAAAAATTTGAAAACATTTTTTAAAAGTGCAAGGATGTGCAAGTTTTAGGCGGCTATAGGCATTAGGGGGGCTTGGCAACTTTCTATCTGTTATATTTTGGAAGTGACAAACAGGTTCTTTTTTCGTCTTGGGCAACTATTATAATATATTATATTATATACTAAATAACAAGTTTACAAAGAATTCACTACACTAGTAATAAAAGCTATCACTACTTCAAAGTTAGCAGACCCAATACGAAATTCAATGACCAAATAGAAGTCAGCACCAAAACTTAATTACTTAAAAATTTCTTTGAGTGACAGAAGGAAAACTTATATTAGGACAGTATATTTCTTAGATTAGATTTATGGAAGATAACAATGTACTAATTTCTGAATTGTTTAAATAATATCGAACGAGTCAACTACCTTATCCAAACCGCTACCGGAGCACTATCCCTTCGAAAGCTTAGTCTCATTTCTCAACAGCTAACTATAATTTGAAAATATTTAGAATAAAGTTATTGTTCGATAGGCTCATGTTTTTTTTGGGATGAAAGGGGATTTTTATTAAATGTCCGAAAATAATTTTTCGTCACTAAAGTTTGGTATGGTATTTGGCATGATGCGATCGTCAAATGTTTTTACCGAGTCACTAACTTGGACATAGTCTCTAAAACATACTTTTGATTTTATTTTTACTTAGTTCCGAACTAGGGGTCAATAATTTAAGTTATTGAAATTCAGTTGCCCCGCGTGGGACAATCTAATCGAATGCTAATTGTAATTCGGTTATTTATCCTGCGCACTTCATTGGGGTCGTACAAATAATGAGTTCTGATTACAGCGATTGTGCCCAAGTCTAGTGTTGCCGATAAGATAGCCGCAATAGATACTAAGCAGAGCTACATGCACACCCAAAGTGCCGTTGTGACTCATCGACTCCTCGACCATTGTTGCGGGTCCGACAATAGGCCTGTACTCGATCAGCGATTTTTAAAAGGTGTGTGAACCGCGCAGAAAGCTTTGGAAAGCTTGTAGAGTTTGTGCCAATGCCTCGGCAGAGAACTTGTTCTTATGGATTGTGGCTGACCTTGCCGTAGAAGCCCATTATGTTTTTATTTGCATAATACCTTAGAACAGTCGAAGGGTTTTCGGGCTATCGCATTTCAATATCTTGGAGATTATGAAAAGCTTTGCCAGCTGTTTTGAAGTTCGCAGCTGTGCTCTGGAAAACTCCCTCTCCATTACCAACTTGCGGCATTGACGCTCTCGCCGTAACCGTTACCCGTTAACCGTTTTGAGCTCGGCGACCTAAGCTTTTGGCTGCGTCGCGAGGTTTAGTTAATATTATTAACCGGAGTGACGGCCAAGTTGTCGCAACGTTTCTCGTGGATCGCAGATCGTGGCGGTAAGGCGAGCTTTTTGCCGGGGGCTCAAAGTGTGAGTGTGAGGTGTCTTCAGTTTGGTTTTTTTCACATAGCGTGGCATTACTCTCTTTGACGAATTCAATGCGACGTCGCGCTTTTTTCGGTTCTGCAACTTCCGTTAGTCGGTGGCTCGAAAAGTAAACAAAGTGCTGCATATCGCATGCAAACGTGACAATCTTTCAGACGCACTCCAACTTGATAACTTGATAAGCATCTGTGAGATGCAAAGATACAAGTTATAAAGCACCATCTCGCGAAGCCATGTAGCCGAGTGAAAAAAGTAAAATATGCGAAAGCAGAAAAACAAAAAATTTGTGCGTGTGTTAGTTGGC'..b'ATTACCTTATACGTATAAATTTTATCATTCAATTCCGAAAGCATTTTGGGCGAAAATAAAGTACTTACTTTTAGGGCGAAAAATAAGTAAGTTGCCATTAAATGGAATATTTTTTTGTTACGATGATTAGTCATTTATAATAAAAATTTAAAATATGGGCAATTTGGTCCCCTAATCAACATGCACATATGTACATACATATATTTACATTTTCCCAAATGTGTCTGTAATTTTTTTTTTAGTATGGAAACGCAGACAGTAGGAAAAACGTAGCCAACAAAAAAGGCAAAAAATGCGTTTGCCGCAGACACAAATTATCGATCCGAACATTACACAAACACGCACACGGACAGAATTAAGCAGCACCGCAAAGTAAAACACTTGGGTAAACCCCCAAAAATGGTTGGAGCTGAGTGGGGGTGGCAAGGGCACTTTTTTTTGTTGCGGCAACTTCTTTAAGTTGTTCTTGATAAAAAAGTCATGACCTAACACAATATGTCCGTAAATAAGCCTGTGTAACAAAATAAGGCCATTGGCCCTGAAATGTACCTGATATATTGTTTTTTGTTAGTATTTAGAGGTGTTAGAAAAGATGAAGGTATTTGCTTAAAAATTGTGATTAATCTCAATCCCTTACATTTTTTAAAATAATAATCACAAAGCTTCGTTTCGCGTTGAAACTGAATTTTTTGCAATTCAACCCTTCCCACTTATTATAGTTTTCGTTCTGTTCTCACTAGCAAATGTTCTCACTCCAGTTTCTCTCGCCTCTCCCTCTTTATATTTGTTGTTACGGCCTGGTAAACCAACTGACCGTGTGGCCTAATGGATAAGGCGTCGGACTTCGGATCCGAAGATTGCAGGTTCGAGTCCTGTCACGGTCGACCGTTCTATGCTTTTTTTTAATATTCATATTTTTCCTTGAGCTATGAATATTACAGCTTTCATTAATTGGCCAAGTCAATTGCTGAAAAAAATATTTATTAGTTCTTTAAGGAACTAGAAGCTTAAATAGTGTATTGGGCTTGCGTAAGGACAAGTAGCAGTCGTGGCCGAGTGGTTAAGGCGTCTGACTCGAAATCAGATTCCCTCTGGGAGCGTAGGTTCGAATCCTACCGGCTGCGAATGAGAATGTATATTTTATTTCATATGTTTTTATTTTCTGAAATTAAATAAAAACGTTCTGCATAGCAAAACAAATGAGTGCTAGGTGTTTAAAAATACATTATTTTATTGCCATACGGAATTATCCTATTTAACGATCAATTTATATTTATAAGGTAGAGAATTAACCTTTTTTTTAATTGTCTTATAGAATTATCCTATTTAACGATCAAACTATATTTAAAAGTATAAAAAATAGTAGGAAACGTAGGAAATTAACCTTTGGCCCTGTAATATGCATAAACTCCGGAAGATTGTTGGGATTTGATCAAAAATAAGCAGTCGTGGCCGAGTGGTTAAGGCGTCTGACTCGAAATCAGATTCCCTCTGGGAGCGTAGGTTCGAATCCTACCGGCTGCGGAAGGGTAGTCCTATATTTTTTATGTTTTAATTTTTAAAAGGAGCATTCTTTCAGTTTTGAATATGTTTATTATATTACACACTGTGCCTTTGTTTGGCAATTACTTTCTGTCTAATGAATTTCTTAATTCAATTATAATCCGCATTTTGATCATATTTCGTATTCAAGGAACCACATCTCTAATTTTTTTACCTTGCCTATTTGTCTCGCATTGTGTAGCCCAAACACAACAACACCACCCACCAGACACGCACAAAATTATTTACATTTGCTGCTGACGAGTTCGTTGAACCTTTGATAACCTTTTTGGTCTGCTCCTCGGCAATTTTATTTCTCTATATACTAAATTTTTCGGCTGTCTTTCCTTTACTTTCGTTTTGCTCTTCCGTCTGTGGGCGTATATCGCCGTCCACAAAAAGCCTCAAAATGTCTTTGGTCCTTTTGCACCATTGACGTTGTTGTTTCCGCAGGTCCGAGCCCGCAGGAATCTTTGATAAAGATCTTTATATTATCAATGTCTAAGTATAGATAAAATGAATAAATAATTATGAAATAAGAATGTAAATACAATTTTCAATCAATCGTTTTAAGCAAGGTTCATTTGCAATATTATAAACTATGATAGACCGTTTTGTATCATTGATCTTGGGAATTTGGGACGCCGGTTGCGTAACTGACCGTGTGGCCCAATGGATAAGGCGTCGGACTTCGGATCCGAAGATTGCAGGTTCGAGTCCTGTCACGGTCGAAGCTCAGGCTATATTTTTTTAAATTATATTTTGTTCGTCCTAGAATATATTAATATGGGAGATTCCCTAGCCCAACCCAAACACACCAACACCACCCACCAGACACGTACAAAATTATTTACATTTGCTGCTGACGAGTTCGTTGAACCTTTGATAACCTTTTTGGTCTGCTCCTCGGCAATTTTATTTCTCTATATACTAAATTTTTCGTCTTTCTTTCCTTTACTTTCGTTTTGCTCTTTCGTCTGTGGGCGTATATCGCCGTCCACAAAAAGCCTCAAAATGTCTTTGGTCCTTTTGCACCATTGACGTTGTTGTTTCCGCAGGTCAGAGCCCGCAGGAATCTTTGATAATGATCTTTCTATTATTAATGTCTAAGTATAGATAAAATGAATAAATAATTATGAAAAAAGAATGTAAATACAATTTTCAATCAATCGTTTTAAGCAAGGTTCATTTGCAATATTATAAACTATAATAGACCGTTTTGTATCATTGATCTTGGGAATTTGGGACGCCGGTTGCGTAACTGACCGTGTGGCCCAATGGATAAGGCGTCGGACTTCGGATCCGAAGATTGCAGGTTCGAGTCCTGTCACGGTCGAAGCTCAGGCTACATTTTTTTTAAATTATATTTTGTTCGTCCTAGAATATATTAATATGGGAGATTCCCTAGCCCAACCCATTTGTGTAACCTGAGAAATTGGGAATTTGGGACGGCGGTTGCGTAACTGACCGTGTGGCCCAATGGATAAGGCGTCGGACTTCGGATCCGAAGATTGCAGGTTCGAGTCCTGTCACGGTCGAAGCTCAGGCTATATTTTTTTTAAATTATATTTTGTTCGTCCTAGAATATATTTATATGGGAGATTCCCTAGCCCAACCCATTTGTGTAACCTGAGAAATTGGGAATTTGGGACGGGGGTTACGTAACCGACCGTGTGGCCCAATGGATAAGGCGTCGGACTTCGGATCCGAAGATTGCAGGTTCGAGTCCTGTCACGGTCGTACCTCAGTATTTAATTTTTTTTGAACTTATTTTTCGTTCGTCCTATAATATATTAATATGGGAGATTCCCTAGCCCCACTCATTTGTGTAACCTGAGTGCGGTAAGCAGCAATCGTAACCAATTGGCATACCGAATTGAAAGATTTATTGGACTTTTACATGGGTCGTCCATGGACGAATCAACATGTGGCTGCCACCGCAAGAAGCCCAACTTTGTTCGTTGGCTCTTGCTGCCTGGGCTTGCACTGAAACAAATCTCTTTAACGTCAGCAAAAAATAAAAAGATATTTTTTCTAAAGTATGTATTGTCGTACATTTGGTTTATAATTTTAATATTTAGCGTATCAATTAAATCAATGTGTCTATGTGTCCGATACTTTCGTGTATTTTGTTATGTTTCTGTGTATCTGCTGGTGTCGTTGCTGCAATTGTTGCTAGCTTGAATAGCTATATATTTTTTATTCTCTTTTGTCAGCAAGCAGACTGAGGAGCAAGTTTTAAGCAACAAGAACGACACGCGGAGGAACAAGCTGGTCTACAAAGTGGAGGACGAGGCTGCAATTTATGTGGAGGTCCGGCTGTCCACAGTCCGCGGTCCAAAAGAGATCCGAGGGCCCACAGAGTCGGCTTAGCATAATAAACGTCAGAATTAATTGGATTTTAATTGTCTGTTAAGCGCTGAAATTAAGTGCAGCAAAACTAGATTGTCGGCCAG\n' |
| b |
| diff -r 9645d995fb3c -r 9185ca0a7b43 test-data/mirbase-21-dme-hairpins-16jul2015.fa --- a/test-data/mirbase-21-dme-hairpins-16jul2015.fa Wed Oct 24 07:40:20 2018 -0400 +++ b/test-data/mirbase-21-dme-hairpins-16jul2015.fa Wed Jan 16 08:18:13 2019 -0500 |
| b |
| b'@@ -1,512 +1,512 @@\n->dme-mir-1_MI0000116 Drosophila melanogaster miR-1 stem-loop\r\n-TTCAGCCTTTGAGAGTTCCATGCTTCCTTGCATTCAATAGTTATATTCAAGCATATGGAATGTAAAGAAGTATGGAGCGAAATCTGGCGAG\r\n->dme-mir-2a-1_MI0000117 Drosophila melanogaster miR-2a-1 stem-loop\r\n-GCTGGGCTCTCAAAGTGGTTGTGAAATGCATTTCCGCTTTGCGCGGCATATCACAGCCAGCTTTGATGAGCTTAGC\r\n->dme-mir-2a-2_MI0000118 Drosophila melanogaster miR-2a-2 stem-loop\r\n-ATCTAAGCCTCATCAAGTGGTTGTGATATGGATACCCAACGCATATCACAGCCAGCTTTGATGAGCTAGGAT\r\n->dme-mir-2b-1_MI0000119 Drosophila melanogaster miR-2b-1 stem-loop\r\n-CTTCAACTGTCTTCAAAGTGGCAGTGACATGTTGTCAACAATATTCATATCACAGCCAGCTTTGAGGAGCGTTGCGG\r\n->dme-mir-2b-2_MI0000120 Drosophila melanogaster miR-2b-2 stem-loop\r\n-TTGTGTCATTCTTCAAAGTGGTTGTGAAATGTTTGCCTTTTTATGCCTATTCATATCACAGCCAGCTTTGAGGAGCGACGCGA\r\n->dme-mir-3_MI0000121 Drosophila melanogaster miR-3 stem-loop\r\n-GATCCTGGGATGCATCTTGTGCAGTTATGTTTCAATCTCACATCACTGGGCAAAGTGTGTCTCAAGATC\r\n->dme-mir-4_MI0000122 Drosophila melanogaster miR-4 stem-loop\r\n-TTGCAATTAGTTTCTTTGGTCGTCCAGCCTTAGGTGATTTTTCCGGTCATAAAGCTAGACAACCATTGAAGTTCGTTGTGG\r\n->dme-mir-5_MI0000123 Drosophila melanogaster miR-5 stem-loop\r\n-GCTAAAAGGAACGATCGTTGTGATATGAGTTGTTTCCTAACATATCACAGTGATTTTCCTTTATAACGC\r\n->dme-mir-6-1_MI0000124 Drosophila melanogaster miR-6-1 stem-loop\r\n-TTTAATGTAGAGGGAATAGTTGCTGTGCTGTAAGTTAATATACCATATCTATATCACAGTGGCTGTTCTTTTTGTACCTAAA\r\n->dme-mir-6-2_MI0000125 Drosophila melanogaster miR-6-2 stem-loop\r\n-TAACCCAAGGGAACTTCTGCTGCTGATATATTATTGAAAAACTACTATATCACAGTGGCTGTTCTTTTTGGTTG\r\n->dme-mir-6-3_MI0000126 Drosophila melanogaster miR-6-3 stem-loop\r\n-CAAAAAGAAGGGAACGGTTGCTGATGATGTAGTTTGAAACTCTCACAATTTATATCACAGTGGCTGTTCTTTTTTGTTTG\r\n->dme-mir-7_MI0000127 Drosophila melanogaster miR-7 stem-loop\r\n-GAGTGCATTCCGTATGGAAGACTAGTGATTTTGTTGTTTGGTCTTTGGTAATAACAATAAATCCCTTGTCTTCTTACGGCGTGCATTT\r\n->dme-mir-8_MI0000128 Drosophila melanogaster miR-8 stem-loop\r\n-AAGGACATCTGTTCACATCTTACCGGGCAGCATTAGATCCTTTTTATAACTCTAATACTGTCAGGTAAAGATGTCGTCCGTGTCCTT\r\n->dme-mir-9a_MI0000129 Drosophila melanogaster miR-9a stem-loop\r\n-GCTATGTTGTCTTTGGTTATCTAGCTGTATGAGTGATAAATAACGTCATAAAGCTAGCTTACCGAAGTTAATATTAGC\r\n->dme-mir-10_MI0000130 Drosophila melanogaster miR-10 stem-loop\r\n-CCACGTCTACCCTGTAGATCCGAATTTGTTTTATACTAGCTTTAAGGACAAATTCGGTTCTAGAGAGGTTTGTGTGG\r\n->dme-mir-11_MI0000131 Drosophila melanogaster miR-11 stem-loop\r\n-GCACTTGTCAAGAACTTTCTCTGTGACCCGCGTGTACTTAAAAGCCGCATCACAGTCTGAGTTCTTGCTGAGTGC\r\n->dme-mir-12_MI0000132 Drosophila melanogaster miR-12 stem-loop\r\n-TACGGTTGAGTATTACATCAGGTACTGGTGTGCCTTAAATCCAACAACCAGTACTTATGTCATACTACGCCGTG\r\n->dme-mir-13a_MI0000133 Drosophila melanogaster miR-13a stem-loop\r\n-TACGTAACTCCTCAAAGGGTTGTGAAATGTCGACTATTATCTACTCATATCACAGCCATTTTGATGAGTTTCGTG\r\n->dme-mir-13b-1_MI0000134 Drosophila melanogaster miR-13b-1 stem-loop\r\n-CCATGTCGTTAAAATGTTTGTGAACTTATGTATTCACAATCATATCACAGCCATTTTGACGAGTTTGG\r\n->dme-mir-13b-2_MI0000135 Drosophila melanogaster miR-13b-2 stem-loop\r\n-TATTAACGCGTCAAAATGACTGTGAGCTATGTGGATTTGACTTCATATCACAGCCATTTTGACGAGTTTG\r\n->dme-mir-14_MI0000136 Drosophila melanogaster miR-14 stem-loop\r\n-TGTGGGAGCGAGACGGGGACTCACTGTGCTTATTAAATAGTCAGTCTTTTTCTCTCTCCTATA\r\n->dme-mir-263a_MI0000343 Drosophila melanogaster miR-263a stem-loop\r\n-TAGATCTCGGCACAGTTAATGGCACTGGAAGAATTCACGGGGTAATTTTTATACAACCCGTGATCTCTTAGTGGCATCTATGGTGCGAGAATAA\r\n->dme-mir-184_MI0000354 Drosophila melanogaster miR-184 stem-loop\r\n-GGTTGGCCGGTGCATTCGTACCCTTATCATTCTCTCGCCCCGTGTGCACTTAAAGACAACTGGACGGAGAACTGATAAGGGCTCGTATCACCAATTCATC\r\n->dme-mir-274_MI0000355 Drosophila melanogaster miR-274 stem-loop\r\n-TCCTGTGTTGCAGTTTCGTTTTGTGACCGACACTAACGGGTAATTGTTTGGCCGCCAGGATTACTCGTTTTTGCGATCACAAATTATGAAATTGCAGCAA\r\n->dme-mir-275_MI0000356 Drosophila melanogaster miR-275 stem-loop\r\n-TGTAAAGTCTCCTACCTTGCGCGCTAATCAGTGACCGGGGCTGGTTTTTTATATACAGTCAGGTACCTGAAGTAGCGCGCGTGGTGGCAGACATATAT\r\n->dme-mir-92a_MI0000357 Drosophila melanogaster miR-92a stem-loop\r\n-AATATGAATTTCCCGTAGGACGGGAAGGTGTCAACGTTTTGCATTTCGAATAAACATTGCACTTGTCCCGGCCTATGGGCGGTTTGTAATAAACA\r\n->dme-mir-219_MI0000358 Drosophila melanogaster miR-219 stem-loop\r\n-TAATTCGATTT'..b'TATATCTAGGCCAAATATATATACTTGTTCTATGTATTAGTTATTTGCAAAGGAATACATGTGCCTGTATATATATTCGGTAAAATCACATCTTTGAATT\n+>dme-mir-4980_MI0017766 Drosophila melanogaster miR-4980 stem-loop\n+GAAGAGGCTGAGAGCGGGAAAGTGAGAAGTAGAGAGCGCAGATAGGGAGTGGGAGCTTATACCGTTATAAAGCCAACTTCCGTTCTGCGTTTCGTTCCAACCCCCCACCTCTCTTTCCCTCT\n+>dme-mir-4981_MI0017767 Drosophila melanogaster miR-4981 stem-loop\n+TGGCCACGTGCCCGCAAGACGCCTTCGGCCGGCGCAAAGTTTCAATTTGATATTCCTTGGCCGGTCGAGCAGCGTCTTGGGGTTGTTCGTGGATT\n+>dme-mir-4982_MI0017768 Drosophila melanogaster miR-4982 stem-loop\n+CCAACTTTGCTGGCATTCGGTGGCCAATAATGCAATTGCATGTCCTTGTTGCTGTTGCAATGTTGCAGCTGGAATTGCAATTGCATTTCTAGTTGCCGCTGCTGCTGCTCGAGTGGCAA\n+>dme-mir-4983_MI0017769 Drosophila melanogaster miR-4983 stem-loop\n+GGCTGGCTGTCTTGACCCACTTGCTCGTTTGCATTTCTGAAAAATGTATACGCAAAAACCAAAATCAGAAATTCTTTTGAGCAAGTGTGTCATGAAATTGCCATTCGT\n+>dme-mir-4984_MI0017770 Drosophila melanogaster miR-4984 stem-loop\n+CTTCGCTCGAGGTGTGAAAACCTTTTGGCCAGCGAATACGCCTCGGATCCAATCACGTTTCAAGATCGAGGTGAATTCTTTGACGTATTCGCTGGCCAAATGACACGTTCGCCATGTTTTGCG\n+>dme-mir-4985_MI0017771 Drosophila melanogaster miR-4985 stem-loop\n+TTGGGGGCGCTGCACTGGCATTGAAAAGTGAATTACATTGATCGTGACATGGGAATGGAAAATGTCGCCGAGCCATGTAAATCGTTTGGCCTACCCGTCTA\n+>dme-mir-4986_MI0017772 Drosophila melanogaster miR-4986 stem-loop\n+TTCTGCCGCTTTTGCTGTGGCTTCTCTGCATGGGATTCCCCATTCTGCATGGCGCCGATCTCTGCCAGCCCATCGGATGGCGGAACTTCCAGTGCAGCGAGGTCGCTTCTCTGCAGGATCTG\n+>dme-mir-4987_MI0017773 Drosophila melanogaster miR-4987 stem-loop\n+GCGGTGCCGTTGATGATGACACAGCGCGCTTGCAACAGCGTGCGGCACGATTCTCACAGCAGGGCTCCAGCTCGGCCAAAAAATCGGTCGTCGCCATTGCAAGCTCACCGTTTGGTCTCACCACGGCCAAGA\n+>dme-mir-9369_MI0028918 Drosophila melanogaster miR-9369 stem-loop\n+AGCGAGAGGGTATTATGTATTCATATTTGTAATATCATGATACATATTCTCCTTTCGCTCTA\n+>dme-mir-9370_MI0028919 Drosophila melanogaster miR-9370 stem-loop\n+TTTGGGTTGCCGGTACCGGGTGGTTTCCCCGATATCCACGACCCATACCA\n+>dme-mir-9371_MI0028920 Drosophila melanogaster miR-9371 stem-loop\n+AAATCACTTTGCTTGGAATTCACATTGATGTACGTAAGAATTCATCACGAAGTGGTTTCTG\n+>dme-mir-9372_MI0028921 Drosophila melanogaster miR-9372 stem-loop\n+TAAAAGCACATTTCGCCAGCACGTGTACTTTCCACCTCGTCTGTGATTTTGGTTTTTAACG\n+>dme-mir-9373_MI0028922 Drosophila melanogaster miR-9373 stem-loop\n+AGTTTGTGAGGAGCGTTCGGCGGATACACATCGCACCCATCGCTCTTGGCCAGCTCGTC\n+>dme-mir-9374_MI0028923 Drosophila melanogaster miR-9374 stem-loop\n+CGTGCAATAATTTCCTCGATTGGCATCAAGTGGCTTCCAGTCGGGTACATATTGCACAAGA\n+>dme-mir-9375_MI0028924 Drosophila melanogaster miR-9375 stem-loop\n+CCGAGTATATGGAATTTCTGTTTTGCCTAGTATGAACCGAAACTCGATATAATTCAGAA\n+>dme-mir-9376_MI0028925 Drosophila melanogaster miR-9376 stem-loop\n+ATAGCCAGCATGGCCAAAGCGCTGTGCTTAAGTGGTCCAAGCGACCGAAAGCACTTTGACCATGCGGTGGTGGCCA\n+>dme-mir-9377_MI0028926 Drosophila melanogaster miR-9377 stem-loop\n+CGCTCTTTCTCTCTATCTGGCCTGGCCTGGCTTGATGGGGAGAAGGAGAGGG\n+>dme-mir-9378_MI0028927 Drosophila melanogaster miR-9378 stem-loop\n+AGTGGAGTGAGACCTCGAGTTCGGGCAAATCTGATAGCCGAACGGGAGTTTCCTCCATTGGG\n+>dme-mir-9379_MI0028928 Drosophila melanogaster miR-9379 stem-loop\n+CGCATGTCAGGTGGTAATCCATTAGTATAAACATGGTATGGCCACTTGACAGTCGGC\n+>dme-mir-9380_MI0028929 Drosophila melanogaster miR-9380 stem-loop\n+GCTCCTGCTGCATCTGTTGGCGATAGCGCTCGTCACTCTTGGCCGTGTACTCCGCCTCCAACAGATCCAGCAGCAGA\n+>dme-mir-9381_MI0028930 Drosophila melanogaster miR-9381 stem-loop\n+GCCAGGGAAGGGTCGAGTGCGGATCCCTTGCCCCAGCGGCTATTCGCCTGCGCACTCGGTCCATCCCTGGCTCA\n+>dme-mir-9382_MI0028931 Drosophila melanogaster miR-9382 stem-loop\n+ATCACAGTGTGGCTGAGGGATTCCACTTTCCTTATAACTTTTGCCGATCCCCGGCGCCACTGTGATCGT\n+>dme-mir-9383_MI0028932 Drosophila melanogaster miR-9383 stem-loop\n+GGGTGCAGATCAAGTGCGAGCTGCGCATTCTCTCGCAGTTCGCCTTCAATCTGAACCCCGA\n+>dme-mir-9384_MI0028933 Drosophila melanogaster miR-9384 stem-loop\n+AGGCATAATTCAACTCACACGTCTACAGGTACATATGTGTGTGTTCGGTTATGTACTTTG\n+>dme-mir-9385_MI0028934 Drosophila melanogaster miR-9385 stem-loop\n+ACAGTGTATGCAAATGATGAATGTGCCATATCAGAAACTATTCCTCATTGCTATACCTGTGGT\n+>dme-mir-9388_MI0028938 Drosophila melanogaster miR-9388 stem-loop\n+CAAGTATTTTGGTACGTATGTATGTATGTACATACATGTGTATATGGTACATTCATGTAGTACATACATACATATGTATGCAAGTACGTACG\n' |
| b |
| diff -r 9645d995fb3c -r 9185ca0a7b43 test-data/reads-sample-small.fastq --- a/test-data/reads-sample-small.fastq Wed Oct 24 07:40:20 2018 -0400 +++ b/test-data/reads-sample-small.fastq Wed Jan 16 08:18:13 2019 -0500 |
| b |
| b'@@ -1,182280 +1,182280 @@\n-@HWI-ST132:678:C1LFKACXX:6:1103:5043:24327\r\n-TCTGTCGTGCATTGTCGG\r\n-+\r\n-IHFC<HHHHHDFFFFCCB\r\n-@HWI-ST132:678:C1LFKACXX:6:1101:19372:1918\r\n-AGAATTGTGACCTGAATC\r\n-+\r\n-BCCFFFFDFFHHHFHIJJ\r\n-@HWI-ST132:678:C1LFKACXX:6:1101:18439:2762\r\n-CGCGCGCTACACTGACGG\r\n-+\r\n-@@@D?DD@FFFDDEEFGI\r\n-@HWI-ST132:678:C1LFKACXX:6:1101:10715:4477\r\n-TAACTGAGTACCTGGCTC\r\n-+\r\n-:??DDD2222ADDE<CGG\r\n-@HWI-ST132:678:C1LFKACXX:6:1101:20172:4409\r\n-TTCTACAGTCCGACGATC\r\n-+\r\n-=@BF:====DFFHBGGIJ\r\n-@HWI-ST132:678:C1LFKACXX:6:1101:11143:4891\r\n-TTCGAGACAGTAACCACA\r\n-+\r\n-=@@D;D?D>C<DFIIHGG\r\n-@HWI-ST132:678:C1LFKACXX:6:1101:9335:5110\r\n-AAGTAACGAAAGGATTAC\r\n-+\r\n-:?@B4=2=CFHHHJIJJJ\r\n-@HWI-ST132:678:C1LFKACXX:6:1101:16012:5749\r\n-AGATTTACAATTTTGGGC\r\n-+\r\n-BC@DFFFFHDFFHJIJJJ\r\n-@HWI-ST132:678:C1LFKACXX:6:1101:4811:6756\r\n-TGTACTACTCTACTTGTT\r\n-+\r\n-CCCFFFADHHHHHJJCGI\r\n-@HWI-ST132:678:C1LFKACXX:6:1101:7299:9245\r\n-CATTGGAACTAAATGACC\r\n-+\r\n-=BBDA4=BFHHHHJIIHJ\r\n-@HWI-ST132:678:C1LFKACXX:6:1101:13600:10898\r\n-ATCCCGGACGAGCCCCCA\r\n-+\r\n-@CCFFFFFHHH@FHIJJI\r\n-@HWI-ST132:678:C1LFKACXX:6:1101:9047:12024\r\n-ACGACAACCGTCATCCCG\r\n-+\r\n-@CCFFFFFHHHHFJJIJI\r\n-@HWI-ST132:678:C1LFKACXX:6:1101:7548:13223\r\n-ATAGACCTGACAGCGTGC\r\n-+\r\n-?@@FDDFFH:ADAFHCGI\r\n-@HWI-ST132:678:C1LFKACXX:6:1101:7552:14739\r\n-GGAGGAAGTAGCTTTTTT\r\n-+\r\n-BBBDDDFFH2AADFHIJI\r\n-@HWI-ST132:678:C1LFKACXX:6:1101:19574:14871\r\n-TTCCCCGTCGGGGAGCCA\r\n-+\r\n-BBBFFFFDF?FHF:??FH\r\n-@HWI-ST132:678:C1LFKACXX:6:1101:9689:16020\r\n-TGCTGGTCGACTATACTC\r\n-+\r\n-B?@DAAADFFHHHJJ@FG\r\n-@HWI-ST132:678:C1LFKACXX:6:1101:10332:16559\r\n-GCCCGGCTAGCTCAACCC\r\n-+\r\n-=B@FA=@DHFHHHIJIIJ\r\n-@HWI-ST132:678:C1LFKACXX:6:1101:16598:17271\r\n-TCCACCACGTTCCCGTGG\r\n-+\r\n-BBBFFF:AA<CFHIHCGH\r\n-@HWI-ST132:678:C1LFKACXX:6:1101:16473:17908\r\n-TTCTACAGTCCGACGATC\r\n-+\r\n-BBBFFF>AADHFHGHHHI\r\n-@HWI-ST132:678:C1LFKACXX:6:1101:17076:19365\r\n-TCCCCGGCATCTCCACCA\r\n-+\r\n-CC@FFFFFHHHHHJIJJJ\r\n-@HWI-ST132:678:C1LFKACXX:6:1101:2970:20077\r\n-TCCCGGATGGAACCACCA\r\n-+\r\n-B@BFDBAD@DFHHHHIJI\r\n-@HWI-ST132:678:C1LFKACXX:6:1101:19292:22029\r\n-TACAGAGGGCTGCGAGAC\r\n-+\r\n-CCCFFFFFHHHHG@FDHH\r\n-@HWI-ST132:678:C1LFKACXX:6:1101:7403:22551\r\n-GCAGTCGTGGCCGCGCGG\r\n-+\r\n-@@@DDDDDHDHHF12?FH\r\n-@HWI-ST132:678:C1LFKACXX:6:1101:6550:24420\r\n-TCTTTGGTATTCTCGCTG\r\n-+\r\n-@@@DDDDAFHHHF<+AEG\r\n-@HWI-ST132:678:C1LFKACXX:6:1101:15312:25043\r\n-ATGACACCGTTGGAAGAA\r\n-+\r\n-@BCFFFFFHHHHFGHEEF\r\n-@HWI-ST132:678:C1LFKACXX:6:1101:10841:25468\r\n-TCTTTGGTATTCTCGCTG\r\n-+\r\n-BCCFFFFBFHHHHEIJJJ\r\n-@HWI-ST132:678:C1LFKACXX:6:1101:6460:26533\r\n-TCCCGGGTTTCGGCACCA\r\n-+\r\n-CCCFFFFDHHH<DGHIJJ\r\n-@HWI-ST132:678:C1LFKACXX:6:1101:8169:26973\r\n-ATCCTGGTCACGGCACCA\r\n-+\r\n-@CCFFFFEHBH@FHIJJJ\r\n-@HWI-ST132:678:C1LFKACXX:6:1101:17561:28189\r\n-TCCCGGATGGAACCACCA\r\n-+\r\n-BBCFFFDD?FDFHJIJJJ\r\n-@HWI-ST132:678:C1LFKACXX:6:1101:11670:30039\r\n-TTCTACAGTCCGACGATC\r\n-+\r\n-CCCFFFFFHHHHGJJIIJ\r\n-@HWI-ST132:678:C1LFKACXX:6:1101:5395:30961\r\n-TACGGACCAATGGCAAAA\r\n-+\r\n-@B@FDDDDH=FHDHIGIG\r\n-@HWI-ST132:678:C1LFKACXX:6:1101:8747:33935\r\n-CGCATGAATGGATTAAAA\r\n-+\r\n-@@@DDF<DHH>FHGGBHG\r\n-@HWI-ST132:678:C1LFKACXX:6:1101:9941:34387\r\n-ATCCCATCCTCGTCGCCA\r\n-+\r\n-BCBDFFFFHHHHHH@FHI\r\n-@HWI-ST132:678:C1LFKACXX:6:1101:14543:34442\r\n-TCCACCACGTTCCCGTGG\r\n-+\r\n-@C@FFFADFFHGHJJEHI\r\n-@HWI-ST132:678:C1LFKACXX:6:1101:5887:34986\r\n-AAACTTTCAACAACGGAT\r\n-+\r\n-@@@DFFFFH<FHHIICGI\r\n-@HWI-ST132:678:C1LFKACXX:6:1101:9891:35111\r\n-AAGAGTCTTGTCTGGTAC\r\n-+\r\n-BCCFFBDFHHHHHJFHHI\r\n-@HWI-ST132:678:C1LFKACXX:6:1101:10051:35463\r\n-TCTTGATCGAAGCCCCGG\r\n-+\r\n-B@BFFFFFHFFHGJJJJJ\r\n-@HWI-ST132:678:C1LFKACXX:6:1101:4680:35647\r\n-CGGGATGTAGCGCAGCTT\r\n-+\r\n-BB@FADFDFHGFHEIIJJ\r\n-@HWI-ST132:678:C1LFKACXX:6:1101:14569:35583\r\n-AAGATAGAGTAGTTTTTT\r\n-+\r\n-BBCDFFFFHCHHHHIJJJ\r\n-@HWI-ST132:678:C1LFKACXX:6:1101:13960:37817\r\n-AAAGTTCGGAAAACTGGC\r\n-+\r\n-@CCFDFDFHHHHHBGFGI\r\n-@HWI-ST132:678:C1LFKACXX:6:1101:16007:38099\r\n-GATGACTGGGGTGAAGTC\r\n-+\r\n-B@BDDFFFHG?CFBGIEG\r\n-@HWI-ST132:678:C1LFKACXX:6:1101:8213:39438\r\n-TAATGATTCCTGTACTGA\r\n-+\r\n-BBBFFFFFHHHHFHIJIJ\r\n-@HWI-ST132:678:C1LFKACXX:6:1101:15318:43042\r\n-CCGCTGCTGATCACACTG\r\n-+\r\n-CCCFFFFFHDHHHJJJJJ\r\n-@HWI-ST132:678:C1LFKACXX:6:1101:16708:44453\r\n'..b'276\n+GATCCCAGATCCGCTGTGTTT\n++\n+CCCFFFFFHHHHHIJFGHHIJ\n+@HWI-ST132:678:C1LFKACXX:6:1213:14045:90482\n+ATACTAGATTCGTTGAAAAGT\n++\n+@@@F7DDDFA<CC?;FAEBH?\n+@HWI-ST132:678:C1LFKACXX:6:1302:4633:32096\n+TGTTGCGGCAACTTCTTTAAGTTG\n++\n+CCCFFFFFHHHHHJJJJJJJJHIJ\n+@HWI-ST132:678:C1LFKACXX:6:2107:6041:64276\n+TGGCCTAATGGATAAGGCGTCGGACT\n++\n+@CCFFFDFHHHHHIJJJJ<FHIJJJJ\n+@HWI-ST132:678:C1LFKACXX:6:1112:9014:81599\n+TTCGGATCCGAAGATTGCAGG\n++\n+@CCFFDFFHGGGGDCEGIJJJ\n+@HWI-ST132:678:C1LFKACXX:6:2105:11875:25254\n+CGAAGATTGCAGGTTCGAGTC\n++\n+CC@FFFFFHHHFCAFHIJ+AH\n+@HWI-ST132:678:C1LFKACXX:6:2101:16974:2305\n+ACCGTTCTATGCTTTTTTTT\n++\n+:BBDDDDFHH<2<CFHIIJJ\n+@HWI-ST132:678:C1LFKACXX:6:1313:11404:80054\n+ACCGTTCTATGCTTTTTTTTA\n++\n+@@CFBDFF?FHHGIIIIGIIC\n+@HWI-ST132:678:C1LFKACXX:6:1116:12125:58757\n+AAGTAGCAGTCGTGGCCGAGTG\n++\n+??+4=B?DDHHF<EGHGGGIDG\n+@HWI-ST132:678:C1LFKACXX:6:1205:9493:45438\n+GCAGTCGTGGCCGAGTGG\n++\n+BCCFDFFFHHHHHIDCFH\n+@HWI-ST132:678:C1LFKACXX:6:1207:2720:86231\n+GCAGTCGTGGCCGAGTGG\n++\n+@@@FFFFDHHHGFIG2AF\n+@HWI-ST132:678:C1LFKACXX:6:1214:18091:41339\n+GCAGTCGTGGCCGAGTGGTTAAGG\n++\n+?@:4ABDDHHFHFDGCGDFHFGIG\n+@HWI-ST132:678:C1LFKACXX:6:1309:18921:24185\n+GCAGTCGTGGCCGAGTGGTTAAGG\n++\n+@CCFDFFFHHHHHI@ACGFHIIIJ\n+@HWI-ST132:678:C1LFKACXX:6:1106:1391:88663\n+GCAGTCGTGGCCGAGTGGTTAAGGC\n++\n+@@@FDEDDAFHHHJH+AFFHIJEHG\n+@HWI-ST132:678:C1LFKACXX:6:1310:15410:68712\n+GCAGTCGTGGCCGAGTGGTTAAGGC\n++\n+@@@DDFFFHHHHH?EEGHIJHIEEH\n+@HWI-ST132:678:C1LFKACXX:6:1202:15769:84946\n+AGCGTAGGTTCGAATCCT\n++\n+?@@D=ADDHHFDHFGGIG\n+@HWI-ST132:678:C1LFKACXX:6:2105:13686:25294\n+AGCGTAGGTTCGAATCCT\n++\n+BCCFFFFFFHHDDHHIJJ\n+@HWI-ST132:678:C1LFKACXX:6:1106:17247:63193\n+AATCCTACCGGCTGCGAATGA\n++\n+@BBFFDEFHFHHHFFFFHGHJ\n+@HWI-ST132:678:C1LFKACXX:6:1107:17291:97995\n+ATCCTACCGGCTGCGAATGA\n++\n+@CCFFFFFDFFHHJGEHGBG\n+@HWI-ST132:678:C1LFKACXX:6:2105:5531:13237\n+ACCGGCTGCGAATGAGAA\n++\n+B@BFFFFFGHDFCFHEGI\n+@HWI-ST132:678:C1LFKACXX:6:1111:11783:45506\n+ACCGGCTGCGAATGAGAATGT\n++\n+???DFFFFFHF:CCCGHHBG<\n+@HWI-ST132:678:C1LFKACXX:6:2105:11033:71535\n+CGGCTGCGAATGAGAATGTATATTT\n++\n+?BBDFFFF@<@ACAAEHHHGGIJJI\n+@HWI-ST132:678:C1LFKACXX:6:2103:20548:80488\n+AATGAGAATGTATATTTT\n++\n+BCBDDFFFHHFHHJJJJJ\n+@HWI-ST132:678:C1LFKACXX:6:1213:10954:88904\n+GCAGTCGTGGCCGAGTGG\n++\n+B@CFFFFFFHGFHGIFHI\n+@HWI-ST132:678:C1LFKACXX:6:1301:8478:85932\n+GCAGTCGTGGCCGAGTGG\n++\n+@CCFDFFDFHHHHGHAFG\n+@HWI-ST132:678:C1LFKACXX:6:2101:5467:98324\n+GCAGTCGTGGCCGAGTGG\n++\n+@@CFFDFFHHGHH>GAGH\n+@HWI-ST132:678:C1LFKACXX:6:2107:20194:63182\n+GCAGTCGTGGCCGAGTGG\n++\n+BCCFFFFFHGHHHBH<EH\n+@HWI-ST132:678:C1LFKACXX:6:1116:13015:74545\n+GCAGTCGTGGCCGAGTGGTTAAGGC\n++\n+B@:BDDFDFHFFFBG2CDHGGGFHI\n+@HWI-ST132:678:C1LFKACXX:6:1209:1463:48119\n+GCAGTCGTGGCCGAGTGGTTAAGGC\n++\n+BCCFDFDDHHHHHJJFHIIJJJIJJ\n+@HWI-ST132:678:C1LFKACXX:6:1313:4928:7411\n+GCAGTCGTGGCCGAGTGGTTAAGGC\n++\n+@C@FFDFFHHFHHJJAEGGHGIIJI\n+@HWI-ST132:678:C1LFKACXX:6:1113:20573:45425\n+AGTCGTGGCCGAGTGGTTAAGGC\n++\n+CCCFFFFFFHHHH?EHHHIIJJJ\n+@HWI-ST132:678:C1LFKACXX:6:2109:6492:70002\n+GTCGTGGCCGAGTGGTTAAGGC\n++\n+CCCFFFFFGHG@2<EAFHGGJI\n+@HWI-ST132:678:C1LFKACXX:6:1104:13333:89311\n+TTAAGGCGTCTGACTCGAAATCAGA\n++\n+CCCFFFFFHHHHHIIJJGGIJJJJJ\n+@HWI-ST132:678:C1LFKACXX:6:1306:7606:88539\n+TGACTCGAAATCAGATTCCCTCTG\n++\n+CCCFFFFFHHHHHJJJIJGIJJJJ\n+@HWI-ST132:678:C1LFKACXX:6:2108:19159:27727\n+ATATAGCCTGAGCTTCGACC\n++\n+JJJJJIHF?HHHFDFFFCCC\n+@HWI-ST132:678:C1LFKACXX:6:1211:6213:41030\n+TCGGATCCGAAGATTGCAGG\n++\n+@@CFFFFFDHHGHEHEFFHI\n+@HWI-ST132:678:C1LFKACXX:6:1203:8956:45599\n+AGATTGCAGGTTCGAGTCCT\n++\n+@@@DFFFFHHFHH<A<AEHH\n+@HWI-ST132:678:C1LFKACXX:6:1303:5477:98042\n+GTAACTGACCGTGTGGCCCAATGGA\n++\n+??@DFFFFGHDHGG?GGIEH3<FGH\n+@HWI-ST132:678:C1LFKACXX:6:1315:9507:45115\n+AAGATTGCAGGTTCGAGTC\n++\n+@@@:BDDDAFHHFIIGHFA\n+@HWI-ST132:678:C1LFKACXX:6:1306:9972:7484\n+AAGATTGCAGGTTCGAGTCCT\n++\n+@@CFFFFAFFHHHG@GEBGHH\n+@HWI-ST132:678:C1LFKACXX:6:1303:16006:44426\n+AGATTGCAGGTTCGAGTCCT\n++\n+@@@FFFFFDHDFHCE<AEHI\n+@HWI-ST132:678:C1LFKACXX:6:1214:13442:64117\n+AATGGATAAGGCGTCGGA\n++\n+818A:3ADHHFBFC1@FB\n+@HWI-ST132:678:C1LFKACXX:6:1214:1663:16969\n+ATTGCAGGTTCGAGTCCTG\n++\n+@@@FDFFFCFFHHIGHIIJ\n' |
| b |
| diff -r 9645d995fb3c -r 9185ca0a7b43 test-data/res.html --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/res.html Wed Jan 16 08:18:13 2019 -0500 |
| b |
| b'@@ -0,0 +1,411 @@\n+\n+ <!DOCTYPE html>\n+ <html lang="en">\n+ <head>\n+ <meta charset="utf-8">\n+ <title>pipeline</title>\n+ <meta name="viewport" content="width=device-width, initial-scale=1.0">\n+ <meta name="description" content="">\n+ <meta name="author" content="">\n+ <!-- Le styles -->\n+ <link href="css/bootstrap.css" rel="stylesheet">\n+ <link href="css/bootstrap-table.css" rel="stylesheet">\n+ <style type="text/css">\n+ body {\n+ padding-top: 60px;\n+ padding-bottom: 40px;\n+ }\n+ div#page {\n+ width: 940px;\n+ background-color: #fff;\n+ margin: 0 auto;\n+ text-align: left;\n+ border-color: #fff;\n+ border-style: none solid solid;\n+ border-width: medium 1px 1px;\n+ }\n+\n+ div.content {\n+ \tdisplay: none;\n+\t float: right;\n+\t width: 550px;\n+ }\n+ div.content a, div.navigation a {\n+ text-decoration: none;\n+ \tcolor: #777;\n+ }\n+ div.content a:focus, div.content a:hover, div.content a:active {\n+ text-decoration: underline;\n+ }\n+ \n+ div.controls {\n+ margin-top: 5px;\n+\t height: 23px;\n+ }\n+ \n+ div.controls a {\n+\t padding: 5px;\n+ }\n+ div.ss-controls {\n+\t float: left;\n+ }\n+ div.nav-controls {\n+\t float: right;\n+ }\n+ div.slideshow-container {\n+\t position: relative;\n+\t clear: both;\n+\t height: 502px; /* This should be set to be at least the height of the largest image in the slideshow */\n+ }\n+ div.loader {\n+ \tposition: absolute;\n+ \ttop: 0;\n+ \tleft: 0;\n+ background-image: url(\'loader.gif\');\n+ background-repeat: no-repeat;\n+ background-position: center;\n+ \twidth: 550px;\n+ \theight: 502px; /* This should be set to be at least the height of the largest image in the slideshow */\n+ }\n+ div.slideshow {\n+ \n+ }\n+ \n+ div.slideshow span.image-wrapper {\n+\t display: block;\n+\t position: absolute;\n+\t top: 0;\n+\t left: 0;\n+ }\n+ div.slideshow a.advance-link {\n+\t display: block;\n+ \t width: 550px;\n+ height: 502px; /* This should be set to be at least the height of the largest image in the slideshow */\n+ line-height: 502px; /* This should be set to be at least the height of the largest image in the slideshow */\n+ text-align: center;\n+ }\n+ div.slideshow a.advance-link:hover, div.slideshow a.advance-link:active, div.slideshow a.advance-link:visited {\n+ text-decoration: none;\n+ }\n+ div.slideshow img {\n+ vertical-align: middle;\n+\tborder: 1px solid #ccc;\n+ }\n+\n+ div.image-title {\n+ font-weight: bold;\n+ font-size: 1.4em;\n+ }\n+\n+ div.image-desc {\n+ line-height: 1.3em;\n+ padding-top: 12px;\n+ }\n+ div.navigation {\n+\n+ }\n+ ul.thumbs {\n+\tclear: both;\n+\tmargin: 0;\n+\tpadding: 0;\n+ }\n+ ul.thumbs li {\n+\tfloat: none;\n+\tpadding: 0;\n+\tmargin: 0;\n+ list-style: none;\n+ }\n+ a.thumb {\n+\tpadding: 0;\n+\tdisplay: inline;\n+\tborder: none;\n+ }\n+ ul.thumbs li.selected a.thumb {\n+\tcolor: #000;\n+ font-weight: bold;\n+ }\n+ a.thumb:focus {\n+\toutline: none;\n+ }\n+ ul.thumbs img {\n+\tborder: none;\n+\tdisplay: block;\n+ }\n+ div.pagination {\n+\tclear: both;\n+ }\n+ div.navigation div.top {\n+ margin-bottom: 12px;\n+\theight: 11px;\n+ }\n+ div.navigation div.bottom {\n+ margin-top: 12px;\n+ }\n+ div.pagination a, div.pagination span.current, div.pagination span.ellipsis {\n+\tdisplay: block;\n+\tfloat: left;\n+ margin-right: 2px;\n+\tpadding: 4px 7px 2px 7px;\n+\tborder: 1px solid #ccc;\n+ }\n+ div.pagination a:hover {\n+ background-color: #eee;\n+ text-decoration: none;\n+ }\n+ div.pagination span.current {\n+ font-weight: bold;\n+ background-color: #000;\n+ border-color: #000;\n+\tcolor: #fff;\n+ }\n+ div.pagination span.ellipsis {\n+\tborder: none;\n+\tpadding: 5px 0 3px 2px;\n+ }\n+ \n+ div.download {\n+\tfloat: right;\n+ }\n+ \n+ div.caption-container {\n+\tposition: relative;\n+\tclear: left;\n+\theight: 75px;\n+ }\n+ span.image-caption {\n+\tdisplay: block;\n+\tposition: absolute;\n+\twidth: 550px;\n+\ttop: 0;\n+\tleft: 0;\n+ }\n+ div.caption {\n+\tpadding: 12px;\n+ }\n+\n+ /* Featurettes\n+ ------------------------- */\n+\n+ .featurette {\n+ padding-top: 20px; /* Vertica'..b'ng" title="chrom_1">chrom_1</a>\n+ </li>\n+ \n+ <li>\n+ <a class="thumb" href="reads-sample-small.fastq/genome//Gviz/rand/chrom_2.png" title="chrom_2">chrom_2</a>\n+ </li>\n+ \n+ <li>\n+ <a class="thumb" href="reads-sample-small.fastq/genome//Gviz/rand/chrom_3.png" title="chrom_3">chrom_3</a>\n+ </li>\n+ \n+ <li>\n+ <a class="thumb" href="reads-sample-small.fastq/genome//Gviz/rand/chrom_4.png" title="chrom_4">chrom_4</a>\n+ </li>\n+ \n+ <li>\n+ <a class="thumb" href="reads-sample-small.fastq/genome//Gviz/rand/chrom_5.png" title="chrom_5">chrom_5</a>\n+ </li>\n+ \n+ <li>\n+ <a class="thumb" href="reads-sample-small.fastq/genome//Gviz/rand/chrom_6.png" title="chrom_6">chrom_6</a>\n+ </li>\n+ \n+ </ul>\n+ </div>\n+ <div style="clear: both;"></div></div>\n+ </div>\n+ </div>\n+ \n+ <!-- FOOTER -->\n+ <div class="container">\n+ <footer>\n+ \n+ </footer>\n+ </div>\n+ <!-- Le javascript\n+ ================================================== -->\n+ <!-- Placed at the end of the document so the pages load faster -->\n+ <script type="text/javascript" src="js/filter.js"></script>\n+ <script type="text/javascript" src="js/jquery.js"></script>\n+ <script type="text/javascript" src="js/jquery-1.3.2.js"></script>\n+ <script type="text/javascript" src="js/jquery.galleriffic.js"></script>\n+ <script type="text/javascript" src="js/jquery.opacityrollover.js"></script>\n+ <script type="text/javascript" src="js/bootstrap-table.js"></script>\n+ <script type="text/javascript" src="js/bootstrap.min.js"></script>\n+ <script type="text/javascript">\n+ jQuery(document).ready(function($) {\n+ // We only want these styles applied when javascript is enabled\n+ $(\'div.navigation\').css({\'width\' : \'300px\', \'float\' : \'left\'});\n+ $(\'div.content\').css(\'display\', \'block\');\n+ \n+ $(".each-gallery").each(function(i){\n+ // Initially set opacity on thumbs and add\n+ // additional styling for hover effect on thumbs\n+ var onMouseOutOpacity = 0.67;\n+ $(\'#thumbs + i + ul.thumbs li\').opacityrollover({\n+ mouseOutOpacity: onMouseOutOpacity,\n+ mouseOverOpacity: 1.0,\n+ fadeSpeed: \'fast\',\n+ exemptionSelector: \'.selected\'\n+ });\n+ \n+ // Initialize Advanced Galleriffic Gallery\n+ var gallery = $(\'#thumbs\'+i).galleriffic({\n+ delay: 2500,\n+ numThumbs: 22,\n+ preloadAhead: 10,\n+ enableTopPager: true,\n+ enableBottomPager: true,\n+ maxPagesToShow: 7,\n+ imageContainerSel: \'#slideshow\'+ i,\n+ controlsContainerSel: \'#controls\' + i,\n+ captionContainerSel: \'#caption\' + i,\n+ loadingContainerSel: \'#loading\' + i,\n+ renderSSControls: true,\n+ renderNavControls: true,\n+ playLinkText: \'Play\',\n+ pauseLinkText: \'Pause\',\n+ prevLinkText: \'‹ Previous\',\n+ nextLinkText: \'Next ›\',\n+ nextPageLinkText: \'Next ›\',\n+ prevPageLinkText: \'‹ Prev\',\n+ enableHistory: false,\n+ autoStart: false,\n+ syncTransitions: true,\n+ defaultTransitionDuration: 900,\n+ onSlideChange: function(prevIndex, nextIndex) {\n+ // \'this\' refers to the gallery, which is an extension of $(\'#thumbs\')\n+ this.find(\'ul.thumbs\').children()\n+ .eq(prevIndex).fadeTo(\'fast\', onMouseOutOpacity).end()\n+ .eq(nextIndex).fadeTo(\'fast\', 1.0);\n+ },\n+ onPageTransitionOut: function(callback) {\n+ this.fadeTo(\'fast\', 0.0, callback);\n+ },\n+ onPageTransitionIn: function() {\n+ this.fadeTo(\'fast\', 1.0);\n+ }\n+ });\n+ });\n+ });\n+ </script>\n+ </body>\n+ </html>\n+ \n\\ No newline at end of file\n' |
| b |
| diff -r 9645d995fb3c -r 9185ca0a7b43 test-data/res_files/css/bootstrap-responsive.css --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/res_files/css/bootstrap-responsive.css Wed Jan 16 08:18:13 2019 -0500 |
| [ |
| b'@@ -0,0 +1,1109 @@\n+/*!\r\n+ * Bootstrap Responsive v2.3.2\r\n+ *\r\n+ * Copyright 2012 Twitter, Inc\r\n+ * Licensed under the Apache License v2.0\r\n+ * http://www.apache.org/licenses/LICENSE-2.0\r\n+ *\r\n+ * Designed and built with all the love in the world @twitter by @mdo and @fat.\r\n+ */\r\n+\r\n+.clearfix {\r\n+ *zoom: 1;\r\n+}\r\n+\r\n+.clearfix:before,\r\n+.clearfix:after {\r\n+ display: table;\r\n+ line-height: 0;\r\n+ content: "";\r\n+}\r\n+\r\n+.clearfix:after {\r\n+ clear: both;\r\n+}\r\n+\r\n+.hide-text {\r\n+ font: 0/0 a;\r\n+ color: transparent;\r\n+ text-shadow: none;\r\n+ background-color: transparent;\r\n+ border: 0;\r\n+}\r\n+\r\n+.input-block-level {\r\n+ display: block;\r\n+ width: 100%;\r\n+ min-height: 30px;\r\n+ -webkit-box-sizing: border-box;\r\n+ -moz-box-sizing: border-box;\r\n+ box-sizing: border-box;\r\n+}\r\n+\r\n+@-ms-viewport {\r\n+ width: device-width;\r\n+}\r\n+\r\n+.hidden {\r\n+ display: none;\r\n+ visibility: hidden;\r\n+}\r\n+\r\n+.visible-phone {\r\n+ display: none !important;\r\n+}\r\n+\r\n+.visible-tablet {\r\n+ display: none !important;\r\n+}\r\n+\r\n+.hidden-desktop {\r\n+ display: none !important;\r\n+}\r\n+\r\n+.visible-desktop {\r\n+ display: inherit !important;\r\n+}\r\n+\r\n+@media (min-width: 768px) and (max-width: 979px) {\r\n+ .hidden-desktop {\r\n+ display: inherit !important;\r\n+ }\r\n+ .visible-desktop {\r\n+ display: none !important ;\r\n+ }\r\n+ .visible-tablet {\r\n+ display: inherit !important;\r\n+ }\r\n+ .hidden-tablet {\r\n+ display: none !important;\r\n+ }\r\n+}\r\n+\r\n+@media (max-width: 767px) {\r\n+ .hidden-desktop {\r\n+ display: inherit !important;\r\n+ }\r\n+ .visible-desktop {\r\n+ display: none !important;\r\n+ }\r\n+ .visible-phone {\r\n+ display: inherit !important;\r\n+ }\r\n+ .hidden-phone {\r\n+ display: none !important;\r\n+ }\r\n+}\r\n+\r\n+.visible-print {\r\n+ display: none !important;\r\n+}\r\n+\r\n+@media print {\r\n+ .visible-print {\r\n+ display: inherit !important;\r\n+ }\r\n+ .hidden-print {\r\n+ display: none !important;\r\n+ }\r\n+}\r\n+\r\n+@media (min-width: 1200px) {\r\n+ .row {\r\n+ margin-left: -30px;\r\n+ *zoom: 1;\r\n+ }\r\n+ .row:before,\r\n+ .row:after {\r\n+ display: table;\r\n+ line-height: 0;\r\n+ content: "";\r\n+ }\r\n+ .row:after {\r\n+ clear: both;\r\n+ }\r\n+ [class*="span"] {\r\n+ float: left;\r\n+ min-height: 1px;\r\n+ margin-left: 30px;\r\n+ }\r\n+ .container,\r\n+ .navbar-static-top .container,\r\n+ .navbar-fixed-top .container,\r\n+ .navbar-fixed-bottom .container {\r\n+ width: 1170px;\r\n+ }\r\n+ .span12 {\r\n+ width: 1170px;\r\n+ }\r\n+ .span11 {\r\n+ width: 1070px;\r\n+ }\r\n+ .span10 {\r\n+ width: 970px;\r\n+ }\r\n+ .span9 {\r\n+ width: 870px;\r\n+ }\r\n+ .span8 {\r\n+ width: 770px;\r\n+ }\r\n+ .span7 {\r\n+ width: 670px;\r\n+ }\r\n+ .span6 {\r\n+ width: 570px;\r\n+ }\r\n+ .span5 {\r\n+ width: 470px;\r\n+ }\r\n+ .span4 {\r\n+ width: 370px;\r\n+ }\r\n+ .span3 {\r\n+ width: 270px;\r\n+ }\r\n+ .span2 {\r\n+ width: 170px;\r\n+ }\r\n+ .span1 {\r\n+ width: 70px;\r\n+ }\r\n+ .offset12 {\r\n+ margin-left: 1230px;\r\n+ }\r\n+ .offset11 {\r\n+ margin-left: 1130px;\r\n+ }\r\n+ .offset10 {\r\n+ margin-left: 1030px;\r\n+ }\r\n+ .offset9 {\r\n+ margin-left: 930px;\r\n+ }\r\n+ .offset8 {\r\n+ margin-left: 830px;\r\n+ }\r\n+ .offset7 {\r\n+ margin-left: 730px;\r\n+ }\r\n+ .offset6 {\r\n+ margin-left: 630px;\r\n+ }\r\n+ .offset5 {\r\n+ margin-left: 530px;\r\n+ }\r\n+ .offset4 {\r\n+ margin-left: 430px;\r\n+ }\r\n+ .offset3 {\r\n+ margin-left: 330px;\r\n+ }\r\n+ .offset2 {\r\n+ margin-left: 230px;\r\n+ }\r\n+ .offset1 {\r\n+ margin-left: 130px;\r\n+ }\r\n+ .row-fluid {\r\n+ width: 100%;\r\n+ *zoom: 1;\r\n+ }\r\n+ .row-fluid:before,\r\n+ .row-fluid:after {\r\n+ display: table;\r\n+ line-height: 0;\r\n+ content: "";\r\n+ }\r\n+ .row-fluid:after {\r\n+ clear: both;\r\n+ }\r\n+ .row-fluid [class*="span"] {\r\n+ display: block;\r\n+ float: left;\r\n+ width: 100%;\r\n+ min-height: 30px;\r\n+ margin-left: 2.564102564102564%;\r\n+ *margin-left: 2.5109110747408616%;\r\n+ -webkit-box-sizing: border-box;\r\n+ -moz-box-sizing: border-box;\r\n+ box-sizing: border-box;\r\n+ }\r\n+ .row-'..b'+ }\r\n+ .navbar-fixed-top {\r\n+ margin-bottom: 20px;\r\n+ }\r\n+ .navbar-fixed-bottom {\r\n+ margin-top: 20px;\r\n+ }\r\n+ .navbar-fixed-top .navbar-inner,\r\n+ .navbar-fixed-bottom .navbar-inner {\r\n+ padding: 5px;\r\n+ }\r\n+ .navbar .container {\r\n+ width: auto;\r\n+ padding: 0;\r\n+ }\r\n+ .navbar .brand {\r\n+ padding-right: 10px;\r\n+ padding-left: 10px;\r\n+ margin: 0 0 0 -5px;\r\n+ }\r\n+ .nav-collapse {\r\n+ clear: both;\r\n+ }\r\n+ .nav-collapse .nav {\r\n+ float: none;\r\n+ margin: 0 0 10px;\r\n+ }\r\n+ .nav-collapse .nav > li {\r\n+ float: none;\r\n+ }\r\n+ .nav-collapse .nav > li > a {\r\n+ margin-bottom: 2px;\r\n+ }\r\n+ .nav-collapse .nav > .divider-vertical {\r\n+ display: none;\r\n+ }\r\n+ .nav-collapse .nav .nav-header {\r\n+ color: #777777;\r\n+ text-shadow: none;\r\n+ }\r\n+ .nav-collapse .nav > li > a,\r\n+ .nav-collapse .dropdown-menu a {\r\n+ padding: 9px 15px;\r\n+ font-weight: bold;\r\n+ color: #777777;\r\n+ -webkit-border-radius: 3px;\r\n+ -moz-border-radius: 3px;\r\n+ border-radius: 3px;\r\n+ }\r\n+ .nav-collapse .btn {\r\n+ padding: 4px 10px 4px;\r\n+ font-weight: normal;\r\n+ -webkit-border-radius: 4px;\r\n+ -moz-border-radius: 4px;\r\n+ border-radius: 4px;\r\n+ }\r\n+ .nav-collapse .dropdown-menu li + li a {\r\n+ margin-bottom: 2px;\r\n+ }\r\n+ .nav-collapse .nav > li > a:hover,\r\n+ .nav-collapse .nav > li > a:focus,\r\n+ .nav-collapse .dropdown-menu a:hover,\r\n+ .nav-collapse .dropdown-menu a:focus {\r\n+ background-color: #f2f2f2;\r\n+ }\r\n+ .navbar-inverse .nav-collapse .nav > li > a,\r\n+ .navbar-inverse .nav-collapse .dropdown-menu a {\r\n+ color: #999999;\r\n+ }\r\n+ .navbar-inverse .nav-collapse .nav > li > a:hover,\r\n+ .navbar-inverse .nav-collapse .nav > li > a:focus,\r\n+ .navbar-inverse .nav-collapse .dropdown-menu a:hover,\r\n+ .navbar-inverse .nav-collapse .dropdown-menu a:focus {\r\n+ background-color: #111111;\r\n+ }\r\n+ .nav-collapse.in .btn-group {\r\n+ padding: 0;\r\n+ margin-top: 5px;\r\n+ }\r\n+ .nav-collapse .dropdown-menu {\r\n+ position: static;\r\n+ top: auto;\r\n+ left: auto;\r\n+ display: none;\r\n+ float: none;\r\n+ max-width: none;\r\n+ padding: 0;\r\n+ margin: 0 15px;\r\n+ background-color: transparent;\r\n+ border: none;\r\n+ -webkit-border-radius: 0;\r\n+ -moz-border-radius: 0;\r\n+ border-radius: 0;\r\n+ -webkit-box-shadow: none;\r\n+ -moz-box-shadow: none;\r\n+ box-shadow: none;\r\n+ }\r\n+ .nav-collapse .open > .dropdown-menu {\r\n+ display: block;\r\n+ }\r\n+ .nav-collapse .dropdown-menu:before,\r\n+ .nav-collapse .dropdown-menu:after {\r\n+ display: none;\r\n+ }\r\n+ .nav-collapse .dropdown-menu .divider {\r\n+ display: none;\r\n+ }\r\n+ .nav-collapse .nav > li > .dropdown-menu:before,\r\n+ .nav-collapse .nav > li > .dropdown-menu:after {\r\n+ display: none;\r\n+ }\r\n+ .nav-collapse .navbar-form,\r\n+ .nav-collapse .navbar-search {\r\n+ float: none;\r\n+ padding: 10px 15px;\r\n+ margin: 10px 0;\r\n+ border-top: 1px solid #f2f2f2;\r\n+ border-bottom: 1px solid #f2f2f2;\r\n+ -webkit-box-shadow: inset 0 1px 0 rgba(255, 255, 255, 0.1), 0 1px 0 rgba(255, 255, 255, 0.1);\r\n+ -moz-box-shadow: inset 0 1px 0 rgba(255, 255, 255, 0.1), 0 1px 0 rgba(255, 255, 255, 0.1);\r\n+ box-shadow: inset 0 1px 0 rgba(255, 255, 255, 0.1), 0 1px 0 rgba(255, 255, 255, 0.1);\r\n+ }\r\n+ .navbar-inverse .nav-collapse .navbar-form,\r\n+ .navbar-inverse .nav-collapse .navbar-search {\r\n+ border-top-color: #111111;\r\n+ border-bottom-color: #111111;\r\n+ }\r\n+ .navbar .nav-collapse .nav.pull-right {\r\n+ float: none;\r\n+ margin-left: 0;\r\n+ }\r\n+ .nav-collapse,\r\n+ .nav-collapse.collapse {\r\n+ height: 0;\r\n+ overflow: hidden;\r\n+ }\r\n+ .navbar .btn-navbar {\r\n+ display: block;\r\n+ }\r\n+ .navbar-static .navbar-inner {\r\n+ padding-right: 10px;\r\n+ padding-left: 10px;\r\n+ }\r\n+}\r\n+\r\n+@media (min-width: 980px) {\r\n+ .nav-collapse.collapse {\r\n+ height: auto !important;\r\n+ overflow: visible !important;\r\n+ }\r\n+}\r\n' |
| b |
| diff -r 9645d995fb3c -r 9185ca0a7b43 test-data/res_files/css/bootstrap-table.css --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/res_files/css/bootstrap-table.css Wed Jan 16 08:18:13 2019 -0500 |
| [ |
| @@ -0,0 +1,313 @@ +/** + * @author zhixin wen <wenzhixin2010@gmail.com> + * version: 1.11.1 + * https://github.com/wenzhixin/bootstrap-table/ + */ + +.bootstrap-table .table { + margin-bottom: 0 !important; + border-bottom: 1px solid #dddddd; + border-collapse: collapse !important; + border-radius: 1px; +} + +.bootstrap-table .table:not(.table-condensed), +.bootstrap-table .table:not(.table-condensed) > tbody > tr > th, +.bootstrap-table .table:not(.table-condensed) > tfoot > tr > th, +.bootstrap-table .table:not(.table-condensed) > thead > tr > td, +.bootstrap-table .table:not(.table-condensed) > tbody > tr > td, +.bootstrap-table .table:not(.table-condensed) > tfoot > tr > td { + padding: 8px; +} + +.bootstrap-table .table.table-no-bordered > thead > tr > th, +.bootstrap-table .table.table-no-bordered > tbody > tr > td { + border-right: 2px solid transparent; +} + +.bootstrap-table .table.table-no-bordered > tbody > tr > td:last-child { + border-right: none; +} + +.fixed-table-container { + position: relative; + clear: both; + border: 1px solid #dddddd; + border-radius: 4px; + -webkit-border-radius: 4px; + -moz-border-radius: 4px; +} + +.fixed-table-container.table-no-bordered { + border: 1px solid transparent; +} + +.fixed-table-footer, +.fixed-table-header { + overflow: hidden; +} + +.fixed-table-footer { + border-top: 1px solid #dddddd; +} + +.fixed-table-body { + overflow-x: auto; + overflow-y: auto; + height: 100%; +} + +.fixed-table-container table { + width: 100%; +} + +.fixed-table-container thead th { + height: 0; + padding: 0; + margin: 0; + border-left: 1px solid #dddddd; +} + +.fixed-table-container thead th:focus { + outline: 0 solid transparent; +} + +.fixed-table-container thead th:first-child { + border-left: none; + border-top-left-radius: 4px; + -webkit-border-top-left-radius: 4px; + -moz-border-radius-topleft: 4px; +} + +.fixed-table-container thead th .th-inner, +.fixed-table-container tbody td .th-inner { + padding: 8px; + line-height: 24px; + vertical-align: top; + overflow: hidden; + text-overflow: ellipsis; + white-space: nowrap; +} + +.fixed-table-container thead th .sortable { + cursor: pointer; + background-position: right; + background-repeat: no-repeat; + padding-right: 30px; +} + +.fixed-table-container thead th .both { + background-image: url('data:image/png;base64,iVBORw0KGgoAAAANSUhEUgAAABMAAAATCAQAAADYWf5HAAAAkElEQVQoz7X QMQ5AQBCF4dWQSJxC5wwax1Cq1e7BAdxD5SL+Tq/QCM1oNiJidwox0355mXnG/DrEtIQ6azioNZQxI0ykPhTQIwhCR+BmBYtlK7kLJYwWCcJA9M4qdrZrd8pPjZWPtOqdRQy320YSV17OatFC4euts6z39GYMKRPCTKY9UnPQ6P+GtMRfGtPnBCiqhAeJPmkqAAAAAElFTkSuQmCC'); +} + +.fixed-table-container thead th .asc { + background-image: url('data:image/png;base64,iVBORw0KGgoAAAANSUhEUgAAABMAAAATCAYAAAByUDbMAAAAZ0lEQVQ4y2NgGLKgquEuFxBPAGI2ahhWCsS/gDibUoO0gPgxEP8H4ttArEyuQYxAPBdqEAxPBImTY5gjEL9DM+wTENuQahAvEO9DMwiGdwAxOymGJQLxTyD+jgWDxCMZRsEoGAVoAADeemwtPcZI2wAAAABJRU5ErkJggg=='); +} + +.fixed-table-container thead th .desc { + background-image: url('data:image/png;base64,iVBORw0KGgoAAAANSUhEUgAAABMAAAATCAYAAAByUDbMAAAAZUlEQVQ4y2NgGAWjYBSggaqGu5FA/BOIv2PBIPFEUgxjB+IdQPwfC94HxLykus4GiD+hGfQOiB3J8SojEE9EM2wuSJzcsFMG4ttQgx4DsRalkZENxL+AuJQaMcsGxBOAmGvopk8AVz1sLZgg0bsAAAAASUVORK5CYII= '); +} + +.fixed-table-container th.detail { + width: 30px; +} + +.fixed-table-container tbody td { + border-left: 1px solid #dddddd; +} + +.fixed-table-container tbody tr:first-child td { + border-top: none; +} + +.fixed-table-container tbody td:first-child { + border-left: none; +} + +/* the same color with .active */ +.fixed-table-container tbody .selected td { + background-color: #f5f5f5; +} + +.fixed-table-container .bs-checkbox { + text-align: center; +} + +.fixed-table-container .bs-checkbox .th-inner { + padding: 8px 0; +} + +.fixed-table-container input[type="radio"], +.fixed-table-container input[type="checkbox"] { + margin: 0 auto !important; +} + +.fixed-table-container .no-records-found { + text-align: center; +} + +.fixed-table-pagination div.pagination, +.fixed-table-pagination .pagination-detail { + margin-top: 10px; + margin-bottom: 10px; +} + +.fixed-table-pagination div.pagination .pagination { + margin: 0; +} + +.fixed-table-pagination .pagination a { + padding: 6px 12px; + line-height: 1.428571429; +} + +.fixed-table-pagination .pagination-info { + line-height: 34px; + margin-right: 5px; +} + +.fixed-table-pagination .btn-group { + position: relative; + display: inline-block; + vertical-align: middle; +} + +.fixed-table-pagination .dropup .dropdown-menu { + margin-bottom: 0; +} + +.fixed-table-pagination .page-list { + display: inline-block; +} + +.fixed-table-toolbar .columns-left { + margin-right: 5px; +} + +.fixed-table-toolbar .columns-right { + margin-left: 5px; +} + +.fixed-table-toolbar .columns label { + display: block; + padding: 3px 20px; + clear: both; + font-weight: normal; + line-height: 1.428571429; +} + +.fixed-table-toolbar .bs-bars, +.fixed-table-toolbar .search, +.fixed-table-toolbar .columns { + position: relative; + margin-top: 10px; + margin-bottom: 10px; + line-height: 34px; +} + +.fixed-table-pagination li.disabled a { + pointer-events: none; + cursor: default; +} + +.fixed-table-loading { + display: none; + position: absolute; + top: 42px; + right: 0; + bottom: 0; + left: 0; + z-index: 99; + background-color: #fff; + text-align: center; +} + +.fixed-table-body .card-view .title { + font-weight: bold; + display: inline-block; + min-width: 30%; + text-align: left !important; +} + +/* support bootstrap 2 */ +.fixed-table-body thead th .th-inner { + box-sizing: border-box; +} + +.table th, .table td { + vertical-align: middle; + box-sizing: border-box; +} + +.fixed-table-toolbar .dropdown-menu { + text-align: left; + max-height: 300px; + overflow: auto; +} + +.fixed-table-toolbar .btn-group > .btn-group { + display: inline-block; + margin-left: -1px !important; +} + +.fixed-table-toolbar .btn-group > .btn-group > .btn { + border-radius: 0; +} + +.fixed-table-toolbar .btn-group > .btn-group:first-child > .btn { + border-top-left-radius: 4px; + border-bottom-left-radius: 4px; +} + +.fixed-table-toolbar .btn-group > .btn-group:last-child > .btn { + border-top-right-radius: 4px; + border-bottom-right-radius: 4px; +} + +.bootstrap-table .table > thead > tr > th { + vertical-align: bottom; + border-bottom: 1px solid #ddd; +} + +/* support bootstrap 3 */ +.bootstrap-table .table thead > tr > th { + padding: 0; + margin: 0; +} + +.bootstrap-table .fixed-table-footer tbody > tr > td { + padding: 0 !important; +} + +.bootstrap-table .fixed-table-footer .table { + border-bottom: none; + border-radius: 0; + padding: 0 !important; +} + +.bootstrap-table .pull-right .dropdown-menu { + right: 0; + left: auto; +} + +/* calculate scrollbar width */ +p.fixed-table-scroll-inner { + width: 100%; + height: 200px; +} + +div.fixed-table-scroll-outer { + top: 0; + left: 0; + visibility: hidden; + width: 200px; + height: 150px; + overflow: hidden; +} + +/* for get correct heights */ +.fixed-table-toolbar:after, .fixed-table-pagination:after { + content: ""; + display: block; + clear: both; +} |
| b |
| diff -r 9645d995fb3c -r 9185ca0a7b43 test-data/res_files/css/bootstrap.css --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/res_files/css/bootstrap.css Wed Jan 16 08:18:13 2019 -0500 |
| [ |
| b'@@ -0,0 +1,6167 @@\n+/*!\r\n+ * Bootstrap v2.3.2\r\n+ *\r\n+ * Copyright 2012 Twitter, Inc\r\n+ * Licensed under the Apache License v2.0\r\n+ * http://www.apache.org/licenses/LICENSE-2.0\r\n+ *\r\n+ * Designed and built with all the love in the world @twitter by @mdo and @fat.\r\n+ */\r\n+\r\n+.clearfix {\r\n+ *zoom: 1;\r\n+}\r\n+\r\n+.clearfix:before,\r\n+.clearfix:after {\r\n+ display: table;\r\n+ line-height: 0;\r\n+ content: "";\r\n+}\r\n+\r\n+.clearfix:after {\r\n+ clear: both;\r\n+}\r\n+\r\n+.hide-text {\r\n+ font: 0/0 a;\r\n+ color: transparent;\r\n+ text-shadow: none;\r\n+ background-color: transparent;\r\n+ border: 0;\r\n+}\r\n+\r\n+.input-block-level {\r\n+ display: block;\r\n+ width: 100%;\r\n+ min-height: 30px;\r\n+ -webkit-box-sizing: border-box;\r\n+ -moz-box-sizing: border-box;\r\n+ box-sizing: border-box;\r\n+}\r\n+\r\n+article,\r\n+aside,\r\n+details,\r\n+figcaption,\r\n+figure,\r\n+footer,\r\n+header,\r\n+hgroup,\r\n+nav,\r\n+section {\r\n+ display: block;\r\n+}\r\n+\r\n+audio,\r\n+canvas,\r\n+video {\r\n+ display: inline-block;\r\n+ *display: inline;\r\n+ *zoom: 1;\r\n+}\r\n+\r\n+audio:not([controls]) {\r\n+ display: none;\r\n+}\r\n+\r\n+html {\r\n+ font-size: 100%;\r\n+ -webkit-text-size-adjust: 100%;\r\n+ -ms-text-size-adjust: 100%;\r\n+}\r\n+\r\n+a:focus {\r\n+ outline: thin dotted #333;\r\n+ outline: 5px auto -webkit-focus-ring-color;\r\n+ outline-offset: -2px;\r\n+}\r\n+\r\n+a:hover,\r\n+a:active {\r\n+ outline: 0;\r\n+}\r\n+\r\n+sub,\r\n+sup {\r\n+ position: relative;\r\n+ font-size: 75%;\r\n+ line-height: 0;\r\n+ vertical-align: baseline;\r\n+}\r\n+\r\n+sup {\r\n+ top: -0.5em;\r\n+}\r\n+\r\n+sub {\r\n+ bottom: -0.25em;\r\n+}\r\n+\r\n+img {\r\n+ width: auto\\9;\r\n+ height: auto;\r\n+ max-width: 100%;\r\n+ vertical-align: middle;\r\n+ border: 0;\r\n+ -ms-interpolation-mode: bicubic;\r\n+}\r\n+\r\n+#map_canvas img,\r\n+.google-maps img {\r\n+ max-width: none;\r\n+}\r\n+\r\n+button,\r\n+input,\r\n+select,\r\n+textarea {\r\n+ margin: 0;\r\n+ font-size: 100%;\r\n+ vertical-align: middle;\r\n+}\r\n+\r\n+button,\r\n+input {\r\n+ *overflow: visible;\r\n+ line-height: normal;\r\n+}\r\n+\r\n+button::-moz-focus-inner,\r\n+input::-moz-focus-inner {\r\n+ padding: 0;\r\n+ border: 0;\r\n+}\r\n+\r\n+button,\r\n+html input[type="button"],\r\n+input[type="reset"],\r\n+input[type="submit"] {\r\n+ cursor: pointer;\r\n+ -webkit-appearance: button;\r\n+}\r\n+\r\n+label,\r\n+select,\r\n+button,\r\n+input[type="button"],\r\n+input[type="reset"],\r\n+input[type="submit"],\r\n+input[type="radio"],\r\n+input[type="checkbox"] {\r\n+ cursor: pointer;\r\n+}\r\n+\r\n+input[type="search"] {\r\n+ -webkit-box-sizing: content-box;\r\n+ -moz-box-sizing: content-box;\r\n+ box-sizing: content-box;\r\n+ -webkit-appearance: textfield;\r\n+}\r\n+\r\n+input[type="search"]::-webkit-search-decoration,\r\n+input[type="search"]::-webkit-search-cancel-button {\r\n+ -webkit-appearance: none;\r\n+}\r\n+\r\n+textarea {\r\n+ overflow: auto;\r\n+ vertical-align: top;\r\n+}\r\n+\r\n+@media print {\r\n+ * {\r\n+ color: #000 !important;\r\n+ text-shadow: none !important;\r\n+ background: transparent !important;\r\n+ box-shadow: none !important;\r\n+ }\r\n+ a,\r\n+ a:visited {\r\n+ text-decoration: underline;\r\n+ }\r\n+ a[href]:after {\r\n+ content: " (" attr(href) ")";\r\n+ }\r\n+ abbr[title]:after {\r\n+ content: " (" attr(title) ")";\r\n+ }\r\n+ .ir a:after,\r\n+ a[href^="javascript:"]:after,\r\n+ a[href^="#"]:after {\r\n+ content: "";\r\n+ }\r\n+ pre,\r\n+ blockquote {\r\n+ border: 1px solid #999;\r\n+ page-break-inside: avoid;\r\n+ }\r\n+ thead {\r\n+ display: table-header-group;\r\n+ }\r\n+ tr,\r\n+ img {\r\n+ page-break-inside: avoid;\r\n+ }\r\n+ img {\r\n+ max-width: 100% !important;\r\n+ }\r\n+ @page {\r\n+ margin: 0.5cm;\r\n+ }\r\n+ p,\r\n+ h2,\r\n+ h3 {\r\n+ orphans: 3;\r\n+ widows: 3;\r\n+ }\r\n+ h2,\r\n+ h3 {\r\n+ page-break-after: avoid;\r\n+ }\r\n+}\r\n+\r\n+body {\r\n+ margin: 0;\r\n+ font-family: "Helvetica Neue", Helvetica, Arial, sans-serif;\r\n+ font-size: 14px;\r\n+ line-height: 20px;\r\n+ color: #333333;\r\n+ background-color: #ffffff;\r\n+}\r\n+\r\n+a {\r\n+ color: #0088cc;\r\n+ text-decoration: none;\r\n+}\r\n+\r\n+a:hover,\r\n+a:focus {\r\n+ color: #005580;\r\n+ text-decoration: underline;\r\n+}\r\n+\r\n+.img-rounded {\r\n+ -webkit-bo'..b'nt 25%, transparent 50%, rgba(255, 255, 255, 0.15) 50%, rgba(255, 255, 255, 0.15) 75%, transparent 75%, transparent);\r\n+}\r\n+\r\n+.accordion {\r\n+ margin-bottom: 20px;\r\n+}\r\n+\r\n+.accordion-group {\r\n+ margin-bottom: 2px;\r\n+ border: 1px solid #e5e5e5;\r\n+ -webkit-border-radius: 4px;\r\n+ -moz-border-radius: 4px;\r\n+ border-radius: 4px;\r\n+}\r\n+\r\n+.accordion-heading {\r\n+ border-bottom: 0;\r\n+}\r\n+\r\n+.accordion-heading .accordion-toggle {\r\n+ display: block;\r\n+ padding: 8px 15px;\r\n+}\r\n+\r\n+.accordion-toggle {\r\n+ cursor: pointer;\r\n+}\r\n+\r\n+.accordion-inner {\r\n+ padding: 9px 15px;\r\n+ border-top: 1px solid #e5e5e5;\r\n+}\r\n+\r\n+.carousel {\r\n+ position: relative;\r\n+ margin-bottom: 20px;\r\n+ line-height: 1;\r\n+}\r\n+\r\n+.carousel-inner {\r\n+ position: relative;\r\n+ width: 100%;\r\n+ overflow: hidden;\r\n+}\r\n+\r\n+.carousel-inner > .item {\r\n+ position: relative;\r\n+ display: none;\r\n+ -webkit-transition: 0.6s ease-in-out left;\r\n+ -moz-transition: 0.6s ease-in-out left;\r\n+ -o-transition: 0.6s ease-in-out left;\r\n+ transition: 0.6s ease-in-out left;\r\n+}\r\n+\r\n+.carousel-inner > .item > img,\r\n+.carousel-inner > .item > a > img {\r\n+ display: block;\r\n+ line-height: 1;\r\n+}\r\n+\r\n+.carousel-inner > .active,\r\n+.carousel-inner > .next,\r\n+.carousel-inner > .prev {\r\n+ display: block;\r\n+}\r\n+\r\n+.carousel-inner > .active {\r\n+ left: 0;\r\n+}\r\n+\r\n+.carousel-inner > .next,\r\n+.carousel-inner > .prev {\r\n+ position: absolute;\r\n+ top: 0;\r\n+ width: 100%;\r\n+}\r\n+\r\n+.carousel-inner > .next {\r\n+ left: 100%;\r\n+}\r\n+\r\n+.carousel-inner > .prev {\r\n+ left: -100%;\r\n+}\r\n+\r\n+.carousel-inner > .next.left,\r\n+.carousel-inner > .prev.right {\r\n+ left: 0;\r\n+}\r\n+\r\n+.carousel-inner > .active.left {\r\n+ left: -100%;\r\n+}\r\n+\r\n+.carousel-inner > .active.right {\r\n+ left: 100%;\r\n+}\r\n+\r\n+.carousel-control {\r\n+ position: absolute;\r\n+ top: 40%;\r\n+ left: 15px;\r\n+ width: 40px;\r\n+ height: 40px;\r\n+ margin-top: -20px;\r\n+ font-size: 60px;\r\n+ font-weight: 100;\r\n+ line-height: 30px;\r\n+ color: #ffffff;\r\n+ text-align: center;\r\n+ background: #222222;\r\n+ border: 3px solid #ffffff;\r\n+ -webkit-border-radius: 23px;\r\n+ -moz-border-radius: 23px;\r\n+ border-radius: 23px;\r\n+ opacity: 0.5;\r\n+ filter: alpha(opacity=50);\r\n+}\r\n+\r\n+.carousel-control.right {\r\n+ right: 15px;\r\n+ left: auto;\r\n+}\r\n+\r\n+.carousel-control:hover,\r\n+.carousel-control:focus {\r\n+ color: #ffffff;\r\n+ text-decoration: none;\r\n+ opacity: 0.9;\r\n+ filter: alpha(opacity=90);\r\n+}\r\n+\r\n+.carousel-indicators {\r\n+ position: absolute;\r\n+ top: 15px;\r\n+ right: 15px;\r\n+ z-index: 5;\r\n+ margin: 0;\r\n+ list-style: none;\r\n+}\r\n+\r\n+.carousel-indicators li {\r\n+ display: block;\r\n+ float: left;\r\n+ width: 10px;\r\n+ height: 10px;\r\n+ margin-left: 5px;\r\n+ text-indent: -999px;\r\n+ background-color: #ccc;\r\n+ background-color: rgba(255, 255, 255, 0.25);\r\n+ border-radius: 5px;\r\n+}\r\n+\r\n+.carousel-indicators .active {\r\n+ background-color: #fff;\r\n+}\r\n+\r\n+.carousel-caption {\r\n+ position: absolute;\r\n+ right: 0;\r\n+ bottom: 0;\r\n+ left: 0;\r\n+ padding: 15px;\r\n+ background: #333333;\r\n+ background: rgba(0, 0, 0, 0.75);\r\n+}\r\n+\r\n+.carousel-caption h4,\r\n+.carousel-caption p {\r\n+ line-height: 20px;\r\n+ color: #ffffff;\r\n+}\r\n+\r\n+.carousel-caption h4 {\r\n+ margin: 0 0 5px;\r\n+}\r\n+\r\n+.carousel-caption p {\r\n+ margin-bottom: 0;\r\n+}\r\n+\r\n+.hero-unit {\r\n+ padding: 60px;\r\n+ margin-bottom: 30px;\r\n+ font-size: 18px;\r\n+ font-weight: 200;\r\n+ line-height: 30px;\r\n+ color: inherit;\r\n+ background-color: #eeeeee;\r\n+ -webkit-border-radius: 6px;\r\n+ -moz-border-radius: 6px;\r\n+ border-radius: 6px;\r\n+}\r\n+\r\n+.hero-unit h1 {\r\n+ margin-bottom: 0;\r\n+ font-size: 60px;\r\n+ line-height: 1;\r\n+ letter-spacing: -1px;\r\n+ color: inherit;\r\n+}\r\n+\r\n+.hero-unit li {\r\n+ line-height: 30px;\r\n+}\r\n+\r\n+.pull-right {\r\n+ float: right;\r\n+}\r\n+\r\n+.pull-left {\r\n+ float: left;\r\n+}\r\n+\r\n+.hide {\r\n+ display: none;\r\n+}\r\n+\r\n+.show {\r\n+ display: block;\r\n+}\r\n+\r\n+.invisible {\r\n+ visibility: hidden;\r\n+}\r\n+\r\n+.affix {\r\n+ position: fixed;\r\n+}\r\n' |
| b |
| diff -r 9645d995fb3c -r 9185ca0a7b43 test-data/res_files/js/bootstrap-table.js --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/res_files/js/bootstrap-table.js Wed Jan 16 08:18:13 2019 -0500 |
| [ |
| b"@@ -0,0 +1,3094 @@\n+/**\r\n+ * @author zhixin wen <wenzhixin2010@gmail.com>\r\n+ * version: 1.11.1\r\n+ * https://github.com/wenzhixin/bootstrap-table/\r\n+ */\r\n+\r\n+(function ($) {\r\n+ 'use strict';\r\n+\r\n+ // TOOLS DEFINITION\r\n+ // ======================\r\n+\r\n+ var cachedWidth = null;\r\n+\r\n+ // it only does '%s', and return '' when arguments are undefined\r\n+ var sprintf = function (str) {\r\n+ var args = arguments,\r\n+ flag = true,\r\n+ i = 1;\r\n+\r\n+ str = str.replace(/%s/g, function () {\r\n+ var arg = args[i++];\r\n+\r\n+ if (typeof arg === 'undefined') {\r\n+ flag = false;\r\n+ return '';\r\n+ }\r\n+ return arg;\r\n+ });\r\n+ return flag ? str : '';\r\n+ };\r\n+\r\n+ var getPropertyFromOther = function (list, from, to, value) {\r\n+ var result = '';\r\n+ $.each(list, function (i, item) {\r\n+ if (item[from] === value) {\r\n+ result = item[to];\r\n+ return false;\r\n+ }\r\n+ return true;\r\n+ });\r\n+ return result;\r\n+ };\r\n+\r\n+ var getFieldIndex = function (columns, field) {\r\n+ var index = -1;\r\n+\r\n+ $.each(columns, function (i, column) {\r\n+ if (column.field === field) {\r\n+ index = i;\r\n+ return false;\r\n+ }\r\n+ return true;\r\n+ });\r\n+ return index;\r\n+ };\r\n+\r\n+ // http://jsfiddle.net/wenyi/47nz7ez9/3/\r\n+ var setFieldIndex = function (columns) {\r\n+ var i, j, k,\r\n+ totalCol = 0,\r\n+ flag = [];\r\n+\r\n+ for (i = 0; i < columns[0].length; i++) {\r\n+ totalCol += columns[0][i].colspan || 1;\r\n+ }\r\n+\r\n+ for (i = 0; i < columns.length; i++) {\r\n+ flag[i] = [];\r\n+ for (j = 0; j < totalCol; j++) {\r\n+ flag[i][j] = false;\r\n+ }\r\n+ }\r\n+\r\n+ for (i = 0; i < columns.length; i++) {\r\n+ for (j = 0; j < columns[i].length; j++) {\r\n+ var r = columns[i][j],\r\n+ rowspan = r.rowspan || 1,\r\n+ colspan = r.colspan || 1,\r\n+ index = $.inArray(false, flag[i]);\r\n+\r\n+ if (colspan === 1) {\r\n+ r.fieldIndex = index;\r\n+ // when field is undefined, use index instead\r\n+ if (typeof r.field === 'undefined') {\r\n+ r.field = index;\r\n+ }\r\n+ }\r\n+\r\n+ for (k = 0; k < rowspan; k++) {\r\n+ flag[i + k][index] = true;\r\n+ }\r\n+ for (k = 0; k < colspan; k++) {\r\n+ flag[i][index + k] = true;\r\n+ }\r\n+ }\r\n+ }\r\n+ };\r\n+\r\n+ var getScrollBarWidth = function () {\r\n+ if (cachedWidth === null) {\r\n+ var inner = $('<p/>').addClass('fixed-table-scroll-inner'),\r\n+ outer = $('<div/>').addClass('fixed-table-scroll-outer'),\r\n+ w1, w2;\r\n+\r\n+ outer.append(inner);\r\n+ $('body').append(outer);\r\n+\r\n+ w1 = inner[0].offsetWidth;\r\n+ outer.css('overflow', 'scroll');\r\n+ w2 = inner[0].offsetWidth;\r\n+\r\n+ if (w1 === w2) {\r\n+ w2 = outer[0].clientWidth;\r\n+ }\r\n+\r\n+ outer.remove();\r\n+ cachedWidth = w1 - w2;\r\n+ }\r\n+ return cachedWidth;\r\n+ };\r\n+\r\n+ var calculateObjectValue = function (self, name, args, defaultValue) {\r\n+ var func = name;\r\n+\r\n+ if (typeof name === 'string') {\r\n+ // support obj.func1.func2\r\n+ var names = name.split('.');\r\n+\r\n+ if (names.length > 1) {\r\n+ func = window;\r\n+ $.each(names, function (i, f) {\r\n+ func = func[f];\r\n+ });\r\n+ } else {\r\n+ func = window[name];\r\n+ "..b' };\r\n+\r\n+ BootstrapTable.prototype.collapseAllRows = function (isSubTable) {\r\n+ if (isSubTable) {\r\n+ this.expandRow_(false, 0);\r\n+ } else {\r\n+ var trs = this.$body.children();\r\n+ for (var i = 0; i < trs.length; i++) {\r\n+ this.expandRow_(false, $(trs[i]).data("index"));\r\n+ }\r\n+ }\r\n+ };\r\n+\r\n+ BootstrapTable.prototype.updateFormatText = function (name, text) {\r\n+ if (this.options[sprintf(\'format%s\', name)]) {\r\n+ if (typeof text === \'string\') {\r\n+ this.options[sprintf(\'format%s\', name)] = function () {\r\n+ return text;\r\n+ };\r\n+ } else if (typeof text === \'function\') {\r\n+ this.options[sprintf(\'format%s\', name)] = text;\r\n+ }\r\n+ }\r\n+ this.initToolbar();\r\n+ this.initPagination();\r\n+ this.initBody();\r\n+ };\r\n+\r\n+ // BOOTSTRAP TABLE PLUGIN DEFINITION\r\n+ // =======================\r\n+\r\n+ var allowedMethods = [\r\n+ \'getOptions\',\r\n+ \'getSelections\', \'getAllSelections\', \'getData\',\r\n+ \'load\', \'append\', \'prepend\', \'remove\', \'removeAll\',\r\n+ \'insertRow\', \'updateRow\', \'updateCell\', \'updateByUniqueId\', \'removeByUniqueId\',\r\n+ \'getRowByUniqueId\', \'showRow\', \'hideRow\', \'getHiddenRows\',\r\n+ \'mergeCells\',\r\n+ \'checkAll\', \'uncheckAll\', \'checkInvert\',\r\n+ \'check\', \'uncheck\',\r\n+ \'checkBy\', \'uncheckBy\',\r\n+ \'refresh\',\r\n+ \'resetView\',\r\n+ \'resetWidth\',\r\n+ \'destroy\',\r\n+ \'showLoading\', \'hideLoading\',\r\n+ \'showColumn\', \'hideColumn\', \'getHiddenColumns\', \'getVisibleColumns\',\r\n+ \'showAllColumns\', \'hideAllColumns\',\r\n+ \'filterBy\',\r\n+ \'scrollTo\',\r\n+ \'getScrollPosition\',\r\n+ \'selectPage\', \'prevPage\', \'nextPage\',\r\n+ \'togglePagination\',\r\n+ \'toggleView\',\r\n+ \'refreshOptions\',\r\n+ \'resetSearch\',\r\n+ \'expandRow\', \'collapseRow\', \'expandAllRows\', \'collapseAllRows\',\r\n+ \'updateFormatText\'\r\n+ ];\r\n+\r\n+ $.fn.bootstrapTable = function (option) {\r\n+ var value,\r\n+ args = Array.prototype.slice.call(arguments, 1);\r\n+\r\n+ this.each(function () {\r\n+ var $this = $(this),\r\n+ data = $this.data(\'bootstrap.table\'),\r\n+ options = $.extend({}, BootstrapTable.DEFAULTS, $this.data(),\r\n+ typeof option === \'object\' && option);\r\n+\r\n+ if (typeof option === \'string\') {\r\n+ if ($.inArray(option, allowedMethods) < 0) {\r\n+ throw new Error("Unknown method: " + option);\r\n+ }\r\n+\r\n+ if (!data) {\r\n+ return;\r\n+ }\r\n+\r\n+ value = data[option].apply(data, args);\r\n+\r\n+ if (option === \'destroy\') {\r\n+ $this.removeData(\'bootstrap.table\');\r\n+ }\r\n+ }\r\n+\r\n+ if (!data) {\r\n+ $this.data(\'bootstrap.table\', (data = new BootstrapTable(this, options)));\r\n+ }\r\n+ });\r\n+\r\n+ return typeof value === \'undefined\' ? this : value;\r\n+ };\r\n+\r\n+ $.fn.bootstrapTable.Constructor = BootstrapTable;\r\n+ $.fn.bootstrapTable.defaults = BootstrapTable.DEFAULTS;\r\n+ $.fn.bootstrapTable.columnDefaults = BootstrapTable.COLUMN_DEFAULTS;\r\n+ $.fn.bootstrapTable.locales = BootstrapTable.LOCALES;\r\n+ $.fn.bootstrapTable.methods = allowedMethods;\r\n+ $.fn.bootstrapTable.utils = {\r\n+ sprintf: sprintf,\r\n+ getFieldIndex: getFieldIndex,\r\n+ compareObjects: compareObjects,\r\n+ calculateObjectValue: calculateObjectValue,\r\n+ getItemField: getItemField,\r\n+ objectKeys: objectKeys,\r\n+ isIEBrowser: isIEBrowser\r\n+ };\r\n+\r\n+ // BOOTSTRAP TABLE INIT\r\n+ // =======================\r\n+\r\n+ $(function () {\r\n+ $(\'[data-toggle="table"]\').bootstrapTable();\r\n+ });\r\n+})(jQuery);\r\n' |
| b |
| diff -r 9645d995fb3c -r 9185ca0a7b43 test-data/res_files/js/bootstrap.min.js --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/res_files/js/bootstrap.min.js Wed Jan 16 08:18:13 2019 -0500 |
| [ |
| b'@@ -0,0 +1,6 @@\n+/**\r\n+* Bootstrap.js v2.3.2 by @fat & @mdo\r\n+* Copyright 2013 Twitter, Inc.\r\n+* http://www.apache.org/licenses/LICENSE-2.0.txt\r\n+*/\r\n+!function(e){"use strict";e(function(){e.support.transition=function(){var e=function(){var e=document.createElement("bootstrap"),t={WebkitTransition:"webkitTransitionEnd",MozTransition:"transitionend",OTransition:"oTransitionEnd otransitionend",transition:"transitionend"},n;for(n in t)if(e.style[n]!==undefined)return t[n]}();return e&&{end:e}}()})}(window.jQuery),!function(e){"use strict";var t=\'[data-dismiss="alert"]\',n=function(n){e(n).on("click",t,this.close)};n.prototype.close=function(t){function s(){i.trigger("closed").remove()}var n=e(this),r=n.attr("data-target"),i;r||(r=n.attr("href"),r=r&&r.replace(/.*(?=#[^\\s]*$)/,"")),i=e(r),t&&t.preventDefault(),i.length||(i=n.hasClass("alert")?n:n.parent()),i.trigger(t=e.Event("close"));if(t.isDefaultPrevented())return;i.removeClass("in"),e.support.transition&&i.hasClass("fade")?i.on(e.support.transition.end,s):s()};var r=e.fn.alert;e.fn.alert=function(t){return this.each(function(){var r=e(this),i=r.data("alert");i||r.data("alert",i=new n(this)),typeof t=="string"&&i[t].call(r)})},e.fn.alert.Constructor=n,e.fn.alert.noConflict=function(){return e.fn.alert=r,this},e(document).on("click.alert.data-api",t,n.prototype.close)}(window.jQuery),!function(e){"use strict";var t=function(t,n){this.$element=e(t),this.options=e.extend({},e.fn.button.defaults,n)};t.prototype.setState=function(e){var t="disabled",n=this.$element,r=n.data(),i=n.is("input")?"val":"html";e+="Text",r.resetText||n.data("resetText",n[i]()),n[i](r[e]||this.options[e]),setTimeout(function(){e=="loadingText"?n.addClass(t).attr(t,t):n.removeClass(t).removeAttr(t)},0)},t.prototype.toggle=function(){var e=this.$element.closest(\'[data-toggle="buttons-radio"]\');e&&e.find(".active").removeClass("active"),this.$element.toggleClass("active")};var n=e.fn.button;e.fn.button=function(n){return this.each(function(){var r=e(this),i=r.data("button"),s=typeof n=="object"&&n;i||r.data("button",i=new t(this,s)),n=="toggle"?i.toggle():n&&i.setState(n)})},e.fn.button.defaults={loadingText:"loading..."},e.fn.button.Constructor=t,e.fn.button.noConflict=function(){return e.fn.button=n,this},e(document).on("click.button.data-api","[data-toggle^=button]",function(t){var n=e(t.target);n.hasClass("btn")||(n=n.closest(".btn")),n.button("toggle")})}(window.jQuery),!function(e){"use strict";var t=function(t,n){this.$element=e(t),this.$indicators=this.$element.find(".carousel-indicators"),this.options=n,this.options.pause=="hover"&&this.$element.on("mouseenter",e.proxy(this.pause,this)).on("mouseleave",e.proxy(this.cycle,this))};t.prototype={cycle:function(t){return t||(this.paused=!1),this.interval&&clearInterval(this.interval),this.options.interval&&!this.paused&&(this.interval=setInterval(e.proxy(this.next,this),this.options.interval)),this},getActiveIndex:function(){return this.$active=this.$element.find(".item.active"),this.$items=this.$active.parent().children(),this.$items.index(this.$active)},to:function(t){var n=this.getActiveIndex(),r=this;if(t>this.$items.length-1||t<0)return;return this.sliding?this.$element.one("slid",function(){r.to(t)}):n==t?this.pause().cycle():this.slide(t>n?"next":"prev",e(this.$items[t]))},pause:function(t){return t||(this.paused=!0),this.$element.find(".next, .prev").length&&e.support.transition.end&&(this.$element.trigger(e.support.transition.end),this.cycle(!0)),clearInterval(this.interval),this.interval=null,this},next:function(){if(this.sliding)return;return this.slide("next")},prev:function(){if(this.sliding)return;return this.slide("prev")},slide:function(t,n){var r=this.$element.find(".item.active"),i=n||r[t](),s=this.interval,o=t=="next"?"left":"right",u=t=="next"?"first":"last",a=this,f;this.sliding=!0,s&&this.pause(),i=i.length?i:this.$element.find(".item")[u](),f=e.Event("slide",{relatedTarget:i[0],direction:o});if(i.hasClass("active"))return;this.$in'..b',next:function(t){var n=this.$menu.find(".active").removeClass("active"),r=n.next();r.length||(r=e(this.$menu.find("li")[0])),r.addClass("active")},prev:function(e){var t=this.$menu.find(".active").removeClass("active"),n=t.prev();n.length||(n=this.$menu.find("li").last()),n.addClass("active")},listen:function(){this.$element.on("focus",e.proxy(this.focus,this)).on("blur",e.proxy(this.blur,this)).on("keypress",e.proxy(this.keypress,this)).on("keyup",e.proxy(this.keyup,this)),this.eventSupported("keydown")&&this.$element.on("keydown",e.proxy(this.keydown,this)),this.$menu.on("click",e.proxy(this.click,this)).on("mouseenter","li",e.proxy(this.mouseenter,this)).on("mouseleave","li",e.proxy(this.mouseleave,this))},eventSupported:function(e){var t=e in this.$element;return t||(this.$element.setAttribute(e,"return;"),t=typeof this.$element[e]=="function"),t},move:function(e){if(!this.shown)return;switch(e.keyCode){case 9:case 13:case 27:e.preventDefault();break;case 38:e.preventDefault(),this.prev();break;case 40:e.preventDefault(),this.next()}e.stopPropagation()},keydown:function(t){this.suppressKeyPressRepeat=~e.inArray(t.keyCode,[40,38,9,13,27]),this.move(t)},keypress:function(e){if(this.suppressKeyPressRepeat)return;this.move(e)},keyup:function(e){switch(e.keyCode){case 40:case 38:case 16:case 17:case 18:break;case 9:case 13:if(!this.shown)return;this.select();break;case 27:if(!this.shown)return;this.hide();break;default:this.lookup()}e.stopPropagation(),e.preventDefault()},focus:function(e){this.focused=!0},blur:function(e){this.focused=!1,!this.mousedover&&this.shown&&this.hide()},click:function(e){e.stopPropagation(),e.preventDefault(),this.select(),this.$element.focus()},mouseenter:function(t){this.mousedover=!0,this.$menu.find(".active").removeClass("active"),e(t.currentTarget).addClass("active")},mouseleave:function(e){this.mousedover=!1,!this.focused&&this.shown&&this.hide()}};var n=e.fn.typeahead;e.fn.typeahead=function(n){return this.each(function(){var r=e(this),i=r.data("typeahead"),s=typeof n=="object"&&n;i||r.data("typeahead",i=new t(this,s)),typeof n=="string"&&i[n]()})},e.fn.typeahead.defaults={source:[],items:8,menu:\'<ul class="typeahead dropdown-menu"></ul>\',item:\'<li><a href="#"></a></li>\',minLength:1},e.fn.typeahead.Constructor=t,e.fn.typeahead.noConflict=function(){return e.fn.typeahead=n,this},e(document).on("focus.typeahead.data-api",\'[data-provide="typeahead"]\',function(t){var n=e(this);if(n.data("typeahead"))return;n.typeahead(n.data())})}(window.jQuery),!function(e){"use strict";var t=function(t,n){this.options=e.extend({},e.fn.affix.defaults,n),this.$window=e(window).on("scroll.affix.data-api",e.proxy(this.checkPosition,this)).on("click.affix.data-api",e.proxy(function(){setTimeout(e.proxy(this.checkPosition,this),1)},this)),this.$element=e(t),this.checkPosition()};t.prototype.checkPosition=function(){if(!this.$element.is(":visible"))return;var t=e(document).height(),n=this.$window.scrollTop(),r=this.$element.offset(),i=this.options.offset,s=i.bottom,o=i.top,u="affix affix-top affix-bottom",a;typeof i!="object"&&(s=o=i),typeof o=="function"&&(o=i.top()),typeof s=="function"&&(s=i.bottom()),a=this.unpin!=null&&n+this.unpin<=r.top?!1:s!=null&&r.top+this.$element.height()>=t-s?"bottom":o!=null&&n<=o?"top":!1;if(this.affixed===a)return;this.affixed=a,this.unpin=a=="bottom"?r.top-n:null,this.$element.removeClass(u).addClass("affix"+(a?"-"+a:""))};var n=e.fn.affix;e.fn.affix=function(n){return this.each(function(){var r=e(this),i=r.data("affix"),s=typeof n=="object"&&n;i||r.data("affix",i=new t(this,s)),typeof n=="string"&&i[n]()})},e.fn.affix.Constructor=t,e.fn.affix.defaults={offset:0},e.fn.affix.noConflict=function(){return e.fn.affix=n,this},e(window).on("load",function(){e(\'[data-spy="affix"]\').each(function(){var t=e(this),n=t.data();n.offset=n.offset||{},n.offsetBottom&&(n.offset.bottom=n.offsetBottom),n.offsetTop&&(n.offset.top=n.offsetTop),t.affix(n)})})}(window.jQuery);\n\\ No newline at end of file\n' |
| b |
| diff -r 9645d995fb3c -r 9185ca0a7b43 test-data/res_files/js/filter.js --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/res_files/js/filter.js Wed Jan 16 08:18:13 2019 -0500 |
| [ |
| @@ -0,0 +1,20 @@ +function search(input) { + // Declare variables + var elt, filter, uls, li, a, i; + elt = input.parentElement; + filter = input.value.toUpperCase(); + uls = elt.getElementsByClassName('thumbs'); + + // Loop through all list items, and hide those who don't match the search query + for (j = 0; j < uls.length; j++) { + li = uls[j].getElementsByTagName('li'); + for (i = 0; i < li.length; i++) { + a = li[i].getElementsByTagName("a")[0]; + if (a.innerHTML.toUpperCase().indexOf(filter) > -1) { + li[i].style.display = ""; + } else { + li[i].style.display = "none"; + } + } + } +} |
| b |
| diff -r 9645d995fb3c -r 9185ca0a7b43 test-data/res_files/js/jquery.galleriffic.js --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/res_files/js/jquery.galleriffic.js Wed Jan 16 08:18:13 2019 -0500 |
| [ |
| b"@@ -0,0 +1,979 @@\n+/**\r\n+ * jQuery Galleriffic plugin\r\n+ *\r\n+ * Copyright (c) 2008 Trent Foley (http://trentacular.com)\r\n+ * Licensed under the MIT License:\r\n+ * http://www.opensource.org/licenses/mit-license.php\r\n+ *\r\n+ * Much thanks to primary contributer Ponticlaro (http://www.ponticlaro.com)\r\n+ */\r\n+;(function($) {\r\n+\t// Globally keep track of all images by their unique hash. Each item is an image data object.\r\n+\tvar allImages = {};\r\n+\tvar imageCounter = 0;\r\n+\n+\t// Galleriffic static class\r\n+\t$.galleriffic = {\n+\t\tversion: '2.0.1',\n+\n+\t\t// Strips invalid characters and any leading # characters\n+\t\tnormalizeHash: function(hash) {\r\n+\t\t\treturn hash.replace(/^.*#/, '').replace(/\\?.*$/, '');\n+\t\t},\n+\n+\t\tgetImage: function(hash) {\n+\t\t\tif (!hash)\n+\t\t\t\treturn undefined;\n+\n+\t\t\thash = $.galleriffic.normalizeHash(hash);\r\n+\t\t\treturn allImages[hash];\n+\t\t},\n+\r\n+\t\t// Global function that looks up an image by its hash and displays the image.\n+\t\t// Returns false when an image is not found for the specified hash.\n+\t\t// @param {String} hash This is the unique hash value assigned to an image.\n+\t\tgotoImage: function(hash) {\r\n+\t\t\tvar imageData = $.galleriffic.getImage(hash);\r\n+\t\t\tif (!imageData)\n+\t\t\t\treturn false;\r\n+\n+\t\t\tvar gallery = imageData.gallery;\n+\t\t\tgallery.gotoImage(imageData);\n+\t\t\t\n+\t\t\treturn true;\r\n+\t\t},\n+\n+\t\t// Removes an image from its respective gallery by its hash.\n+\t\t// Returns false when an image is not found for the specified hash or the\n+\t\t// specified owner gallery does match the located images gallery.\n+\t\t// @param {String} hash This is the unique hash value assigned to an image.\n+\t\t// @param {Object} ownerGallery (Optional) When supplied, the located images\n+\t\t// gallery is verified to be the same as the specified owning gallery before\n+\t\t// performing the remove operation.\n+\t\tremoveImageByHash: function(hash, ownerGallery) {\n+\t\t\tvar imageData = $.galleriffic.getImage(hash);\n+\t\t\tif (!imageData)\n+\t\t\t\treturn false;\n+\n+\t\t\tvar gallery = imageData.gallery;\n+\t\t\tif (ownerGallery && ownerGallery != gallery)\n+\t\t\t\treturn false;\n+\n+\t\t\treturn gallery.removeImageByIndex(imageData.index);\n+\t\t}\r\n+\t};\n+\r\n+\tvar defaults = {\r\n+\t\tdelay: 3000,\r\n+\t\tnumThumbs: 20,\r\n+\t\tpreloadAhead: 40, // Set to -1 to preload all images\r\n+\t\tenableTopPager: false,\r\n+\t\tenableBottomPager: true,\r\n+\t\tmaxPagesToShow: 7,\r\n+\t\timageContainerSel: '',\r\n+\t\tcaptionContainerSel: '',\r\n+\t\tcontrolsContainerSel: '',\r\n+\t\tloadingContainerSel: '',\r\n+\t\trenderSSControls: true,\r\n+\t\trenderNavControls: true,\r\n+\t\tplayLinkText: 'Play',\r\n+\t\tpauseLinkText: 'Pause',\r\n+\t\tprevLinkText: 'Previous',\r\n+\t\tnextLinkText: 'Next',\r\n+\t\tnextPageLinkText: 'Next ›',\r\n+\t\tprevPageLinkText: '‹ Prev',\r\n+\t\tenableHistory: false,\n+\t\tenableKeyboardNavigation: true,\r\n+\t\tautoStart: false,\r\n+\t\tsyncTransitions: false,\r\n+\t\tdefaultTransitionDuration: 1000,\r\n+\t\tonSlideChange: undefined, // accepts a delegate like such: function(prevIndex, nextIndex) { ... }\r\n+\t\tonTransitionOut: undefined, // accepts a delegate like such: function(slide, caption, isSync, callback) { ... }\r\n+\t\tonTransitionIn: undefined, // accepts a delegate like such: function(slide, caption, isSync) { ... }\r\n+\t\tonPageTransitionOut: undefined, // accepts a delegate like such: function(callback) { ... }\r\n+\t\tonPageTransitionIn: undefined, // accepts a delegate like such: function() { ... }\n+\t\tonImageAdded: undefined, // accepts a delegate like such: function(imageData, $li) { ... }\n+\t\tonImageRemoved: undefined // accepts a delegate like such: function(imageData, $li) { ... }\r\n+\t};\r\n+\n+\t// Primary Galleriffic initialization function that should be called on the thumbnail container.\r\n+\t$.fn.galleriffic = function(settings) {\r\n+\t\t// Extend Gallery O"..b'display all thumbnails.\r\n+\t\t\tbuildPageLink: function(pager, pageNum, numPages) {\r\n+\t\t\t\tvar pageLabel = pageNum + 1;\r\n+\t\t\t\tvar currentPage = this.getCurrentPage();\r\n+\t\t\t\tif (pageNum == currentPage)\r\n+\t\t\t\t\tpager.append(\'<span class="current">\'+pageLabel+\'</span>\');\r\n+\t\t\t\telse if (pageNum < numPages) {\r\n+\t\t\t\t\tvar imageIndex = pageNum*this.numThumbs;\r\n+\t\t\t\t\tpager.append(\'<a rel="history" href="#\'+this.data[imageIndex].hash+\'" title="\'+pageLabel+\'">\'+pageLabel+\'</a>\');\r\n+\t\t\t\t}\n+\t\t\t\t\n+\t\t\t\treturn this;\r\n+\t\t\t}\r\n+\t\t});\r\n+\r\n+\t\t// Now initialize the gallery\r\n+\t\t$.extend(this, defaults, settings);\r\n+\t\t\r\n+\t\t// Verify the history plugin is available\r\n+\t\tif (this.enableHistory && !$.historyInit)\r\n+\t\t\tthis.enableHistory = false;\r\n+\t\t\r\n+\t\t// Select containers\r\n+\t\tif (this.imageContainerSel) this.$imageContainer = $(this.imageContainerSel);\r\n+\t\tif (this.captionContainerSel) this.$captionContainer = $(this.captionContainerSel);\r\n+\t\tif (this.loadingContainerSel) this.$loadingContainer = $(this.loadingContainerSel);\r\n+\n+\t\t// Initialize the thumbails\r\n+\t\tthis.initializeThumbs();\r\n+\t\t\r\n+\t\tif (this.maxPagesToShow < 3)\r\n+\t\t\tthis.maxPagesToShow = 3;\r\n+\r\n+\t\tthis.displayedPage = -1;\n+\t\tthis.currentImage = this.data[0];\r\n+\t\tvar gallery = this;\r\n+\r\n+\t\t// Hide the loadingContainer\r\n+\t\tif (this.$loadingContainer)\r\n+\t\t\tthis.$loadingContainer.hide();\r\n+\r\n+\t\t// Setup controls\r\n+\t\tif (this.controlsContainerSel) {\r\n+\t\t\tthis.$controlsContainer = $(this.controlsContainerSel).empty();\r\n+\t\t\t\r\n+\t\t\tif (this.renderSSControls) {\r\n+\t\t\t\tif (this.autoStart) {\r\n+\t\t\t\t\tthis.$controlsContainer\r\n+\t\t\t\t\t\t.append(\'<div class="ss-controls"><a href="#pause" class="pause" title="\'+this.pauseLinkText+\'">\'+this.pauseLinkText+\'</a></div>\');\r\n+\t\t\t\t} else {\r\n+\t\t\t\t\tthis.$controlsContainer\r\n+\t\t\t\t\t\t.append(\'<div class="ss-controls"><a href="#play" class="play" title="\'+this.playLinkText+\'">\'+this.playLinkText+\'</a></div>\');\r\n+\t\t\t\t}\r\n+\r\n+\t\t\t\tthis.$controlsContainer.find(\'div.ss-controls a\')\r\n+\t\t\t\t\t.click(function(e) {\r\n+\t\t\t\t\t\tgallery.toggleSlideshow();\r\n+\t\t\t\t\t\te.preventDefault();\r\n+\t\t\t\t\t\treturn false;\r\n+\t\t\t\t\t});\r\n+\t\t\t}\r\n+\t\t\r\n+\t\t\tif (this.renderNavControls) {\r\n+\t\t\t\tthis.$controlsContainer\r\n+\t\t\t\t\t.append(\'<div class="nav-controls"><a class="prev" rel="history" title="\'+this.prevLinkText+\'">\'+this.prevLinkText+\'</a><a class="next" rel="history" title="\'+this.nextLinkText+\'">\'+this.nextLinkText+\'</a></div>\')\r\n+\t\t\t\t\t.find(\'div.nav-controls a\')\r\n+\t\t\t\t\t.click(function(e) {\r\n+\t\t\t\t\t\tgallery.clickHandler(e, this);\r\n+\t\t\t\t\t});\r\n+\t\t\t}\r\n+\t\t}\r\n+\n+\t\tvar initFirstImage = !this.enableHistory || !location.hash;\n+\t\tif (this.enableHistory && location.hash) {\n+\t\t\tvar hash = $.galleriffic.normalizeHash(location.hash);\n+\t\t\tvar imageData = allImages[hash];\r\n+\t\t\tif (!imageData)\n+\t\t\t\tinitFirstImage = true;\n+\t\t}\n+\r\n+\t\t// Setup gallery to show the first image\n+\t\tif (initFirstImage)\r\n+\t\t\tthis.gotoIndex(0, false, true);\r\n+\n+\t\t// Setup Keyboard Navigation\n+\t\tif (this.enableKeyboardNavigation) {\n+\t\t\t$(document).keydown(function(e) {\n+\t\t\t\tvar key = e.charCode ? e.charCode : e.keyCode ? e.keyCode : 0;\n+\t\t\t\tswitch(key) {\n+\t\t\t\t\tcase 32: // space\n+\t\t\t\t\t\tgallery.next();\n+\t\t\t\t\t\te.preventDefault();\n+\t\t\t\t\t\tbreak;\n+\t\t\t\t\tcase 33: // Page Up\n+\t\t\t\t\t\tgallery.previousPage();\n+\t\t\t\t\t\te.preventDefault();\n+\t\t\t\t\t\tbreak;\n+\t\t\t\t\tcase 34: // Page Down\n+\t\t\t\t\t\tgallery.nextPage();\n+\t\t\t\t\t\te.preventDefault();\n+\t\t\t\t\t\tbreak;\n+\t\t\t\t\tcase 35: // End\n+\t\t\t\t\t\tgallery.gotoIndex(gallery.data.length-1);\n+\t\t\t\t\t\te.preventDefault();\n+\t\t\t\t\t\tbreak;\n+\t\t\t\t\tcase 36: // Home\n+\t\t\t\t\t\tgallery.gotoIndex(0);\n+\t\t\t\t\t\te.preventDefault();\n+\t\t\t\t\t\tbreak;\n+\t\t\t\t\tcase 37: // left arrow\n+\t\t\t\t\t\tgallery.previous();\n+\t\t\t\t\t\te.preventDefault();\n+\t\t\t\t\t\tbreak;\n+\t\t\t\t\tcase 39: // right arrow\n+\t\t\t\t\t\tgallery.next();\n+\t\t\t\t\t\te.preventDefault();\n+\t\t\t\t\t\tbreak;\n+\t\t\t\t}\n+\t\t\t});\n+\t\t}\n+\n+\t\t// Auto start the slideshow\r\n+\t\tif (this.autoStart)\r\n+\t\t\tthis.play();\r\n+\r\n+\t\t// Kickoff Image Preloader after 1 second\r\n+\t\tsetTimeout(function() { gallery.preloadInit(); }, 1000);\r\n+\r\n+\t\treturn this;\r\n+\t};\r\n+})(jQuery);\r\n' |
| b |
| diff -r 9645d995fb3c -r 9185ca0a7b43 test-data/res_files/js/jquery.js --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/res_files/js/jquery.js Wed Jan 16 08:18:13 2019 -0500 |
| [ |
| b'@@ -0,0 +1,5 @@\n+/*! jQuery v1.9.1 | (c) 2005, 2012 jQuery Foundation, Inc. | jquery.org/license\r\n+//@ sourceMappingURL=jquery.min.map\r\n+*/(function(e,t){var n,r,i=typeof t,o=e.document,a=e.location,s=e.jQuery,u=e.$,l={},c=[],p="1.9.1",f=c.concat,d=c.push,h=c.slice,g=c.indexOf,m=l.toString,y=l.hasOwnProperty,v=p.trim,b=function(e,t){return new b.fn.init(e,t,r)},x=/[+-]?(?:\\d*\\.|)\\d+(?:[eE][+-]?\\d+|)/.source,w=/\\S+/g,T=/^[\\s\\uFEFF\\xA0]+|[\\s\\uFEFF\\xA0]+$/g,N=/^(?:(<[\\w\\W]+>)[^>]*|#([\\w-]*))$/,C=/^<(\\w+)\\s*\\/?>(?:<\\/\\1>|)$/,k=/^[\\],:{}\\s]*$/,E=/(?:^|:|,)(?:\\s*\\[)+/g,S=/\\\\(?:["\\\\\\/bfnrt]|u[\\da-fA-F]{4})/g,A=/"[^"\\\\\\r\\n]*"|true|false|null|-?(?:\\d+\\.|)\\d+(?:[eE][+-]?\\d+|)/g,j=/^-ms-/,D=/-([\\da-z])/gi,L=function(e,t){return t.toUpperCase()},H=function(e){(o.addEventListener||"load"===e.type||"complete"===o.readyState)&&(q(),b.ready())},q=function(){o.addEventListener?(o.removeEventListener("DOMContentLoaded",H,!1),e.removeEventListener("load",H,!1)):(o.detachEvent("onreadystatechange",H),e.detachEvent("onload",H))};b.fn=b.prototype={jquery:p,constructor:b,init:function(e,n,r){var i,a;if(!e)return this;if("string"==typeof e){if(i="<"===e.charAt(0)&&">"===e.charAt(e.length-1)&&e.length>=3?[null,e,null]:N.exec(e),!i||!i[1]&&n)return!n||n.jquery?(n||r).find(e):this.constructor(n).find(e);if(i[1]){if(n=n instanceof b?n[0]:n,b.merge(this,b.parseHTML(i[1],n&&n.nodeType?n.ownerDocument||n:o,!0)),C.test(i[1])&&b.isPlainObject(n))for(i in n)b.isFunction(this[i])?this[i](n[i]):this.attr(i,n[i]);return this}if(a=o.getElementById(i[2]),a&&a.parentNode){if(a.id!==i[2])return r.find(e);this.length=1,this[0]=a}return this.context=o,this.selector=e,this}return e.nodeType?(this.context=this[0]=e,this.length=1,this):b.isFunction(e)?r.ready(e):(e.selector!==t&&(this.selector=e.selector,this.context=e.context),b.makeArray(e,this))},selector:"",length:0,size:function(){return this.length},toArray:function(){return h.call(this)},get:function(e){return null==e?this.toArray():0>e?this[this.length+e]:this[e]},pushStack:function(e){var t=b.merge(this.constructor(),e);return t.prevObject=this,t.context=this.context,t},each:function(e,t){return b.each(this,e,t)},ready:function(e){return b.ready.promise().done(e),this},slice:function(){return this.pushStack(h.apply(this,arguments))},first:function(){return this.eq(0)},last:function(){return this.eq(-1)},eq:function(e){var t=this.length,n=+e+(0>e?t:0);return this.pushStack(n>=0&&t>n?[this[n]]:[])},map:function(e){return this.pushStack(b.map(this,function(t,n){return e.call(t,n,t)}))},end:function(){return this.prevObject||this.constructor(null)},push:d,sort:[].sort,splice:[].splice},b.fn.init.prototype=b.fn,b.extend=b.fn.extend=function(){var e,n,r,i,o,a,s=arguments[0]||{},u=1,l=arguments.length,c=!1;for("boolean"==typeof s&&(c=s,s=arguments[1]||{},u=2),"object"==typeof s||b.isFunction(s)||(s={}),l===u&&(s=this,--u);l>u;u++)if(null!=(o=arguments[u]))for(i in o)e=s[i],r=o[i],s!==r&&(c&&r&&(b.isPlainObject(r)||(n=b.isArray(r)))?(n?(n=!1,a=e&&b.isArray(e)?e:[]):a=e&&b.isPlainObject(e)?e:{},s[i]=b.extend(c,a,r)):r!==t&&(s[i]=r));return s},b.extend({noConflict:function(t){return e.$===b&&(e.$=u),t&&e.jQuery===b&&(e.jQuery=s),b},isReady:!1,readyWait:1,holdReady:function(e){e?b.readyWait++:b.ready(!0)},ready:function(e){if(e===!0?!--b.readyWait:!b.isReady){if(!o.body)return setTimeout(b.ready);b.isReady=!0,e!==!0&&--b.readyWait>0||(n.resolveWith(o,[b]),b.fn.trigger&&b(o).trigger("ready").off("ready"))}},isFunction:function(e){return"function"===b.type(e)},isArray:Array.isArray||function(e){return"array"===b.type(e)},isWindow:function(e){return null!=e&&e==e.window},isNumeric:function(e){return!isNaN(parseFloat(e))&&isFinite(e)},type:function(e){return null==e?e+"":"object"==typeof e||"function"==typeof e?l[m.call(e)]||"object":typeof e},isPlainObject:function(e){if(!e||"object"!==b.type(e)||e.nodeType||b.isWindow(e))return!1;try{if(e.constructor&&!y.call(e,"constructor")&&!y.call(e.constructor.prototype,"isPrototypeOf")'..b' ir(e,t){var n,r={height:e},i=0;for(t=t?1:0;4>i;i+=2-t)n=Zt[i],r["margin"+n]=r["padding"+n]=e;return t&&(r.opacity=r.width=e),r}b.each({slideDown:ir("show"),slideUp:ir("hide"),slideToggle:ir("toggle"),fadeIn:{opacity:"show"},fadeOut:{opacity:"hide"},fadeToggle:{opacity:"toggle"}},function(e,t){b.fn[e]=function(e,n,r){return this.animate(t,e,n,r)}}),b.speed=function(e,t,n){var r=e&&"object"==typeof e?b.extend({},e):{complete:n||!n&&t||b.isFunction(e)&&e,duration:e,easing:n&&t||t&&!b.isFunction(t)&&t};return r.duration=b.fx.off?0:"number"==typeof r.duration?r.duration:r.duration in b.fx.speeds?b.fx.speeds[r.duration]:b.fx.speeds._default,(null==r.queue||r.queue===!0)&&(r.queue="fx"),r.old=r.complete,r.complete=function(){b.isFunction(r.old)&&r.old.call(this),r.queue&&b.dequeue(this,r.queue)},r},b.easing={linear:function(e){return e},swing:function(e){return.5-Math.cos(e*Math.PI)/2}},b.timers=[],b.fx=rr.prototype.init,b.fx.tick=function(){var e,n=b.timers,r=0;for(Xn=b.now();n.length>r;r++)e=n[r],e()||n[r]!==e||n.splice(r--,1);n.length||b.fx.stop(),Xn=t},b.fx.timer=function(e){e()&&b.timers.push(e)&&b.fx.start()},b.fx.interval=13,b.fx.start=function(){Un||(Un=setInterval(b.fx.tick,b.fx.interval))},b.fx.stop=function(){clearInterval(Un),Un=null},b.fx.speeds={slow:600,fast:200,_default:400},b.fx.step={},b.expr&&b.expr.filters&&(b.expr.filters.animated=function(e){return b.grep(b.timers,function(t){return e===t.elem}).length}),b.fn.offset=function(e){if(arguments.length)return e===t?this:this.each(function(t){b.offset.setOffset(this,e,t)});var n,r,o={top:0,left:0},a=this[0],s=a&&a.ownerDocument;if(s)return n=s.documentElement,b.contains(n,a)?(typeof a.getBoundingClientRect!==i&&(o=a.getBoundingClientRect()),r=or(s),{top:o.top+(r.pageYOffset||n.scrollTop)-(n.clientTop||0),left:o.left+(r.pageXOffset||n.scrollLeft)-(n.clientLeft||0)}):o},b.offset={setOffset:function(e,t,n){var r=b.css(e,"position");"static"===r&&(e.style.position="relative");var i=b(e),o=i.offset(),a=b.css(e,"top"),s=b.css(e,"left"),u=("absolute"===r||"fixed"===r)&&b.inArray("auto",[a,s])>-1,l={},c={},p,f;u?(c=i.position(),p=c.top,f=c.left):(p=parseFloat(a)||0,f=parseFloat(s)||0),b.isFunction(t)&&(t=t.call(e,n,o)),null!=t.top&&(l.top=t.top-o.top+p),null!=t.left&&(l.left=t.left-o.left+f),"using"in t?t.using.call(e,l):i.css(l)}},b.fn.extend({position:function(){if(this[0]){var e,t,n={top:0,left:0},r=this[0];return"fixed"===b.css(r,"position")?t=r.getBoundingClientRect():(e=this.offsetParent(),t=this.offset(),b.nodeName(e[0],"html")||(n=e.offset()),n.top+=b.css(e[0],"borderTopWidth",!0),n.left+=b.css(e[0],"borderLeftWidth",!0)),{top:t.top-n.top-b.css(r,"marginTop",!0),left:t.left-n.left-b.css(r,"marginLeft",!0)}}},offsetParent:function(){return this.map(function(){var e=this.offsetParent||o.documentElement;while(e&&!b.nodeName(e,"html")&&"static"===b.css(e,"position"))e=e.offsetParent;return e||o.documentElement})}}),b.each({scrollLeft:"pageXOffset",scrollTop:"pageYOffset"},function(e,n){var r=/Y/.test(n);b.fn[e]=function(i){return b.access(this,function(e,i,o){var a=or(e);return o===t?a?n in a?a[n]:a.document.documentElement[i]:e[i]:(a?a.scrollTo(r?b(a).scrollLeft():o,r?o:b(a).scrollTop()):e[i]=o,t)},e,i,arguments.length,null)}});function or(e){return b.isWindow(e)?e:9===e.nodeType?e.defaultView||e.parentWindow:!1}b.each({Height:"height",Width:"width"},function(e,n){b.each({padding:"inner"+e,content:n,"":"outer"+e},function(r,i){b.fn[i]=function(i,o){var a=arguments.length&&(r||"boolean"!=typeof i),s=r||(i===!0||o===!0?"margin":"border");return b.access(this,function(n,r,i){var o;return b.isWindow(n)?n.document.documentElement["client"+e]:9===n.nodeType?(o=n.documentElement,Math.max(n.body["scroll"+e],o["scroll"+e],n.body["offset"+e],o["offset"+e],o["client"+e])):i===t?b.css(n,r,s):b.style(n,r,i,s)},n,a?i:t,a,null)}})}),e.jQuery=e.$=b,"function"==typeof define&&define.amd&&define.amd.jQuery&&define("jquery",[],function(){return b})})(window);\n\\ No newline at end of file\n' |
| b |
| diff -r 9645d995fb3c -r 9185ca0a7b43 test-data/res_files/js/jquery.opacityrollover.js --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/res_files/js/jquery.opacityrollover.js Wed Jan 16 08:18:13 2019 -0500 |
| b |
| @@ -0,0 +1,42 @@ +/** + * jQuery Opacity Rollover plugin + * + * Copyright (c) 2009 Trent Foley (http://trentacular.com) + * Licensed under the MIT License: + * http://www.opensource.org/licenses/mit-license.php + */ +;(function($) { + var defaults = { + mouseOutOpacity: 0.67, + mouseOverOpacity: 1.0, + fadeSpeed: 'fast', + exemptionSelector: '.selected' + }; + + $.fn.opacityrollover = function(settings) { + // Initialize the effect + $.extend(this, defaults, settings); + + var config = this; + + function fadeTo(element, opacity) { + var $target = $(element); + + if (config.exemptionSelector) + $target = $target.not(config.exemptionSelector); + + $target.fadeTo(config.fadeSpeed, opacity); + } + + this.css('opacity', this.mouseOutOpacity) + .hover( + function () { + fadeTo(this, config.mouseOverOpacity); + }, + function () { + fadeTo(this, config.mouseOutOpacity); + }); + + return this; + }; +})(jQuery); |
| b |
| diff -r 9645d995fb3c -r 9185ca0a7b43 test-data/res_files/reads-sample-small.fastq-bonafide_reads-TEs.html --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/res_files/reads-sample-small.fastq-bonafide_reads-TEs.html Wed Jan 16 08:18:13 2019 -0500 |
| b |
| b'@@ -0,0 +1,388 @@\n+\n+ <!DOCTYPE html>\n+ <html lang="en">\n+ <head>\n+ <meta charset="utf-8">\n+ <title>pipeline</title>\n+ <meta name="viewport" content="width=device-width, initial-scale=1.0">\n+ <meta name="description" content="">\n+ <meta name="author" content="">\n+ <!-- Le styles -->\n+ <link href="css/bootstrap.css" rel="stylesheet">\n+ <link href="css/bootstrap-table.css" rel="stylesheet">\n+ <style type="text/css">\n+ body {\n+ padding-top: 60px;\n+ padding-bottom: 40px;\n+ }\n+ div#page {\n+ width: 940px;\n+ background-color: #fff;\n+ margin: 0 auto;\n+ text-align: left;\n+ border-color: #fff;\n+ border-style: none solid solid;\n+ border-width: medium 1px 1px;\n+ }\n+\n+ div.content {\n+ \tdisplay: none;\n+\t float: right;\n+\t width: 550px;\n+ }\n+ div.content a, div.navigation a {\n+ text-decoration: none;\n+ \tcolor: #777;\n+ }\n+ div.content a:focus, div.content a:hover, div.content a:active {\n+ text-decoration: underline;\n+ }\n+ \n+ div.controls {\n+ margin-top: 5px;\n+\t height: 23px;\n+ }\n+ \n+ div.controls a {\n+\t padding: 5px;\n+ }\n+ div.ss-controls {\n+\t float: left;\n+ }\n+ div.nav-controls {\n+\t float: right;\n+ }\n+ div.slideshow-container {\n+\t position: relative;\n+\t clear: both;\n+\t height: 502px; /* This should be set to be at least the height of the largest image in the slideshow */\n+ }\n+ div.loader {\n+ \tposition: absolute;\n+ \ttop: 0;\n+ \tleft: 0;\n+ background-image: url(\'loader.gif\');\n+ background-repeat: no-repeat;\n+ background-position: center;\n+ \twidth: 550px;\n+ \theight: 502px; /* This should be set to be at least the height of the largest image in the slideshow */\n+ }\n+ div.slideshow {\n+ \n+ }\n+ \n+ div.slideshow span.image-wrapper {\n+\t display: block;\n+\t position: absolute;\n+\t top: 0;\n+\t left: 0;\n+ }\n+ div.slideshow a.advance-link {\n+\t display: block;\n+ \t width: 550px;\n+ height: 502px; /* This should be set to be at least the height of the largest image in the slideshow */\n+ line-height: 502px; /* This should be set to be at least the height of the largest image in the slideshow */\n+ text-align: center;\n+ }\n+ div.slideshow a.advance-link:hover, div.slideshow a.advance-link:active, div.slideshow a.advance-link:visited {\n+ text-decoration: none;\n+ }\n+ div.slideshow img {\n+ vertical-align: middle;\n+\tborder: 1px solid #ccc;\n+ }\n+\n+ div.image-title {\n+ font-weight: bold;\n+ font-size: 1.4em;\n+ }\n+\n+ div.image-desc {\n+ line-height: 1.3em;\n+ padding-top: 12px;\n+ }\n+ div.navigation {\n+\n+ }\n+ ul.thumbs {\n+\tclear: both;\n+\tmargin: 0;\n+\tpadding: 0;\n+ }\n+ ul.thumbs li {\n+\tfloat: none;\n+\tpadding: 0;\n+\tmargin: 0;\n+ list-style: none;\n+ }\n+ a.thumb {\n+\tpadding: 0;\n+\tdisplay: inline;\n+\tborder: none;\n+ }\n+ ul.thumbs li.selected a.thumb {\n+\tcolor: #000;\n+ font-weight: bold;\n+ }\n+ a.thumb:focus {\n+\toutline: none;\n+ }\n+ ul.thumbs img {\n+\tborder: none;\n+\tdisplay: block;\n+ }\n+ div.pagination {\n+\tclear: both;\n+ }\n+ div.navigation div.top {\n+ margin-bottom: 12px;\n+\theight: 11px;\n+ }\n+ div.navigation div.bottom {\n+ margin-top: 12px;\n+ }\n+ div.pagination a, div.pagination span.current, div.pagination span.ellipsis {\n+\tdisplay: block;\n+\tfloat: left;\n+ margin-right: 2px;\n+\tpadding: 4px 7px 2px 7px;\n+\tborder: 1px solid #ccc;\n+ }\n+ div.pagination a:hover {\n+ background-color: #eee;\n+ text-decoration: none;\n+ }\n+ div.pagination span.current {\n+ font-weight: bold;\n+ background-color: #000;\n+ border-color: #000;\n+\tcolor: #fff;\n+ }\n+ div.pagination span.ellipsis {\n+\tborder: none;\n+\tpadding: 5px 0 3px 2px;\n+ }\n+ \n+ div.download {\n+\tfloat: right;\n+ }\n+ \n+ div.caption-container {\n+\tposition: relative;\n+\tclear: left;\n+\theight: 75px;\n+ }\n+ span.image-caption {\n+\tdisplay: block;\n+\tposition: absolute;\n+\twidth: 550px;\n+\ttop: 0;\n+\tleft: 0;\n+ }\n+ div.caption {\n+\tpadding: 12px;\n+ }\n+\n+ /* Featurettes\n+ ------------------------- */\n+\n+ .featurette {\n+ padding-top: 20px; /* Vertica'..b'z_TEs/G6_DM.png" title="G6_DM">G6_DM</a>\n+ </li>\n+ \t\n+ <li>\n+ <a class="thumb" href="reads-sample-small.fastq/subgroups/bonafide_reads//Gviz_TEs/Gypsy2-LTR_DM.png" title="Gypsy2-LTR_DM">Gypsy2-LTR_DM</a>\n+ </li>\n+ \t\n+ <li>\n+ <a class="thumb" href="reads-sample-small.fastq/subgroups/bonafide_reads//Gviz_TEs/I_DM.png" title="I_DM">I_DM</a>\n+ </li>\n+ \t\n+ <li>\n+ <a class="thumb" href="reads-sample-small.fastq/subgroups/bonafide_reads//Gviz_TEs/MAX_I.png" title="MAX_I">MAX_I</a>\n+ </li>\n+ \t\n+ <li>\n+ <a class="thumb" href="reads-sample-small.fastq/subgroups/bonafide_reads//Gviz_TEs/MAX_LTR.png" title="MAX_LTR">MAX_LTR</a>\n+ </li>\n+ \t\n+ <li>\n+ <a class="thumb" href="reads-sample-small.fastq/subgroups/bonafide_reads//Gviz_TEs/PROTOP.png" title="PROTOP">PROTOP</a>\n+ </li>\n+ \t\n+ </ul>\n+ </div>\n+ <div style="clear: both;"></div></div>\n+ </div>\n+ </div>\n+ \n+ <!-- FOOTER -->\n+ <div class="container">\n+ <footer>\n+ \n+ </footer>\n+ </div>\n+ <!-- Le javascript\n+ ================================================== -->\n+ <!-- Placed at the end of the document so the pages load faster -->\n+ <script type="text/javascript" src="js/filter.js"></script>\n+ <script type="text/javascript" src="js/jquery.js"></script>\n+ <script type="text/javascript" src="js/jquery-1.3.2.js"></script>\n+ <script type="text/javascript" src="js/jquery.galleriffic.js"></script>\n+ <script type="text/javascript" src="js/jquery.opacityrollover.js"></script>\n+ <script type="text/javascript" src="js/bootstrap-table.js"></script>\n+ <script type="text/javascript" src="js/bootstrap.min.js"></script>\n+ <script type="text/javascript">\n+ jQuery(document).ready(function($) {\n+ // We only want these styles applied when javascript is enabled\n+ $(\'div.navigation\').css({\'width\' : \'300px\', \'float\' : \'left\'});\n+ $(\'div.content\').css(\'display\', \'block\');\n+ \n+ $(".each-gallery").each(function(i){\n+ // Initially set opacity on thumbs and add\n+ // additional styling for hover effect on thumbs\n+ var onMouseOutOpacity = 0.67;\n+ $(\'#thumbs + i + ul.thumbs li\').opacityrollover({\n+ mouseOutOpacity: onMouseOutOpacity,\n+ mouseOverOpacity: 1.0,\n+ fadeSpeed: \'fast\',\n+ exemptionSelector: \'.selected\'\n+ });\n+ \n+ // Initialize Advanced Galleriffic Gallery\n+ var gallery = $(\'#thumbs\'+i).galleriffic({\n+ delay: 2500,\n+ numThumbs: 22,\n+ preloadAhead: 10,\n+ enableTopPager: true,\n+ enableBottomPager: true,\n+ maxPagesToShow: 7,\n+ imageContainerSel: \'#slideshow\'+ i,\n+ controlsContainerSel: \'#controls\' + i,\n+ captionContainerSel: \'#caption\' + i,\n+ loadingContainerSel: \'#loading\' + i,\n+ renderSSControls: true,\n+ renderNavControls: true,\n+ playLinkText: \'Play\',\n+ pauseLinkText: \'Pause\',\n+ prevLinkText: \'‹ Previous\',\n+ nextLinkText: \'Next ›\',\n+ nextPageLinkText: \'Next ›\',\n+ prevPageLinkText: \'‹ Prev\',\n+ enableHistory: false,\n+ autoStart: false,\n+ syncTransitions: true,\n+ defaultTransitionDuration: 900,\n+ onSlideChange: function(prevIndex, nextIndex) {\n+ // \'this\' refers to the gallery, which is an extension of $(\'#thumbs\')\n+ this.find(\'ul.thumbs\').children()\n+ .eq(prevIndex).fadeTo(\'fast\', onMouseOutOpacity).end()\n+ .eq(nextIndex).fadeTo(\'fast\', 1.0);\n+ },\n+ onPageTransitionOut: function(callback) {\n+ this.fadeTo(\'fast\', 0.0, callback);\n+ },\n+ onPageTransitionIn: function() {\n+ this.fadeTo(\'fast\', 1.0);\n+ }\n+ });\n+ });\n+ });\n+ </script>\n+ </body>\n+ </html>\n+ \n\\ No newline at end of file\n' |
| b |
| diff -r 9645d995fb3c -r 9185ca0a7b43 test-data/res_files/reads-sample-small.fastq-bonafide_reads-genome.html --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/res_files/reads-sample-small.fastq-bonafide_reads-genome.html Wed Jan 16 08:18:13 2019 -0500 |
| b |
| b'@@ -0,0 +1,397 @@\n+\n+ <!DOCTYPE html>\n+ <html lang="en">\n+ <head>\n+ <meta charset="utf-8">\n+ <title>pipeline</title>\n+ <meta name="viewport" content="width=device-width, initial-scale=1.0">\n+ <meta name="description" content="">\n+ <meta name="author" content="">\n+ <!-- Le styles -->\n+ <link href="css/bootstrap.css" rel="stylesheet">\n+ <link href="css/bootstrap-table.css" rel="stylesheet">\n+ <style type="text/css">\n+ body {\n+ padding-top: 60px;\n+ padding-bottom: 40px;\n+ }\n+ div#page {\n+ width: 940px;\n+ background-color: #fff;\n+ margin: 0 auto;\n+ text-align: left;\n+ border-color: #fff;\n+ border-style: none solid solid;\n+ border-width: medium 1px 1px;\n+ }\n+\n+ div.content {\n+ \tdisplay: none;\n+\t float: right;\n+\t width: 550px;\n+ }\n+ div.content a, div.navigation a {\n+ text-decoration: none;\n+ \tcolor: #777;\n+ }\n+ div.content a:focus, div.content a:hover, div.content a:active {\n+ text-decoration: underline;\n+ }\n+ \n+ div.controls {\n+ margin-top: 5px;\n+\t height: 23px;\n+ }\n+ \n+ div.controls a {\n+\t padding: 5px;\n+ }\n+ div.ss-controls {\n+\t float: left;\n+ }\n+ div.nav-controls {\n+\t float: right;\n+ }\n+ div.slideshow-container {\n+\t position: relative;\n+\t clear: both;\n+\t height: 502px; /* This should be set to be at least the height of the largest image in the slideshow */\n+ }\n+ div.loader {\n+ \tposition: absolute;\n+ \ttop: 0;\n+ \tleft: 0;\n+ background-image: url(\'loader.gif\');\n+ background-repeat: no-repeat;\n+ background-position: center;\n+ \twidth: 550px;\n+ \theight: 502px; /* This should be set to be at least the height of the largest image in the slideshow */\n+ }\n+ div.slideshow {\n+ \n+ }\n+ \n+ div.slideshow span.image-wrapper {\n+\t display: block;\n+\t position: absolute;\n+\t top: 0;\n+\t left: 0;\n+ }\n+ div.slideshow a.advance-link {\n+\t display: block;\n+ \t width: 550px;\n+ height: 502px; /* This should be set to be at least the height of the largest image in the slideshow */\n+ line-height: 502px; /* This should be set to be at least the height of the largest image in the slideshow */\n+ text-align: center;\n+ }\n+ div.slideshow a.advance-link:hover, div.slideshow a.advance-link:active, div.slideshow a.advance-link:visited {\n+ text-decoration: none;\n+ }\n+ div.slideshow img {\n+ vertical-align: middle;\n+\tborder: 1px solid #ccc;\n+ }\n+\n+ div.image-title {\n+ font-weight: bold;\n+ font-size: 1.4em;\n+ }\n+\n+ div.image-desc {\n+ line-height: 1.3em;\n+ padding-top: 12px;\n+ }\n+ div.navigation {\n+\n+ }\n+ ul.thumbs {\n+\tclear: both;\n+\tmargin: 0;\n+\tpadding: 0;\n+ }\n+ ul.thumbs li {\n+\tfloat: none;\n+\tpadding: 0;\n+\tmargin: 0;\n+ list-style: none;\n+ }\n+ a.thumb {\n+\tpadding: 0;\n+\tdisplay: inline;\n+\tborder: none;\n+ }\n+ ul.thumbs li.selected a.thumb {\n+\tcolor: #000;\n+ font-weight: bold;\n+ }\n+ a.thumb:focus {\n+\toutline: none;\n+ }\n+ ul.thumbs img {\n+\tborder: none;\n+\tdisplay: block;\n+ }\n+ div.pagination {\n+\tclear: both;\n+ }\n+ div.navigation div.top {\n+ margin-bottom: 12px;\n+\theight: 11px;\n+ }\n+ div.navigation div.bottom {\n+ margin-top: 12px;\n+ }\n+ div.pagination a, div.pagination span.current, div.pagination span.ellipsis {\n+\tdisplay: block;\n+\tfloat: left;\n+ margin-right: 2px;\n+\tpadding: 4px 7px 2px 7px;\n+\tborder: 1px solid #ccc;\n+ }\n+ div.pagination a:hover {\n+ background-color: #eee;\n+ text-decoration: none;\n+ }\n+ div.pagination span.current {\n+ font-weight: bold;\n+ background-color: #000;\n+ border-color: #000;\n+\tcolor: #fff;\n+ }\n+ div.pagination span.ellipsis {\n+\tborder: none;\n+\tpadding: 5px 0 3px 2px;\n+ }\n+ \n+ div.download {\n+\tfloat: right;\n+ }\n+ \n+ div.caption-container {\n+\tposition: relative;\n+\tclear: left;\n+\theight: 75px;\n+ }\n+ span.image-caption {\n+\tdisplay: block;\n+\tposition: absolute;\n+\twidth: 550px;\n+\ttop: 0;\n+\tleft: 0;\n+ }\n+ div.caption {\n+\tpadding: 12px;\n+ }\n+\n+ /* Featurettes\n+ ------------------------- */\n+\n+ .featurette {\n+ padding-top: 20px; /* Vertica'..b'stq/subgroups/bonafide_reads//Gviz_genome/rand/chrom_1.png" title="chrom_1">chrom_1</a>\n+ </li>\n+ \n+ <li>\n+ <a class="thumb" href="reads-sample-small.fastq/subgroups/bonafide_reads//Gviz_genome/rand/chrom_2.png" title="chrom_2">chrom_2</a>\n+ </li>\n+ \n+ <li>\n+ <a class="thumb" href="reads-sample-small.fastq/subgroups/bonafide_reads//Gviz_genome/rand/chrom_4.png" title="chrom_4">chrom_4</a>\n+ </li>\n+ \n+ <li>\n+ <a class="thumb" href="reads-sample-small.fastq/subgroups/bonafide_reads//Gviz_genome/rand/chrom_5.png" title="chrom_5">chrom_5</a>\n+ </li>\n+ \n+ <li>\n+ <a class="thumb" href="reads-sample-small.fastq/subgroups/bonafide_reads//Gviz_genome/rand/chrom_6.png" title="chrom_6">chrom_6</a>\n+ </li>\n+ \n+ </ul>\n+ </div>\n+ <div style="clear: both;"></div></div>\n+ </div>\n+ </div>\n+ \n+ <!-- FOOTER -->\n+ <div class="container">\n+ <footer>\n+ \n+ </footer>\n+ </div>\n+ <!-- Le javascript\n+ ================================================== -->\n+ <!-- Placed at the end of the document so the pages load faster -->\n+ <script type="text/javascript" src="js/filter.js"></script>\n+ <script type="text/javascript" src="js/jquery.js"></script>\n+ <script type="text/javascript" src="js/jquery-1.3.2.js"></script>\n+ <script type="text/javascript" src="js/jquery.galleriffic.js"></script>\n+ <script type="text/javascript" src="js/jquery.opacityrollover.js"></script>\n+ <script type="text/javascript" src="js/bootstrap-table.js"></script>\n+ <script type="text/javascript" src="js/bootstrap.min.js"></script>\n+ <script type="text/javascript">\n+ jQuery(document).ready(function($) {\n+ // We only want these styles applied when javascript is enabled\n+ $(\'div.navigation\').css({\'width\' : \'300px\', \'float\' : \'left\'});\n+ $(\'div.content\').css(\'display\', \'block\');\n+ \n+ $(".each-gallery").each(function(i){\n+ // Initially set opacity on thumbs and add\n+ // additional styling for hover effect on thumbs\n+ var onMouseOutOpacity = 0.67;\n+ $(\'#thumbs + i + ul.thumbs li\').opacityrollover({\n+ mouseOutOpacity: onMouseOutOpacity,\n+ mouseOverOpacity: 1.0,\n+ fadeSpeed: \'fast\',\n+ exemptionSelector: \'.selected\'\n+ });\n+ \n+ // Initialize Advanced Galleriffic Gallery\n+ var gallery = $(\'#thumbs\'+i).galleriffic({\n+ delay: 2500,\n+ numThumbs: 22,\n+ preloadAhead: 10,\n+ enableTopPager: true,\n+ enableBottomPager: true,\n+ maxPagesToShow: 7,\n+ imageContainerSel: \'#slideshow\'+ i,\n+ controlsContainerSel: \'#controls\' + i,\n+ captionContainerSel: \'#caption\' + i,\n+ loadingContainerSel: \'#loading\' + i,\n+ renderSSControls: true,\n+ renderNavControls: true,\n+ playLinkText: \'Play\',\n+ pauseLinkText: \'Pause\',\n+ prevLinkText: \'‹ Previous\',\n+ nextLinkText: \'Next ›\',\n+ nextPageLinkText: \'Next ›\',\n+ prevPageLinkText: \'‹ Prev\',\n+ enableHistory: false,\n+ autoStart: false,\n+ syncTransitions: true,\n+ defaultTransitionDuration: 900,\n+ onSlideChange: function(prevIndex, nextIndex) {\n+ // \'this\' refers to the gallery, which is an extension of $(\'#thumbs\')\n+ this.find(\'ul.thumbs\').children()\n+ .eq(prevIndex).fadeTo(\'fast\', onMouseOutOpacity).end()\n+ .eq(nextIndex).fadeTo(\'fast\', 1.0);\n+ },\n+ onPageTransitionOut: function(callback) {\n+ this.fadeTo(\'fast\', 0.0, callback);\n+ },\n+ onPageTransitionIn: function() {\n+ this.fadeTo(\'fast\', 1.0);\n+ }\n+ });\n+ });\n+ });\n+ </script>\n+ </body>\n+ </html>\n+ \n\\ No newline at end of file\n' |
| b |
| diff -r 9645d995fb3c -r 9185ca0a7b43 test-data/res_files/reads-sample-small.fastq-bonafide_reads-transcripts.html --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/res_files/reads-sample-small.fastq-bonafide_reads-transcripts.html Wed Jan 16 08:18:13 2019 -0500 |
| b |
| b'@@ -0,0 +1,315 @@\n+\n+ <!DOCTYPE html>\n+ <html lang="en">\n+ <head>\n+ <meta charset="utf-8">\n+ <title>pipeline</title>\n+ <meta name="viewport" content="width=device-width, initial-scale=1.0">\n+ <meta name="description" content="">\n+ <meta name="author" content="">\n+ <!-- Le styles -->\n+ <link href="css/bootstrap.css" rel="stylesheet">\n+ <link href="css/bootstrap-table.css" rel="stylesheet">\n+ <style type="text/css">\n+ body {\n+ padding-top: 60px;\n+ padding-bottom: 40px;\n+ }\n+ div#page {\n+ width: 940px;\n+ background-color: #fff;\n+ margin: 0 auto;\n+ text-align: left;\n+ border-color: #fff;\n+ border-style: none solid solid;\n+ border-width: medium 1px 1px;\n+ }\n+\n+ div.content {\n+ \tdisplay: none;\n+\t float: right;\n+\t width: 550px;\n+ }\n+ div.content a, div.navigation a {\n+ text-decoration: none;\n+ \tcolor: #777;\n+ }\n+ div.content a:focus, div.content a:hover, div.content a:active {\n+ text-decoration: underline;\n+ }\n+ \n+ div.controls {\n+ margin-top: 5px;\n+\t height: 23px;\n+ }\n+ \n+ div.controls a {\n+\t padding: 5px;\n+ }\n+ div.ss-controls {\n+\t float: left;\n+ }\n+ div.nav-controls {\n+\t float: right;\n+ }\n+ div.slideshow-container {\n+\t position: relative;\n+\t clear: both;\n+\t height: 502px; /* This should be set to be at least the height of the largest image in the slideshow */\n+ }\n+ div.loader {\n+ \tposition: absolute;\n+ \ttop: 0;\n+ \tleft: 0;\n+ background-image: url(\'loader.gif\');\n+ background-repeat: no-repeat;\n+ background-position: center;\n+ \twidth: 550px;\n+ \theight: 502px; /* This should be set to be at least the height of the largest image in the slideshow */\n+ }\n+ div.slideshow {\n+ \n+ }\n+ \n+ div.slideshow span.image-wrapper {\n+\t display: block;\n+\t position: absolute;\n+\t top: 0;\n+\t left: 0;\n+ }\n+ div.slideshow a.advance-link {\n+\t display: block;\n+ \t width: 550px;\n+ height: 502px; /* This should be set to be at least the height of the largest image in the slideshow */\n+ line-height: 502px; /* This should be set to be at least the height of the largest image in the slideshow */\n+ text-align: center;\n+ }\n+ div.slideshow a.advance-link:hover, div.slideshow a.advance-link:active, div.slideshow a.advance-link:visited {\n+ text-decoration: none;\n+ }\n+ div.slideshow img {\n+ vertical-align: middle;\n+\tborder: 1px solid #ccc;\n+ }\n+\n+ div.image-title {\n+ font-weight: bold;\n+ font-size: 1.4em;\n+ }\n+\n+ div.image-desc {\n+ line-height: 1.3em;\n+ padding-top: 12px;\n+ }\n+ div.navigation {\n+\n+ }\n+ ul.thumbs {\n+\tclear: both;\n+\tmargin: 0;\n+\tpadding: 0;\n+ }\n+ ul.thumbs li {\n+\tfloat: none;\n+\tpadding: 0;\n+\tmargin: 0;\n+ list-style: none;\n+ }\n+ a.thumb {\n+\tpadding: 0;\n+\tdisplay: inline;\n+\tborder: none;\n+ }\n+ ul.thumbs li.selected a.thumb {\n+\tcolor: #000;\n+ font-weight: bold;\n+ }\n+ a.thumb:focus {\n+\toutline: none;\n+ }\n+ ul.thumbs img {\n+\tborder: none;\n+\tdisplay: block;\n+ }\n+ div.pagination {\n+\tclear: both;\n+ }\n+ div.navigation div.top {\n+ margin-bottom: 12px;\n+\theight: 11px;\n+ }\n+ div.navigation div.bottom {\n+ margin-top: 12px;\n+ }\n+ div.pagination a, div.pagination span.current, div.pagination span.ellipsis {\n+\tdisplay: block;\n+\tfloat: left;\n+ margin-right: 2px;\n+\tpadding: 4px 7px 2px 7px;\n+\tborder: 1px solid #ccc;\n+ }\n+ div.pagination a:hover {\n+ background-color: #eee;\n+ text-decoration: none;\n+ }\n+ div.pagination span.current {\n+ font-weight: bold;\n+ background-color: #000;\n+ border-color: #000;\n+\tcolor: #fff;\n+ }\n+ div.pagination span.ellipsis {\n+\tborder: none;\n+\tpadding: 5px 0 3px 2px;\n+ }\n+ \n+ div.download {\n+\tfloat: right;\n+ }\n+ \n+ div.caption-container {\n+\tposition: relative;\n+\tclear: left;\n+\theight: 75px;\n+ }\n+ span.image-caption {\n+\tdisplay: block;\n+\tposition: absolute;\n+\twidth: 550px;\n+\ttop: 0;\n+\tleft: 0;\n+ }\n+ div.caption {\n+\tpadding: 12px;\n+ }\n+\n+ /* Featurettes\n+ ------------------------- */\n+\n+ .featurette {\n+ padding-top: 20px; /* Vertica'..b'</span>\n+ <span class="icon-bar"></span>\n+ </button>\n+ <a class="brand" href="report.txt">Report</a>\n+ <div class="nav-collapse collapse">\n+ <ul class="nav">\n+ <li class="active"><a href="reads-sample-small.fastq.html">reads-sample-small.fastq</a></li>\n+ </ul>\n+ </div><!--/.nav-collapse -->\n+ </div>\n+ </div>\n+ </div>\n+ <div class="container">\n+ <div class="featurette">\n+ <h1>transcripts</h1>\n+ <p class="featurette-p">\n+ <A HREF="reads-sample-small.fastq/subgroups/bonafide_reads//bonafide_reads-transcripts_reads_counts.txt">read number per transcript (txt)</A><br/> \n+<A HREF="reads-sample-small.fastq/subgroups/bonafide_reads//bonafide_reads-transcripts_sorted.bam">transcripts mappers (sorted bam)</A><br/> \n+<A HREF="reads-sample-small.fastq/subgroups/bonafide_reads//bonafide_reads-transcripts_unique_sorted.bam">transcripts unique mappers (sorted bam)</A><br/> \n+\n+ </p>\n+ </div>\n+ </div>\n+ \n+ <!-- FOOTER -->\n+ <div class="container">\n+ <footer>\n+ \n+ </footer>\n+ </div>\n+ <!-- Le javascript\n+ ================================================== -->\n+ <!-- Placed at the end of the document so the pages load faster -->\n+ <script type="text/javascript" src="js/filter.js"></script>\n+ <script type="text/javascript" src="js/jquery.js"></script>\n+ <script type="text/javascript" src="js/jquery-1.3.2.js"></script>\n+ <script type="text/javascript" src="js/jquery.galleriffic.js"></script>\n+ <script type="text/javascript" src="js/jquery.opacityrollover.js"></script>\n+ <script type="text/javascript" src="js/bootstrap-table.js"></script>\n+ <script type="text/javascript" src="js/bootstrap.min.js"></script>\n+ <script type="text/javascript">\n+ jQuery(document).ready(function($) {\n+ // We only want these styles applied when javascript is enabled\n+ $(\'div.navigation\').css({\'width\' : \'300px\', \'float\' : \'left\'});\n+ $(\'div.content\').css(\'display\', \'block\');\n+ \n+ $(".each-gallery").each(function(i){\n+ // Initially set opacity on thumbs and add\n+ // additional styling for hover effect on thumbs\n+ var onMouseOutOpacity = 0.67;\n+ $(\'#thumbs + i + ul.thumbs li\').opacityrollover({\n+ mouseOutOpacity: onMouseOutOpacity,\n+ mouseOverOpacity: 1.0,\n+ fadeSpeed: \'fast\',\n+ exemptionSelector: \'.selected\'\n+ });\n+ \n+ // Initialize Advanced Galleriffic Gallery\n+ var gallery = $(\'#thumbs\'+i).galleriffic({\n+ delay: 2500,\n+ numThumbs: 22,\n+ preloadAhead: 10,\n+ enableTopPager: true,\n+ enableBottomPager: true,\n+ maxPagesToShow: 7,\n+ imageContainerSel: \'#slideshow\'+ i,\n+ controlsContainerSel: \'#controls\' + i,\n+ captionContainerSel: \'#caption\' + i,\n+ loadingContainerSel: \'#loading\' + i,\n+ renderSSControls: true,\n+ renderNavControls: true,\n+ playLinkText: \'Play\',\n+ pauseLinkText: \'Pause\',\n+ prevLinkText: \'‹ Previous\',\n+ nextLinkText: \'Next ›\',\n+ nextPageLinkText: \'Next ›\',\n+ prevPageLinkText: \'‹ Prev\',\n+ enableHistory: false,\n+ autoStart: false,\n+ syncTransitions: true,\n+ defaultTransitionDuration: 900,\n+ onSlideChange: function(prevIndex, nextIndex) {\n+ // \'this\' refers to the gallery, which is an extension of $(\'#thumbs\')\n+ this.find(\'ul.thumbs\').children()\n+ .eq(prevIndex).fadeTo(\'fast\', onMouseOutOpacity).end()\n+ .eq(nextIndex).fadeTo(\'fast\', 1.0);\n+ },\n+ onPageTransitionOut: function(callback) {\n+ this.fadeTo(\'fast\', 0.0, callback);\n+ },\n+ onPageTransitionIn: function() {\n+ this.fadeTo(\'fast\', 1.0);\n+ }\n+ });\n+ });\n+ });\n+ </script>\n+ </body>\n+ </html>\n+ \n\\ No newline at end of file\n' |
| b |
| diff -r 9645d995fb3c -r 9185ca0a7b43 test-data/res_files/reads-sample-small.fastq-miRNAs-TEs.html --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/res_files/reads-sample-small.fastq-miRNAs-TEs.html Wed Jan 16 08:18:13 2019 -0500 |
| b |
| b'@@ -0,0 +1,340 @@\n+\n+ <!DOCTYPE html>\n+ <html lang="en">\n+ <head>\n+ <meta charset="utf-8">\n+ <title>pipeline</title>\n+ <meta name="viewport" content="width=device-width, initial-scale=1.0">\n+ <meta name="description" content="">\n+ <meta name="author" content="">\n+ <!-- Le styles -->\n+ <link href="css/bootstrap.css" rel="stylesheet">\n+ <link href="css/bootstrap-table.css" rel="stylesheet">\n+ <style type="text/css">\n+ body {\n+ padding-top: 60px;\n+ padding-bottom: 40px;\n+ }\n+ div#page {\n+ width: 940px;\n+ background-color: #fff;\n+ margin: 0 auto;\n+ text-align: left;\n+ border-color: #fff;\n+ border-style: none solid solid;\n+ border-width: medium 1px 1px;\n+ }\n+\n+ div.content {\n+ \tdisplay: none;\n+\t float: right;\n+\t width: 550px;\n+ }\n+ div.content a, div.navigation a {\n+ text-decoration: none;\n+ \tcolor: #777;\n+ }\n+ div.content a:focus, div.content a:hover, div.content a:active {\n+ text-decoration: underline;\n+ }\n+ \n+ div.controls {\n+ margin-top: 5px;\n+\t height: 23px;\n+ }\n+ \n+ div.controls a {\n+\t padding: 5px;\n+ }\n+ div.ss-controls {\n+\t float: left;\n+ }\n+ div.nav-controls {\n+\t float: right;\n+ }\n+ div.slideshow-container {\n+\t position: relative;\n+\t clear: both;\n+\t height: 502px; /* This should be set to be at least the height of the largest image in the slideshow */\n+ }\n+ div.loader {\n+ \tposition: absolute;\n+ \ttop: 0;\n+ \tleft: 0;\n+ background-image: url(\'loader.gif\');\n+ background-repeat: no-repeat;\n+ background-position: center;\n+ \twidth: 550px;\n+ \theight: 502px; /* This should be set to be at least the height of the largest image in the slideshow */\n+ }\n+ div.slideshow {\n+ \n+ }\n+ \n+ div.slideshow span.image-wrapper {\n+\t display: block;\n+\t position: absolute;\n+\t top: 0;\n+\t left: 0;\n+ }\n+ div.slideshow a.advance-link {\n+\t display: block;\n+ \t width: 550px;\n+ height: 502px; /* This should be set to be at least the height of the largest image in the slideshow */\n+ line-height: 502px; /* This should be set to be at least the height of the largest image in the slideshow */\n+ text-align: center;\n+ }\n+ div.slideshow a.advance-link:hover, div.slideshow a.advance-link:active, div.slideshow a.advance-link:visited {\n+ text-decoration: none;\n+ }\n+ div.slideshow img {\n+ vertical-align: middle;\n+\tborder: 1px solid #ccc;\n+ }\n+\n+ div.image-title {\n+ font-weight: bold;\n+ font-size: 1.4em;\n+ }\n+\n+ div.image-desc {\n+ line-height: 1.3em;\n+ padding-top: 12px;\n+ }\n+ div.navigation {\n+\n+ }\n+ ul.thumbs {\n+\tclear: both;\n+\tmargin: 0;\n+\tpadding: 0;\n+ }\n+ ul.thumbs li {\n+\tfloat: none;\n+\tpadding: 0;\n+\tmargin: 0;\n+ list-style: none;\n+ }\n+ a.thumb {\n+\tpadding: 0;\n+\tdisplay: inline;\n+\tborder: none;\n+ }\n+ ul.thumbs li.selected a.thumb {\n+\tcolor: #000;\n+ font-weight: bold;\n+ }\n+ a.thumb:focus {\n+\toutline: none;\n+ }\n+ ul.thumbs img {\n+\tborder: none;\n+\tdisplay: block;\n+ }\n+ div.pagination {\n+\tclear: both;\n+ }\n+ div.navigation div.top {\n+ margin-bottom: 12px;\n+\theight: 11px;\n+ }\n+ div.navigation div.bottom {\n+ margin-top: 12px;\n+ }\n+ div.pagination a, div.pagination span.current, div.pagination span.ellipsis {\n+\tdisplay: block;\n+\tfloat: left;\n+ margin-right: 2px;\n+\tpadding: 4px 7px 2px 7px;\n+\tborder: 1px solid #ccc;\n+ }\n+ div.pagination a:hover {\n+ background-color: #eee;\n+ text-decoration: none;\n+ }\n+ div.pagination span.current {\n+ font-weight: bold;\n+ background-color: #000;\n+ border-color: #000;\n+\tcolor: #fff;\n+ }\n+ div.pagination span.ellipsis {\n+\tborder: none;\n+\tpadding: 5px 0 3px 2px;\n+ }\n+ \n+ div.download {\n+\tfloat: right;\n+ }\n+ \n+ div.caption-container {\n+\tposition: relative;\n+\tclear: left;\n+\theight: 75px;\n+ }\n+ span.image-caption {\n+\tdisplay: block;\n+\tposition: absolute;\n+\twidth: 550px;\n+\ttop: 0;\n+\tleft: 0;\n+ }\n+ div.caption {\n+\tpadding: 12px;\n+ }\n+\n+ /* Featurettes\n+ ------------------------- */\n+\n+ .featurette {\n+ padding-top: 20px; /* Vertica'..b'/A><br/> \n+<A HREF="reads-sample-small.fastq/subgroups/miRNAs//miRNAs-TEs_sorted.bam">TEs mappers (sorted bam)</A><br/> \n+<A HREF="reads-sample-small.fastq/subgroups/miRNAs//miRNAs-TEs_unique_sorted.bam">TEs unique mappers (sorted bam)</A><br/> \n+\n+ </p>\n+ </div>\n+ </div>\n+ \n+ <div id="page">\n+ <div id="container">\n+ <div class="each-gallery">\n+ <div id="gallery" class="content">\n+ <div id="controls0" class="controls"></div>\n+ <div class="slideshow-container">\n+ <div id="loading0" class="loader"></div>\n+ <div id="slideshow0" class="slideshow"></div>\n+ </div>\n+ <div id="caption0" class="caption-container">Reads randomly assigned</div>\n+ </div>\n+ <div id="thumbs0" class="navigation">\n+ <input type="text" id="myInput0" onkeyup="search(this)" placeholder="Search for names...">\n+ <ul class="thumbs noscript">\n+ \n+ </ul>\n+ </div>\n+ <div style="clear: both;"></div></div>\n+ </div>\n+ </div>\n+ \n+ <!-- FOOTER -->\n+ <div class="container">\n+ <footer>\n+ \n+ </footer>\n+ </div>\n+ <!-- Le javascript\n+ ================================================== -->\n+ <!-- Placed at the end of the document so the pages load faster -->\n+ <script type="text/javascript" src="js/filter.js"></script>\n+ <script type="text/javascript" src="js/jquery.js"></script>\n+ <script type="text/javascript" src="js/jquery-1.3.2.js"></script>\n+ <script type="text/javascript" src="js/jquery.galleriffic.js"></script>\n+ <script type="text/javascript" src="js/jquery.opacityrollover.js"></script>\n+ <script type="text/javascript" src="js/bootstrap-table.js"></script>\n+ <script type="text/javascript" src="js/bootstrap.min.js"></script>\n+ <script type="text/javascript">\n+ jQuery(document).ready(function($) {\n+ // We only want these styles applied when javascript is enabled\n+ $(\'div.navigation\').css({\'width\' : \'300px\', \'float\' : \'left\'});\n+ $(\'div.content\').css(\'display\', \'block\');\n+ \n+ $(".each-gallery").each(function(i){\n+ // Initially set opacity on thumbs and add\n+ // additional styling for hover effect on thumbs\n+ var onMouseOutOpacity = 0.67;\n+ $(\'#thumbs + i + ul.thumbs li\').opacityrollover({\n+ mouseOutOpacity: onMouseOutOpacity,\n+ mouseOverOpacity: 1.0,\n+ fadeSpeed: \'fast\',\n+ exemptionSelector: \'.selected\'\n+ });\n+ \n+ // Initialize Advanced Galleriffic Gallery\n+ var gallery = $(\'#thumbs\'+i).galleriffic({\n+ delay: 2500,\n+ numThumbs: 22,\n+ preloadAhead: 10,\n+ enableTopPager: true,\n+ enableBottomPager: true,\n+ maxPagesToShow: 7,\n+ imageContainerSel: \'#slideshow\'+ i,\n+ controlsContainerSel: \'#controls\' + i,\n+ captionContainerSel: \'#caption\' + i,\n+ loadingContainerSel: \'#loading\' + i,\n+ renderSSControls: true,\n+ renderNavControls: true,\n+ playLinkText: \'Play\',\n+ pauseLinkText: \'Pause\',\n+ prevLinkText: \'‹ Previous\',\n+ nextLinkText: \'Next ›\',\n+ nextPageLinkText: \'Next ›\',\n+ prevPageLinkText: \'‹ Prev\',\n+ enableHistory: false,\n+ autoStart: false,\n+ syncTransitions: true,\n+ defaultTransitionDuration: 900,\n+ onSlideChange: function(prevIndex, nextIndex) {\n+ // \'this\' refers to the gallery, which is an extension of $(\'#thumbs\')\n+ this.find(\'ul.thumbs\').children()\n+ .eq(prevIndex).fadeTo(\'fast\', onMouseOutOpacity).end()\n+ .eq(nextIndex).fadeTo(\'fast\', 1.0);\n+ },\n+ onPageTransitionOut: function(callback) {\n+ this.fadeTo(\'fast\', 0.0, callback);\n+ },\n+ onPageTransitionIn: function() {\n+ this.fadeTo(\'fast\', 1.0);\n+ }\n+ });\n+ });\n+ });\n+ </script>\n+ </body>\n+ </html>\n+ \n\\ No newline at end of file\n' |
| b |
| diff -r 9645d995fb3c -r 9185ca0a7b43 test-data/res_files/reads-sample-small.fastq-miRNAs-genome.html --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/res_files/reads-sample-small.fastq-miRNAs-genome.html Wed Jan 16 08:18:13 2019 -0500 |
| b |
| b'@@ -0,0 +1,366 @@\n+\n+ <!DOCTYPE html>\n+ <html lang="en">\n+ <head>\n+ <meta charset="utf-8">\n+ <title>pipeline</title>\n+ <meta name="viewport" content="width=device-width, initial-scale=1.0">\n+ <meta name="description" content="">\n+ <meta name="author" content="">\n+ <!-- Le styles -->\n+ <link href="css/bootstrap.css" rel="stylesheet">\n+ <link href="css/bootstrap-table.css" rel="stylesheet">\n+ <style type="text/css">\n+ body {\n+ padding-top: 60px;\n+ padding-bottom: 40px;\n+ }\n+ div#page {\n+ width: 940px;\n+ background-color: #fff;\n+ margin: 0 auto;\n+ text-align: left;\n+ border-color: #fff;\n+ border-style: none solid solid;\n+ border-width: medium 1px 1px;\n+ }\n+\n+ div.content {\n+ \tdisplay: none;\n+\t float: right;\n+\t width: 550px;\n+ }\n+ div.content a, div.navigation a {\n+ text-decoration: none;\n+ \tcolor: #777;\n+ }\n+ div.content a:focus, div.content a:hover, div.content a:active {\n+ text-decoration: underline;\n+ }\n+ \n+ div.controls {\n+ margin-top: 5px;\n+\t height: 23px;\n+ }\n+ \n+ div.controls a {\n+\t padding: 5px;\n+ }\n+ div.ss-controls {\n+\t float: left;\n+ }\n+ div.nav-controls {\n+\t float: right;\n+ }\n+ div.slideshow-container {\n+\t position: relative;\n+\t clear: both;\n+\t height: 502px; /* This should be set to be at least the height of the largest image in the slideshow */\n+ }\n+ div.loader {\n+ \tposition: absolute;\n+ \ttop: 0;\n+ \tleft: 0;\n+ background-image: url(\'loader.gif\');\n+ background-repeat: no-repeat;\n+ background-position: center;\n+ \twidth: 550px;\n+ \theight: 502px; /* This should be set to be at least the height of the largest image in the slideshow */\n+ }\n+ div.slideshow {\n+ \n+ }\n+ \n+ div.slideshow span.image-wrapper {\n+\t display: block;\n+\t position: absolute;\n+\t top: 0;\n+\t left: 0;\n+ }\n+ div.slideshow a.advance-link {\n+\t display: block;\n+ \t width: 550px;\n+ height: 502px; /* This should be set to be at least the height of the largest image in the slideshow */\n+ line-height: 502px; /* This should be set to be at least the height of the largest image in the slideshow */\n+ text-align: center;\n+ }\n+ div.slideshow a.advance-link:hover, div.slideshow a.advance-link:active, div.slideshow a.advance-link:visited {\n+ text-decoration: none;\n+ }\n+ div.slideshow img {\n+ vertical-align: middle;\n+\tborder: 1px solid #ccc;\n+ }\n+\n+ div.image-title {\n+ font-weight: bold;\n+ font-size: 1.4em;\n+ }\n+\n+ div.image-desc {\n+ line-height: 1.3em;\n+ padding-top: 12px;\n+ }\n+ div.navigation {\n+\n+ }\n+ ul.thumbs {\n+\tclear: both;\n+\tmargin: 0;\n+\tpadding: 0;\n+ }\n+ ul.thumbs li {\n+\tfloat: none;\n+\tpadding: 0;\n+\tmargin: 0;\n+ list-style: none;\n+ }\n+ a.thumb {\n+\tpadding: 0;\n+\tdisplay: inline;\n+\tborder: none;\n+ }\n+ ul.thumbs li.selected a.thumb {\n+\tcolor: #000;\n+ font-weight: bold;\n+ }\n+ a.thumb:focus {\n+\toutline: none;\n+ }\n+ ul.thumbs img {\n+\tborder: none;\n+\tdisplay: block;\n+ }\n+ div.pagination {\n+\tclear: both;\n+ }\n+ div.navigation div.top {\n+ margin-bottom: 12px;\n+\theight: 11px;\n+ }\n+ div.navigation div.bottom {\n+ margin-top: 12px;\n+ }\n+ div.pagination a, div.pagination span.current, div.pagination span.ellipsis {\n+\tdisplay: block;\n+\tfloat: left;\n+ margin-right: 2px;\n+\tpadding: 4px 7px 2px 7px;\n+\tborder: 1px solid #ccc;\n+ }\n+ div.pagination a:hover {\n+ background-color: #eee;\n+ text-decoration: none;\n+ }\n+ div.pagination span.current {\n+ font-weight: bold;\n+ background-color: #000;\n+ border-color: #000;\n+\tcolor: #fff;\n+ }\n+ div.pagination span.ellipsis {\n+\tborder: none;\n+\tpadding: 5px 0 3px 2px;\n+ }\n+ \n+ div.download {\n+\tfloat: right;\n+ }\n+ \n+ div.caption-container {\n+\tposition: relative;\n+\tclear: left;\n+\theight: 75px;\n+ }\n+ span.image-caption {\n+\tdisplay: block;\n+\tposition: absolute;\n+\twidth: 550px;\n+\ttop: 0;\n+\tleft: 0;\n+ }\n+ div.caption {\n+\tpadding: 12px;\n+ }\n+\n+ /* Featurettes\n+ ------------------------- */\n+\n+ .featurette {\n+ padding-top: 20px; /* Vertica'..b'/Gviz_genome/unique/chrom_3.png" title="chrom_3">chrom_3</a>\n+ </li>\n+ \n+ </ul>\n+ </div>\n+ </div>\n+ <div id="page">\n+ <div id="container">\n+ <div class="each-gallery">\n+ <div id="gallery" class="content">\n+ <div id="controls1" class="controls"></div>\n+ <div class="slideshow-container">\n+ <div id="loading1" class="loader"></div>\n+ <div id="slideshow1" class="slideshow"></div>\n+ </div>\n+ <div id="caption1" class="caption-container">Reads randomly assigned</div>\n+ </div>\n+ <div id="thumbs1" class="navigation">\n+ <input type="text" id="myInput1" onkeyup="search(this)" placeholder="Search for names...">\n+ <ul class="thumbs noscript">\n+ \n+ <li>\n+ <a class="thumb" href="reads-sample-small.fastq/subgroups/miRNAs//Gviz_genome/rand/chrom_3.png" title="chrom_3">chrom_3</a>\n+ </li>\n+ \n+ </ul>\n+ </div>\n+ <div style="clear: both;"></div></div>\n+ </div>\n+ </div>\n+ \n+ <!-- FOOTER -->\n+ <div class="container">\n+ <footer>\n+ \n+ </footer>\n+ </div>\n+ <!-- Le javascript\n+ ================================================== -->\n+ <!-- Placed at the end of the document so the pages load faster -->\n+ <script type="text/javascript" src="js/filter.js"></script>\n+ <script type="text/javascript" src="js/jquery.js"></script>\n+ <script type="text/javascript" src="js/jquery-1.3.2.js"></script>\n+ <script type="text/javascript" src="js/jquery.galleriffic.js"></script>\n+ <script type="text/javascript" src="js/jquery.opacityrollover.js"></script>\n+ <script type="text/javascript" src="js/bootstrap-table.js"></script>\n+ <script type="text/javascript" src="js/bootstrap.min.js"></script>\n+ <script type="text/javascript">\n+ jQuery(document).ready(function($) {\n+ // We only want these styles applied when javascript is enabled\n+ $(\'div.navigation\').css({\'width\' : \'300px\', \'float\' : \'left\'});\n+ $(\'div.content\').css(\'display\', \'block\');\n+ \n+ $(".each-gallery").each(function(i){\n+ // Initially set opacity on thumbs and add\n+ // additional styling for hover effect on thumbs\n+ var onMouseOutOpacity = 0.67;\n+ $(\'#thumbs + i + ul.thumbs li\').opacityrollover({\n+ mouseOutOpacity: onMouseOutOpacity,\n+ mouseOverOpacity: 1.0,\n+ fadeSpeed: \'fast\',\n+ exemptionSelector: \'.selected\'\n+ });\n+ \n+ // Initialize Advanced Galleriffic Gallery\n+ var gallery = $(\'#thumbs\'+i).galleriffic({\n+ delay: 2500,\n+ numThumbs: 22,\n+ preloadAhead: 10,\n+ enableTopPager: true,\n+ enableBottomPager: true,\n+ maxPagesToShow: 7,\n+ imageContainerSel: \'#slideshow\'+ i,\n+ controlsContainerSel: \'#controls\' + i,\n+ captionContainerSel: \'#caption\' + i,\n+ loadingContainerSel: \'#loading\' + i,\n+ renderSSControls: true,\n+ renderNavControls: true,\n+ playLinkText: \'Play\',\n+ pauseLinkText: \'Pause\',\n+ prevLinkText: \'‹ Previous\',\n+ nextLinkText: \'Next ›\',\n+ nextPageLinkText: \'Next ›\',\n+ prevPageLinkText: \'‹ Prev\',\n+ enableHistory: false,\n+ autoStart: false,\n+ syncTransitions: true,\n+ defaultTransitionDuration: 900,\n+ onSlideChange: function(prevIndex, nextIndex) {\n+ // \'this\' refers to the gallery, which is an extension of $(\'#thumbs\')\n+ this.find(\'ul.thumbs\').children()\n+ .eq(prevIndex).fadeTo(\'fast\', onMouseOutOpacity).end()\n+ .eq(nextIndex).fadeTo(\'fast\', 1.0);\n+ },\n+ onPageTransitionOut: function(callback) {\n+ this.fadeTo(\'fast\', 0.0, callback);\n+ },\n+ onPageTransitionIn: function() {\n+ this.fadeTo(\'fast\', 1.0);\n+ }\n+ });\n+ });\n+ });\n+ </script>\n+ </body>\n+ </html>\n+ \n\\ No newline at end of file\n' |
| b |
| diff -r 9645d995fb3c -r 9185ca0a7b43 test-data/res_files/reads-sample-small.fastq-miRNAs-transcripts.html --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/res_files/reads-sample-small.fastq-miRNAs-transcripts.html Wed Jan 16 08:18:13 2019 -0500 |
| b |
| b'@@ -0,0 +1,315 @@\n+\n+ <!DOCTYPE html>\n+ <html lang="en">\n+ <head>\n+ <meta charset="utf-8">\n+ <title>pipeline</title>\n+ <meta name="viewport" content="width=device-width, initial-scale=1.0">\n+ <meta name="description" content="">\n+ <meta name="author" content="">\n+ <!-- Le styles -->\n+ <link href="css/bootstrap.css" rel="stylesheet">\n+ <link href="css/bootstrap-table.css" rel="stylesheet">\n+ <style type="text/css">\n+ body {\n+ padding-top: 60px;\n+ padding-bottom: 40px;\n+ }\n+ div#page {\n+ width: 940px;\n+ background-color: #fff;\n+ margin: 0 auto;\n+ text-align: left;\n+ border-color: #fff;\n+ border-style: none solid solid;\n+ border-width: medium 1px 1px;\n+ }\n+\n+ div.content {\n+ \tdisplay: none;\n+\t float: right;\n+\t width: 550px;\n+ }\n+ div.content a, div.navigation a {\n+ text-decoration: none;\n+ \tcolor: #777;\n+ }\n+ div.content a:focus, div.content a:hover, div.content a:active {\n+ text-decoration: underline;\n+ }\n+ \n+ div.controls {\n+ margin-top: 5px;\n+\t height: 23px;\n+ }\n+ \n+ div.controls a {\n+\t padding: 5px;\n+ }\n+ div.ss-controls {\n+\t float: left;\n+ }\n+ div.nav-controls {\n+\t float: right;\n+ }\n+ div.slideshow-container {\n+\t position: relative;\n+\t clear: both;\n+\t height: 502px; /* This should be set to be at least the height of the largest image in the slideshow */\n+ }\n+ div.loader {\n+ \tposition: absolute;\n+ \ttop: 0;\n+ \tleft: 0;\n+ background-image: url(\'loader.gif\');\n+ background-repeat: no-repeat;\n+ background-position: center;\n+ \twidth: 550px;\n+ \theight: 502px; /* This should be set to be at least the height of the largest image in the slideshow */\n+ }\n+ div.slideshow {\n+ \n+ }\n+ \n+ div.slideshow span.image-wrapper {\n+\t display: block;\n+\t position: absolute;\n+\t top: 0;\n+\t left: 0;\n+ }\n+ div.slideshow a.advance-link {\n+\t display: block;\n+ \t width: 550px;\n+ height: 502px; /* This should be set to be at least the height of the largest image in the slideshow */\n+ line-height: 502px; /* This should be set to be at least the height of the largest image in the slideshow */\n+ text-align: center;\n+ }\n+ div.slideshow a.advance-link:hover, div.slideshow a.advance-link:active, div.slideshow a.advance-link:visited {\n+ text-decoration: none;\n+ }\n+ div.slideshow img {\n+ vertical-align: middle;\n+\tborder: 1px solid #ccc;\n+ }\n+\n+ div.image-title {\n+ font-weight: bold;\n+ font-size: 1.4em;\n+ }\n+\n+ div.image-desc {\n+ line-height: 1.3em;\n+ padding-top: 12px;\n+ }\n+ div.navigation {\n+\n+ }\n+ ul.thumbs {\n+\tclear: both;\n+\tmargin: 0;\n+\tpadding: 0;\n+ }\n+ ul.thumbs li {\n+\tfloat: none;\n+\tpadding: 0;\n+\tmargin: 0;\n+ list-style: none;\n+ }\n+ a.thumb {\n+\tpadding: 0;\n+\tdisplay: inline;\n+\tborder: none;\n+ }\n+ ul.thumbs li.selected a.thumb {\n+\tcolor: #000;\n+ font-weight: bold;\n+ }\n+ a.thumb:focus {\n+\toutline: none;\n+ }\n+ ul.thumbs img {\n+\tborder: none;\n+\tdisplay: block;\n+ }\n+ div.pagination {\n+\tclear: both;\n+ }\n+ div.navigation div.top {\n+ margin-bottom: 12px;\n+\theight: 11px;\n+ }\n+ div.navigation div.bottom {\n+ margin-top: 12px;\n+ }\n+ div.pagination a, div.pagination span.current, div.pagination span.ellipsis {\n+\tdisplay: block;\n+\tfloat: left;\n+ margin-right: 2px;\n+\tpadding: 4px 7px 2px 7px;\n+\tborder: 1px solid #ccc;\n+ }\n+ div.pagination a:hover {\n+ background-color: #eee;\n+ text-decoration: none;\n+ }\n+ div.pagination span.current {\n+ font-weight: bold;\n+ background-color: #000;\n+ border-color: #000;\n+\tcolor: #fff;\n+ }\n+ div.pagination span.ellipsis {\n+\tborder: none;\n+\tpadding: 5px 0 3px 2px;\n+ }\n+ \n+ div.download {\n+\tfloat: right;\n+ }\n+ \n+ div.caption-container {\n+\tposition: relative;\n+\tclear: left;\n+\theight: 75px;\n+ }\n+ span.image-caption {\n+\tdisplay: block;\n+\tposition: absolute;\n+\twidth: 550px;\n+\ttop: 0;\n+\tleft: 0;\n+ }\n+ div.caption {\n+\tpadding: 12px;\n+ }\n+\n+ /* Featurettes\n+ ------------------------- */\n+\n+ .featurette {\n+ padding-top: 20px; /* Vertica'..b'ss="icon-bar"></span>\n+ <span class="icon-bar"></span>\n+ <span class="icon-bar"></span>\n+ </button>\n+ <a class="brand" href="report.txt">Report</a>\n+ <div class="nav-collapse collapse">\n+ <ul class="nav">\n+ <li class="active"><a href="reads-sample-small.fastq.html">reads-sample-small.fastq</a></li>\n+ </ul>\n+ </div><!--/.nav-collapse -->\n+ </div>\n+ </div>\n+ </div>\n+ <div class="container">\n+ <div class="featurette">\n+ <h1>transcripts</h1>\n+ <p class="featurette-p">\n+ <A HREF="reads-sample-small.fastq/subgroups/miRNAs//miRNAs-transcripts_reads_counts.txt">read number per transcript (txt)</A><br/> \n+<A HREF="reads-sample-small.fastq/subgroups/miRNAs//miRNAs-transcripts_sorted.bam">transcripts mappers (sorted bam)</A><br/> \n+<A HREF="reads-sample-small.fastq/subgroups/miRNAs//miRNAs-transcripts_unique_sorted.bam">transcripts unique mappers (sorted bam)</A><br/> \n+\n+ </p>\n+ </div>\n+ </div>\n+ \n+ <!-- FOOTER -->\n+ <div class="container">\n+ <footer>\n+ \n+ </footer>\n+ </div>\n+ <!-- Le javascript\n+ ================================================== -->\n+ <!-- Placed at the end of the document so the pages load faster -->\n+ <script type="text/javascript" src="js/filter.js"></script>\n+ <script type="text/javascript" src="js/jquery.js"></script>\n+ <script type="text/javascript" src="js/jquery-1.3.2.js"></script>\n+ <script type="text/javascript" src="js/jquery.galleriffic.js"></script>\n+ <script type="text/javascript" src="js/jquery.opacityrollover.js"></script>\n+ <script type="text/javascript" src="js/bootstrap-table.js"></script>\n+ <script type="text/javascript" src="js/bootstrap.min.js"></script>\n+ <script type="text/javascript">\n+ jQuery(document).ready(function($) {\n+ // We only want these styles applied when javascript is enabled\n+ $(\'div.navigation\').css({\'width\' : \'300px\', \'float\' : \'left\'});\n+ $(\'div.content\').css(\'display\', \'block\');\n+ \n+ $(".each-gallery").each(function(i){\n+ // Initially set opacity on thumbs and add\n+ // additional styling for hover effect on thumbs\n+ var onMouseOutOpacity = 0.67;\n+ $(\'#thumbs + i + ul.thumbs li\').opacityrollover({\n+ mouseOutOpacity: onMouseOutOpacity,\n+ mouseOverOpacity: 1.0,\n+ fadeSpeed: \'fast\',\n+ exemptionSelector: \'.selected\'\n+ });\n+ \n+ // Initialize Advanced Galleriffic Gallery\n+ var gallery = $(\'#thumbs\'+i).galleriffic({\n+ delay: 2500,\n+ numThumbs: 22,\n+ preloadAhead: 10,\n+ enableTopPager: true,\n+ enableBottomPager: true,\n+ maxPagesToShow: 7,\n+ imageContainerSel: \'#slideshow\'+ i,\n+ controlsContainerSel: \'#controls\' + i,\n+ captionContainerSel: \'#caption\' + i,\n+ loadingContainerSel: \'#loading\' + i,\n+ renderSSControls: true,\n+ renderNavControls: true,\n+ playLinkText: \'Play\',\n+ pauseLinkText: \'Pause\',\n+ prevLinkText: \'‹ Previous\',\n+ nextLinkText: \'Next ›\',\n+ nextPageLinkText: \'Next ›\',\n+ prevPageLinkText: \'‹ Prev\',\n+ enableHistory: false,\n+ autoStart: false,\n+ syncTransitions: true,\n+ defaultTransitionDuration: 900,\n+ onSlideChange: function(prevIndex, nextIndex) {\n+ // \'this\' refers to the gallery, which is an extension of $(\'#thumbs\')\n+ this.find(\'ul.thumbs\').children()\n+ .eq(prevIndex).fadeTo(\'fast\', onMouseOutOpacity).end()\n+ .eq(nextIndex).fadeTo(\'fast\', 1.0);\n+ },\n+ onPageTransitionOut: function(callback) {\n+ this.fadeTo(\'fast\', 0.0, callback);\n+ },\n+ onPageTransitionIn: function() {\n+ this.fadeTo(\'fast\', 1.0);\n+ }\n+ });\n+ });\n+ });\n+ </script>\n+ </body>\n+ </html>\n+ \n\\ No newline at end of file\n' |
| b |
| diff -r 9645d995fb3c -r 9185ca0a7b43 test-data/res_files/reads-sample-small.fastq-piRNAs-PPP.html --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/res_files/reads-sample-small.fastq-piRNAs-PPP.html Wed Jan 16 08:18:13 2019 -0500 |
| b |
| b'@@ -0,0 +1,337 @@\n+\n+ <!DOCTYPE html>\n+ <html lang="en">\n+ <head>\n+ <meta charset="utf-8">\n+ <title>pipeline</title>\n+ <meta name="viewport" content="width=device-width, initial-scale=1.0">\n+ <meta name="description" content="">\n+ <meta name="author" content="">\n+ <!-- Le styles -->\n+ <link href="css/bootstrap.css" rel="stylesheet">\n+ <link href="css/bootstrap-table.css" rel="stylesheet">\n+ <style type="text/css">\n+ body {\n+ padding-top: 60px;\n+ padding-bottom: 40px;\n+ }\n+ div#page {\n+ width: 940px;\n+ background-color: #fff;\n+ margin: 0 auto;\n+ text-align: left;\n+ border-color: #fff;\n+ border-style: none solid solid;\n+ border-width: medium 1px 1px;\n+ }\n+\n+ div.content {\n+ \tdisplay: none;\n+\t float: right;\n+\t width: 550px;\n+ }\n+ div.content a, div.navigation a {\n+ text-decoration: none;\n+ \tcolor: #777;\n+ }\n+ div.content a:focus, div.content a:hover, div.content a:active {\n+ text-decoration: underline;\n+ }\n+ \n+ div.controls {\n+ margin-top: 5px;\n+\t height: 23px;\n+ }\n+ \n+ div.controls a {\n+\t padding: 5px;\n+ }\n+ div.ss-controls {\n+\t float: left;\n+ }\n+ div.nav-controls {\n+\t float: right;\n+ }\n+ div.slideshow-container {\n+\t position: relative;\n+\t clear: both;\n+\t height: 502px; /* This should be set to be at least the height of the largest image in the slideshow */\n+ }\n+ div.loader {\n+ \tposition: absolute;\n+ \ttop: 0;\n+ \tleft: 0;\n+ background-image: url(\'loader.gif\');\n+ background-repeat: no-repeat;\n+ background-position: center;\n+ \twidth: 550px;\n+ \theight: 502px; /* This should be set to be at least the height of the largest image in the slideshow */\n+ }\n+ div.slideshow {\n+ \n+ }\n+ \n+ div.slideshow span.image-wrapper {\n+\t display: block;\n+\t position: absolute;\n+\t top: 0;\n+\t left: 0;\n+ }\n+ div.slideshow a.advance-link {\n+\t display: block;\n+ \t width: 550px;\n+ height: 502px; /* This should be set to be at least the height of the largest image in the slideshow */\n+ line-height: 502px; /* This should be set to be at least the height of the largest image in the slideshow */\n+ text-align: center;\n+ }\n+ div.slideshow a.advance-link:hover, div.slideshow a.advance-link:active, div.slideshow a.advance-link:visited {\n+ text-decoration: none;\n+ }\n+ div.slideshow img {\n+ vertical-align: middle;\n+\tborder: 1px solid #ccc;\n+ }\n+\n+ div.image-title {\n+ font-weight: bold;\n+ font-size: 1.4em;\n+ }\n+\n+ div.image-desc {\n+ line-height: 1.3em;\n+ padding-top: 12px;\n+ }\n+ div.navigation {\n+\n+ }\n+ ul.thumbs {\n+\tclear: both;\n+\tmargin: 0;\n+\tpadding: 0;\n+ }\n+ ul.thumbs li {\n+\tfloat: none;\n+\tpadding: 0;\n+\tmargin: 0;\n+ list-style: none;\n+ }\n+ a.thumb {\n+\tpadding: 0;\n+\tdisplay: inline;\n+\tborder: none;\n+ }\n+ ul.thumbs li.selected a.thumb {\n+\tcolor: #000;\n+ font-weight: bold;\n+ }\n+ a.thumb:focus {\n+\toutline: none;\n+ }\n+ ul.thumbs img {\n+\tborder: none;\n+\tdisplay: block;\n+ }\n+ div.pagination {\n+\tclear: both;\n+ }\n+ div.navigation div.top {\n+ margin-bottom: 12px;\n+\theight: 11px;\n+ }\n+ div.navigation div.bottom {\n+ margin-top: 12px;\n+ }\n+ div.pagination a, div.pagination span.current, div.pagination span.ellipsis {\n+\tdisplay: block;\n+\tfloat: left;\n+ margin-right: 2px;\n+\tpadding: 4px 7px 2px 7px;\n+\tborder: 1px solid #ccc;\n+ }\n+ div.pagination a:hover {\n+ background-color: #eee;\n+ text-decoration: none;\n+ }\n+ div.pagination span.current {\n+ font-weight: bold;\n+ background-color: #000;\n+ border-color: #000;\n+\tcolor: #fff;\n+ }\n+ div.pagination span.ellipsis {\n+\tborder: none;\n+\tpadding: 5px 0 3px 2px;\n+ }\n+ \n+ div.download {\n+\tfloat: right;\n+ }\n+ \n+ div.caption-container {\n+\tposition: relative;\n+\tclear: left;\n+\theight: 75px;\n+ }\n+ span.image-caption {\n+\tdisplay: block;\n+\tposition: absolute;\n+\twidth: 550px;\n+\ttop: 0;\n+\tleft: 0;\n+ }\n+ div.caption {\n+\tpadding: 12px;\n+ }\n+\n+ /* Featurettes\n+ ------------------------- */\n+\n+ .featurette {\n+ padding-top: 20px; /* Vertica'..b'eads-sample-small.fastq/subgroups/PPPartners/MAX_I.html">MAX_I</a> </td><td> 54 </td><td> 11 </td><td> 2.34782608695652 </td><td> 2.44253424438055 </td><td> 3.5422938011818 </td><td> 0.00019833170283523 </td>\n+</tr><tr><td> <a href="reads-sample-small.fastq/subgroups/PPPartners/MAX_LTR.html">MAX_LTR</a> </td><td> 16 </td><td> 0 </td><td> 0.695652173913043 </td><td> 1.75535906419012 </td><td> -0.396301923694456 </td><td> 0.654058845865745 </td>\n+</tr><tr><td> <a href="reads-sample-small.fastq/subgroups/PPPartners/PROTOP.html">PROTOP</a> </td><td> 49 </td><td> 11 </td><td> 2.1304347826087 </td><td> 2.30885531258291 </td><td> 3.84154224348902 </td><td> 6.11318444337927e-05 </td>\n+</tr><tr><td> ZAM_I </td>\n+<td> 0 </td><td> 0 </td><td> 0 </td><td> 0 </td><td> NA </td><td> NA </td>\n+</tr><tr><td> ZAM_LTR </td>\n+<td> 0 </td><td> 0 </td><td> 0 </td><td> 0 </td><td> NA </td><td> NA </td>\n+</tr></tbody></table></div>\n+ <!-- FOOTER -->\n+ <div class="container">\n+ <footer>\n+ \n+ </footer>\n+ </div>\n+ <!-- Le javascript\n+ ================================================== -->\n+ <!-- Placed at the end of the document so the pages load faster -->\n+ <script type="text/javascript" src="js/filter.js"></script>\n+ <script type="text/javascript" src="js/jquery.js"></script>\n+ <script type="text/javascript" src="js/jquery-1.3.2.js"></script>\n+ <script type="text/javascript" src="js/jquery.galleriffic.js"></script>\n+ <script type="text/javascript" src="js/jquery.opacityrollover.js"></script>\n+ <script type="text/javascript" src="js/bootstrap-table.js"></script>\n+ <script type="text/javascript" src="js/bootstrap.min.js"></script>\n+ <script type="text/javascript">\n+ jQuery(document).ready(function($) {\n+ // We only want these styles applied when javascript is enabled\n+ $(\'div.navigation\').css({\'width\' : \'300px\', \'float\' : \'left\'});\n+ $(\'div.content\').css(\'display\', \'block\');\n+ \n+ $(".each-gallery").each(function(i){\n+ // Initially set opacity on thumbs and add\n+ // additional styling for hover effect on thumbs\n+ var onMouseOutOpacity = 0.67;\n+ $(\'#thumbs + i + ul.thumbs li\').opacityrollover({\n+ mouseOutOpacity: onMouseOutOpacity,\n+ mouseOverOpacity: 1.0,\n+ fadeSpeed: \'fast\',\n+ exemptionSelector: \'.selected\'\n+ });\n+ \n+ // Initialize Advanced Galleriffic Gallery\n+ var gallery = $(\'#thumbs\'+i).galleriffic({\n+ delay: 2500,\n+ numThumbs: 22,\n+ preloadAhead: 10,\n+ enableTopPager: true,\n+ enableBottomPager: true,\n+ maxPagesToShow: 7,\n+ imageContainerSel: \'#slideshow\'+ i,\n+ controlsContainerSel: \'#controls\' + i,\n+ captionContainerSel: \'#caption\' + i,\n+ loadingContainerSel: \'#loading\' + i,\n+ renderSSControls: true,\n+ renderNavControls: true,\n+ playLinkText: \'Play\',\n+ pauseLinkText: \'Pause\',\n+ prevLinkText: \'‹ Previous\',\n+ nextLinkText: \'Next ›\',\n+ nextPageLinkText: \'Next ›\',\n+ prevPageLinkText: \'‹ Prev\',\n+ enableHistory: false,\n+ autoStart: false,\n+ syncTransitions: true,\n+ defaultTransitionDuration: 900,\n+ onSlideChange: function(prevIndex, nextIndex) {\n+ // \'this\' refers to the gallery, which is an extension of $(\'#thumbs\')\n+ this.find(\'ul.thumbs\').children()\n+ .eq(prevIndex).fadeTo(\'fast\', onMouseOutOpacity).end()\n+ .eq(nextIndex).fadeTo(\'fast\', 1.0);\n+ },\n+ onPageTransitionOut: function(callback) {\n+ this.fadeTo(\'fast\', 0.0, callback);\n+ },\n+ onPageTransitionIn: function() {\n+ this.fadeTo(\'fast\', 1.0);\n+ }\n+ });\n+ });\n+ });\n+ </script>\n+ </body>\n+ </html>\n+ \n\\ No newline at end of file\n' |
| b |
| diff -r 9645d995fb3c -r 9185ca0a7b43 test-data/res_files/reads-sample-small.fastq-piRNAs-TEs.html --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/res_files/reads-sample-small.fastq-piRNAs-TEs.html Wed Jan 16 08:18:13 2019 -0500 |
| b |
| b'@@ -0,0 +1,389 @@\n+\n+ <!DOCTYPE html>\n+ <html lang="en">\n+ <head>\n+ <meta charset="utf-8">\n+ <title>pipeline</title>\n+ <meta name="viewport" content="width=device-width, initial-scale=1.0">\n+ <meta name="description" content="">\n+ <meta name="author" content="">\n+ <!-- Le styles -->\n+ <link href="css/bootstrap.css" rel="stylesheet">\n+ <link href="css/bootstrap-table.css" rel="stylesheet">\n+ <style type="text/css">\n+ body {\n+ padding-top: 60px;\n+ padding-bottom: 40px;\n+ }\n+ div#page {\n+ width: 940px;\n+ background-color: #fff;\n+ margin: 0 auto;\n+ text-align: left;\n+ border-color: #fff;\n+ border-style: none solid solid;\n+ border-width: medium 1px 1px;\n+ }\n+\n+ div.content {\n+ \tdisplay: none;\n+\t float: right;\n+\t width: 550px;\n+ }\n+ div.content a, div.navigation a {\n+ text-decoration: none;\n+ \tcolor: #777;\n+ }\n+ div.content a:focus, div.content a:hover, div.content a:active {\n+ text-decoration: underline;\n+ }\n+ \n+ div.controls {\n+ margin-top: 5px;\n+\t height: 23px;\n+ }\n+ \n+ div.controls a {\n+\t padding: 5px;\n+ }\n+ div.ss-controls {\n+\t float: left;\n+ }\n+ div.nav-controls {\n+\t float: right;\n+ }\n+ div.slideshow-container {\n+\t position: relative;\n+\t clear: both;\n+\t height: 502px; /* This should be set to be at least the height of the largest image in the slideshow */\n+ }\n+ div.loader {\n+ \tposition: absolute;\n+ \ttop: 0;\n+ \tleft: 0;\n+ background-image: url(\'loader.gif\');\n+ background-repeat: no-repeat;\n+ background-position: center;\n+ \twidth: 550px;\n+ \theight: 502px; /* This should be set to be at least the height of the largest image in the slideshow */\n+ }\n+ div.slideshow {\n+ \n+ }\n+ \n+ div.slideshow span.image-wrapper {\n+\t display: block;\n+\t position: absolute;\n+\t top: 0;\n+\t left: 0;\n+ }\n+ div.slideshow a.advance-link {\n+\t display: block;\n+ \t width: 550px;\n+ height: 502px; /* This should be set to be at least the height of the largest image in the slideshow */\n+ line-height: 502px; /* This should be set to be at least the height of the largest image in the slideshow */\n+ text-align: center;\n+ }\n+ div.slideshow a.advance-link:hover, div.slideshow a.advance-link:active, div.slideshow a.advance-link:visited {\n+ text-decoration: none;\n+ }\n+ div.slideshow img {\n+ vertical-align: middle;\n+\tborder: 1px solid #ccc;\n+ }\n+\n+ div.image-title {\n+ font-weight: bold;\n+ font-size: 1.4em;\n+ }\n+\n+ div.image-desc {\n+ line-height: 1.3em;\n+ padding-top: 12px;\n+ }\n+ div.navigation {\n+\n+ }\n+ ul.thumbs {\n+\tclear: both;\n+\tmargin: 0;\n+\tpadding: 0;\n+ }\n+ ul.thumbs li {\n+\tfloat: none;\n+\tpadding: 0;\n+\tmargin: 0;\n+ list-style: none;\n+ }\n+ a.thumb {\n+\tpadding: 0;\n+\tdisplay: inline;\n+\tborder: none;\n+ }\n+ ul.thumbs li.selected a.thumb {\n+\tcolor: #000;\n+ font-weight: bold;\n+ }\n+ a.thumb:focus {\n+\toutline: none;\n+ }\n+ ul.thumbs img {\n+\tborder: none;\n+\tdisplay: block;\n+ }\n+ div.pagination {\n+\tclear: both;\n+ }\n+ div.navigation div.top {\n+ margin-bottom: 12px;\n+\theight: 11px;\n+ }\n+ div.navigation div.bottom {\n+ margin-top: 12px;\n+ }\n+ div.pagination a, div.pagination span.current, div.pagination span.ellipsis {\n+\tdisplay: block;\n+\tfloat: left;\n+ margin-right: 2px;\n+\tpadding: 4px 7px 2px 7px;\n+\tborder: 1px solid #ccc;\n+ }\n+ div.pagination a:hover {\n+ background-color: #eee;\n+ text-decoration: none;\n+ }\n+ div.pagination span.current {\n+ font-weight: bold;\n+ background-color: #000;\n+ border-color: #000;\n+\tcolor: #fff;\n+ }\n+ div.pagination span.ellipsis {\n+\tborder: none;\n+\tpadding: 5px 0 3px 2px;\n+ }\n+ \n+ div.download {\n+\tfloat: right;\n+ }\n+ \n+ div.caption-container {\n+\tposition: relative;\n+\tclear: left;\n+\theight: 75px;\n+ }\n+ span.image-caption {\n+\tdisplay: block;\n+\tposition: absolute;\n+\twidth: 550px;\n+\ttop: 0;\n+\tleft: 0;\n+ }\n+ div.caption {\n+\tpadding: 12px;\n+ }\n+\n+ /* Featurettes\n+ ------------------------- */\n+\n+ .featurette {\n+ padding-top: 20px; /* Vertica'..b'sample-small.fastq/subgroups/piRNAs//Gviz_TEs/G6_DM.png" title="G6_DM">G6_DM</a>\n+ </li>\n+ \t\n+ <li>\n+ <a class="thumb" href="reads-sample-small.fastq/subgroups/piRNAs//Gviz_TEs/Gypsy2-LTR_DM.png" title="Gypsy2-LTR_DM">Gypsy2-LTR_DM</a>\n+ </li>\n+ \t\n+ <li>\n+ <a class="thumb" href="reads-sample-small.fastq/subgroups/piRNAs//Gviz_TEs/I_DM.png" title="I_DM">I_DM</a>\n+ </li>\n+ \t\n+ <li>\n+ <a class="thumb" href="reads-sample-small.fastq/subgroups/piRNAs//Gviz_TEs/MAX_I.png" title="MAX_I">MAX_I</a>\n+ </li>\n+ \t\n+ <li>\n+ <a class="thumb" href="reads-sample-small.fastq/subgroups/piRNAs//Gviz_TEs/MAX_LTR.png" title="MAX_LTR">MAX_LTR</a>\n+ </li>\n+ \t\n+ <li>\n+ <a class="thumb" href="reads-sample-small.fastq/subgroups/piRNAs//Gviz_TEs/PROTOP.png" title="PROTOP">PROTOP</a>\n+ </li>\n+ \t\n+ </ul>\n+ </div>\n+ <div style="clear: both;"></div></div>\n+ </div>\n+ </div>\n+ \n+ <!-- FOOTER -->\n+ <div class="container">\n+ <footer>\n+ \n+ </footer>\n+ </div>\n+ <!-- Le javascript\n+ ================================================== -->\n+ <!-- Placed at the end of the document so the pages load faster -->\n+ <script type="text/javascript" src="js/filter.js"></script>\n+ <script type="text/javascript" src="js/jquery.js"></script>\n+ <script type="text/javascript" src="js/jquery-1.3.2.js"></script>\n+ <script type="text/javascript" src="js/jquery.galleriffic.js"></script>\n+ <script type="text/javascript" src="js/jquery.opacityrollover.js"></script>\n+ <script type="text/javascript" src="js/bootstrap-table.js"></script>\n+ <script type="text/javascript" src="js/bootstrap.min.js"></script>\n+ <script type="text/javascript">\n+ jQuery(document).ready(function($) {\n+ // We only want these styles applied when javascript is enabled\n+ $(\'div.navigation\').css({\'width\' : \'300px\', \'float\' : \'left\'});\n+ $(\'div.content\').css(\'display\', \'block\');\n+ \n+ $(".each-gallery").each(function(i){\n+ // Initially set opacity on thumbs and add\n+ // additional styling for hover effect on thumbs\n+ var onMouseOutOpacity = 0.67;\n+ $(\'#thumbs + i + ul.thumbs li\').opacityrollover({\n+ mouseOutOpacity: onMouseOutOpacity,\n+ mouseOverOpacity: 1.0,\n+ fadeSpeed: \'fast\',\n+ exemptionSelector: \'.selected\'\n+ });\n+ \n+ // Initialize Advanced Galleriffic Gallery\n+ var gallery = $(\'#thumbs\'+i).galleriffic({\n+ delay: 2500,\n+ numThumbs: 22,\n+ preloadAhead: 10,\n+ enableTopPager: true,\n+ enableBottomPager: true,\n+ maxPagesToShow: 7,\n+ imageContainerSel: \'#slideshow\'+ i,\n+ controlsContainerSel: \'#controls\' + i,\n+ captionContainerSel: \'#caption\' + i,\n+ loadingContainerSel: \'#loading\' + i,\n+ renderSSControls: true,\n+ renderNavControls: true,\n+ playLinkText: \'Play\',\n+ pauseLinkText: \'Pause\',\n+ prevLinkText: \'‹ Previous\',\n+ nextLinkText: \'Next ›\',\n+ nextPageLinkText: \'Next ›\',\n+ prevPageLinkText: \'‹ Prev\',\n+ enableHistory: false,\n+ autoStart: false,\n+ syncTransitions: true,\n+ defaultTransitionDuration: 900,\n+ onSlideChange: function(prevIndex, nextIndex) {\n+ // \'this\' refers to the gallery, which is an extension of $(\'#thumbs\')\n+ this.find(\'ul.thumbs\').children()\n+ .eq(prevIndex).fadeTo(\'fast\', onMouseOutOpacity).end()\n+ .eq(nextIndex).fadeTo(\'fast\', 1.0);\n+ },\n+ onPageTransitionOut: function(callback) {\n+ this.fadeTo(\'fast\', 0.0, callback);\n+ },\n+ onPageTransitionIn: function() {\n+ this.fadeTo(\'fast\', 1.0);\n+ }\n+ });\n+ });\n+ });\n+ </script>\n+ </body>\n+ </html>\n+ \n\\ No newline at end of file\n' |
| b |
| diff -r 9645d995fb3c -r 9185ca0a7b43 test-data/res_files/reads-sample-small.fastq-piRNAs-genome.html --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/res_files/reads-sample-small.fastq-piRNAs-genome.html Wed Jan 16 08:18:13 2019 -0500 |
| b |
| b'@@ -0,0 +1,389 @@\n+\n+ <!DOCTYPE html>\n+ <html lang="en">\n+ <head>\n+ <meta charset="utf-8">\n+ <title>pipeline</title>\n+ <meta name="viewport" content="width=device-width, initial-scale=1.0">\n+ <meta name="description" content="">\n+ <meta name="author" content="">\n+ <!-- Le styles -->\n+ <link href="css/bootstrap.css" rel="stylesheet">\n+ <link href="css/bootstrap-table.css" rel="stylesheet">\n+ <style type="text/css">\n+ body {\n+ padding-top: 60px;\n+ padding-bottom: 40px;\n+ }\n+ div#page {\n+ width: 940px;\n+ background-color: #fff;\n+ margin: 0 auto;\n+ text-align: left;\n+ border-color: #fff;\n+ border-style: none solid solid;\n+ border-width: medium 1px 1px;\n+ }\n+\n+ div.content {\n+ \tdisplay: none;\n+\t float: right;\n+\t width: 550px;\n+ }\n+ div.content a, div.navigation a {\n+ text-decoration: none;\n+ \tcolor: #777;\n+ }\n+ div.content a:focus, div.content a:hover, div.content a:active {\n+ text-decoration: underline;\n+ }\n+ \n+ div.controls {\n+ margin-top: 5px;\n+\t height: 23px;\n+ }\n+ \n+ div.controls a {\n+\t padding: 5px;\n+ }\n+ div.ss-controls {\n+\t float: left;\n+ }\n+ div.nav-controls {\n+\t float: right;\n+ }\n+ div.slideshow-container {\n+\t position: relative;\n+\t clear: both;\n+\t height: 502px; /* This should be set to be at least the height of the largest image in the slideshow */\n+ }\n+ div.loader {\n+ \tposition: absolute;\n+ \ttop: 0;\n+ \tleft: 0;\n+ background-image: url(\'loader.gif\');\n+ background-repeat: no-repeat;\n+ background-position: center;\n+ \twidth: 550px;\n+ \theight: 502px; /* This should be set to be at least the height of the largest image in the slideshow */\n+ }\n+ div.slideshow {\n+ \n+ }\n+ \n+ div.slideshow span.image-wrapper {\n+\t display: block;\n+\t position: absolute;\n+\t top: 0;\n+\t left: 0;\n+ }\n+ div.slideshow a.advance-link {\n+\t display: block;\n+ \t width: 550px;\n+ height: 502px; /* This should be set to be at least the height of the largest image in the slideshow */\n+ line-height: 502px; /* This should be set to be at least the height of the largest image in the slideshow */\n+ text-align: center;\n+ }\n+ div.slideshow a.advance-link:hover, div.slideshow a.advance-link:active, div.slideshow a.advance-link:visited {\n+ text-decoration: none;\n+ }\n+ div.slideshow img {\n+ vertical-align: middle;\n+\tborder: 1px solid #ccc;\n+ }\n+\n+ div.image-title {\n+ font-weight: bold;\n+ font-size: 1.4em;\n+ }\n+\n+ div.image-desc {\n+ line-height: 1.3em;\n+ padding-top: 12px;\n+ }\n+ div.navigation {\n+\n+ }\n+ ul.thumbs {\n+\tclear: both;\n+\tmargin: 0;\n+\tpadding: 0;\n+ }\n+ ul.thumbs li {\n+\tfloat: none;\n+\tpadding: 0;\n+\tmargin: 0;\n+ list-style: none;\n+ }\n+ a.thumb {\n+\tpadding: 0;\n+\tdisplay: inline;\n+\tborder: none;\n+ }\n+ ul.thumbs li.selected a.thumb {\n+\tcolor: #000;\n+ font-weight: bold;\n+ }\n+ a.thumb:focus {\n+\toutline: none;\n+ }\n+ ul.thumbs img {\n+\tborder: none;\n+\tdisplay: block;\n+ }\n+ div.pagination {\n+\tclear: both;\n+ }\n+ div.navigation div.top {\n+ margin-bottom: 12px;\n+\theight: 11px;\n+ }\n+ div.navigation div.bottom {\n+ margin-top: 12px;\n+ }\n+ div.pagination a, div.pagination span.current, div.pagination span.ellipsis {\n+\tdisplay: block;\n+\tfloat: left;\n+ margin-right: 2px;\n+\tpadding: 4px 7px 2px 7px;\n+\tborder: 1px solid #ccc;\n+ }\n+ div.pagination a:hover {\n+ background-color: #eee;\n+ text-decoration: none;\n+ }\n+ div.pagination span.current {\n+ font-weight: bold;\n+ background-color: #000;\n+ border-color: #000;\n+\tcolor: #fff;\n+ }\n+ div.pagination span.ellipsis {\n+\tborder: none;\n+\tpadding: 5px 0 3px 2px;\n+ }\n+ \n+ div.download {\n+\tfloat: right;\n+ }\n+ \n+ div.caption-container {\n+\tposition: relative;\n+\tclear: left;\n+\theight: 75px;\n+ }\n+ span.image-caption {\n+\tdisplay: block;\n+\tposition: absolute;\n+\twidth: 550px;\n+\ttop: 0;\n+\tleft: 0;\n+ }\n+ div.caption {\n+\tpadding: 12px;\n+ }\n+\n+ /* Featurettes\n+ ------------------------- */\n+\n+ .featurette {\n+ padding-top: 20px; /* Vertica'..b'="navigation">\n+ <input type="text" id="myInput1" onkeyup="search(this)" placeholder="Search for names...">\n+ <ul class="thumbs noscript">\n+ \n+ <li>\n+ <a class="thumb" href="reads-sample-small.fastq/subgroups/piRNAs//Gviz_genome/rand/chrom_1.png" title="chrom_1">chrom_1</a>\n+ </li>\n+ \n+ <li>\n+ <a class="thumb" href="reads-sample-small.fastq/subgroups/piRNAs//Gviz_genome/rand/chrom_2.png" title="chrom_2">chrom_2</a>\n+ </li>\n+ \n+ <li>\n+ <a class="thumb" href="reads-sample-small.fastq/subgroups/piRNAs//Gviz_genome/rand/chrom_4.png" title="chrom_4">chrom_4</a>\n+ </li>\n+ \n+ <li>\n+ <a class="thumb" href="reads-sample-small.fastq/subgroups/piRNAs//Gviz_genome/rand/chrom_6.png" title="chrom_6">chrom_6</a>\n+ </li>\n+ \n+ </ul>\n+ </div>\n+ <div style="clear: both;"></div></div>\n+ </div>\n+ </div>\n+ \n+ <!-- FOOTER -->\n+ <div class="container">\n+ <footer>\n+ \n+ </footer>\n+ </div>\n+ <!-- Le javascript\n+ ================================================== -->\n+ <!-- Placed at the end of the document so the pages load faster -->\n+ <script type="text/javascript" src="js/filter.js"></script>\n+ <script type="text/javascript" src="js/jquery.js"></script>\n+ <script type="text/javascript" src="js/jquery-1.3.2.js"></script>\n+ <script type="text/javascript" src="js/jquery.galleriffic.js"></script>\n+ <script type="text/javascript" src="js/jquery.opacityrollover.js"></script>\n+ <script type="text/javascript" src="js/bootstrap-table.js"></script>\n+ <script type="text/javascript" src="js/bootstrap.min.js"></script>\n+ <script type="text/javascript">\n+ jQuery(document).ready(function($) {\n+ // We only want these styles applied when javascript is enabled\n+ $(\'div.navigation\').css({\'width\' : \'300px\', \'float\' : \'left\'});\n+ $(\'div.content\').css(\'display\', \'block\');\n+ \n+ $(".each-gallery").each(function(i){\n+ // Initially set opacity on thumbs and add\n+ // additional styling for hover effect on thumbs\n+ var onMouseOutOpacity = 0.67;\n+ $(\'#thumbs + i + ul.thumbs li\').opacityrollover({\n+ mouseOutOpacity: onMouseOutOpacity,\n+ mouseOverOpacity: 1.0,\n+ fadeSpeed: \'fast\',\n+ exemptionSelector: \'.selected\'\n+ });\n+ \n+ // Initialize Advanced Galleriffic Gallery\n+ var gallery = $(\'#thumbs\'+i).galleriffic({\n+ delay: 2500,\n+ numThumbs: 22,\n+ preloadAhead: 10,\n+ enableTopPager: true,\n+ enableBottomPager: true,\n+ maxPagesToShow: 7,\n+ imageContainerSel: \'#slideshow\'+ i,\n+ controlsContainerSel: \'#controls\' + i,\n+ captionContainerSel: \'#caption\' + i,\n+ loadingContainerSel: \'#loading\' + i,\n+ renderSSControls: true,\n+ renderNavControls: true,\n+ playLinkText: \'Play\',\n+ pauseLinkText: \'Pause\',\n+ prevLinkText: \'‹ Previous\',\n+ nextLinkText: \'Next ›\',\n+ nextPageLinkText: \'Next ›\',\n+ prevPageLinkText: \'‹ Prev\',\n+ enableHistory: false,\n+ autoStart: false,\n+ syncTransitions: true,\n+ defaultTransitionDuration: 900,\n+ onSlideChange: function(prevIndex, nextIndex) {\n+ // \'this\' refers to the gallery, which is an extension of $(\'#thumbs\')\n+ this.find(\'ul.thumbs\').children()\n+ .eq(prevIndex).fadeTo(\'fast\', onMouseOutOpacity).end()\n+ .eq(nextIndex).fadeTo(\'fast\', 1.0);\n+ },\n+ onPageTransitionOut: function(callback) {\n+ this.fadeTo(\'fast\', 0.0, callback);\n+ },\n+ onPageTransitionIn: function() {\n+ this.fadeTo(\'fast\', 1.0);\n+ }\n+ });\n+ });\n+ });\n+ </script>\n+ </body>\n+ </html>\n+ \n\\ No newline at end of file\n' |
| b |
| diff -r 9645d995fb3c -r 9185ca0a7b43 test-data/res_files/reads-sample-small.fastq-piRNAs-transcripts.html --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/res_files/reads-sample-small.fastq-piRNAs-transcripts.html Wed Jan 16 08:18:13 2019 -0500 |
| b |
| b'@@ -0,0 +1,315 @@\n+\n+ <!DOCTYPE html>\n+ <html lang="en">\n+ <head>\n+ <meta charset="utf-8">\n+ <title>pipeline</title>\n+ <meta name="viewport" content="width=device-width, initial-scale=1.0">\n+ <meta name="description" content="">\n+ <meta name="author" content="">\n+ <!-- Le styles -->\n+ <link href="css/bootstrap.css" rel="stylesheet">\n+ <link href="css/bootstrap-table.css" rel="stylesheet">\n+ <style type="text/css">\n+ body {\n+ padding-top: 60px;\n+ padding-bottom: 40px;\n+ }\n+ div#page {\n+ width: 940px;\n+ background-color: #fff;\n+ margin: 0 auto;\n+ text-align: left;\n+ border-color: #fff;\n+ border-style: none solid solid;\n+ border-width: medium 1px 1px;\n+ }\n+\n+ div.content {\n+ \tdisplay: none;\n+\t float: right;\n+\t width: 550px;\n+ }\n+ div.content a, div.navigation a {\n+ text-decoration: none;\n+ \tcolor: #777;\n+ }\n+ div.content a:focus, div.content a:hover, div.content a:active {\n+ text-decoration: underline;\n+ }\n+ \n+ div.controls {\n+ margin-top: 5px;\n+\t height: 23px;\n+ }\n+ \n+ div.controls a {\n+\t padding: 5px;\n+ }\n+ div.ss-controls {\n+\t float: left;\n+ }\n+ div.nav-controls {\n+\t float: right;\n+ }\n+ div.slideshow-container {\n+\t position: relative;\n+\t clear: both;\n+\t height: 502px; /* This should be set to be at least the height of the largest image in the slideshow */\n+ }\n+ div.loader {\n+ \tposition: absolute;\n+ \ttop: 0;\n+ \tleft: 0;\n+ background-image: url(\'loader.gif\');\n+ background-repeat: no-repeat;\n+ background-position: center;\n+ \twidth: 550px;\n+ \theight: 502px; /* This should be set to be at least the height of the largest image in the slideshow */\n+ }\n+ div.slideshow {\n+ \n+ }\n+ \n+ div.slideshow span.image-wrapper {\n+\t display: block;\n+\t position: absolute;\n+\t top: 0;\n+\t left: 0;\n+ }\n+ div.slideshow a.advance-link {\n+\t display: block;\n+ \t width: 550px;\n+ height: 502px; /* This should be set to be at least the height of the largest image in the slideshow */\n+ line-height: 502px; /* This should be set to be at least the height of the largest image in the slideshow */\n+ text-align: center;\n+ }\n+ div.slideshow a.advance-link:hover, div.slideshow a.advance-link:active, div.slideshow a.advance-link:visited {\n+ text-decoration: none;\n+ }\n+ div.slideshow img {\n+ vertical-align: middle;\n+\tborder: 1px solid #ccc;\n+ }\n+\n+ div.image-title {\n+ font-weight: bold;\n+ font-size: 1.4em;\n+ }\n+\n+ div.image-desc {\n+ line-height: 1.3em;\n+ padding-top: 12px;\n+ }\n+ div.navigation {\n+\n+ }\n+ ul.thumbs {\n+\tclear: both;\n+\tmargin: 0;\n+\tpadding: 0;\n+ }\n+ ul.thumbs li {\n+\tfloat: none;\n+\tpadding: 0;\n+\tmargin: 0;\n+ list-style: none;\n+ }\n+ a.thumb {\n+\tpadding: 0;\n+\tdisplay: inline;\n+\tborder: none;\n+ }\n+ ul.thumbs li.selected a.thumb {\n+\tcolor: #000;\n+ font-weight: bold;\n+ }\n+ a.thumb:focus {\n+\toutline: none;\n+ }\n+ ul.thumbs img {\n+\tborder: none;\n+\tdisplay: block;\n+ }\n+ div.pagination {\n+\tclear: both;\n+ }\n+ div.navigation div.top {\n+ margin-bottom: 12px;\n+\theight: 11px;\n+ }\n+ div.navigation div.bottom {\n+ margin-top: 12px;\n+ }\n+ div.pagination a, div.pagination span.current, div.pagination span.ellipsis {\n+\tdisplay: block;\n+\tfloat: left;\n+ margin-right: 2px;\n+\tpadding: 4px 7px 2px 7px;\n+\tborder: 1px solid #ccc;\n+ }\n+ div.pagination a:hover {\n+ background-color: #eee;\n+ text-decoration: none;\n+ }\n+ div.pagination span.current {\n+ font-weight: bold;\n+ background-color: #000;\n+ border-color: #000;\n+\tcolor: #fff;\n+ }\n+ div.pagination span.ellipsis {\n+\tborder: none;\n+\tpadding: 5px 0 3px 2px;\n+ }\n+ \n+ div.download {\n+\tfloat: right;\n+ }\n+ \n+ div.caption-container {\n+\tposition: relative;\n+\tclear: left;\n+\theight: 75px;\n+ }\n+ span.image-caption {\n+\tdisplay: block;\n+\tposition: absolute;\n+\twidth: 550px;\n+\ttop: 0;\n+\tleft: 0;\n+ }\n+ div.caption {\n+\tpadding: 12px;\n+ }\n+\n+ /* Featurettes\n+ ------------------------- */\n+\n+ .featurette {\n+ padding-top: 20px; /* Vertica'..b'ss="icon-bar"></span>\n+ <span class="icon-bar"></span>\n+ <span class="icon-bar"></span>\n+ </button>\n+ <a class="brand" href="report.txt">Report</a>\n+ <div class="nav-collapse collapse">\n+ <ul class="nav">\n+ <li class="active"><a href="reads-sample-small.fastq.html">reads-sample-small.fastq</a></li>\n+ </ul>\n+ </div><!--/.nav-collapse -->\n+ </div>\n+ </div>\n+ </div>\n+ <div class="container">\n+ <div class="featurette">\n+ <h1>transcripts</h1>\n+ <p class="featurette-p">\n+ <A HREF="reads-sample-small.fastq/subgroups/piRNAs//piRNAs-transcripts_reads_counts.txt">read number per transcript (txt)</A><br/> \n+<A HREF="reads-sample-small.fastq/subgroups/piRNAs//piRNAs-transcripts_sorted.bam">transcripts mappers (sorted bam)</A><br/> \n+<A HREF="reads-sample-small.fastq/subgroups/piRNAs//piRNAs-transcripts_unique_sorted.bam">transcripts unique mappers (sorted bam)</A><br/> \n+\n+ </p>\n+ </div>\n+ </div>\n+ \n+ <!-- FOOTER -->\n+ <div class="container">\n+ <footer>\n+ \n+ </footer>\n+ </div>\n+ <!-- Le javascript\n+ ================================================== -->\n+ <!-- Placed at the end of the document so the pages load faster -->\n+ <script type="text/javascript" src="js/filter.js"></script>\n+ <script type="text/javascript" src="js/jquery.js"></script>\n+ <script type="text/javascript" src="js/jquery-1.3.2.js"></script>\n+ <script type="text/javascript" src="js/jquery.galleriffic.js"></script>\n+ <script type="text/javascript" src="js/jquery.opacityrollover.js"></script>\n+ <script type="text/javascript" src="js/bootstrap-table.js"></script>\n+ <script type="text/javascript" src="js/bootstrap.min.js"></script>\n+ <script type="text/javascript">\n+ jQuery(document).ready(function($) {\n+ // We only want these styles applied when javascript is enabled\n+ $(\'div.navigation\').css({\'width\' : \'300px\', \'float\' : \'left\'});\n+ $(\'div.content\').css(\'display\', \'block\');\n+ \n+ $(".each-gallery").each(function(i){\n+ // Initially set opacity on thumbs and add\n+ // additional styling for hover effect on thumbs\n+ var onMouseOutOpacity = 0.67;\n+ $(\'#thumbs + i + ul.thumbs li\').opacityrollover({\n+ mouseOutOpacity: onMouseOutOpacity,\n+ mouseOverOpacity: 1.0,\n+ fadeSpeed: \'fast\',\n+ exemptionSelector: \'.selected\'\n+ });\n+ \n+ // Initialize Advanced Galleriffic Gallery\n+ var gallery = $(\'#thumbs\'+i).galleriffic({\n+ delay: 2500,\n+ numThumbs: 22,\n+ preloadAhead: 10,\n+ enableTopPager: true,\n+ enableBottomPager: true,\n+ maxPagesToShow: 7,\n+ imageContainerSel: \'#slideshow\'+ i,\n+ controlsContainerSel: \'#controls\' + i,\n+ captionContainerSel: \'#caption\' + i,\n+ loadingContainerSel: \'#loading\' + i,\n+ renderSSControls: true,\n+ renderNavControls: true,\n+ playLinkText: \'Play\',\n+ pauseLinkText: \'Pause\',\n+ prevLinkText: \'‹ Previous\',\n+ nextLinkText: \'Next ›\',\n+ nextPageLinkText: \'Next ›\',\n+ prevPageLinkText: \'‹ Prev\',\n+ enableHistory: false,\n+ autoStart: false,\n+ syncTransitions: true,\n+ defaultTransitionDuration: 900,\n+ onSlideChange: function(prevIndex, nextIndex) {\n+ // \'this\' refers to the gallery, which is an extension of $(\'#thumbs\')\n+ this.find(\'ul.thumbs\').children()\n+ .eq(prevIndex).fadeTo(\'fast\', onMouseOutOpacity).end()\n+ .eq(nextIndex).fadeTo(\'fast\', 1.0);\n+ },\n+ onPageTransitionOut: function(callback) {\n+ this.fadeTo(\'fast\', 0.0, callback);\n+ },\n+ onPageTransitionIn: function() {\n+ this.fadeTo(\'fast\', 1.0);\n+ }\n+ });\n+ });\n+ });\n+ </script>\n+ </body>\n+ </html>\n+ \n\\ No newline at end of file\n' |
| b |
| diff -r 9645d995fb3c -r 9185ca0a7b43 test-data/res_files/reads-sample-small.fastq-siRNAs-TEs.html --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/res_files/reads-sample-small.fastq-siRNAs-TEs.html Wed Jan 16 08:18:13 2019 -0500 |
| b |
| b'@@ -0,0 +1,388 @@\n+\n+ <!DOCTYPE html>\n+ <html lang="en">\n+ <head>\n+ <meta charset="utf-8">\n+ <title>pipeline</title>\n+ <meta name="viewport" content="width=device-width, initial-scale=1.0">\n+ <meta name="description" content="">\n+ <meta name="author" content="">\n+ <!-- Le styles -->\n+ <link href="css/bootstrap.css" rel="stylesheet">\n+ <link href="css/bootstrap-table.css" rel="stylesheet">\n+ <style type="text/css">\n+ body {\n+ padding-top: 60px;\n+ padding-bottom: 40px;\n+ }\n+ div#page {\n+ width: 940px;\n+ background-color: #fff;\n+ margin: 0 auto;\n+ text-align: left;\n+ border-color: #fff;\n+ border-style: none solid solid;\n+ border-width: medium 1px 1px;\n+ }\n+\n+ div.content {\n+ \tdisplay: none;\n+\t float: right;\n+\t width: 550px;\n+ }\n+ div.content a, div.navigation a {\n+ text-decoration: none;\n+ \tcolor: #777;\n+ }\n+ div.content a:focus, div.content a:hover, div.content a:active {\n+ text-decoration: underline;\n+ }\n+ \n+ div.controls {\n+ margin-top: 5px;\n+\t height: 23px;\n+ }\n+ \n+ div.controls a {\n+\t padding: 5px;\n+ }\n+ div.ss-controls {\n+\t float: left;\n+ }\n+ div.nav-controls {\n+\t float: right;\n+ }\n+ div.slideshow-container {\n+\t position: relative;\n+\t clear: both;\n+\t height: 502px; /* This should be set to be at least the height of the largest image in the slideshow */\n+ }\n+ div.loader {\n+ \tposition: absolute;\n+ \ttop: 0;\n+ \tleft: 0;\n+ background-image: url(\'loader.gif\');\n+ background-repeat: no-repeat;\n+ background-position: center;\n+ \twidth: 550px;\n+ \theight: 502px; /* This should be set to be at least the height of the largest image in the slideshow */\n+ }\n+ div.slideshow {\n+ \n+ }\n+ \n+ div.slideshow span.image-wrapper {\n+\t display: block;\n+\t position: absolute;\n+\t top: 0;\n+\t left: 0;\n+ }\n+ div.slideshow a.advance-link {\n+\t display: block;\n+ \t width: 550px;\n+ height: 502px; /* This should be set to be at least the height of the largest image in the slideshow */\n+ line-height: 502px; /* This should be set to be at least the height of the largest image in the slideshow */\n+ text-align: center;\n+ }\n+ div.slideshow a.advance-link:hover, div.slideshow a.advance-link:active, div.slideshow a.advance-link:visited {\n+ text-decoration: none;\n+ }\n+ div.slideshow img {\n+ vertical-align: middle;\n+\tborder: 1px solid #ccc;\n+ }\n+\n+ div.image-title {\n+ font-weight: bold;\n+ font-size: 1.4em;\n+ }\n+\n+ div.image-desc {\n+ line-height: 1.3em;\n+ padding-top: 12px;\n+ }\n+ div.navigation {\n+\n+ }\n+ ul.thumbs {\n+\tclear: both;\n+\tmargin: 0;\n+\tpadding: 0;\n+ }\n+ ul.thumbs li {\n+\tfloat: none;\n+\tpadding: 0;\n+\tmargin: 0;\n+ list-style: none;\n+ }\n+ a.thumb {\n+\tpadding: 0;\n+\tdisplay: inline;\n+\tborder: none;\n+ }\n+ ul.thumbs li.selected a.thumb {\n+\tcolor: #000;\n+ font-weight: bold;\n+ }\n+ a.thumb:focus {\n+\toutline: none;\n+ }\n+ ul.thumbs img {\n+\tborder: none;\n+\tdisplay: block;\n+ }\n+ div.pagination {\n+\tclear: both;\n+ }\n+ div.navigation div.top {\n+ margin-bottom: 12px;\n+\theight: 11px;\n+ }\n+ div.navigation div.bottom {\n+ margin-top: 12px;\n+ }\n+ div.pagination a, div.pagination span.current, div.pagination span.ellipsis {\n+\tdisplay: block;\n+\tfloat: left;\n+ margin-right: 2px;\n+\tpadding: 4px 7px 2px 7px;\n+\tborder: 1px solid #ccc;\n+ }\n+ div.pagination a:hover {\n+ background-color: #eee;\n+ text-decoration: none;\n+ }\n+ div.pagination span.current {\n+ font-weight: bold;\n+ background-color: #000;\n+ border-color: #000;\n+\tcolor: #fff;\n+ }\n+ div.pagination span.ellipsis {\n+\tborder: none;\n+\tpadding: 5px 0 3px 2px;\n+ }\n+ \n+ div.download {\n+\tfloat: right;\n+ }\n+ \n+ div.caption-container {\n+\tposition: relative;\n+\tclear: left;\n+\theight: 75px;\n+ }\n+ span.image-caption {\n+\tdisplay: block;\n+\tposition: absolute;\n+\twidth: 550px;\n+\ttop: 0;\n+\tleft: 0;\n+ }\n+ div.caption {\n+\tpadding: 12px;\n+ }\n+\n+ /* Featurettes\n+ ------------------------- */\n+\n+ .featurette {\n+ padding-top: 20px; /* Vertica'..b'sample-small.fastq/subgroups/siRNAs//Gviz_TEs/G6_DM.png" title="G6_DM">G6_DM</a>\n+ </li>\n+ \t\n+ <li>\n+ <a class="thumb" href="reads-sample-small.fastq/subgroups/siRNAs//Gviz_TEs/Gypsy2-LTR_DM.png" title="Gypsy2-LTR_DM">Gypsy2-LTR_DM</a>\n+ </li>\n+ \t\n+ <li>\n+ <a class="thumb" href="reads-sample-small.fastq/subgroups/siRNAs//Gviz_TEs/I_DM.png" title="I_DM">I_DM</a>\n+ </li>\n+ \t\n+ <li>\n+ <a class="thumb" href="reads-sample-small.fastq/subgroups/siRNAs//Gviz_TEs/MAX_I.png" title="MAX_I">MAX_I</a>\n+ </li>\n+ \t\n+ <li>\n+ <a class="thumb" href="reads-sample-small.fastq/subgroups/siRNAs//Gviz_TEs/MAX_LTR.png" title="MAX_LTR">MAX_LTR</a>\n+ </li>\n+ \t\n+ <li>\n+ <a class="thumb" href="reads-sample-small.fastq/subgroups/siRNAs//Gviz_TEs/PROTOP.png" title="PROTOP">PROTOP</a>\n+ </li>\n+ \t\n+ </ul>\n+ </div>\n+ <div style="clear: both;"></div></div>\n+ </div>\n+ </div>\n+ \n+ <!-- FOOTER -->\n+ <div class="container">\n+ <footer>\n+ \n+ </footer>\n+ </div>\n+ <!-- Le javascript\n+ ================================================== -->\n+ <!-- Placed at the end of the document so the pages load faster -->\n+ <script type="text/javascript" src="js/filter.js"></script>\n+ <script type="text/javascript" src="js/jquery.js"></script>\n+ <script type="text/javascript" src="js/jquery-1.3.2.js"></script>\n+ <script type="text/javascript" src="js/jquery.galleriffic.js"></script>\n+ <script type="text/javascript" src="js/jquery.opacityrollover.js"></script>\n+ <script type="text/javascript" src="js/bootstrap-table.js"></script>\n+ <script type="text/javascript" src="js/bootstrap.min.js"></script>\n+ <script type="text/javascript">\n+ jQuery(document).ready(function($) {\n+ // We only want these styles applied when javascript is enabled\n+ $(\'div.navigation\').css({\'width\' : \'300px\', \'float\' : \'left\'});\n+ $(\'div.content\').css(\'display\', \'block\');\n+ \n+ $(".each-gallery").each(function(i){\n+ // Initially set opacity on thumbs and add\n+ // additional styling for hover effect on thumbs\n+ var onMouseOutOpacity = 0.67;\n+ $(\'#thumbs + i + ul.thumbs li\').opacityrollover({\n+ mouseOutOpacity: onMouseOutOpacity,\n+ mouseOverOpacity: 1.0,\n+ fadeSpeed: \'fast\',\n+ exemptionSelector: \'.selected\'\n+ });\n+ \n+ // Initialize Advanced Galleriffic Gallery\n+ var gallery = $(\'#thumbs\'+i).galleriffic({\n+ delay: 2500,\n+ numThumbs: 22,\n+ preloadAhead: 10,\n+ enableTopPager: true,\n+ enableBottomPager: true,\n+ maxPagesToShow: 7,\n+ imageContainerSel: \'#slideshow\'+ i,\n+ controlsContainerSel: \'#controls\' + i,\n+ captionContainerSel: \'#caption\' + i,\n+ loadingContainerSel: \'#loading\' + i,\n+ renderSSControls: true,\n+ renderNavControls: true,\n+ playLinkText: \'Play\',\n+ pauseLinkText: \'Pause\',\n+ prevLinkText: \'‹ Previous\',\n+ nextLinkText: \'Next ›\',\n+ nextPageLinkText: \'Next ›\',\n+ prevPageLinkText: \'‹ Prev\',\n+ enableHistory: false,\n+ autoStart: false,\n+ syncTransitions: true,\n+ defaultTransitionDuration: 900,\n+ onSlideChange: function(prevIndex, nextIndex) {\n+ // \'this\' refers to the gallery, which is an extension of $(\'#thumbs\')\n+ this.find(\'ul.thumbs\').children()\n+ .eq(prevIndex).fadeTo(\'fast\', onMouseOutOpacity).end()\n+ .eq(nextIndex).fadeTo(\'fast\', 1.0);\n+ },\n+ onPageTransitionOut: function(callback) {\n+ this.fadeTo(\'fast\', 0.0, callback);\n+ },\n+ onPageTransitionIn: function() {\n+ this.fadeTo(\'fast\', 1.0);\n+ }\n+ });\n+ });\n+ });\n+ </script>\n+ </body>\n+ </html>\n+ \n\\ No newline at end of file\n' |
| b |
| diff -r 9645d995fb3c -r 9185ca0a7b43 test-data/res_files/reads-sample-small.fastq-siRNAs-genome.html --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/res_files/reads-sample-small.fastq-siRNAs-genome.html Wed Jan 16 08:18:13 2019 -0500 |
| b |
| b'@@ -0,0 +1,397 @@\n+\n+ <!DOCTYPE html>\n+ <html lang="en">\n+ <head>\n+ <meta charset="utf-8">\n+ <title>pipeline</title>\n+ <meta name="viewport" content="width=device-width, initial-scale=1.0">\n+ <meta name="description" content="">\n+ <meta name="author" content="">\n+ <!-- Le styles -->\n+ <link href="css/bootstrap.css" rel="stylesheet">\n+ <link href="css/bootstrap-table.css" rel="stylesheet">\n+ <style type="text/css">\n+ body {\n+ padding-top: 60px;\n+ padding-bottom: 40px;\n+ }\n+ div#page {\n+ width: 940px;\n+ background-color: #fff;\n+ margin: 0 auto;\n+ text-align: left;\n+ border-color: #fff;\n+ border-style: none solid solid;\n+ border-width: medium 1px 1px;\n+ }\n+\n+ div.content {\n+ \tdisplay: none;\n+\t float: right;\n+\t width: 550px;\n+ }\n+ div.content a, div.navigation a {\n+ text-decoration: none;\n+ \tcolor: #777;\n+ }\n+ div.content a:focus, div.content a:hover, div.content a:active {\n+ text-decoration: underline;\n+ }\n+ \n+ div.controls {\n+ margin-top: 5px;\n+\t height: 23px;\n+ }\n+ \n+ div.controls a {\n+\t padding: 5px;\n+ }\n+ div.ss-controls {\n+\t float: left;\n+ }\n+ div.nav-controls {\n+\t float: right;\n+ }\n+ div.slideshow-container {\n+\t position: relative;\n+\t clear: both;\n+\t height: 502px; /* This should be set to be at least the height of the largest image in the slideshow */\n+ }\n+ div.loader {\n+ \tposition: absolute;\n+ \ttop: 0;\n+ \tleft: 0;\n+ background-image: url(\'loader.gif\');\n+ background-repeat: no-repeat;\n+ background-position: center;\n+ \twidth: 550px;\n+ \theight: 502px; /* This should be set to be at least the height of the largest image in the slideshow */\n+ }\n+ div.slideshow {\n+ \n+ }\n+ \n+ div.slideshow span.image-wrapper {\n+\t display: block;\n+\t position: absolute;\n+\t top: 0;\n+\t left: 0;\n+ }\n+ div.slideshow a.advance-link {\n+\t display: block;\n+ \t width: 550px;\n+ height: 502px; /* This should be set to be at least the height of the largest image in the slideshow */\n+ line-height: 502px; /* This should be set to be at least the height of the largest image in the slideshow */\n+ text-align: center;\n+ }\n+ div.slideshow a.advance-link:hover, div.slideshow a.advance-link:active, div.slideshow a.advance-link:visited {\n+ text-decoration: none;\n+ }\n+ div.slideshow img {\n+ vertical-align: middle;\n+\tborder: 1px solid #ccc;\n+ }\n+\n+ div.image-title {\n+ font-weight: bold;\n+ font-size: 1.4em;\n+ }\n+\n+ div.image-desc {\n+ line-height: 1.3em;\n+ padding-top: 12px;\n+ }\n+ div.navigation {\n+\n+ }\n+ ul.thumbs {\n+\tclear: both;\n+\tmargin: 0;\n+\tpadding: 0;\n+ }\n+ ul.thumbs li {\n+\tfloat: none;\n+\tpadding: 0;\n+\tmargin: 0;\n+ list-style: none;\n+ }\n+ a.thumb {\n+\tpadding: 0;\n+\tdisplay: inline;\n+\tborder: none;\n+ }\n+ ul.thumbs li.selected a.thumb {\n+\tcolor: #000;\n+ font-weight: bold;\n+ }\n+ a.thumb:focus {\n+\toutline: none;\n+ }\n+ ul.thumbs img {\n+\tborder: none;\n+\tdisplay: block;\n+ }\n+ div.pagination {\n+\tclear: both;\n+ }\n+ div.navigation div.top {\n+ margin-bottom: 12px;\n+\theight: 11px;\n+ }\n+ div.navigation div.bottom {\n+ margin-top: 12px;\n+ }\n+ div.pagination a, div.pagination span.current, div.pagination span.ellipsis {\n+\tdisplay: block;\n+\tfloat: left;\n+ margin-right: 2px;\n+\tpadding: 4px 7px 2px 7px;\n+\tborder: 1px solid #ccc;\n+ }\n+ div.pagination a:hover {\n+ background-color: #eee;\n+ text-decoration: none;\n+ }\n+ div.pagination span.current {\n+ font-weight: bold;\n+ background-color: #000;\n+ border-color: #000;\n+\tcolor: #fff;\n+ }\n+ div.pagination span.ellipsis {\n+\tborder: none;\n+\tpadding: 5px 0 3px 2px;\n+ }\n+ \n+ div.download {\n+\tfloat: right;\n+ }\n+ \n+ div.caption-container {\n+\tposition: relative;\n+\tclear: left;\n+\theight: 75px;\n+ }\n+ span.image-caption {\n+\tdisplay: block;\n+\tposition: absolute;\n+\twidth: 550px;\n+\ttop: 0;\n+\tleft: 0;\n+ }\n+ div.caption {\n+\tpadding: 12px;\n+ }\n+\n+ /* Featurettes\n+ ------------------------- */\n+\n+ .featurette {\n+ padding-top: 20px; /* Vertica'..b'ass="thumb" href="reads-sample-small.fastq/subgroups/siRNAs//Gviz_genome/rand/chrom_1.png" title="chrom_1">chrom_1</a>\n+ </li>\n+ \n+ <li>\n+ <a class="thumb" href="reads-sample-small.fastq/subgroups/siRNAs//Gviz_genome/rand/chrom_2.png" title="chrom_2">chrom_2</a>\n+ </li>\n+ \n+ <li>\n+ <a class="thumb" href="reads-sample-small.fastq/subgroups/siRNAs//Gviz_genome/rand/chrom_4.png" title="chrom_4">chrom_4</a>\n+ </li>\n+ \n+ <li>\n+ <a class="thumb" href="reads-sample-small.fastq/subgroups/siRNAs//Gviz_genome/rand/chrom_5.png" title="chrom_5">chrom_5</a>\n+ </li>\n+ \n+ <li>\n+ <a class="thumb" href="reads-sample-small.fastq/subgroups/siRNAs//Gviz_genome/rand/chrom_6.png" title="chrom_6">chrom_6</a>\n+ </li>\n+ \n+ </ul>\n+ </div>\n+ <div style="clear: both;"></div></div>\n+ </div>\n+ </div>\n+ \n+ <!-- FOOTER -->\n+ <div class="container">\n+ <footer>\n+ \n+ </footer>\n+ </div>\n+ <!-- Le javascript\n+ ================================================== -->\n+ <!-- Placed at the end of the document so the pages load faster -->\n+ <script type="text/javascript" src="js/filter.js"></script>\n+ <script type="text/javascript" src="js/jquery.js"></script>\n+ <script type="text/javascript" src="js/jquery-1.3.2.js"></script>\n+ <script type="text/javascript" src="js/jquery.galleriffic.js"></script>\n+ <script type="text/javascript" src="js/jquery.opacityrollover.js"></script>\n+ <script type="text/javascript" src="js/bootstrap-table.js"></script>\n+ <script type="text/javascript" src="js/bootstrap.min.js"></script>\n+ <script type="text/javascript">\n+ jQuery(document).ready(function($) {\n+ // We only want these styles applied when javascript is enabled\n+ $(\'div.navigation\').css({\'width\' : \'300px\', \'float\' : \'left\'});\n+ $(\'div.content\').css(\'display\', \'block\');\n+ \n+ $(".each-gallery").each(function(i){\n+ // Initially set opacity on thumbs and add\n+ // additional styling for hover effect on thumbs\n+ var onMouseOutOpacity = 0.67;\n+ $(\'#thumbs + i + ul.thumbs li\').opacityrollover({\n+ mouseOutOpacity: onMouseOutOpacity,\n+ mouseOverOpacity: 1.0,\n+ fadeSpeed: \'fast\',\n+ exemptionSelector: \'.selected\'\n+ });\n+ \n+ // Initialize Advanced Galleriffic Gallery\n+ var gallery = $(\'#thumbs\'+i).galleriffic({\n+ delay: 2500,\n+ numThumbs: 22,\n+ preloadAhead: 10,\n+ enableTopPager: true,\n+ enableBottomPager: true,\n+ maxPagesToShow: 7,\n+ imageContainerSel: \'#slideshow\'+ i,\n+ controlsContainerSel: \'#controls\' + i,\n+ captionContainerSel: \'#caption\' + i,\n+ loadingContainerSel: \'#loading\' + i,\n+ renderSSControls: true,\n+ renderNavControls: true,\n+ playLinkText: \'Play\',\n+ pauseLinkText: \'Pause\',\n+ prevLinkText: \'‹ Previous\',\n+ nextLinkText: \'Next ›\',\n+ nextPageLinkText: \'Next ›\',\n+ prevPageLinkText: \'‹ Prev\',\n+ enableHistory: false,\n+ autoStart: false,\n+ syncTransitions: true,\n+ defaultTransitionDuration: 900,\n+ onSlideChange: function(prevIndex, nextIndex) {\n+ // \'this\' refers to the gallery, which is an extension of $(\'#thumbs\')\n+ this.find(\'ul.thumbs\').children()\n+ .eq(prevIndex).fadeTo(\'fast\', onMouseOutOpacity).end()\n+ .eq(nextIndex).fadeTo(\'fast\', 1.0);\n+ },\n+ onPageTransitionOut: function(callback) {\n+ this.fadeTo(\'fast\', 0.0, callback);\n+ },\n+ onPageTransitionIn: function() {\n+ this.fadeTo(\'fast\', 1.0);\n+ }\n+ });\n+ });\n+ });\n+ </script>\n+ </body>\n+ </html>\n+ \n\\ No newline at end of file\n' |
| b |
| diff -r 9645d995fb3c -r 9185ca0a7b43 test-data/res_files/reads-sample-small.fastq-siRNAs-transcripts.html --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/res_files/reads-sample-small.fastq-siRNAs-transcripts.html Wed Jan 16 08:18:13 2019 -0500 |
| b |
| b'@@ -0,0 +1,315 @@\n+\n+ <!DOCTYPE html>\n+ <html lang="en">\n+ <head>\n+ <meta charset="utf-8">\n+ <title>pipeline</title>\n+ <meta name="viewport" content="width=device-width, initial-scale=1.0">\n+ <meta name="description" content="">\n+ <meta name="author" content="">\n+ <!-- Le styles -->\n+ <link href="css/bootstrap.css" rel="stylesheet">\n+ <link href="css/bootstrap-table.css" rel="stylesheet">\n+ <style type="text/css">\n+ body {\n+ padding-top: 60px;\n+ padding-bottom: 40px;\n+ }\n+ div#page {\n+ width: 940px;\n+ background-color: #fff;\n+ margin: 0 auto;\n+ text-align: left;\n+ border-color: #fff;\n+ border-style: none solid solid;\n+ border-width: medium 1px 1px;\n+ }\n+\n+ div.content {\n+ \tdisplay: none;\n+\t float: right;\n+\t width: 550px;\n+ }\n+ div.content a, div.navigation a {\n+ text-decoration: none;\n+ \tcolor: #777;\n+ }\n+ div.content a:focus, div.content a:hover, div.content a:active {\n+ text-decoration: underline;\n+ }\n+ \n+ div.controls {\n+ margin-top: 5px;\n+\t height: 23px;\n+ }\n+ \n+ div.controls a {\n+\t padding: 5px;\n+ }\n+ div.ss-controls {\n+\t float: left;\n+ }\n+ div.nav-controls {\n+\t float: right;\n+ }\n+ div.slideshow-container {\n+\t position: relative;\n+\t clear: both;\n+\t height: 502px; /* This should be set to be at least the height of the largest image in the slideshow */\n+ }\n+ div.loader {\n+ \tposition: absolute;\n+ \ttop: 0;\n+ \tleft: 0;\n+ background-image: url(\'loader.gif\');\n+ background-repeat: no-repeat;\n+ background-position: center;\n+ \twidth: 550px;\n+ \theight: 502px; /* This should be set to be at least the height of the largest image in the slideshow */\n+ }\n+ div.slideshow {\n+ \n+ }\n+ \n+ div.slideshow span.image-wrapper {\n+\t display: block;\n+\t position: absolute;\n+\t top: 0;\n+\t left: 0;\n+ }\n+ div.slideshow a.advance-link {\n+\t display: block;\n+ \t width: 550px;\n+ height: 502px; /* This should be set to be at least the height of the largest image in the slideshow */\n+ line-height: 502px; /* This should be set to be at least the height of the largest image in the slideshow */\n+ text-align: center;\n+ }\n+ div.slideshow a.advance-link:hover, div.slideshow a.advance-link:active, div.slideshow a.advance-link:visited {\n+ text-decoration: none;\n+ }\n+ div.slideshow img {\n+ vertical-align: middle;\n+\tborder: 1px solid #ccc;\n+ }\n+\n+ div.image-title {\n+ font-weight: bold;\n+ font-size: 1.4em;\n+ }\n+\n+ div.image-desc {\n+ line-height: 1.3em;\n+ padding-top: 12px;\n+ }\n+ div.navigation {\n+\n+ }\n+ ul.thumbs {\n+\tclear: both;\n+\tmargin: 0;\n+\tpadding: 0;\n+ }\n+ ul.thumbs li {\n+\tfloat: none;\n+\tpadding: 0;\n+\tmargin: 0;\n+ list-style: none;\n+ }\n+ a.thumb {\n+\tpadding: 0;\n+\tdisplay: inline;\n+\tborder: none;\n+ }\n+ ul.thumbs li.selected a.thumb {\n+\tcolor: #000;\n+ font-weight: bold;\n+ }\n+ a.thumb:focus {\n+\toutline: none;\n+ }\n+ ul.thumbs img {\n+\tborder: none;\n+\tdisplay: block;\n+ }\n+ div.pagination {\n+\tclear: both;\n+ }\n+ div.navigation div.top {\n+ margin-bottom: 12px;\n+\theight: 11px;\n+ }\n+ div.navigation div.bottom {\n+ margin-top: 12px;\n+ }\n+ div.pagination a, div.pagination span.current, div.pagination span.ellipsis {\n+\tdisplay: block;\n+\tfloat: left;\n+ margin-right: 2px;\n+\tpadding: 4px 7px 2px 7px;\n+\tborder: 1px solid #ccc;\n+ }\n+ div.pagination a:hover {\n+ background-color: #eee;\n+ text-decoration: none;\n+ }\n+ div.pagination span.current {\n+ font-weight: bold;\n+ background-color: #000;\n+ border-color: #000;\n+\tcolor: #fff;\n+ }\n+ div.pagination span.ellipsis {\n+\tborder: none;\n+\tpadding: 5px 0 3px 2px;\n+ }\n+ \n+ div.download {\n+\tfloat: right;\n+ }\n+ \n+ div.caption-container {\n+\tposition: relative;\n+\tclear: left;\n+\theight: 75px;\n+ }\n+ span.image-caption {\n+\tdisplay: block;\n+\tposition: absolute;\n+\twidth: 550px;\n+\ttop: 0;\n+\tleft: 0;\n+ }\n+ div.caption {\n+\tpadding: 12px;\n+ }\n+\n+ /* Featurettes\n+ ------------------------- */\n+\n+ .featurette {\n+ padding-top: 20px; /* Vertica'..b'ss="icon-bar"></span>\n+ <span class="icon-bar"></span>\n+ <span class="icon-bar"></span>\n+ </button>\n+ <a class="brand" href="report.txt">Report</a>\n+ <div class="nav-collapse collapse">\n+ <ul class="nav">\n+ <li class="active"><a href="reads-sample-small.fastq.html">reads-sample-small.fastq</a></li>\n+ </ul>\n+ </div><!--/.nav-collapse -->\n+ </div>\n+ </div>\n+ </div>\n+ <div class="container">\n+ <div class="featurette">\n+ <h1>transcripts</h1>\n+ <p class="featurette-p">\n+ <A HREF="reads-sample-small.fastq/subgroups/siRNAs//siRNAs-transcripts_reads_counts.txt">read number per transcript (txt)</A><br/> \n+<A HREF="reads-sample-small.fastq/subgroups/siRNAs//siRNAs-transcripts_sorted.bam">transcripts mappers (sorted bam)</A><br/> \n+<A HREF="reads-sample-small.fastq/subgroups/siRNAs//siRNAs-transcripts_unique_sorted.bam">transcripts unique mappers (sorted bam)</A><br/> \n+\n+ </p>\n+ </div>\n+ </div>\n+ \n+ <!-- FOOTER -->\n+ <div class="container">\n+ <footer>\n+ \n+ </footer>\n+ </div>\n+ <!-- Le javascript\n+ ================================================== -->\n+ <!-- Placed at the end of the document so the pages load faster -->\n+ <script type="text/javascript" src="js/filter.js"></script>\n+ <script type="text/javascript" src="js/jquery.js"></script>\n+ <script type="text/javascript" src="js/jquery-1.3.2.js"></script>\n+ <script type="text/javascript" src="js/jquery.galleriffic.js"></script>\n+ <script type="text/javascript" src="js/jquery.opacityrollover.js"></script>\n+ <script type="text/javascript" src="js/bootstrap-table.js"></script>\n+ <script type="text/javascript" src="js/bootstrap.min.js"></script>\n+ <script type="text/javascript">\n+ jQuery(document).ready(function($) {\n+ // We only want these styles applied when javascript is enabled\n+ $(\'div.navigation\').css({\'width\' : \'300px\', \'float\' : \'left\'});\n+ $(\'div.content\').css(\'display\', \'block\');\n+ \n+ $(".each-gallery").each(function(i){\n+ // Initially set opacity on thumbs and add\n+ // additional styling for hover effect on thumbs\n+ var onMouseOutOpacity = 0.67;\n+ $(\'#thumbs + i + ul.thumbs li\').opacityrollover({\n+ mouseOutOpacity: onMouseOutOpacity,\n+ mouseOverOpacity: 1.0,\n+ fadeSpeed: \'fast\',\n+ exemptionSelector: \'.selected\'\n+ });\n+ \n+ // Initialize Advanced Galleriffic Gallery\n+ var gallery = $(\'#thumbs\'+i).galleriffic({\n+ delay: 2500,\n+ numThumbs: 22,\n+ preloadAhead: 10,\n+ enableTopPager: true,\n+ enableBottomPager: true,\n+ maxPagesToShow: 7,\n+ imageContainerSel: \'#slideshow\'+ i,\n+ controlsContainerSel: \'#controls\' + i,\n+ captionContainerSel: \'#caption\' + i,\n+ loadingContainerSel: \'#loading\' + i,\n+ renderSSControls: true,\n+ renderNavControls: true,\n+ playLinkText: \'Play\',\n+ pauseLinkText: \'Pause\',\n+ prevLinkText: \'‹ Previous\',\n+ nextLinkText: \'Next ›\',\n+ nextPageLinkText: \'Next ›\',\n+ prevPageLinkText: \'‹ Prev\',\n+ enableHistory: false,\n+ autoStart: false,\n+ syncTransitions: true,\n+ defaultTransitionDuration: 900,\n+ onSlideChange: function(prevIndex, nextIndex) {\n+ // \'this\' refers to the gallery, which is an extension of $(\'#thumbs\')\n+ this.find(\'ul.thumbs\').children()\n+ .eq(prevIndex).fadeTo(\'fast\', onMouseOutOpacity).end()\n+ .eq(nextIndex).fadeTo(\'fast\', 1.0);\n+ },\n+ onPageTransitionOut: function(callback) {\n+ this.fadeTo(\'fast\', 0.0, callback);\n+ },\n+ onPageTransitionIn: function() {\n+ this.fadeTo(\'fast\', 1.0);\n+ }\n+ });\n+ });\n+ });\n+ </script>\n+ </body>\n+ </html>\n+ \n\\ No newline at end of file\n' |
| b |
| diff -r 9645d995fb3c -r 9185ca0a7b43 test-data/res_files/reads-sample-small.fastq-sub.html --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/res_files/reads-sample-small.fastq-sub.html Wed Jan 16 08:18:13 2019 -0500 |
| b |
| b'@@ -0,0 +1,339 @@\n+\n+ <!DOCTYPE html>\n+ <html lang="en">\n+ <head>\n+ <meta charset="utf-8">\n+ <title>pipeline</title>\n+ <meta name="viewport" content="width=device-width, initial-scale=1.0">\n+ <meta name="description" content="">\n+ <meta name="author" content="">\n+ <!-- Le styles -->\n+ <link href="css/bootstrap.css" rel="stylesheet">\n+ <link href="css/bootstrap-table.css" rel="stylesheet">\n+ <style type="text/css">\n+ body {\n+ padding-top: 60px;\n+ padding-bottom: 40px;\n+ }\n+ div#page {\n+ width: 940px;\n+ background-color: #fff;\n+ margin: 0 auto;\n+ text-align: left;\n+ border-color: #fff;\n+ border-style: none solid solid;\n+ border-width: medium 1px 1px;\n+ }\n+\n+ div.content {\n+ \tdisplay: none;\n+\t float: right;\n+\t width: 550px;\n+ }\n+ div.content a, div.navigation a {\n+ text-decoration: none;\n+ \tcolor: #777;\n+ }\n+ div.content a:focus, div.content a:hover, div.content a:active {\n+ text-decoration: underline;\n+ }\n+ \n+ div.controls {\n+ margin-top: 5px;\n+\t height: 23px;\n+ }\n+ \n+ div.controls a {\n+\t padding: 5px;\n+ }\n+ div.ss-controls {\n+\t float: left;\n+ }\n+ div.nav-controls {\n+\t float: right;\n+ }\n+ div.slideshow-container {\n+\t position: relative;\n+\t clear: both;\n+\t height: 502px; /* This should be set to be at least the height of the largest image in the slideshow */\n+ }\n+ div.loader {\n+ \tposition: absolute;\n+ \ttop: 0;\n+ \tleft: 0;\n+ background-image: url(\'loader.gif\');\n+ background-repeat: no-repeat;\n+ background-position: center;\n+ \twidth: 550px;\n+ \theight: 502px; /* This should be set to be at least the height of the largest image in the slideshow */\n+ }\n+ div.slideshow {\n+ \n+ }\n+ \n+ div.slideshow span.image-wrapper {\n+\t display: block;\n+\t position: absolute;\n+\t top: 0;\n+\t left: 0;\n+ }\n+ div.slideshow a.advance-link {\n+\t display: block;\n+ \t width: 550px;\n+ height: 502px; /* This should be set to be at least the height of the largest image in the slideshow */\n+ line-height: 502px; /* This should be set to be at least the height of the largest image in the slideshow */\n+ text-align: center;\n+ }\n+ div.slideshow a.advance-link:hover, div.slideshow a.advance-link:active, div.slideshow a.advance-link:visited {\n+ text-decoration: none;\n+ }\n+ div.slideshow img {\n+ vertical-align: middle;\n+\tborder: 1px solid #ccc;\n+ }\n+\n+ div.image-title {\n+ font-weight: bold;\n+ font-size: 1.4em;\n+ }\n+\n+ div.image-desc {\n+ line-height: 1.3em;\n+ padding-top: 12px;\n+ }\n+ div.navigation {\n+\n+ }\n+ ul.thumbs {\n+\tclear: both;\n+\tmargin: 0;\n+\tpadding: 0;\n+ }\n+ ul.thumbs li {\n+\tfloat: none;\n+\tpadding: 0;\n+\tmargin: 0;\n+ list-style: none;\n+ }\n+ a.thumb {\n+\tpadding: 0;\n+\tdisplay: inline;\n+\tborder: none;\n+ }\n+ ul.thumbs li.selected a.thumb {\n+\tcolor: #000;\n+ font-weight: bold;\n+ }\n+ a.thumb:focus {\n+\toutline: none;\n+ }\n+ ul.thumbs img {\n+\tborder: none;\n+\tdisplay: block;\n+ }\n+ div.pagination {\n+\tclear: both;\n+ }\n+ div.navigation div.top {\n+ margin-bottom: 12px;\n+\theight: 11px;\n+ }\n+ div.navigation div.bottom {\n+ margin-top: 12px;\n+ }\n+ div.pagination a, div.pagination span.current, div.pagination span.ellipsis {\n+\tdisplay: block;\n+\tfloat: left;\n+ margin-right: 2px;\n+\tpadding: 4px 7px 2px 7px;\n+\tborder: 1px solid #ccc;\n+ }\n+ div.pagination a:hover {\n+ background-color: #eee;\n+ text-decoration: none;\n+ }\n+ div.pagination span.current {\n+ font-weight: bold;\n+ background-color: #000;\n+ border-color: #000;\n+\tcolor: #fff;\n+ }\n+ div.pagination span.ellipsis {\n+\tborder: none;\n+\tpadding: 5px 0 3px 2px;\n+ }\n+ \n+ div.download {\n+\tfloat: right;\n+ }\n+ \n+ div.caption-container {\n+\tposition: relative;\n+\tclear: left;\n+\theight: 75px;\n+ }\n+ span.image-caption {\n+\tdisplay: block;\n+\tposition: absolute;\n+\twidth: 550px;\n+\ttop: 0;\n+\tleft: 0;\n+ }\n+ div.caption {\n+\tpadding: 12px;\n+ }\n+\n+ /* Featurettes\n+ ------------------------- */\n+\n+ .featurette {\n+ padding-top: 20px; /* Vertica'..b' <p><a class="btn" href="reads-sample-small.fastq-piRNAs-genome.html">Genome</a></p>\n+ <p><a class="btn" href="reads-sample-small.fastq-piRNAs-TEs.html">TE</a></p>\n+ <p><a class="btn" href="reads-sample-small.fastq-piRNAs-transcripts.html">Transcripts</a></p>\n+ </div>\n+ </div>\n+ </div>\n+ <div class="span6">\n+ <h2>miRNAs</h2>\n+ <p><a class="btn" href="reads-sample-small.fastq-miRNAs-genome.html">Genome</a></p>\n+ <p><a class="btn" href="reads-sample-small.fastq-miRNAs-TEs.html">TE</a></p>\n+ <p><a class="btn" href="reads-sample-small.fastq-miRNAs-transcripts.html">Transcripts</a></p>\n+ </div>\n+ </div>\n+</div>\n+ <div class="container"> <div class="row text-center"> <img src="reads-sample-small.fastq/subgroups//pie_chart.png"/><br />\n+ <A HREF="reads-sample-small.fastq/subgroups//repartition.txt">text file</A><br/>\n+ </div></div>\n+ <!-- FOOTER -->\n+ <div class="container">\n+ <footer>\n+ \n+ </footer>\n+ </div>\n+ <!-- Le javascript\n+ ================================================== -->\n+ <!-- Placed at the end of the document so the pages load faster -->\n+ <script type="text/javascript" src="js/filter.js"></script>\n+ <script type="text/javascript" src="js/jquery.js"></script>\n+ <script type="text/javascript" src="js/jquery-1.3.2.js"></script>\n+ <script type="text/javascript" src="js/jquery.galleriffic.js"></script>\n+ <script type="text/javascript" src="js/jquery.opacityrollover.js"></script>\n+ <script type="text/javascript" src="js/bootstrap-table.js"></script>\n+ <script type="text/javascript" src="js/bootstrap.min.js"></script>\n+ <script type="text/javascript">\n+ jQuery(document).ready(function($) {\n+ // We only want these styles applied when javascript is enabled\n+ $(\'div.navigation\').css({\'width\' : \'300px\', \'float\' : \'left\'});\n+ $(\'div.content\').css(\'display\', \'block\');\n+ \n+ $(".each-gallery").each(function(i){\n+ // Initially set opacity on thumbs and add\n+ // additional styling for hover effect on thumbs\n+ var onMouseOutOpacity = 0.67;\n+ $(\'#thumbs + i + ul.thumbs li\').opacityrollover({\n+ mouseOutOpacity: onMouseOutOpacity,\n+ mouseOverOpacity: 1.0,\n+ fadeSpeed: \'fast\',\n+ exemptionSelector: \'.selected\'\n+ });\n+ \n+ // Initialize Advanced Galleriffic Gallery\n+ var gallery = $(\'#thumbs\'+i).galleriffic({\n+ delay: 2500,\n+ numThumbs: 22,\n+ preloadAhead: 10,\n+ enableTopPager: true,\n+ enableBottomPager: true,\n+ maxPagesToShow: 7,\n+ imageContainerSel: \'#slideshow\'+ i,\n+ controlsContainerSel: \'#controls\' + i,\n+ captionContainerSel: \'#caption\' + i,\n+ loadingContainerSel: \'#loading\' + i,\n+ renderSSControls: true,\n+ renderNavControls: true,\n+ playLinkText: \'Play\',\n+ pauseLinkText: \'Pause\',\n+ prevLinkText: \'‹ Previous\',\n+ nextLinkText: \'Next ›\',\n+ nextPageLinkText: \'Next ›\',\n+ prevPageLinkText: \'‹ Prev\',\n+ enableHistory: false,\n+ autoStart: false,\n+ syncTransitions: true,\n+ defaultTransitionDuration: 900,\n+ onSlideChange: function(prevIndex, nextIndex) {\n+ // \'this\' refers to the gallery, which is an extension of $(\'#thumbs\')\n+ this.find(\'ul.thumbs\').children()\n+ .eq(prevIndex).fadeTo(\'fast\', onMouseOutOpacity).end()\n+ .eq(nextIndex).fadeTo(\'fast\', 1.0);\n+ },\n+ onPageTransitionOut: function(callback) {\n+ this.fadeTo(\'fast\', 0.0, callback);\n+ },\n+ onPageTransitionIn: function() {\n+ this.fadeTo(\'fast\', 1.0);\n+ }\n+ });\n+ });\n+ });\n+ </script>\n+ </body>\n+ </html>\n+ \n\\ No newline at end of file\n' |
| b |
| diff -r 9645d995fb3c -r 9185ca0a7b43 test-data/res_files/reads-sample-small.fastq.html --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/res_files/reads-sample-small.fastq.html Wed Jan 16 08:18:13 2019 -0500 |
| b |
| b'@@ -0,0 +1,411 @@\n+\n+ <!DOCTYPE html>\n+ <html lang="en">\n+ <head>\n+ <meta charset="utf-8">\n+ <title>pipeline</title>\n+ <meta name="viewport" content="width=device-width, initial-scale=1.0">\n+ <meta name="description" content="">\n+ <meta name="author" content="">\n+ <!-- Le styles -->\n+ <link href="css/bootstrap.css" rel="stylesheet">\n+ <link href="css/bootstrap-table.css" rel="stylesheet">\n+ <style type="text/css">\n+ body {\n+ padding-top: 60px;\n+ padding-bottom: 40px;\n+ }\n+ div#page {\n+ width: 940px;\n+ background-color: #fff;\n+ margin: 0 auto;\n+ text-align: left;\n+ border-color: #fff;\n+ border-style: none solid solid;\n+ border-width: medium 1px 1px;\n+ }\n+\n+ div.content {\n+ \tdisplay: none;\n+\t float: right;\n+\t width: 550px;\n+ }\n+ div.content a, div.navigation a {\n+ text-decoration: none;\n+ \tcolor: #777;\n+ }\n+ div.content a:focus, div.content a:hover, div.content a:active {\n+ text-decoration: underline;\n+ }\n+ \n+ div.controls {\n+ margin-top: 5px;\n+\t height: 23px;\n+ }\n+ \n+ div.controls a {\n+\t padding: 5px;\n+ }\n+ div.ss-controls {\n+\t float: left;\n+ }\n+ div.nav-controls {\n+\t float: right;\n+ }\n+ div.slideshow-container {\n+\t position: relative;\n+\t clear: both;\n+\t height: 502px; /* This should be set to be at least the height of the largest image in the slideshow */\n+ }\n+ div.loader {\n+ \tposition: absolute;\n+ \ttop: 0;\n+ \tleft: 0;\n+ background-image: url(\'loader.gif\');\n+ background-repeat: no-repeat;\n+ background-position: center;\n+ \twidth: 550px;\n+ \theight: 502px; /* This should be set to be at least the height of the largest image in the slideshow */\n+ }\n+ div.slideshow {\n+ \n+ }\n+ \n+ div.slideshow span.image-wrapper {\n+\t display: block;\n+\t position: absolute;\n+\t top: 0;\n+\t left: 0;\n+ }\n+ div.slideshow a.advance-link {\n+\t display: block;\n+ \t width: 550px;\n+ height: 502px; /* This should be set to be at least the height of the largest image in the slideshow */\n+ line-height: 502px; /* This should be set to be at least the height of the largest image in the slideshow */\n+ text-align: center;\n+ }\n+ div.slideshow a.advance-link:hover, div.slideshow a.advance-link:active, div.slideshow a.advance-link:visited {\n+ text-decoration: none;\n+ }\n+ div.slideshow img {\n+ vertical-align: middle;\n+\tborder: 1px solid #ccc;\n+ }\n+\n+ div.image-title {\n+ font-weight: bold;\n+ font-size: 1.4em;\n+ }\n+\n+ div.image-desc {\n+ line-height: 1.3em;\n+ padding-top: 12px;\n+ }\n+ div.navigation {\n+\n+ }\n+ ul.thumbs {\n+\tclear: both;\n+\tmargin: 0;\n+\tpadding: 0;\n+ }\n+ ul.thumbs li {\n+\tfloat: none;\n+\tpadding: 0;\n+\tmargin: 0;\n+ list-style: none;\n+ }\n+ a.thumb {\n+\tpadding: 0;\n+\tdisplay: inline;\n+\tborder: none;\n+ }\n+ ul.thumbs li.selected a.thumb {\n+\tcolor: #000;\n+ font-weight: bold;\n+ }\n+ a.thumb:focus {\n+\toutline: none;\n+ }\n+ ul.thumbs img {\n+\tborder: none;\n+\tdisplay: block;\n+ }\n+ div.pagination {\n+\tclear: both;\n+ }\n+ div.navigation div.top {\n+ margin-bottom: 12px;\n+\theight: 11px;\n+ }\n+ div.navigation div.bottom {\n+ margin-top: 12px;\n+ }\n+ div.pagination a, div.pagination span.current, div.pagination span.ellipsis {\n+\tdisplay: block;\n+\tfloat: left;\n+ margin-right: 2px;\n+\tpadding: 4px 7px 2px 7px;\n+\tborder: 1px solid #ccc;\n+ }\n+ div.pagination a:hover {\n+ background-color: #eee;\n+ text-decoration: none;\n+ }\n+ div.pagination span.current {\n+ font-weight: bold;\n+ background-color: #000;\n+ border-color: #000;\n+\tcolor: #fff;\n+ }\n+ div.pagination span.ellipsis {\n+\tborder: none;\n+\tpadding: 5px 0 3px 2px;\n+ }\n+ \n+ div.download {\n+\tfloat: right;\n+ }\n+ \n+ div.caption-container {\n+\tposition: relative;\n+\tclear: left;\n+\theight: 75px;\n+ }\n+ span.image-caption {\n+\tdisplay: block;\n+\tposition: absolute;\n+\twidth: 550px;\n+\ttop: 0;\n+\tleft: 0;\n+ }\n+ div.caption {\n+\tpadding: 12px;\n+ }\n+\n+ /* Featurettes\n+ ------------------------- */\n+\n+ .featurette {\n+ padding-top: 20px; /* Vertica'..b'ng" title="chrom_1">chrom_1</a>\n+ </li>\n+ \n+ <li>\n+ <a class="thumb" href="reads-sample-small.fastq/genome//Gviz/rand/chrom_2.png" title="chrom_2">chrom_2</a>\n+ </li>\n+ \n+ <li>\n+ <a class="thumb" href="reads-sample-small.fastq/genome//Gviz/rand/chrom_3.png" title="chrom_3">chrom_3</a>\n+ </li>\n+ \n+ <li>\n+ <a class="thumb" href="reads-sample-small.fastq/genome//Gviz/rand/chrom_4.png" title="chrom_4">chrom_4</a>\n+ </li>\n+ \n+ <li>\n+ <a class="thumb" href="reads-sample-small.fastq/genome//Gviz/rand/chrom_5.png" title="chrom_5">chrom_5</a>\n+ </li>\n+ \n+ <li>\n+ <a class="thumb" href="reads-sample-small.fastq/genome//Gviz/rand/chrom_6.png" title="chrom_6">chrom_6</a>\n+ </li>\n+ \n+ </ul>\n+ </div>\n+ <div style="clear: both;"></div></div>\n+ </div>\n+ </div>\n+ \n+ <!-- FOOTER -->\n+ <div class="container">\n+ <footer>\n+ \n+ </footer>\n+ </div>\n+ <!-- Le javascript\n+ ================================================== -->\n+ <!-- Placed at the end of the document so the pages load faster -->\n+ <script type="text/javascript" src="js/filter.js"></script>\n+ <script type="text/javascript" src="js/jquery.js"></script>\n+ <script type="text/javascript" src="js/jquery-1.3.2.js"></script>\n+ <script type="text/javascript" src="js/jquery.galleriffic.js"></script>\n+ <script type="text/javascript" src="js/jquery.opacityrollover.js"></script>\n+ <script type="text/javascript" src="js/bootstrap-table.js"></script>\n+ <script type="text/javascript" src="js/bootstrap.min.js"></script>\n+ <script type="text/javascript">\n+ jQuery(document).ready(function($) {\n+ // We only want these styles applied when javascript is enabled\n+ $(\'div.navigation\').css({\'width\' : \'300px\', \'float\' : \'left\'});\n+ $(\'div.content\').css(\'display\', \'block\');\n+ \n+ $(".each-gallery").each(function(i){\n+ // Initially set opacity on thumbs and add\n+ // additional styling for hover effect on thumbs\n+ var onMouseOutOpacity = 0.67;\n+ $(\'#thumbs + i + ul.thumbs li\').opacityrollover({\n+ mouseOutOpacity: onMouseOutOpacity,\n+ mouseOverOpacity: 1.0,\n+ fadeSpeed: \'fast\',\n+ exemptionSelector: \'.selected\'\n+ });\n+ \n+ // Initialize Advanced Galleriffic Gallery\n+ var gallery = $(\'#thumbs\'+i).galleriffic({\n+ delay: 2500,\n+ numThumbs: 22,\n+ preloadAhead: 10,\n+ enableTopPager: true,\n+ enableBottomPager: true,\n+ maxPagesToShow: 7,\n+ imageContainerSel: \'#slideshow\'+ i,\n+ controlsContainerSel: \'#controls\' + i,\n+ captionContainerSel: \'#caption\' + i,\n+ loadingContainerSel: \'#loading\' + i,\n+ renderSSControls: true,\n+ renderNavControls: true,\n+ playLinkText: \'Play\',\n+ pauseLinkText: \'Pause\',\n+ prevLinkText: \'‹ Previous\',\n+ nextLinkText: \'Next ›\',\n+ nextPageLinkText: \'Next ›\',\n+ prevPageLinkText: \'‹ Prev\',\n+ enableHistory: false,\n+ autoStart: false,\n+ syncTransitions: true,\n+ defaultTransitionDuration: 900,\n+ onSlideChange: function(prevIndex, nextIndex) {\n+ // \'this\' refers to the gallery, which is an extension of $(\'#thumbs\')\n+ this.find(\'ul.thumbs\').children()\n+ .eq(prevIndex).fadeTo(\'fast\', onMouseOutOpacity).end()\n+ .eq(nextIndex).fadeTo(\'fast\', 1.0);\n+ },\n+ onPageTransitionOut: function(callback) {\n+ this.fadeTo(\'fast\', 0.0, callback);\n+ },\n+ onPageTransitionIn: function() {\n+ this.fadeTo(\'fast\', 1.0);\n+ }\n+ });\n+ });\n+ });\n+ </script>\n+ </body>\n+ </html>\n+ \n\\ No newline at end of file\n' |
| b |
| diff -r 9645d995fb3c -r 9185ca0a7b43 test-data/res_files/reads-sample-small.fastq/dataset_35117_18-29.fastq --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/res_files/reads-sample-small.fastq/dataset_35117_18-29.fastq Wed Jan 16 08:18:13 2019 -0500 |
| b |
| b'@@ -0,0 +1,182280 @@\n+@HWI-ST132:678:C1LFKACXX:6:1103:5043:24327\n+TCTGTCGTGCATTGTCGG\n++\n+IHFC<HHHHHDFFFFCCB\n+@HWI-ST132:678:C1LFKACXX:6:1101:19372:1918\n+AGAATTGTGACCTGAATC\n++\n+BCCFFFFDFFHHHFHIJJ\n+@HWI-ST132:678:C1LFKACXX:6:1101:18439:2762\n+CGCGCGCTACACTGACGG\n++\n+@@@D?DD@FFFDDEEFGI\n+@HWI-ST132:678:C1LFKACXX:6:1101:10715:4477\n+TAACTGAGTACCTGGCTC\n++\n+:??DDD2222ADDE<CGG\n+@HWI-ST132:678:C1LFKACXX:6:1101:20172:4409\n+TTCTACAGTCCGACGATC\n++\n+=@BF:====DFFHBGGIJ\n+@HWI-ST132:678:C1LFKACXX:6:1101:11143:4891\n+TTCGAGACAGTAACCACA\n++\n+=@@D;D?D>C<DFIIHGG\n+@HWI-ST132:678:C1LFKACXX:6:1101:9335:5110\n+AAGTAACGAAAGGATTAC\n++\n+:?@B4=2=CFHHHJIJJJ\n+@HWI-ST132:678:C1LFKACXX:6:1101:16012:5749\n+AGATTTACAATTTTGGGC\n++\n+BC@DFFFFHDFFHJIJJJ\n+@HWI-ST132:678:C1LFKACXX:6:1101:4811:6756\n+TGTACTACTCTACTTGTT\n++\n+CCCFFFADHHHHHJJCGI\n+@HWI-ST132:678:C1LFKACXX:6:1101:7299:9245\n+CATTGGAACTAAATGACC\n++\n+=BBDA4=BFHHHHJIIHJ\n+@HWI-ST132:678:C1LFKACXX:6:1101:13600:10898\n+ATCCCGGACGAGCCCCCA\n++\n+@CCFFFFFHHH@FHIJJI\n+@HWI-ST132:678:C1LFKACXX:6:1101:9047:12024\n+ACGACAACCGTCATCCCG\n++\n+@CCFFFFFHHHHFJJIJI\n+@HWI-ST132:678:C1LFKACXX:6:1101:7548:13223\n+ATAGACCTGACAGCGTGC\n++\n+?@@FDDFFH:ADAFHCGI\n+@HWI-ST132:678:C1LFKACXX:6:1101:7552:14739\n+GGAGGAAGTAGCTTTTTT\n++\n+BBBDDDFFH2AADFHIJI\n+@HWI-ST132:678:C1LFKACXX:6:1101:19574:14871\n+TTCCCCGTCGGGGAGCCA\n++\n+BBBFFFFDF?FHF:??FH\n+@HWI-ST132:678:C1LFKACXX:6:1101:9689:16020\n+TGCTGGTCGACTATACTC\n++\n+B?@DAAADFFHHHJJ@FG\n+@HWI-ST132:678:C1LFKACXX:6:1101:10332:16559\n+GCCCGGCTAGCTCAACCC\n++\n+=B@FA=@DHFHHHIJIIJ\n+@HWI-ST132:678:C1LFKACXX:6:1101:16598:17271\n+TCCACCACGTTCCCGTGG\n++\n+BBBFFF:AA<CFHIHCGH\n+@HWI-ST132:678:C1LFKACXX:6:1101:16473:17908\n+TTCTACAGTCCGACGATC\n++\n+BBBFFF>AADHFHGHHHI\n+@HWI-ST132:678:C1LFKACXX:6:1101:17076:19365\n+TCCCCGGCATCTCCACCA\n++\n+CC@FFFFFHHHHHJIJJJ\n+@HWI-ST132:678:C1LFKACXX:6:1101:2970:20077\n+TCCCGGATGGAACCACCA\n++\n+B@BFDBAD@DFHHHHIJI\n+@HWI-ST132:678:C1LFKACXX:6:1101:19292:22029\n+TACAGAGGGCTGCGAGAC\n++\n+CCCFFFFFHHHHG@FDHH\n+@HWI-ST132:678:C1LFKACXX:6:1101:7403:22551\n+GCAGTCGTGGCCGCGCGG\n++\n+@@@DDDDDHDHHF12?FH\n+@HWI-ST132:678:C1LFKACXX:6:1101:6550:24420\n+TCTTTGGTATTCTCGCTG\n++\n+@@@DDDDAFHHHF<+AEG\n+@HWI-ST132:678:C1LFKACXX:6:1101:15312:25043\n+ATGACACCGTTGGAAGAA\n++\n+@BCFFFFFHHHHFGHEEF\n+@HWI-ST132:678:C1LFKACXX:6:1101:10841:25468\n+TCTTTGGTATTCTCGCTG\n++\n+BCCFFFFBFHHHHEIJJJ\n+@HWI-ST132:678:C1LFKACXX:6:1101:6460:26533\n+TCCCGGGTTTCGGCACCA\n++\n+CCCFFFFDHHH<DGHIJJ\n+@HWI-ST132:678:C1LFKACXX:6:1101:8169:26973\n+ATCCTGGTCACGGCACCA\n++\n+@CCFFFFEHBH@FHIJJJ\n+@HWI-ST132:678:C1LFKACXX:6:1101:17561:28189\n+TCCCGGATGGAACCACCA\n++\n+BBCFFFDD?FDFHJIJJJ\n+@HWI-ST132:678:C1LFKACXX:6:1101:11670:30039\n+TTCTACAGTCCGACGATC\n++\n+CCCFFFFFHHHHGJJIIJ\n+@HWI-ST132:678:C1LFKACXX:6:1101:5395:30961\n+TACGGACCAATGGCAAAA\n++\n+@B@FDDDDH=FHDHIGIG\n+@HWI-ST132:678:C1LFKACXX:6:1101:8747:33935\n+CGCATGAATGGATTAAAA\n++\n+@@@DDF<DHH>FHGGBHG\n+@HWI-ST132:678:C1LFKACXX:6:1101:9941:34387\n+ATCCCATCCTCGTCGCCA\n++\n+BCBDFFFFHHHHHH@FHI\n+@HWI-ST132:678:C1LFKACXX:6:1101:14543:34442\n+TCCACCACGTTCCCGTGG\n++\n+@C@FFFADFFHGHJJEHI\n+@HWI-ST132:678:C1LFKACXX:6:1101:5887:34986\n+AAACTTTCAACAACGGAT\n++\n+@@@DFFFFH<FHHIICGI\n+@HWI-ST132:678:C1LFKACXX:6:1101:9891:35111\n+AAGAGTCTTGTCTGGTAC\n++\n+BCCFFBDFHHHHHJFHHI\n+@HWI-ST132:678:C1LFKACXX:6:1101:10051:35463\n+TCTTGATCGAAGCCCCGG\n++\n+B@BFFFFFHFFHGJJJJJ\n+@HWI-ST132:678:C1LFKACXX:6:1101:4680:35647\n+CGGGATGTAGCGCAGCTT\n++\n+BB@FADFDFHGFHEIIJJ\n+@HWI-ST132:678:C1LFKACXX:6:1101:14569:35583\n+AAGATAGAGTAGTTTTTT\n++\n+BBCDFFFFHCHHHHIJJJ\n+@HWI-ST132:678:C1LFKACXX:6:1101:13960:37817\n+AAAGTTCGGAAAACTGGC\n++\n+@CCFDFDFHHHHHBGFGI\n+@HWI-ST132:678:C1LFKACXX:6:1101:16007:38099\n+GATGACTGGGGTGAAGTC\n++\n+B@BDDFFFHG?CFBGIEG\n+@HWI-ST132:678:C1LFKACXX:6:1101:8213:39438\n+TAATGATTCCTGTACTGA\n++\n+BBBFFFFFHHHHFHIJIJ\n+@HWI-ST132:678:C1LFKACXX:6:1101:15318:43042\n+CCGCTGCTGATCACACTG\n++\n+CCCFFFFFHDHHHJJJJJ\n+@HWI-ST132:678:C1LFKACXX:6:1101:16708:44453\n+TGCTAGAGGGTCTCGGTA\n++\n+?BBF;A=DFH<DHIE<<C\n+@HWI-ST132:678:C1LFKACXX:6:1101:8544:45645\n+TGCGGCTGGATCACCTCC\n++\n+@CCFFFFF:FHHHIJJJI\n+@HWI-ST132:678:C1LFKACXX:6:1101:16382:46217\n+AT'..b'276\n+GATCCCAGATCCGCTGTGTTT\n++\n+CCCFFFFFHHHHHIJFGHHIJ\n+@HWI-ST132:678:C1LFKACXX:6:1213:14045:90482\n+ATACTAGATTCGTTGAAAAGT\n++\n+@@@F7DDDFA<CC?;FAEBH?\n+@HWI-ST132:678:C1LFKACXX:6:1302:4633:32096\n+TGTTGCGGCAACTTCTTTAAGTTG\n++\n+CCCFFFFFHHHHHJJJJJJJJHIJ\n+@HWI-ST132:678:C1LFKACXX:6:2107:6041:64276\n+TGGCCTAATGGATAAGGCGTCGGACT\n++\n+@CCFFFDFHHHHHIJJJJ<FHIJJJJ\n+@HWI-ST132:678:C1LFKACXX:6:1112:9014:81599\n+TTCGGATCCGAAGATTGCAGG\n++\n+@CCFFDFFHGGGGDCEGIJJJ\n+@HWI-ST132:678:C1LFKACXX:6:2105:11875:25254\n+CGAAGATTGCAGGTTCGAGTC\n++\n+CC@FFFFFHHHFCAFHIJ+AH\n+@HWI-ST132:678:C1LFKACXX:6:2101:16974:2305\n+ACCGTTCTATGCTTTTTTTT\n++\n+:BBDDDDFHH<2<CFHIIJJ\n+@HWI-ST132:678:C1LFKACXX:6:1313:11404:80054\n+ACCGTTCTATGCTTTTTTTTA\n++\n+@@CFBDFF?FHHGIIIIGIIC\n+@HWI-ST132:678:C1LFKACXX:6:1116:12125:58757\n+AAGTAGCAGTCGTGGCCGAGTG\n++\n+??+4=B?DDHHF<EGHGGGIDG\n+@HWI-ST132:678:C1LFKACXX:6:1205:9493:45438\n+GCAGTCGTGGCCGAGTGG\n++\n+BCCFDFFFHHHHHIDCFH\n+@HWI-ST132:678:C1LFKACXX:6:1207:2720:86231\n+GCAGTCGTGGCCGAGTGG\n++\n+@@@FFFFDHHHGFIG2AF\n+@HWI-ST132:678:C1LFKACXX:6:1214:18091:41339\n+GCAGTCGTGGCCGAGTGGTTAAGG\n++\n+?@:4ABDDHHFHFDGCGDFHFGIG\n+@HWI-ST132:678:C1LFKACXX:6:1309:18921:24185\n+GCAGTCGTGGCCGAGTGGTTAAGG\n++\n+@CCFDFFFHHHHHI@ACGFHIIIJ\n+@HWI-ST132:678:C1LFKACXX:6:1106:1391:88663\n+GCAGTCGTGGCCGAGTGGTTAAGGC\n++\n+@@@FDEDDAFHHHJH+AFFHIJEHG\n+@HWI-ST132:678:C1LFKACXX:6:1310:15410:68712\n+GCAGTCGTGGCCGAGTGGTTAAGGC\n++\n+@@@DDFFFHHHHH?EEGHIJHIEEH\n+@HWI-ST132:678:C1LFKACXX:6:1202:15769:84946\n+AGCGTAGGTTCGAATCCT\n++\n+?@@D=ADDHHFDHFGGIG\n+@HWI-ST132:678:C1LFKACXX:6:2105:13686:25294\n+AGCGTAGGTTCGAATCCT\n++\n+BCCFFFFFFHHDDHHIJJ\n+@HWI-ST132:678:C1LFKACXX:6:1106:17247:63193\n+AATCCTACCGGCTGCGAATGA\n++\n+@BBFFDEFHFHHHFFFFHGHJ\n+@HWI-ST132:678:C1LFKACXX:6:1107:17291:97995\n+ATCCTACCGGCTGCGAATGA\n++\n+@CCFFFFFDFFHHJGEHGBG\n+@HWI-ST132:678:C1LFKACXX:6:2105:5531:13237\n+ACCGGCTGCGAATGAGAA\n++\n+B@BFFFFFGHDFCFHEGI\n+@HWI-ST132:678:C1LFKACXX:6:1111:11783:45506\n+ACCGGCTGCGAATGAGAATGT\n++\n+???DFFFFFHF:CCCGHHBG<\n+@HWI-ST132:678:C1LFKACXX:6:2105:11033:71535\n+CGGCTGCGAATGAGAATGTATATTT\n++\n+?BBDFFFF@<@ACAAEHHHGGIJJI\n+@HWI-ST132:678:C1LFKACXX:6:2103:20548:80488\n+AATGAGAATGTATATTTT\n++\n+BCBDDFFFHHFHHJJJJJ\n+@HWI-ST132:678:C1LFKACXX:6:1213:10954:88904\n+GCAGTCGTGGCCGAGTGG\n++\n+B@CFFFFFFHGFHGIFHI\n+@HWI-ST132:678:C1LFKACXX:6:1301:8478:85932\n+GCAGTCGTGGCCGAGTGG\n++\n+@CCFDFFDFHHHHGHAFG\n+@HWI-ST132:678:C1LFKACXX:6:2101:5467:98324\n+GCAGTCGTGGCCGAGTGG\n++\n+@@CFFDFFHHGHH>GAGH\n+@HWI-ST132:678:C1LFKACXX:6:2107:20194:63182\n+GCAGTCGTGGCCGAGTGG\n++\n+BCCFFFFFHGHHHBH<EH\n+@HWI-ST132:678:C1LFKACXX:6:1116:13015:74545\n+GCAGTCGTGGCCGAGTGGTTAAGGC\n++\n+B@:BDDFDFHFFFBG2CDHGGGFHI\n+@HWI-ST132:678:C1LFKACXX:6:1209:1463:48119\n+GCAGTCGTGGCCGAGTGGTTAAGGC\n++\n+BCCFDFDDHHHHHJJFHIIJJJIJJ\n+@HWI-ST132:678:C1LFKACXX:6:1313:4928:7411\n+GCAGTCGTGGCCGAGTGGTTAAGGC\n++\n+@C@FFDFFHHFHHJJAEGGHGIIJI\n+@HWI-ST132:678:C1LFKACXX:6:1113:20573:45425\n+AGTCGTGGCCGAGTGGTTAAGGC\n++\n+CCCFFFFFFHHHH?EHHHIIJJJ\n+@HWI-ST132:678:C1LFKACXX:6:2109:6492:70002\n+GTCGTGGCCGAGTGGTTAAGGC\n++\n+CCCFFFFFGHG@2<EAFHGGJI\n+@HWI-ST132:678:C1LFKACXX:6:1104:13333:89311\n+TTAAGGCGTCTGACTCGAAATCAGA\n++\n+CCCFFFFFHHHHHIIJJGGIJJJJJ\n+@HWI-ST132:678:C1LFKACXX:6:1306:7606:88539\n+TGACTCGAAATCAGATTCCCTCTG\n++\n+CCCFFFFFHHHHHJJJIJGIJJJJ\n+@HWI-ST132:678:C1LFKACXX:6:2108:19159:27727\n+ATATAGCCTGAGCTTCGACC\n++\n+JJJJJIHF?HHHFDFFFCCC\n+@HWI-ST132:678:C1LFKACXX:6:1211:6213:41030\n+TCGGATCCGAAGATTGCAGG\n++\n+@@CFFFFFDHHGHEHEFFHI\n+@HWI-ST132:678:C1LFKACXX:6:1203:8956:45599\n+AGATTGCAGGTTCGAGTCCT\n++\n+@@@DFFFFHHFHH<A<AEHH\n+@HWI-ST132:678:C1LFKACXX:6:1303:5477:98042\n+GTAACTGACCGTGTGGCCCAATGGA\n++\n+??@DFFFFGHDHGG?GGIEH3<FGH\n+@HWI-ST132:678:C1LFKACXX:6:1315:9507:45115\n+AAGATTGCAGGTTCGAGTC\n++\n+@@@:BDDDAFHHFIIGHFA\n+@HWI-ST132:678:C1LFKACXX:6:1306:9972:7484\n+AAGATTGCAGGTTCGAGTCCT\n++\n+@@CFFFFAFFHHHG@GEBGHH\n+@HWI-ST132:678:C1LFKACXX:6:1303:16006:44426\n+AGATTGCAGGTTCGAGTCCT\n++\n+@@@FFFFFDHDFHCE<AEHI\n+@HWI-ST132:678:C1LFKACXX:6:1214:13442:64117\n+AATGGATAAGGCGTCGGA\n++\n+818A:3ADHHFBFC1@FB\n+@HWI-ST132:678:C1LFKACXX:6:1214:1663:16969\n+ATTGCAGGTTCGAGTCCTG\n++\n+@@@FDFFFCFFHHIGHIIJ\n' |
| b |
| diff -r 9645d995fb3c -r 9185ca0a7b43 test-data/res_files/reads-sample-small.fastq/genome/Gviz/rand/chrom_1.png |
| b |
| Binary file test-data/res_files/reads-sample-small.fastq/genome/Gviz/rand/chrom_1.png has changed |
| b |
| diff -r 9645d995fb3c -r 9185ca0a7b43 test-data/res_files/reads-sample-small.fastq/genome/Gviz/rand/chrom_2.png |
| b |
| Binary file test-data/res_files/reads-sample-small.fastq/genome/Gviz/rand/chrom_2.png has changed |
| b |
| diff -r 9645d995fb3c -r 9185ca0a7b43 test-data/res_files/reads-sample-small.fastq/genome/Gviz/rand/chrom_3.png |
| b |
| Binary file test-data/res_files/reads-sample-small.fastq/genome/Gviz/rand/chrom_3.png has changed |
| b |
| diff -r 9645d995fb3c -r 9185ca0a7b43 test-data/res_files/reads-sample-small.fastq/genome/Gviz/rand/chrom_4.png |
| b |
| Binary file test-data/res_files/reads-sample-small.fastq/genome/Gviz/rand/chrom_4.png has changed |
| b |
| diff -r 9645d995fb3c -r 9185ca0a7b43 test-data/res_files/reads-sample-small.fastq/genome/Gviz/rand/chrom_5.png |
| b |
| Binary file test-data/res_files/reads-sample-small.fastq/genome/Gviz/rand/chrom_5.png has changed |
| b |
| diff -r 9645d995fb3c -r 9185ca0a7b43 test-data/res_files/reads-sample-small.fastq/genome/Gviz/rand/chrom_6.png |
| b |
| Binary file test-data/res_files/reads-sample-small.fastq/genome/Gviz/rand/chrom_6.png has changed |
| b |
| diff -r 9645d995fb3c -r 9185ca0a7b43 test-data/res_files/reads-sample-small.fastq/genome/Gviz/unique/chrom_1.png |
| b |
| Binary file test-data/res_files/reads-sample-small.fastq/genome/Gviz/unique/chrom_1.png has changed |
| b |
| diff -r 9645d995fb3c -r 9185ca0a7b43 test-data/res_files/reads-sample-small.fastq/genome/Gviz/unique/chrom_2.png |
| b |
| Binary file test-data/res_files/reads-sample-small.fastq/genome/Gviz/unique/chrom_2.png has changed |
| b |
| diff -r 9645d995fb3c -r 9185ca0a7b43 test-data/res_files/reads-sample-small.fastq/genome/Gviz/unique/chrom_3.png |
| b |
| Binary file test-data/res_files/reads-sample-small.fastq/genome/Gviz/unique/chrom_3.png has changed |
| b |
| diff -r 9645d995fb3c -r 9185ca0a7b43 test-data/res_files/reads-sample-small.fastq/genome/Gviz/unique/chrom_4.png |
| b |
| Binary file test-data/res_files/reads-sample-small.fastq/genome/Gviz/unique/chrom_4.png has changed |
| b |
| diff -r 9645d995fb3c -r 9185ca0a7b43 test-data/res_files/reads-sample-small.fastq/genome/Gviz/unique/chrom_5.png |
| b |
| Binary file test-data/res_files/reads-sample-small.fastq/genome/Gviz/unique/chrom_5.png has changed |
| b |
| diff -r 9645d995fb3c -r 9185ca0a7b43 test-data/res_files/reads-sample-small.fastq/genome/Gviz/unique/chrom_6.png |
| b |
| Binary file test-data/res_files/reads-sample-small.fastq/genome/Gviz/unique/chrom_6.png has changed |
| b |
| diff -r 9645d995fb3c -r 9185ca0a7b43 test-data/res_files/reads-sample-small.fastq/genome/distribution.png |
| b |
| Binary file test-data/res_files/reads-sample-small.fastq/genome/distribution.png has changed |
| b |
| diff -r 9645d995fb3c -r 9185ca0a7b43 test-data/res_files/reads-sample-small.fastq/genome/distribution.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/res_files/reads-sample-small.fastq/genome/distribution.txt Wed Jan 16 08:18:13 2019 -0500 |
| b |
| @@ -0,0 +1,13 @@ +size number percentage +18 649 1.66 +19 688 1.76 +20 1317 3.37 +21 3221 8.25 +22 3209 8.22 +23 6730 17.24 +24 10434 26.73 +25 9153 23.45 +26 2895 7.42 +27 439 1.12 +28 283 0.72 +29 22 0.06 |
| b |
| diff -r 9645d995fb3c -r 9185ca0a7b43 test-data/res_files/reads-sample-small.fastq/genome/dup_mapnum.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/res_files/reads-sample-small.fastq/genome/dup_mapnum.txt Wed Jan 16 08:18:13 2019 -0500 |
| b |
| b'@@ -0,0 +1,9998 @@\n+sequence\tcount\tmapnum\n+TGCTTGGACTACATATGGTTGAGG\t1985\t1\n+TGCTTGGACTACATATGGTTGAGGG\t1319\t1\n+TGCTTGGACTACATATGGTTGAG\t943\t1\n+TATAGAATTGTAGAGCAAGACCT\t498\t1\n+TGCTTGGACTACATATGGTTGAGGGT\t300\t1\n+TTGATTAAGATAGCTGCTCCGCCT\t297\t1\n+TATTGGCAAGCCTTTCGTCGAACC\t267\t1\n+ATATCGCAGTCCATGCTG\t240\t1\n+TTTACGGGATAGGACGGTAGCGC\t231\t1\n+TATTGACTGGCGACGCTTTTGAGG\t229\t1\n+TGCTTGGACTACATATGGTTGAGGGTTG\t226\t1\n+TGAAAGACGCAGGATGGTCCGCCT\t226\t1\n+TGAAAGACGCAGGATGGTCCGCCTG\t223\t1\n+TATGTTTAGCGTTGTAGTCGCCT\t193\t1\n+GATTGGACAGCCTCTGTAGTTTGC\t182\t1\n+AACGCATATCGCAGTCCATGCTG\t173\t1\n+TTCGATCTGCCGCGGGCTGCCGAGA\t168\t1\n+TTTCTTCGGTTCGATATCAACGGA\t163\t1\n+GGACTACATATGGTTGAGGGTTGTA\t160\t1\n+TATAGAATTGTAGAGCAAGACCTTG\t144\t1\n+CCATATCTAGGTTCTGTAGCCGAAG\t136\t1\n+TATTTGATTGTTGGGCTACAAGCA\t130\t1\n+TCAGAATCTTTGATTGTGCTCGCT\t128\t1\n+ACTACATATGGTTGAGGGTTGTA\t125\t1\n+TTCAGATGGTGCTCGACTATGGCCT\t117\t1\n+CTGCTTGGACTACATATGGTTGAG\t115\t1\n+TAACTGCGAAGTCGATCAGGTCT\t113\t1\n+GCATATCGCAGTCCATGCTG\t107\t1\n+TTTTTGATCAATTGGCACCATGCGA\t105\t1\n+TTTTTGATCAATTGGCACCATGCGAA\t105\t1\n+TCAGATGAGAGACAAATTAGAATTA\t103\t1\n+TGTAGAGGATCGCTTGTCTGGGC\t99\t1\n+AACTCTAAGCGGTGGATCACTCGGC\t94\t1\n+TAGATGTGGCCTGAAGATGATTTTC\t91\t1\n+TTAGTGTTGAATGTAGGCCAGGGA\t90\t1\n+TGCTTGGACTACATATGGTTGA\t90\t1\n+CTGCTTGGACTACATATGGTTGAGG\t86\t1\n+TCATGAGACGTCTGCTTGTTTGGC\t83\t1\n+GACTACATATGGTTGAGGGTTGTA\t83\t1\n+TGCGTTTGGGATTGTCGGTGAGAC\t82\t1\n+TAATACATCGATTTCGTGACGTCGC\t81\t1\n+TATTTGATTGTTGGGCTACAAGCATT\t81\t1\n+GCTTGGACTACATATGGTTGAGG\t81\t1\n+TGCTTGGACTACATATGGTTG\t80\t1\n+TACATATGGTTGAGGGTTGTA\t78\t1\n+TTTCTTCGGTTCGATATCAACGGAT\t76\t1\n+TATTGGCAAGCCTTTCGTCGAAC\t76\t1\n+TCTTGTAAATACTTTGATTGGCCT\t74\t1\n+TTTTCCGGGCTGAGCTTTCGCTTT\t73\t1\n+TTCGATCGCCGACGTGTGAAGACGT\t73\t1\n+TGCGTTTGGGATTGTCGGTGAGA\t71\t1\n+ACATTTCCGTTTCTCGCGACT\t71\t1\n+AACTCTAAGCGGTGGATCACTC\t70\t1\n+TGCGTTTGGGATTGTCGGTGAGACG\t70\t1\n+CCATGTCCCGTTGCTATCGACTAGA\t69\t1\n+TATTGAAGGAATTGATATATGCC\t68\t1\n+ACATATGGTTGAGGGTTGTA\t67\t1\n+TTGGGTGTTGCAGTAAGAGCTG\t65\t1\n+TACGAGTAGGATATCGATCTGGT\t65\t1\n+TAGAAGACGATTTTCGGGCCGAAAT\t63\t1\n+TGAATGGTTGAAATCGCTCGGCGA\t63\t1\n+TAATGAGATCCCTCGGTTGCCTT\t63\t1\n+TCCGAAAACAAGGCCCGTCGCTA\t62\t1\n+TTCATCAGCGACTTGTGGGATTCC\t61\t1\n+TGTGCTAGAAGACGATTTTCGGGC\t61\t1\n+TTTTTGATCAATTGGCACCATGCG\t59\t1\n+TTTACGGGATAGGACGGTAGCGCG\t58\t1\n+CTACATATGGTTGAGGGTTGTA\t58\t1\n+TCTGATGTTACGCCCGAAGAGA\t58\t1\n+GAACGCATATCGCAGTCCATGCTG\t58\t1\n+TGTATGAACAGTGGAAGTGG\t56\t1\n+CCGTAAAGGCTTACATCTGGCT\t56\t1\n+TGCTAGAAGACGATTTTCGGGC\t54\t1\n+TTAGGACGAAACACAATTGGGGTG\t54\t1\n+TAATTTGACACTGTTTGGAG\t54\t1\n+TAAGTTGTTGGCTTTGAGTTTAAG\t53\t1\n+CAAAGTCCTGGATACCATCGGCT\t52\t1\n+TTGTAATGTAGCGGTCCATTCC\t51\t1\n+TAATAGTCAGGGCGCGAATTTTTAA\t51\t1\n+TATTGGCAAGCCTTTCGTCGAACCA\t50\t1\n+CAGTATGTAGGACTCCCGGGG\t50\t1\n+TTTGGTTAAAGCTGAATGTCTGCC\t50\t1\n+TAATGAGATCCCTCGGTTGCCT\t49\t1\n+TTTTCCGGGCTGAGCTTTCGC\t49\t1\n+TTTGACAAAATATGCCCTTCACCT\t49\t1\n+TGATTGCGTTGGTAACTGATGGGA\t48\t1\n+TTTTAAACATTAGGCCGTCGAGCCAGA\t47\t1\n+TGATTACGCATCATGTCTTGAATG\t46\t1\n+TAGGACGGTAGCGCGAATGTGCTAGT\t46\t1\n+TTTTAAACATTAGGCCGTCGAGCCAG\t45\t1\n+TATCCAGAAAGGACTTCAGCCCTC\t44\t1\n+TAGGACTCCCGGGGGAAACATGGTC\t44\t1\n+TTTCTGTTTGGGTTTGGACT\t44\t1\n+CAAGCATTCGACAAAGTCTGGC\t44\t1\n+TATTGACTGGCGACGCTTTTGAG\t43\t1\n+TACGAGTAGGATATCGATCTGGTG\t43\t1\n+TTAAGTCTCTTTGGATGTTTTCACT\t43\t1\n+TAGGACTCCCGGGGGAAACATGGT\t42\t1\n+TAAAGAGGACAGGCCTTACAGGGTA\t42\t1\n+TTGTAATGTAGCGGTCCATTCCA\t41\t1\n+CCATATCTAGGTTCTGTAGCCGAAGG\t41\t1\n+TTTAAGCTGGTAGGTGTAGAAGCCT\t41\t1\n+CGCTGATGAAATCTCCAGGCTCAG\t41\t1\n+TTCAGTATTGAGTTTTGGGCTTAGC\t41\t1\n+TATGTTTAGCGTTGTAGTCGCCTGC\t41\t1\n+TTTTTGATCAATTGGCACCATGC\t41\t1\n+TCCGGGCTGAGCTTTCGCTTT\t40\t1\n+TCTGATGTTACGCCCGAAGAGATAAC\t40\t1\n+TTTCTGTTTGGGTTTGGAC\t40\t1\n+AACTCTAAGCGGTGGATCACTCG\t40\t1\n+TCAGATGAGAGACAAATTAGAAT\t40\t1\n+TCATACTCTTCGATCTCGAGCCAG\t39\t1\n+TTATTGAATCTTCTTGTATAAGAACT\t39\t1\n+CAAATGTGGATACCGTTAAGCGAC\t38\t1\n+TATTGAAGGAATTGATATATGC\t38\t1\n+TAGAATAACAAGATGCGTAACGGCC\t38\t1\n+TCAAAGTATTTACAAGACGGCTT\t38\t1\n+TTGCGTTGGTAACTGATGGGAT\t38\t1\n+TTGTAATGTAGCGGTCCATTCCAG\t38\t1\n+TAATGAGATCCCTCGGTTGCCTTCT\t37\t1\n+CACAGAGGCCAAGTCATTGAGCGCC\t37\t1\n+TTGATTAAGATAGCTGCTCCGCC\t36\t1\n+TCATACTCTTCGATCTCGAGCCA\t35\t1\n+TAGGACGGTAGCGCGAATGTGCTAG\t35\t1\n+TCTCGGTGGGCAGTAGACCGC\t35\t1\n+AAGATTCTGAGAACCATCACTGGGG\t35\t1\n+TGAATTGAGAGTCGGCGTTCGTCA\t34\t1\n+TTTGACAAAATATGCCCTTCACC\t34\t1\n+TT'..b'CAAGACCTTGTGATCTAGGC\t1\t1\n+TGATCGGCCGGTAGGAGGCGGGCT\t1\t1\n+TCGATGCGTGGCCTGGTACAGTCC\t1\t1\n+AATACGATCTTCGTGCTTCGG\t1\t1\n+ACTACATAAGTTACCATAGGACTTTA\t1\t1\n+TTGAAACCAATCTGGACCTATGGCTC\t1\t1\n+CGCGTGGCAGCTGGGCAGCGGA\t1\t1\n+ATAACGTTAAGGCAATGC\t1\t1\n+CCTCCGCCGCGATCCCGCTACCCTG\t1\t1\n+TTATTGGATTGGGTTTGCTAAGAAG\t1\t1\n+TCCAAGGTACTTTGCTGCGTTCGGC\t1\t1\n+TGCTCGACTATGGCCTTGCTG\t1\t1\n+TATTATTTGAAAATAGATTAGAAA\t1\t1\n+TCTCGAATGTGGATAGCAGGAT\t1\t1\n+TGCATAAGATATTCCGCCTCGAGAA\t1\t1\n+CGCATGGTTCGACGAAAGGCTTGC\t1\t1\n+GAGGTCAATCTGGTTGGTGGTTTC\t1\t1\n+ATTGAAGGAATTGATATATGC\t1\t1\n+GCTGTTCAACAAGAGCGGAGGACA\t1\t1\n+GAAAAAACCCAAATCAACCATCGGC\t1\t1\n+TATATGTATCTGTTTTGGCCC\t1\t1\n+TGCTGTAGGAGCCAAGTTCTCCACCT\t1\t1\n+TTGATTTGTTGGTAGAAGAAGGTT\t1\t1\n+ACCACTATTATCGAAGAAACGCAG\t1\t1\n+TCAGGTCTCTGTGCAGGGT\t1\t1\n+CGTAAGCTTGCTGCGCGCGGAGC\t1\t1\n+GTTATACAATGATCATGTGTT\t1\t1\n+CTTTAATTATCATATATTGTA\t1\t1\n+TGTGATCTAGGCTGAGCGGAG\t1\t1\n+TCGGAGCTAAGCTCAACAACCGCAC\t1\t1\n+TAAGCGGTGGATCACTCGGCT\t1\t1\n+GCTTGATGACTGGTACTG\t1\t1\n+AAGTTAATGATTACTTTGATTGCC\t1\t1\n+ATTTATTGAAGGAATTGATATATGC\t1\t1\n+CTTTCCGCTGTCAACGACCAG\t1\t1\n+TGAATCTGATATAGAGAGCTGCAC\t1\t1\n+AGCGCGAGCATGACGAACGCC\t1\t1\n+TGGCATTGCCCCATAACTGTGAGCC\t1\t1\n+CAATCTGGACCTATGGCTC\t1\t1\n+TACCAGAGGCAGGTGGTCGGAGCTA\t1\t1\n+CGGGAGTGGTATGCTGTTCAACAAGA\t1\t1\n+CATCATCAACGTCCTGTCCAGAG\t1\t1\n+CTCCGACAGAAGCCCCGCTACC\t1\t1\n+CAACTCGTCCACGTAAAACGTCGCT\t1\t1\n+TAACAAAGAGAGCCTGGAGCC\t1\t1\n+TAGCACTTGTAAATTAAGACTCACT\t1\t1\n+TAAAAATAAATGTTCGGGAC\t1\t1\n+TGAGCGGAGAACCAGAGTTGAT\t1\t1\n+ATCCCAAACGCAGACATCG\t1\t1\n+GATGGTGCTCGACTATGGCCT\t1\t1\n+CAAGGTAGTGTCCTCGGCCC\t1\t1\n+AATTCGATCGCCGACGTGTGAA\t1\t1\n+GCTGATCCGACTTAATCAACA\t1\t1\n+TTTTTTCTAGGAGGCTTGTTTTC\t1\t1\n+GTAAAACGTCGCTTACGCAGAG\t1\t1\n+AACTGGCCAACGCTCTGAAACAAGAAG\t1\t1\n+TAAGGCTTTACGCGGCTGACGC\t1\t1\n+CTTGTACTCAAAGCTCCTCCACGGCT\t1\t1\n+TCCTTGGCGGAGGTATCGTAGTGAG\t1\t1\n+TGCTGCGTTCGGCTGTGG\t1\t1\n+GAATCCCACAAGTCGCTGATGAAA\t1\t1\n+TATTGGCGGAGGCTTTGTTTTCTT\t1\t1\n+AACGCATATCGCAGTCCATGCTGT\t1\t1\n+CAATGACTTCGGCTACCTCGCAG\t1\t1\n+TTCTGTAGTCGTCCTCCGTTTTCGT\t1\t1\n+TATTTTTCCAACTGTTCT\t1\t1\n+TGCTTTTCCGTCGGGATG\t1\t1\n+TGGGGGCGTAGCATTACTAGTGC\t1\t1\n+GTTGTTGGCTTTGAGTTTAAG\t1\t1\n+TGCAAGTAGTCCTGAAGG\t1\t1\n+GATAAGCGTCAGCTTCTGCGGACC\t1\t1\n+CCGTTGTGGTTGTTGTTACTG\t1\t1\n+GGGATGTCGGCTGTATAGATGA\t1\t1\n+CACCGTGGTACGTTCGGAGTGAAAAC\t1\t1\n+GATCCCAGATCCGCTGTGTTT\t1\t1\n+TATCGTCGGCAAATGTGGATA\t1\t1\n+TGCCGAGATATGCTGCGAGTTG\t1\t1\n+CCGTGATTGCGTTGGTAACTGAT\t1\t1\n+TGAGGACGTATTTTGAGAGACC\t1\t1\n+TCGCTTCGCTTTCGACTCCGGT\t1\t1\n+CCGGAAATGATCATCCAGC\t1\t1\n+CAAATGATCAACAGGACTCCACAAC\t1\t1\n+TACCGCTGAGGACGTGCCGCTGG\t1\t1\n+TAGATTGGACAGCCTCTGTAGTT\t1\t1\n+CGGGTATCTTGTTGGTCCTCCTG\t1\t1\n+TCTGAGAACCATCACTGGGGCACC\t1\t1\n+CACCATCTGAAGACCCACCAG\t1\t1\n+CTACTAGCACATTCGCGCTAC\t1\t1\n+GCTCGATGCGTGGCCTGGTACAGTC\t1\t1\n+TCGGATCCGAAGATTGCAGG\t1\t5\n+TCAGAACACATGCCATAAAG\t1\t1\n+GTGTGTGAATATCGAGAACCT\t1\t1\n+TTGCCTTTTGTCGGAGAAATCCGT\t1\t1\n+TTTAAAATCAGGTATGACGCC\t1\t1\n+TTCCTTAAGTTCCGTGATTGCGTT\t1\t1\n+AACATCGCTTCTATCTGACCGGA\t1\t1\n+AAAGTCACTGTGGCGAGCCCA\t1\t1\n+TTCGCTGTGGAAGGCCACGCGCGCAAT\t1\t1\n+CTAGAGGTGGCTCCAGGCTCT\t1\t1\n+TGACCTCGTGTGGCCATACTCTT\t1\t1\n+TGTTGCGGCTGCTGCGGCT\t1\t1\n+CACTCCGTTGAGGGCGTCT\t1\t1\n+TTCAGCTCTTTGTAGATTGGACA\t1\t1\n+TTGTTTCAGAGCGTTGGCCAGTTT\t1\t1\n+AAGGAATTCATCAGGTGGCTGGGC\t1\t1\n+GTGAGTTGCTCTATGTATCGGC\t1\t1\n+CAAGCCGGAAAGGGAGCCCGCCTCCTAC\t1\t1\n+TTGATCAAGGTAGAGTTGTCGCGT\t1\t1\n+GACCTTGTGATCTAGGCTGAGCGGA\t1\t1\n+TTCTCCTACGTCTCACCG\t1\t1\n+TACACATCCTGATTCTGCCAGCGCTC\t1\t1\n+AAAACGTCGCTTACGCAGAGA\t1\t1\n+TTGCTGGTAGATACCGCTGAGGA\t1\t1\n+GAAGTACGCGTTGTTGCGCTG\t1\t1\n+ACAACAAATGTTAAACTGATTT\t1\t1\n+TGTGTCCGCACTTCGTGCCT\t1\t1\n+GTAGGATCACGGTAGAAG\t1\t1\n+GCGGAAAGAATGCAGACCTTTGGTCAGC\t1\t1\n+GGCTAGCTCAGTCGGTAGA\t1\t1\n+TGATTTGTTGGTAGAAGAAG\t1\t1\n+ATCAGACGGAGTGCTAGGGGCT\t1\t1\n+CGATAAGGAATTCATCAGGTGGCT\t1\t1\n+CAAATCGAGCAACTCGTCCACG\t1\t1\n+CCACACGGAAACTGGCCAACGCTC\t1\t1\n+GCAAAAATTGAAGTCGATCCCGG\t1\t1\n+TTCAGTCGGTGGGCGAAGA\t1\t1\n+TCCAGAAAGGACTTCAGCCCTC\t1\t1\n+TCGCCTGTACTAATTCACCT\t1\t1\n+ACCGCCGGCGCAAGTTGCACCTTGG\t1\t1\n+TATCGACTAGAGGCGCCTTCCTCGTG\t1\t1\n+TTGTAAGGATTATGGAAGCCCAG\t1\t1\n+GATGAAGCGACTGTGTGGTTCTTACCA\t1\t1\n+GACTTTTCTGTAGTCGTCCTCCGTT\t1\t1\n+TTTCAGGTCTCTGTGCAGGGTGGTG\t1\t1\n+ACCCTTCGGCTACAGAACCTAGATA\t1\t1\n+TAATAATAACGTTAAGGCA\t1\t1\n+TCTTGAAGAGTGGTTGGGGCTGCC\t1\t1\n+CAAAGATTCTGAGAACCATCACT\t1\t1\n+TTCAGGAGATCGTGCACTAATAGAT\t1\t1\n+CGGTAGAGCATGAGACTC\t1\t1\n' |
| b |
| diff -r 9645d995fb3c -r 9185ca0a7b43 test-data/res_files/reads-sample-small.fastq/genome/dup_nonmapp.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/res_files/reads-sample-small.fastq/genome/dup_nonmapp.txt Wed Jan 16 08:18:13 2019 -0500 |
| b |
| b'@@ -0,0 +1,4720 @@\n+sequence\tcount\n+TATTGCACTTGAGCCGGCCTGA\t156\n+TCTTTGGTATTCTCGCTGTAGA\t112\n+TGAGATCATTTTGCAAGCTGATT\t93\n+AAATGAGAGTCAGTAACTGCC\t80\n+TAGTTCTACAGTCCGACGATC\t50\n+TGAGATCATTTTGCAAGCTGAT\t48\n+TGGACGGAGAACTGATAAGGGCA\t47\n+TATTGCACTTGAGACGGCCTGAA\t41\n+TATTGCACTTGAGCCGGCCTG\t39\n+CTAAGGAAATAGTCGCCGTGAT\t35\n+AAAAATGAGAGTCAGTAACTGCC\t33\n+TATTGCACTTGAGACGGCCTGAAA\t30\n+AGTTCTACAGTCCGACGATC\t30\n+TATTGCACCTTCACCGGCCTGA\t22\n+TCTTTGGTATTCTCGCTGTAG\t20\n+TGACTAGATCCACACTCATTAC\t19\n+TGACCACACATTTCAAGGATTAATG\t19\n+AAAATGAGAGTCAGTAACTGCC\t18\n+TGACTAGATCCACACTCATTAAA\t17\n+TGTGATGTGACGTCGTGGAACA\t16\n+TCTTTGGTATTCTAGCTGTAGAAA\t15\n+TTCTACAGTCCGACGATC\t15\n+TGAGCTCATTTTGAAAGCTGATT\t14\n+AGAGTTCTACAGTCCGACGATC\t14\n+TAGCCCCACATGATTCGGCTT\t14\n+TATTGCACTTGAGACGGCCTGT\t13\n+TATTGCACTTGAGCCGGCCTGAAA\t13\n+TAAGATTGGACCCCGTACACTGCCT\t12\n+TATTTGATGACCGGAATTTTGAAA\t12\n+AATGAGAGTCAGTAACTGCC\t11\n+TCTTGGACTGAGCCGCTACTGTT\t11\n+TGAGATCATTTTGCAAGCTGA\t11\n+TGGACGGAGAACTGATAAGGGA\t11\n+GTTCTACAGTCCGACGATC\t11\n+TGGACGGAGAACTGATAAGGGCAA\t11\n+TGGACGGAGAACTGATAATGGC\t11\n+TGGACGGAGAACTTATAAGGGC\t11\n+TATTGCACATTCACCGGCCTGAT\t10\n+AAAAATGAGAGTCAGTAACTGCCA\t10\n+TCTTTGGTCTTCTCGCTGTAGA\t10\n+AAATGAGAGTCAGTAACTGC\t10\n+TATTGCACTTGAGCCGGCCTGAA\t10\n+AAGAGAGCTATCCGTCGACAGTCC\t10\n+TCAGGTACTTAGTGACTCTCACC\t10\n+TGAGATCATTTTGAACGCTGATT\t10\n+TAATACTGTCAGGTACAGATGTC\t10\n+GAAGAACAAAGAACTTTTT\t9\n+AAATGAGAGTCAGTAACTGCCA\t9\n+CAGAGTTCTACAGTCCGACGATC\t9\n+AATTGCACTAGTCCCGGCCTGT\t9\n+TTCTTGACAACCCGATCGGACCTCAA\t9\n+AAAAATGAGAGTCCGTAACTGCC\t8\n+NGGACGGAGAACTGATAAGGGC\t8\n+TGTTAACTGTAAGCCTGTGTCT\t8\n+TGACTAGATCCACCCTCATTAA\t8\n+AAGGGTCGGGTAGTGAGGGCC\t8\n+GAGTTCTACAGTCCGACGATC\t8\n+TATCTGTGGTCTCCCACTAAGGGACA\t8\n+TTACCGTACGATCCGGACAACCGT\t8\n+TAATCCTGTCAGGTAAAGATGTC\t8\n+NCACTGGGCTTTGTTTATCTCA\t8\n+TATTGCACATTCACCGGCCTGAC\t7\n+TTTCTGACGATCGACGACCTCCCGT\t7\n+TCAGGTACTTAGTGACTCTCAAA\t7\n+TCCCGGGTTTCGGCACCA\t7\n+TCCCGGGCGGAAACACCA\t7\n+TACAGATCGTACCTTCACTACC\t7\n+TAATACTGTCAGGTAAAGATGTCT\t7\n+TTCTTTGGATCTCCGCTTAAGACT\t7\n+CGGCACATGTTGACGTACACTC\t6\n+TCTTTGGTCTTCTAGCTGTAGA\t6\n+TGAGTATTACATCCGGTACTGGT\t6\n+TGGACGGAGAACTGATAAGGGT\t6\n+TCAATTCCCCGTCGGGGAGCCA\t6\n+CGGCACATGTTGACGTACACTCA\t6\n+TCAGGTACCTGAAGTCGCGCGC\t6\n+TGCTTCGGCGCCTGGACTTTGGCACC\t6\n+TCAATTTGGTCGTAAGGCTTGGAT\t5\n+TCAGGTACTTAGTGACTCTCAC\t5\n+TGAGATCATTTTGAAAGCTGATTA\t5\n+CGATCTTTTCTCCTCGGACC\t5\n+TCACGGGGCTTTGTTTATCTCA\t5\n+TCACTGGGCTTTGCTTATCTCA\t5\n+TCAGGTACCTGAAGTAGCGCGCGC\t5\n+TGGACGGATAACTGATAAGGGC\t5\n+TGAGATCATTTTGAAAGCTGATA\t5\n+TGAGATCATTTTGAACGCTGAT\t5\n+TACCATAGTAGCTCTGCAGCGAAA\t5\n+TGAAAGACGCAGGATAGTCCGCCTG\t5\n+TTTCTGTACGACGCCGATGATCCT\t5\n+TGAGATAATTTTGAAAGCTGATT\t5\n+ATCCAAAGAATAACGTCGTGAAAC\t4\n+GGAGGAAGTAGCTTTTTT\t4\n+TAGGCACTTCATACCGTGCTCT\t4\n+TAACATCGTAGCCGCTAATGCTGA\t4\n+TTACTGGGCTTTGTTTATCTCA\t4\n+TGAGCTCATTTTGAAAGCTGAT\t4\n+TTCTTGACCACCCGATCGGACCTC\t4\n+GTGCATTGTAGTCGCATTGTCA\t4\n+TCAGGTACCTGAAGTAGCGCGCGA\t4\n+TGAGATCATTTTGAAAGCTGAA\t4\n+TATAGAATTGTAGCGCAAGACCT\t4\n+TCTTTGGTATTCTAGCTGTAGAA\t4\n+TCACTGGGCTTTGTTTATCGCA\t4\n+GAAGAACAAAGAACTTTTTT\t4\n+AATTGCACTAGTCCCGGCCTGCT\t4\n+TGAGATCATTTTGCAAGCTGATA\t4\n+TCCCCGGCATCTCCACCA\t4\n+TGTCTTTTTCCGCTTACTTGCG\t4\n+TTCAATTCCCCGTCGGGGAGCCA\t4\n+TATTGCACATTCACCGGCCTGG\t4\n+TGACTAGATCCACCCTCATTAC\t4\n+TACATATGGTTGAGGGTTGTAT\t4\n+TCACTGGGCTGTGTTTATCTCA\t4\n+CATCTTACCGGGCCGCATTAGA\t4\n+TGTGATGTGACGTCGTGGAAC\t4\n+TCAGGTACCTGAAGTAGCGCGCC\t4\n+TCTCGAATAGCGTTGTGACTGAA\t3\n+TTATCTGTGGTCTCCCACTAAGGGACA\t3\n+TCGTTTCCCGGCCGATGCACCA\t3\n+TAATACTGTCAGGTAAAGCTGTC\t3\n+AATGAGAGTCAGTAACTGCCA\t3\n+TTCTAGTTCGTCTCGGACTGTCCT\t3\n+TCTGAATCACTTTCTACTCGGCATC\t3\n+TGCCGGCTGTTCACACATGAACAC\t3\n+TTTCACCTATCGTTCCATTTGCAGT\t3\n+TGTCTGATGATGACTCGAAAGCCCC\t3\n+TGAGATCATTTTGAACGCTGA\t3\n+TAGGAGTTTTGCGCAAATCTGCCT\t3\n+TCACTGGGCTTTGTTTATCTCG\t3\n+ATTTCCCGGACGAGCCCCCA\t3\n+TTTTCGGCAGGGTTGGTAACTCC\t3\n+TCACTGGGCTTTGTTTATCTCAC\t3\n+TGAAAGACGCAGGCTGGTCCGCCTG\t3\n+ATCCCGGACGAGCCCCCA\t3\n+TGAACACAGCTGGTGGTATCCAGTT\t3\n+TACTTGCATCGCGCCTATCTTATCG\t3\n+CAAGGGACTGACTCGTGTAGTGTG\t3\n+GTGCATTGTAGTCGCATTTTC\t3\n+ATTCCCCGTCGGGGAGCCA\t3\n+TCTTGGACTGAGCCGCTACTGTTTG\t3\n+TGGAAGGAGAACTGATAAGGGC\t3\n+AAGGGTCGGGTAGTGAGGGCCTT\t3\n+TAGGGACGGTCGGGGGCATC\t3\n+CTAAGGAAATAGTAGCCGTGG\t3\n+AATGGCACTGGAAGACTTCACGGG\t3\n+TAAGATTGGACCCCGTACACTGCC\t3\n+GCATGAATGGATTCACGAC\t3'..b'TTTGTACGAGAGTGGGCCGCG\t1\n+TGCATGTGTTGCCCGGTTTAAGAGC\t1\n+GATTCATTCGCGGTATCTCT\t1\n+TCTCTTCGGGCGTAACATCAGAA\t1\n+ACTGTTTGAATTACTCCACCTTGGGA\t1\n+TAACTCTTTCGGATCGCATTCATGTC\t1\n+TCTTCGGTAGAGGTACGCCTTTTAC\t1\n+TTTTGCACTTTTCTCTGCGTAAATG\t1\n+TACGCCTAAAGCAACTCCACTGGT\t1\n+GTCGGTACCTTGGCATCACGGAATT\t1\n+CAATAGTCAAATAGTAGAGTCAACCC\t1\n+TAGTCTCTGATTGGTGTAAAC\t1\n+TATCTTCGGTTTACACGGAGCCC\t1\n+TTCTCCAATTGTCGGTTGACGACCG\t1\n+TCGGAGACTCGCCAATCTATTGCT\t1\n+TATGTTGGCACTACTCTCGCATACGA\t1\n+GAAGGTGAAACTGTTCTGGACGG\t1\n+NTGTCGGACACCGAACCGGGA\t1\n+TTTGCGGCTGTCTGATCAGGC\t1\n+TTCCGCGACTTAGACTTTGTCTGT\t1\n+TTTACTATTTGCATACTCCAGTACT\t1\n+TGGCTGCGAAGGACTCTGGAGTCCC\t1\n+ATGGAGGTGGCTGGTTTGGACC\t1\n+TCCCATATGGTCTCGTGGCTAG\t1\n+TTTCTGAATGTGAACCAAGTTAATCT\t1\n+TTCCCGGCCGATGCACCA\t1\n+TATACTAGGCGTTGCAATCATGCG\t1\n+TACCCGGACGTAGGCAGTCT\t1\n+TCATGACGTCATGGACCATCA\t1\n+ATAGGAGATCTCTATCACTGGCGCC\t1\n+NGCGAAATGACTCTGTCCC\t1\n+AATATTCCTGCACGACTTGTA\t1\n+TGCACACTGTACCCTCTAAA\t1\n+ATAGCATTGGTTGGTGGGGAAACT\t1\n+GACACAAGAGACCCGACCTG\t1\n+CTCGGAGTACCTCCAACTAAACTT\t1\n+TATCGTAGAACCTGTATAGACGACA\t1\n+TACCATAGTAGCTCTGCAGCGAC\t1\n+AATAAGGACAAATTAATA\t1\n+TTGAGGAGGTGCCTGAAAGCC\t1\n+TGACCCGTTCGGCACCTTACGAGA\t1\n+CACCGAGAGCATCCACGGCCTGGCA\t1\n+CGCATCGGGACCTTNAGGTGACGCA\t1\n+CGTCATATCAGGAGGCCTGT\t1\n+TCACTCGGCTTTGTTTATCTCA\t1\n+TAATGAAACGTCTGTAATAATTCC\t1\n+GTGAGTAGAACAGCCGAGCTTCCGT\t1\n+TATAATGATGACTGGCTCTTGAACC\t1\n+CACTTAGGGCTGCTTGCAAA\t1\n+AGCGAAATGACTCTGGCCCAGC\t1\n+GATGCTGCAGATCCACCAGA\t1\n+AAGTGGTTATTTGCTTTGTAAAGGCC\t1\n+TAATGAGACGAATCGTAAGTACGT\t1\n+TAGCTGCGGAACTCGGAAAA\t1\n+AACTCAGACTGTGGGCCATCACC\t1\n+CGAATGCTTGGGATACGTCTAAC\t1\n+TCTGGTGGATCAAGAACTCTTGGGC\t1\n+ATTGGTTTTTGCGGCTGTCCG\t1\n+TTTTGAATAGTATAATCCTGGTA\t1\n+TGCAGAGACTTGAGATCTCT\t1\n+CAGTCCAAGAAGCTCTGCAGTTTT\t1\n+GAAAAGGGTACTCTAGTCTCGGCCT\t1\n+TACCCACGGACAACACGCTGACAAC\t1\n+TGGGTGGGTTGTTCGTTATCTGCT\t1\n+CGAGTATTACATCAGGTACT\t1\n+ACATTTGCTAAATTCCAAGAGGGC\t1\n+GAGGCCTGGATGCACATTTTGT\t1\n+TCAGGTACCTTAAGTAGCGCGCGT\t1\n+TTAATTTGGCCGATCGGAACA\t1\n+TCAAGGGACTGACTCGTGTAGT\t1\n+TAATGCAACTTAACGAACCGAATGTT\t1\n+ACCGGACTCCCATCAGCTTTCAATC\t1\n+TTTTGGAACTCTTCGTTTTAGCCT\t1\n+TAGCTGCTGCAGTCCTCGGATCGC\t1\n+AATGGCACTGGAAGAATTCATGGG\t1\n+AGCGCCGCGTCTTCGGATATGTCTCT\t1\n+TCGGACAAAGAAAACTTGCCAGGCAA\t1\n+TGAGCAGCTATCCCAGACTGC\t1\n+GCTGGGCGTCGCCGGGGGTGGCACAC\t1\n+TGACTAGATCCACACTCATTAAAA\t1\n+TCGAATCCCATCCTCGTCGCCA\t1\n+CTTCCTACAACTGTGTGAGTACT\t1\n+TAGTGGCCGAACACTCGATAGTGAC\t1\n+ACCACACTACAAACTTCTGGAGAACT\t1\n+TTCGGATCAGCGGCAGTTTTGCGC\t1\n+TATTTCTGAAACTAACTATGGTCCT\t1\n+TTACCTAAGAATTGTTGATATTGCA\t1\n+CGGCCCATGTTGAAGTACACTCT\t1\n+TTTAAGGCTCCGTCGATGTTTGAAC\t1\n+AGCTCCTGCGTCATCGTGTGAACT\t1\n+TTTCCTTGGCAAGATCGCGTCGCA\t1\n+ATATTCTGCGTCATCATCG\t1\n+CGGAAGGGATAACCGCTGAAAGC\t1\n+TGAGTGGATCAGGTCTAGGAGG\t1\n+TCTCAAGAGTCCCTAAAGTAGCT\t1\n+GCAAGAATTAAAGCCCCATAAGCTC\t1\n+CCTCTGAGCAGCCAACGCCCGTATT\t1\n+CTCCGAGTCTGAATCTAG\t1\n+TATTGATCCTGATCTTCTATAGAATA\t1\n+ATTCATGTTGGCAGTCAAATGC\t1\n+ATCTGTTACGGCCCTTGAGCAA\t1\n+TGTGCCGGGCTGGCACCAACACTGC\t1\n+AATTCCACCACGTTCCCGTGG\t1\n+CTTAGCAATGCTTAAAGGAGTTGGC\t1\n+TTCATACGGCTGCCATTTTAATAT\t1\n+TGGAGGAGCTGAGCTTTTTCTCT\t1\n+TCCGACCCACTGCCGCGCTGCCGCCA\t1\n+CACCGTATCCCGAGCGTCTTGGCCG\t1\n+TCGGGTGACAAATGCTGTGTACGGCT\t1\n+ACGACAACCGTCATCCCG\t1\n+AATCACGAGGGTTGCATCCCGCCTG\t1\n+TAGGAGTGACTGCACCAAGGCTTGC\t1\n+ATGAGAGTCAGTAACTGC\t1\n+TTATGAATGTCTCCTCTGATCCGG\t1\n+ACCCAAAAAGTAATCGTTGACCTGC\t1\n+AATGTAGTCTGTCTGGTCTGG\t1\n+TTTGACCAGTCGGTCAGCCTCTTGACCC\t1\n+CGTTTCGATAGCCCACTCTGGCGGGA\t1\n+TTGGAGCTCAGAGCCTCTTCTCT\t1\n+TTTTTATTCTGAAGTTAACTT\t1\n+AAGAGAGCTATCCGTCGACAGTCT\t1\n+TCGCCGATCTATGCCTAATTTGGGCT\t1\n+TTTATTAATTTAACTTAGGTCTTGGC\t1\n+AGACTTGTAGAATTAGCGCGGGCGCGT\t1\n+TGAATTCCCGCCTGCCCACAGT\t1\n+TCGTCGCGGCTGATGGCAAAC\t1\n+CGCATGAATGGATTAACGACA\t1\n+ATAGCCCTGACAGCGTGC\t1\n+TTTCGCAAAGATGCAGATGTCGGC\t1\n+ACCCTTGACTACGCCTCTGTAGGCTC\t1\n+NATGCGCATTAACCTGTAGGC\t1\n+AAACAGACTGGACCAACACTC\t1\n+TAGAGCTTTATTACCCAAAACC\t1\n+TCATGACGTTCGGCGTGCCCGAA\t1\n+AAAGGTGCTGAAAGACTATACC\t1\n+TGTGCGATCGCGCGGCAACTGCGCA\t1\n+TCCTGGATCACGCTGTCATATTGA\t1\n+GCCTCGGTGGCGCATCGGCTC\t1\n+TATCCTCTGACTTCACATTATTCCA\t1\n+TCTTTCTCTGTGACTTAATTGGCG\t1\n+AACTGCACTAGTCCCGGCCTGC\t1\n+AGAAAGAACAAAAAGAAAACT\t1\n+AAGAAGCGGGATACTTAACCAT\t1\n+GCTTGGATCGGGGACCTTGAA\t1\n+CAATCGGAGGCCGGTTGACATC\t1\n+AACTGTTCCCTTTGCAAGTGTTAGT\t1\n+CCATATATGACGGCCTCATGGCACC\t1\n' |
| b |
| diff -r 9645d995fb3c -r 9185ca0a7b43 test-data/res_files/reads-sample-small.fastq/genome/dup_unique.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/res_files/reads-sample-small.fastq/genome/dup_unique.txt Wed Jan 16 08:18:13 2019 -0500 |
| b |
| b'@@ -0,0 +1,9974 @@\n+sequence\tcount\n+TGCTTGGACTACATATGGTTGAGG\t1985\n+TGCTTGGACTACATATGGTTGAGGG\t1319\n+TGCTTGGACTACATATGGTTGAG\t943\n+TATAGAATTGTAGAGCAAGACCT\t498\n+TGCTTGGACTACATATGGTTGAGGGT\t300\n+TTGATTAAGATAGCTGCTCCGCCT\t297\n+TATTGGCAAGCCTTTCGTCGAACC\t267\n+ATATCGCAGTCCATGCTG\t240\n+TTTACGGGATAGGACGGTAGCGC\t231\n+TATTGACTGGCGACGCTTTTGAGG\t229\n+TGCTTGGACTACATATGGTTGAGGGTTG\t226\n+TGAAAGACGCAGGATGGTCCGCCT\t226\n+TGAAAGACGCAGGATGGTCCGCCTG\t223\n+TATGTTTAGCGTTGTAGTCGCCT\t193\n+GATTGGACAGCCTCTGTAGTTTGC\t182\n+AACGCATATCGCAGTCCATGCTG\t173\n+TTCGATCTGCCGCGGGCTGCCGAGA\t168\n+TTTCTTCGGTTCGATATCAACGGA\t163\n+GGACTACATATGGTTGAGGGTTGTA\t160\n+TATAGAATTGTAGAGCAAGACCTTG\t144\n+CCATATCTAGGTTCTGTAGCCGAAG\t136\n+TATTTGATTGTTGGGCTACAAGCA\t130\n+TCAGAATCTTTGATTGTGCTCGCT\t128\n+ACTACATATGGTTGAGGGTTGTA\t125\n+TTCAGATGGTGCTCGACTATGGCCT\t117\n+CTGCTTGGACTACATATGGTTGAG\t115\n+TAACTGCGAAGTCGATCAGGTCT\t113\n+GCATATCGCAGTCCATGCTG\t107\n+TTTTTGATCAATTGGCACCATGCGA\t105\n+TTTTTGATCAATTGGCACCATGCGAA\t105\n+TCAGATGAGAGACAAATTAGAATTA\t103\n+TGTAGAGGATCGCTTGTCTGGGC\t99\n+AACTCTAAGCGGTGGATCACTCGGC\t94\n+TAGATGTGGCCTGAAGATGATTTTC\t91\n+TTAGTGTTGAATGTAGGCCAGGGA\t90\n+TGCTTGGACTACATATGGTTGA\t90\n+CTGCTTGGACTACATATGGTTGAGG\t86\n+TCATGAGACGTCTGCTTGTTTGGC\t83\n+GACTACATATGGTTGAGGGTTGTA\t83\n+TGCGTTTGGGATTGTCGGTGAGAC\t82\n+TAATACATCGATTTCGTGACGTCGC\t81\n+TATTTGATTGTTGGGCTACAAGCATT\t81\n+GCTTGGACTACATATGGTTGAGG\t81\n+TGCTTGGACTACATATGGTTG\t80\n+TACATATGGTTGAGGGTTGTA\t78\n+TTTCTTCGGTTCGATATCAACGGAT\t76\n+TATTGGCAAGCCTTTCGTCGAAC\t76\n+TCTTGTAAATACTTTGATTGGCCT\t74\n+TTTTCCGGGCTGAGCTTTCGCTTT\t73\n+TTCGATCGCCGACGTGTGAAGACGT\t73\n+TGCGTTTGGGATTGTCGGTGAGA\t71\n+ACATTTCCGTTTCTCGCGACT\t71\n+AACTCTAAGCGGTGGATCACTC\t70\n+TGCGTTTGGGATTGTCGGTGAGACG\t70\n+CCATGTCCCGTTGCTATCGACTAGA\t69\n+TATTGAAGGAATTGATATATGCC\t68\n+ACATATGGTTGAGGGTTGTA\t67\n+TTGGGTGTTGCAGTAAGAGCTG\t65\n+TACGAGTAGGATATCGATCTGGT\t65\n+TAGAAGACGATTTTCGGGCCGAAAT\t63\n+TGAATGGTTGAAATCGCTCGGCGA\t63\n+TAATGAGATCCCTCGGTTGCCTT\t63\n+TCCGAAAACAAGGCCCGTCGCTA\t62\n+TTCATCAGCGACTTGTGGGATTCC\t61\n+TGTGCTAGAAGACGATTTTCGGGC\t61\n+TTTTTGATCAATTGGCACCATGCG\t59\n+TTTACGGGATAGGACGGTAGCGCG\t58\n+CTACATATGGTTGAGGGTTGTA\t58\n+TCTGATGTTACGCCCGAAGAGA\t58\n+GAACGCATATCGCAGTCCATGCTG\t58\n+TGTATGAACAGTGGAAGTGG\t56\n+CCGTAAAGGCTTACATCTGGCT\t56\n+TGCTAGAAGACGATTTTCGGGC\t54\n+TTAGGACGAAACACAATTGGGGTG\t54\n+TAATTTGACACTGTTTGGAG\t54\n+TAAGTTGTTGGCTTTGAGTTTAAG\t53\n+CAAAGTCCTGGATACCATCGGCT\t52\n+TTGTAATGTAGCGGTCCATTCC\t51\n+TAATAGTCAGGGCGCGAATTTTTAA\t51\n+TATTGGCAAGCCTTTCGTCGAACCA\t50\n+CAGTATGTAGGACTCCCGGGG\t50\n+TTTGGTTAAAGCTGAATGTCTGCC\t50\n+TAATGAGATCCCTCGGTTGCCT\t49\n+TTTTCCGGGCTGAGCTTTCGC\t49\n+TTTGACAAAATATGCCCTTCACCT\t49\n+TGATTGCGTTGGTAACTGATGGGA\t48\n+TTTTAAACATTAGGCCGTCGAGCCAGA\t47\n+TGATTACGCATCATGTCTTGAATG\t46\n+TAGGACGGTAGCGCGAATGTGCTAGT\t46\n+TTTTAAACATTAGGCCGTCGAGCCAG\t45\n+TATCCAGAAAGGACTTCAGCCCTC\t44\n+TAGGACTCCCGGGGGAAACATGGTC\t44\n+TTTCTGTTTGGGTTTGGACT\t44\n+CAAGCATTCGACAAAGTCTGGC\t44\n+TATTGACTGGCGACGCTTTTGAG\t43\n+TACGAGTAGGATATCGATCTGGTG\t43\n+TTAAGTCTCTTTGGATGTTTTCACT\t43\n+TAGGACTCCCGGGGGAAACATGGT\t42\n+TAAAGAGGACAGGCCTTACAGGGTA\t42\n+TTGTAATGTAGCGGTCCATTCCA\t41\n+CCATATCTAGGTTCTGTAGCCGAAGG\t41\n+TTTAAGCTGGTAGGTGTAGAAGCCT\t41\n+CGCTGATGAAATCTCCAGGCTCAG\t41\n+TTCAGTATTGAGTTTTGGGCTTAGC\t41\n+TATGTTTAGCGTTGTAGTCGCCTGC\t41\n+TTTTTGATCAATTGGCACCATGC\t41\n+TCCGGGCTGAGCTTTCGCTTT\t40\n+TCTGATGTTACGCCCGAAGAGATAAC\t40\n+TTTCTGTTTGGGTTTGGAC\t40\n+AACTCTAAGCGGTGGATCACTCG\t40\n+TCAGATGAGAGACAAATTAGAAT\t40\n+TCATACTCTTCGATCTCGAGCCAG\t39\n+TTATTGAATCTTCTTGTATAAGAACT\t39\n+CAAATGTGGATACCGTTAAGCGAC\t38\n+TATTGAAGGAATTGATATATGC\t38\n+TAGAATAACAAGATGCGTAACGGCC\t38\n+TCAAAGTATTTACAAGACGGCTT\t38\n+TTGCGTTGGTAACTGATGGGAT\t38\n+TTGTAATGTAGCGGTCCATTCCAG\t38\n+TAATGAGATCCCTCGGTTGCCTTCT\t37\n+CACAGAGGCCAAGTCATTGAGCGCC\t37\n+TTGATTAAGATAGCTGCTCCGCC\t36\n+TCATACTCTTCGATCTCGAGCCA\t35\n+TAGGACGGTAGCGCGAATGTGCTAG\t35\n+TCTCGGTGGGCAGTAGACCGC\t35\n+AAGATTCTGAGAACCATCACTGGGG\t35\n+TGAATTGAGAGTCGGCGTTCGTCA\t34\n+TTTGACAAAATATGCCCTTCACC\t34\n+TTATTCTAATTAGTTAGGCTCTCCC\t34\n+TATTTGATTGTTGGGCTACAAGC\t34\n+TTTGGGTGTTGCAGTAAGAGCTG\t34\n+TTAAAGAGGACAGGCCTTACAGGGTA\t34\n+TAGGACTCCCGGGGGAAACATGG\t33\n+TGTAGAGGATCGCTTGTCTGGGCAG\t33\n+TCCCTGAGACCCTAACTTGTGA\t32\n+AACTCTAAGCGGTGGATCACTCGGCT\t32\n+TGTAGAGGATCGCTTGTCTGGG\t32\n+TTAGG'..b'GATTGCCCCCA\t1\n+CATAGATTTCCCGTAAAGGCTTACA\t1\n+GCTGTCTGCTGTAGCGCTCTCCG\t1\n+TTTTCTGTAGTCGTCCTCCGTT\t1\n+GCAGCGTCGCAGCAGGCGTCGGC\t1\n+GGTCCTATAAGCTTTGGAGCGGTC\t1\n+CATGTCGTGGCTATACAGGCA\t1\n+TAATGCTTTGATTTGGTCATCAT\t1\n+GTATGTAGGACTCCCGGGG\t1\n+TACGCATCATGTCTTGAATGG\t1\n+CTGCTGCTGCGGCTGGTCCT\t1\n+GTACTCGATCGCCTGAAGAAC\t1\n+GAGCAAGACCTTGTGATCTAGGC\t1\n+TGATCGGCCGGTAGGAGGCGGGCT\t1\n+TCGATGCGTGGCCTGGTACAGTCC\t1\n+AATACGATCTTCGTGCTTCGG\t1\n+ACTACATAAGTTACCATAGGACTTTA\t1\n+TTGAAACCAATCTGGACCTATGGCTC\t1\n+CGCGTGGCAGCTGGGCAGCGGA\t1\n+ATAACGTTAAGGCAATGC\t1\n+CCTCCGCCGCGATCCCGCTACCCTG\t1\n+TTATTGGATTGGGTTTGCTAAGAAG\t1\n+TCCAAGGTACTTTGCTGCGTTCGGC\t1\n+TGCTCGACTATGGCCTTGCTG\t1\n+TATTATTTGAAAATAGATTAGAAA\t1\n+TCTCGAATGTGGATAGCAGGAT\t1\n+TGCATAAGATATTCCGCCTCGAGAA\t1\n+CGCATGGTTCGACGAAAGGCTTGC\t1\n+GAGGTCAATCTGGTTGGTGGTTTC\t1\n+ATTGAAGGAATTGATATATGC\t1\n+GCTGTTCAACAAGAGCGGAGGACA\t1\n+GAAAAAACCCAAATCAACCATCGGC\t1\n+TATATGTATCTGTTTTGGCCC\t1\n+TGCTGTAGGAGCCAAGTTCTCCACCT\t1\n+TTGATTTGTTGGTAGAAGAAGGTT\t1\n+ACCACTATTATCGAAGAAACGCAG\t1\n+TCAGGTCTCTGTGCAGGGT\t1\n+CGTAAGCTTGCTGCGCGCGGAGC\t1\n+GTTATACAATGATCATGTGTT\t1\n+CTTTAATTATCATATATTGTA\t1\n+TGTGATCTAGGCTGAGCGGAG\t1\n+TCGGAGCTAAGCTCAACAACCGCAC\t1\n+TAAGCGGTGGATCACTCGGCT\t1\n+GCTTGATGACTGGTACTG\t1\n+AAGTTAATGATTACTTTGATTGCC\t1\n+ATTTATTGAAGGAATTGATATATGC\t1\n+CTTTCCGCTGTCAACGACCAG\t1\n+TGAATCTGATATAGAGAGCTGCAC\t1\n+AGCGCGAGCATGACGAACGCC\t1\n+TGGCATTGCCCCATAACTGTGAGCC\t1\n+CAATCTGGACCTATGGCTC\t1\n+TACCAGAGGCAGGTGGTCGGAGCTA\t1\n+CGGGAGTGGTATGCTGTTCAACAAGA\t1\n+CATCATCAACGTCCTGTCCAGAG\t1\n+CTCCGACAGAAGCCCCGCTACC\t1\n+CAACTCGTCCACGTAAAACGTCGCT\t1\n+TAACAAAGAGAGCCTGGAGCC\t1\n+TAGCACTTGTAAATTAAGACTCACT\t1\n+TAAAAATAAATGTTCGGGAC\t1\n+TGAGCGGAGAACCAGAGTTGAT\t1\n+ATCCCAAACGCAGACATCG\t1\n+GATGGTGCTCGACTATGGCCT\t1\n+CAAGGTAGTGTCCTCGGCCC\t1\n+AATTCGATCGCCGACGTGTGAA\t1\n+GCTGATCCGACTTAATCAACA\t1\n+TTTTTTCTAGGAGGCTTGTTTTC\t1\n+GTAAAACGTCGCTTACGCAGAG\t1\n+AACTGGCCAACGCTCTGAAACAAGAAG\t1\n+TAAGGCTTTACGCGGCTGACGC\t1\n+CTTGTACTCAAAGCTCCTCCACGGCT\t1\n+TCCTTGGCGGAGGTATCGTAGTGAG\t1\n+TGCTGCGTTCGGCTGTGG\t1\n+GAATCCCACAAGTCGCTGATGAAA\t1\n+TATTGGCGGAGGCTTTGTTTTCTT\t1\n+AACGCATATCGCAGTCCATGCTGT\t1\n+CAATGACTTCGGCTACCTCGCAG\t1\n+TTCTGTAGTCGTCCTCCGTTTTCGT\t1\n+TATTTTTCCAACTGTTCT\t1\n+TGCTTTTCCGTCGGGATG\t1\n+TGGGGGCGTAGCATTACTAGTGC\t1\n+GTTGTTGGCTTTGAGTTTAAG\t1\n+TGCAAGTAGTCCTGAAGG\t1\n+GATAAGCGTCAGCTTCTGCGGACC\t1\n+CCGTTGTGGTTGTTGTTACTG\t1\n+GGGATGTCGGCTGTATAGATGA\t1\n+CACCGTGGTACGTTCGGAGTGAAAAC\t1\n+GATCCCAGATCCGCTGTGTTT\t1\n+TATCGTCGGCAAATGTGGATA\t1\n+TGCCGAGATATGCTGCGAGTTG\t1\n+CCGTGATTGCGTTGGTAACTGAT\t1\n+TGAGGACGTATTTTGAGAGACC\t1\n+TCGCTTCGCTTTCGACTCCGGT\t1\n+CCGGAAATGATCATCCAGC\t1\n+CAAATGATCAACAGGACTCCACAAC\t1\n+TACCGCTGAGGACGTGCCGCTGG\t1\n+TAGATTGGACAGCCTCTGTAGTT\t1\n+CGGGTATCTTGTTGGTCCTCCTG\t1\n+TCTGAGAACCATCACTGGGGCACC\t1\n+CACCATCTGAAGACCCACCAG\t1\n+CTACTAGCACATTCGCGCTAC\t1\n+GCTCGATGCGTGGCCTGGTACAGTC\t1\n+TCAGAACACATGCCATAAAG\t1\n+GTGTGTGAATATCGAGAACCT\t1\n+TTGCCTTTTGTCGGAGAAATCCGT\t1\n+TTTAAAATCAGGTATGACGCC\t1\n+TTCCTTAAGTTCCGTGATTGCGTT\t1\n+AACATCGCTTCTATCTGACCGGA\t1\n+AAAGTCACTGTGGCGAGCCCA\t1\n+TTCGCTGTGGAAGGCCACGCGCGCAAT\t1\n+CTAGAGGTGGCTCCAGGCTCT\t1\n+TGACCTCGTGTGGCCATACTCTT\t1\n+TGTTGCGGCTGCTGCGGCT\t1\n+CACTCCGTTGAGGGCGTCT\t1\n+TTCAGCTCTTTGTAGATTGGACA\t1\n+TTGTTTCAGAGCGTTGGCCAGTTT\t1\n+AAGGAATTCATCAGGTGGCTGGGC\t1\n+GTGAGTTGCTCTATGTATCGGC\t1\n+CAAGCCGGAAAGGGAGCCCGCCTCCTAC\t1\n+TTGATCAAGGTAGAGTTGTCGCGT\t1\n+GACCTTGTGATCTAGGCTGAGCGGA\t1\n+TTCTCCTACGTCTCACCG\t1\n+TACACATCCTGATTCTGCCAGCGCTC\t1\n+AAAACGTCGCTTACGCAGAGA\t1\n+TTGCTGGTAGATACCGCTGAGGA\t1\n+GAAGTACGCGTTGTTGCGCTG\t1\n+ACAACAAATGTTAAACTGATTT\t1\n+TGTGTCCGCACTTCGTGCCT\t1\n+GTAGGATCACGGTAGAAG\t1\n+GCGGAAAGAATGCAGACCTTTGGTCAGC\t1\n+GGCTAGCTCAGTCGGTAGA\t1\n+TGATTTGTTGGTAGAAGAAG\t1\n+ATCAGACGGAGTGCTAGGGGCT\t1\n+CGATAAGGAATTCATCAGGTGGCT\t1\n+CAAATCGAGCAACTCGTCCACG\t1\n+CCACACGGAAACTGGCCAACGCTC\t1\n+GCAAAAATTGAAGTCGATCCCGG\t1\n+TTCAGTCGGTGGGCGAAGA\t1\n+TCCAGAAAGGACTTCAGCCCTC\t1\n+TCGCCTGTACTAATTCACCT\t1\n+ACCGCCGGCGCAAGTTGCACCTTGG\t1\n+TATCGACTAGAGGCGCCTTCCTCGTG\t1\n+TTGTAAGGATTATGGAAGCCCAG\t1\n+GATGAAGCGACTGTGTGGTTCTTACCA\t1\n+GACTTTTCTGTAGTCGTCCTCCGTT\t1\n+TTTCAGGTCTCTGTGCAGGGTGGTG\t1\n+ACCCTTCGGCTACAGAACCTAGATA\t1\n+TAATAATAACGTTAAGGCA\t1\n+TCTTGAAGAGTGGTTGGGGCTGCC\t1\n+CAAAGATTCTGAGAACCATCACT\t1\n+TTCAGGAGATCGTGCACTAATAGAT\t1\n+CGGTAGAGCATGAGACTC\t1\n' |
| b |
| diff -r 9645d995fb3c -r 9185ca0a7b43 test-data/res_files/reads-sample-small.fastq/genome/reads-sample-small.fastq_18-29_minus.bedgraph --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/res_files/reads-sample-small.fastq/genome/reads-sample-small.fastq_18-29_minus.bedgraph Wed Jan 16 08:18:13 2019 -0500 |
| b |
| b'@@ -0,0 +1,4795 @@\n+chrom_1\t0\t3964\t0\n+chrom_1\t3964\t3988\t25.6148\n+chrom_1\t3988\t8675\t0\n+chrom_1\t8675\t8700\t25.6148\n+chrom_1\t8700\t9636\t0\n+chrom_1\t9636\t9661\t25.6148\n+chrom_1\t9661\t10201\t0\n+chrom_1\t10201\t10226\t25.6148\n+chrom_1\t10226\t11637\t0\n+chrom_1\t11637\t11661\t25.6148\n+chrom_1\t11661\t12140\t0\n+chrom_1\t12140\t12161\t25.6148\n+chrom_1\t12161\t12187\t0\n+chrom_1\t12187\t12211\t25.6148\n+chrom_1\t12211\t12214\t0\n+chrom_1\t12214\t12215\t25.6148\n+chrom_1\t12215\t12238\t51.2295\n+chrom_1\t12238\t13134\t0\n+chrom_1\t13134\t13159\t25.6148\n+chrom_1\t13159\t13465\t0\n+chrom_1\t13465\t13470\t25.6148\n+chrom_1\t13470\t13491\t51.2295\n+chrom_1\t13491\t13493\t25.6148\n+chrom_1\t13493\t14233\t0\n+chrom_1\t14233\t14258\t25.6148\n+chrom_1\t14258\t14318\t0\n+chrom_1\t14318\t14321\t25.6148\n+chrom_1\t14321\t14344\t51.2295\n+chrom_1\t14344\t14438\t0\n+chrom_1\t14438\t14463\t25.6148\n+chrom_1\t14463\t14500\t0\n+chrom_1\t14500\t14523\t25.6148\n+chrom_1\t14523\t14778\t0\n+chrom_1\t14778\t14790\t51.2295\n+chrom_1\t14790\t14803\t76.8443\n+chrom_1\t14803\t14804\t51.2295\n+chrom_1\t14804\t14814\t25.6148\n+chrom_1\t14814\t14840\t0\n+chrom_1\t14840\t14860\t51.2295\n+chrom_1\t14860\t14865\t25.6148\n+chrom_1\t14865\t14968\t0\n+chrom_1\t14968\t14973\t25.6148\n+chrom_1\t14973\t14977\t51.2295\n+chrom_1\t14977\t14985\t76.8443\n+chrom_1\t14985\t14992\t128.074\n+chrom_1\t14992\t14999\t102.459\n+chrom_1\t14999\t15002\t76.8443\n+chrom_1\t15002\t15005\t51.2295\n+chrom_1\t15005\t15009\t76.8443\n+chrom_1\t15009\t15025\t25.6148\n+chrom_1\t15025\t15089\t0\n+chrom_1\t15089\t15112\t25.6148\n+chrom_1\t15112\t15114\t51.2295\n+chrom_1\t15114\t15130\t25.6148\n+chrom_1\t15130\t15132\t76.8443\n+chrom_1\t15132\t15134\t128.074\n+chrom_1\t15134\t15137\t102.459\n+chrom_1\t15137\t15155\t128.074\n+chrom_1\t15155\t15157\t76.8443\n+chrom_1\t15157\t15160\t0\n+chrom_1\t15160\t15161\t51.2295\n+chrom_1\t15161\t15164\t102.459\n+chrom_1\t15164\t15184\t128.074\n+chrom_1\t15184\t15185\t76.8443\n+chrom_1\t15185\t15201\t0\n+chrom_1\t15201\t15225\t25.6148\n+chrom_1\t15225\t15250\t0\n+chrom_1\t15250\t15251\t25.6148\n+chrom_1\t15251\t15255\t76.8443\n+chrom_1\t15255\t15260\t102.459\n+chrom_1\t15260\t15274\t128.074\n+chrom_1\t15274\t15287\t25.6148\n+chrom_1\t15287\t15288\t51.2295\n+chrom_1\t15288\t15289\t76.8443\n+chrom_1\t15289\t15290\t204.918\n+chrom_1\t15290\t15291\t281.762\n+chrom_1\t15291\t15306\t307.377\n+chrom_1\t15306\t15313\t281.762\n+chrom_1\t15313\t15315\t128.074\n+chrom_1\t15315\t15348\t0\n+chrom_1\t15348\t15349\t25.6148\n+chrom_1\t15349\t15350\t51.2295\n+chrom_1\t15350\t15366\t76.8443\n+chrom_1\t15366\t15370\t102.459\n+chrom_1\t15370\t15372\t76.8443\n+chrom_1\t15372\t15390\t25.6148\n+chrom_1\t15390\t15444\t0\n+chrom_1\t15444\t15445\t51.2295\n+chrom_1\t15445\t15446\t76.8443\n+chrom_1\t15446\t15469\t128.074\n+chrom_1\t15469\t15470\t51.2295\n+chrom_1\t15470\t15471\t25.6148\n+chrom_1\t15471\t15476\t0\n+chrom_1\t15476\t15477\t25.6148\n+chrom_1\t15477\t15478\t51.2295\n+chrom_1\t15478\t15482\t102.459\n+chrom_1\t15482\t15499\t128.074\n+chrom_1\t15499\t15500\t153.689\n+chrom_1\t15500\t15504\t102.459\n+chrom_1\t15504\t15506\t51.2295\n+chrom_1\t15506\t15523\t25.6148\n+chrom_1\t15523\t15534\t0\n+chrom_1\t15534\t15535\t51.2295\n+chrom_1\t15535\t15536\t76.8443\n+chrom_1\t15536\t15558\t102.459\n+chrom_1\t15558\t15559\t51.2295\n+chrom_1\t15559\t15560\t128.074\n+chrom_1\t15560\t15580\t76.8443\n+chrom_1\t15580\t15584\t51.2295\n+chrom_1\t15584\t15586\t25.6148\n+chrom_1\t15586\t15587\t281.762\n+chrom_1\t15587\t15594\t307.377\n+chrom_1\t15594\t15598\t358.607\n+chrom_1\t15598\t15609\t461.066\n+chrom_1\t15609\t15620\t153.689\n+chrom_1\t15620\t15622\t102.459\n+chrom_1\t15622\t15623\t25.6148\n+chrom_1\t15623\t15688\t0\n+chrom_1\t15688\t15700\t25.6148\n+chrom_1\t15700\t15714\t76.8443\n+chrom_1\t15714\t15722\t51.2295\n+chrom_1\t15722\t15726\t76.8443\n+chrom_1\t15726\t15727\t51.2295\n+chrom_1\t15727\t15728\t102.459\n+chrom_1\t15728\t15730\t128.074\n+chrom_1\t15730\t15745\t204.918\n+chrom_1\t15745\t15750\t179.303\n+chrom_1\t15750\t15752\t76.8443\n+chrom_1\t15752\t15754\t51.2295\n+chrom_1\t15754\t15791\t0\n+chrom_1\t15791\t15793\t51.2295\n+chrom_1\t15793\t15794\t76.8443\n+chrom_1\t15794\t15796\t153.689\n+chrom_1\t15796\t15805\t179.303\n+chrom_1\t15805\t15806\t281.762\n+chrom_1\t15806\t15815\t307.377\n+chrom_1\t15815\t15816\t256.148\n+chrom_1\t15816\t15817\t230.533\n+chrom_1\t15817\t15819\t153.689\n+chrom_1\t15819\t15825\t128.074\n+chrom_1\t15825\t15828\t76.8443\n+chrom_1\t15828\t15925\t0\n+chrom_1\t15925\t15926\t128.074\n+chrom_1\t15926\t15'..b'\t51.2295\n+chrom_1\t85202\t85205\t25.6148\n+chrom_1\t85205\t85252\t0\n+chrom_1\t85252\t85273\t25.6148\n+chrom_1\t85273\t85366\t0\n+chrom_1\t85366\t85390\t25.6148\n+chrom_1\t85390\t85640\t0\n+chrom_1\t85640\t85662\t25.6148\n+chrom_1\t85662\t85759\t0\n+chrom_1\t85759\t85783\t25.6148\n+chrom_1\t85783\t86402\t0\n+chrom_1\t86402\t86424\t25.6148\n+chrom_1\t86424\t86453\t0\n+chrom_1\t86453\t86474\t25.6148\n+chrom_1\t86474\t86632\t0\n+chrom_1\t86632\t86658\t25.6148\n+chrom_1\t86658\t86941\t0\n+chrom_1\t86941\t86967\t25.6148\n+chrom_1\t86967\t87002\t0\n+chrom_1\t87002\t87022\t25.6148\n+chrom_1\t87022\t87066\t0\n+chrom_1\t87066\t87087\t25.6148\n+chrom_1\t87087\t87142\t0\n+chrom_1\t87142\t87163\t25.6148\n+chrom_1\t87163\t87223\t0\n+chrom_1\t87223\t87244\t25.6148\n+chrom_1\t87244\t87446\t0\n+chrom_1\t87446\t87467\t25.6148\n+chrom_1\t87467\t87524\t0\n+chrom_1\t87524\t87546\t25.6148\n+chrom_1\t87546\t87581\t0\n+chrom_1\t87581\t87582\t25.6148\n+chrom_1\t87582\t87602\t51.2295\n+chrom_1\t87602\t87665\t0\n+chrom_1\t87665\t87683\t25.6148\n+chrom_1\t87683\t87819\t0\n+chrom_1\t87819\t87839\t25.6148\n+chrom_1\t87839\t87853\t0\n+chrom_1\t87853\t87878\t25.6148\n+chrom_1\t87878\t88309\t0\n+chrom_1\t88309\t88330\t25.6148\n+chrom_1\t88330\t88443\t0\n+chrom_1\t88443\t88464\t25.6148\n+chrom_1\t88464\t88710\t0\n+chrom_1\t88710\t88731\t25.6148\n+chrom_1\t88731\t89102\t0\n+chrom_1\t89102\t89120\t25.6148\n+chrom_1\t89120\t89812\t0\n+chrom_1\t89812\t89833\t25.6148\n+chrom_1\t89833\t89999\t0\n+chrom_2\t0\t22924\t0\n+chrom_2\t22924\t22934\t25.6148\n+chrom_2\t22934\t22936\t76.8443\n+chrom_2\t22936\t22940\t102.459\n+chrom_2\t22940\t22942\t128.074\n+chrom_2\t22942\t22946\t102.459\n+chrom_2\t22946\t22956\t153.689\n+chrom_2\t22956\t22958\t537.91\n+chrom_2\t22958\t22961\t563.525\n+chrom_2\t22961\t22962\t614.754\n+chrom_2\t22962\t22963\t691.598\n+chrom_2\t22963\t22964\t1306.35\n+chrom_2\t22964\t22965\t1511.27\n+chrom_2\t22965\t22968\t1664.96\n+chrom_2\t22968\t22970\t2638.32\n+chrom_2\t22970\t22971\t2663.93\n+chrom_2\t22971\t22972\t3586.07\n+chrom_2\t22972\t22973\t3944.67\n+chrom_2\t22973\t22974\t3995.9\n+chrom_2\t22974\t22977\t4021.52\n+chrom_2\t22977\t22980\t4047.13\n+chrom_2\t22980\t22981\t4021.52\n+chrom_2\t22981\t22982\t3381.15\n+chrom_2\t22982\t22983\t2996.93\n+chrom_2\t22983\t22984\t2715.16\n+chrom_2\t22984\t22985\t2689.55\n+chrom_2\t22985\t22986\t2612.7\n+chrom_2\t22986\t22989\t2561.48\n+chrom_2\t22989\t22991\t2382.17\n+chrom_2\t22991\t22992\t2202.87\n+chrom_2\t22992\t22993\t1997.95\n+chrom_2\t22993\t22994\t1203.89\n+chrom_2\t22994\t22995\t76.8443\n+chrom_2\t22995\t22996\t51.2295\n+chrom_2\t22996\t32272\t0\n+chrom_2\t32272\t32289\t25.6148\n+chrom_2\t32289\t32292\t51.2295\n+chrom_2\t32292\t32296\t76.8443\n+chrom_2\t32296\t32310\t51.2295\n+chrom_2\t32310\t39255\t0\n+chrom_2\t39255\t39276\t25.6148\n+chrom_2\t39276\t44459\t0\n+chrom_2\t44459\t44485\t25.6148\n+chrom_2\t44485\t49999\t0\n+chrom_4\t0\t575\t0\n+chrom_4\t575\t596\t25.6148\n+chrom_4\t596\t876\t0\n+chrom_4\t876\t901\t128.074\n+chrom_4\t901\t919\t0\n+chrom_4\t919\t944\t51.2295\n+chrom_4\t944\t1149\t0\n+chrom_4\t1149\t1158\t25.6148\n+chrom_4\t1158\t1174\t51.2295\n+chrom_4\t1174\t1184\t25.6148\n+chrom_4\t1184\t2000\t0\n+chrom_5\t0\t450\t0\n+chrom_5\t450\t468\t51.2295\n+chrom_5\t468\t613\t0\n+chrom_5\t613\t615\t25.6148\n+chrom_5\t615\t616\t102.459\n+chrom_5\t616\t632\t179.303\n+chrom_5\t632\t635\t204.918\n+chrom_5\t635\t638\t51.2295\n+chrom_5\t638\t644\t25.6148\n+chrom_5\t644\t646\t51.2295\n+chrom_5\t646\t649\t76.8443\n+chrom_5\t649\t652\t102.459\n+chrom_5\t652\t654\t76.8443\n+chrom_5\t654\t659\t102.459\n+chrom_5\t659\t665\t128.074\n+chrom_5\t665\t667\t102.459\n+chrom_5\t667\t673\t153.689\n+chrom_5\t673\t675\t204.918\n+chrom_5\t675\t679\t179.303\n+chrom_5\t679\t682\t307.377\n+chrom_5\t682\t688\t281.762\n+chrom_5\t688\t692\t230.533\n+chrom_5\t692\t693\t204.918\n+chrom_5\t693\t695\t179.303\n+chrom_5\t695\t699\t153.689\n+chrom_5\t699\t700\t179.303\n+chrom_5\t700\t712\t51.2295\n+chrom_5\t712\t715\t76.8443\n+chrom_5\t715\t716\t102.459\n+chrom_5\t716\t721\t76.8443\n+chrom_5\t721\t723\t51.2295\n+chrom_5\t723\t739\t102.459\n+chrom_5\t739\t744\t153.689\n+chrom_5\t744\t750\t76.8443\n+chrom_5\t750\t751\t179.303\n+chrom_5\t751\t753\t153.689\n+chrom_5\t753\t756\t179.303\n+chrom_5\t756\t762\t230.533\n+chrom_5\t762\t765\t256.148\n+chrom_5\t765\t771\t230.533\n+chrom_5\t771\t772\t204.918\n+chrom_5\t772\t774\t128.074\n+chrom_5\t774\t778\t102.459\n+chrom_5\t778\t783\t51.2295\n+chrom_5\t783\t786\t76.8443\n+chrom_5\t786\t804\t51.2295\n+chrom_5\t804\t1999\t0\n+chrom_6\t0\t3076\t0\n+chrom_6\t3076\t3096\t25.6148\n+chrom_6\t3096\t3999\t0\n' |
| b |
| diff -r 9645d995fb3c -r 9185ca0a7b43 test-data/res_files/reads-sample-small.fastq/genome/reads-sample-small.fastq_18-29_plus.bedgraph --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/res_files/reads-sample-small.fastq/genome/reads-sample-small.fastq_18-29_plus.bedgraph Wed Jan 16 08:18:13 2019 -0500 |
| b |
| b'@@ -0,0 +1,6111 @@\n+chrom_1\t0\t1967\t0\n+chrom_1\t1967\t1991\t25.6148\n+chrom_1\t1991\t2932\t0\n+chrom_1\t2932\t2954\t25.6148\n+chrom_1\t2954\t3456\t0\n+chrom_1\t3456\t3481\t25.6148\n+chrom_1\t3481\t7648\t0\n+chrom_1\t7648\t7671\t25.6148\n+chrom_1\t7671\t7953\t0\n+chrom_1\t7953\t7978\t25.6148\n+chrom_1\t7978\t8721\t0\n+chrom_1\t8721\t8742\t25.6148\n+chrom_1\t8742\t8747\t51.2295\n+chrom_1\t8747\t8758\t25.6148\n+chrom_1\t8758\t8767\t51.2295\n+chrom_1\t8767\t8783\t25.6148\n+chrom_1\t8783\t9642\t0\n+chrom_1\t9642\t9668\t25.6148\n+chrom_1\t9668\t10407\t0\n+chrom_1\t10407\t10428\t25.6148\n+chrom_1\t10428\t14236\t0\n+chrom_1\t14236\t14261\t25.6148\n+chrom_1\t14261\t14309\t0\n+chrom_1\t14309\t14336\t25.6148\n+chrom_1\t14336\t14439\t0\n+chrom_1\t14439\t14463\t25.6148\n+chrom_1\t14463\t14523\t0\n+chrom_1\t14523\t14544\t25.6148\n+chrom_1\t14544\t14551\t0\n+chrom_1\t14551\t14552\t25.6148\n+chrom_1\t14552\t14554\t76.8443\n+chrom_1\t14554\t14578\t179.303\n+chrom_1\t14578\t14580\t25.6148\n+chrom_1\t14580\t14592\t0\n+chrom_1\t14592\t14616\t25.6148\n+chrom_1\t14616\t14979\t0\n+chrom_1\t14979\t15004\t25.6148\n+chrom_1\t15004\t15062\t0\n+chrom_1\t15062\t15087\t25.6148\n+chrom_1\t15087\t15089\t0\n+chrom_1\t15089\t15092\t25.6148\n+chrom_1\t15092\t15115\t128.074\n+chrom_1\t15115\t15117\t102.459\n+chrom_1\t15117\t15139\t0\n+chrom_1\t15139\t15164\t25.6148\n+chrom_1\t15164\t15258\t0\n+chrom_1\t15258\t15260\t25.6148\n+chrom_1\t15260\t15264\t76.8443\n+chrom_1\t15264\t15269\t102.459\n+chrom_1\t15269\t15283\t128.074\n+chrom_1\t15283\t15284\t102.459\n+chrom_1\t15284\t15290\t51.2295\n+chrom_1\t15290\t15293\t25.6148\n+chrom_1\t15293\t15395\t0\n+chrom_1\t15395\t15399\t25.6148\n+chrom_1\t15399\t15400\t76.8443\n+chrom_1\t15400\t15407\t281.762\n+chrom_1\t15407\t15420\t307.377\n+chrom_1\t15420\t15421\t281.762\n+chrom_1\t15421\t15422\t204.918\n+chrom_1\t15422\t15423\t102.459\n+chrom_1\t15423\t15424\t51.2295\n+chrom_1\t15424\t15433\t25.6148\n+chrom_1\t15433\t15460\t0\n+chrom_1\t15460\t15484\t25.6148\n+chrom_1\t15484\t15528\t0\n+chrom_1\t15528\t15529\t25.6148\n+chrom_1\t15529\t15530\t51.2295\n+chrom_1\t15530\t15545\t76.8443\n+chrom_1\t15545\t15546\t102.459\n+chrom_1\t15546\t15548\t486.68\n+chrom_1\t15548\t15550\t461.066\n+chrom_1\t15550\t15555\t435.451\n+chrom_1\t15555\t15567\t409.836\n+chrom_1\t15567\t15569\t384.221\n+chrom_1\t15569\t15570\t204.918\n+chrom_1\t15570\t15572\t25.6148\n+chrom_1\t15572\t15716\t0\n+chrom_1\t15716\t15739\t25.6148\n+chrom_1\t15739\t15801\t0\n+chrom_1\t15801\t15824\t25.6148\n+chrom_1\t15824\t15970\t0\n+chrom_1\t15970\t15993\t76.8443\n+chrom_1\t15993\t16004\t0\n+chrom_1\t16004\t16027\t76.8443\n+chrom_1\t16027\t16028\t25.6148\n+chrom_1\t16028\t16229\t0\n+chrom_1\t16229\t16232\t25.6148\n+chrom_1\t16232\t16237\t51.2295\n+chrom_1\t16237\t16239\t76.8443\n+chrom_1\t16239\t16250\t128.074\n+chrom_1\t16250\t16256\t102.459\n+chrom_1\t16256\t16262\t76.8443\n+chrom_1\t16262\t16336\t0\n+chrom_1\t16336\t16338\t256.148\n+chrom_1\t16338\t16339\t281.762\n+chrom_1\t16339\t16342\t307.377\n+chrom_1\t16342\t16359\t332.992\n+chrom_1\t16359\t16360\t128.074\n+chrom_1\t16360\t16363\t76.8443\n+chrom_1\t16363\t16364\t51.2295\n+chrom_1\t16364\t16365\t25.6148\n+chrom_1\t16365\t16380\t0\n+chrom_1\t16380\t16402\t25.6148\n+chrom_1\t16402\t16496\t0\n+chrom_1\t16496\t16521\t25.6148\n+chrom_1\t16521\t16619\t0\n+chrom_1\t16619\t16628\t25.6148\n+chrom_1\t16628\t16630\t76.8443\n+chrom_1\t16630\t16643\t256.148\n+chrom_1\t16643\t16653\t230.533\n+chrom_1\t16653\t16654\t153.689\n+chrom_1\t16654\t16655\t76.8443\n+chrom_1\t16655\t16656\t25.6148\n+chrom_1\t16656\t16661\t0\n+chrom_1\t16661\t16685\t25.6148\n+chrom_1\t16685\t16772\t0\n+chrom_1\t16772\t16798\t25.6148\n+chrom_1\t16798\t16800\t51.2295\n+chrom_1\t16800\t16801\t179.303\n+chrom_1\t16801\t16808\t461.066\n+chrom_1\t16808\t16810\t486.68\n+chrom_1\t16810\t16811\t512.295\n+chrom_1\t16811\t16819\t537.91\n+chrom_1\t16819\t16823\t512.295\n+chrom_1\t16823\t16825\t461.066\n+chrom_1\t16825\t16829\t128.074\n+chrom_1\t16829\t16835\t102.459\n+chrom_1\t16835\t16849\t51.2295\n+chrom_1\t16849\t16850\t25.6148\n+chrom_1\t16850\t16864\t0\n+chrom_1\t16864\t16866\t25.6148\n+chrom_1\t16866\t16867\t76.8443\n+chrom_1\t16867\t16868\t179.303\n+chrom_1\t16868\t16869\t307.377\n+chrom_1\t16869\t16870\t332.992\n+chrom_1\t16870\t16875\t358.607\n+chrom_1\t16875\t16881\t384.221\n+chrom_1\t16881\t16883\t435.451\n+chrom_1\t16883\t16884\t461.066\n+chrom_1\t16884\t16885\t537.91\n+chrom_1\t16885\t16886\t589.139\n+chrom_1\t16886\t16887\t640.369\n+chrom_1\t16887\t16892\t614.754\n+chrom_1\t16892\t16893\t435.451\n+chrom_1\t16893\t16894\t33'..b'hrom_4\t1207\t1208\t150615\n+chrom_4\t1208\t1209\t153381\n+chrom_4\t1209\t1210\t155200\n+chrom_4\t1210\t1211\t155712\n+chrom_4\t1211\t1212\t156250\n+chrom_4\t1212\t1215\t156378\n+chrom_4\t1215\t1216\t156506\n+chrom_4\t1216\t1217\t156481\n+chrom_4\t1217\t1218\t156327\n+chrom_4\t1218\t1219\t155891\n+chrom_4\t1219\t1220\t155686\n+chrom_4\t1220\t1221\t153356\n+chrom_4\t1221\t1222\t150768\n+chrom_4\t1222\t1223\t123207\n+chrom_4\t1223\t1224\t67751\n+chrom_4\t1224\t1225\t32786.9\n+chrom_4\t1225\t1226\t24564.5\n+chrom_4\t1226\t1227\t24154.7\n+chrom_4\t1227\t1228\t18032.8\n+chrom_4\t1228\t1229\t17494.9\n+chrom_4\t1229\t1230\t1460.04\n+chrom_4\t1230\t1231\t435.451\n+chrom_4\t1231\t1232\t358.607\n+chrom_4\t1232\t1233\t332.992\n+chrom_4\t1233\t1234\t128.074\n+chrom_4\t1234\t1235\t102.459\n+chrom_4\t1235\t1239\t51.2295\n+chrom_4\t1239\t1242\t25.6148\n+chrom_4\t1242\t1300\t0\n+chrom_4\t1300\t1319\t25.6148\n+chrom_4\t1319\t1376\t0\n+chrom_4\t1376\t1385\t25.6148\n+chrom_4\t1385\t1386\t51.2295\n+chrom_4\t1386\t1387\t102.459\n+chrom_4\t1387\t1388\t332.992\n+chrom_4\t1388\t1389\t537.91\n+chrom_4\t1389\t1390\t1639.34\n+chrom_4\t1390\t1391\t3457.99\n+chrom_4\t1391\t1392\t3509.22\n+chrom_4\t1392\t1396\t3534.84\n+chrom_4\t1396\t1408\t3509.22\n+chrom_4\t1408\t1409\t3483.61\n+chrom_4\t1409\t1410\t3406.76\n+chrom_4\t1410\t1411\t3227.46\n+chrom_4\t1411\t1412\t3125\n+chrom_4\t1412\t1413\t2945.7\n+chrom_4\t1413\t1414\t1946.72\n+chrom_4\t1414\t1415\t819.672\n+chrom_4\t1415\t1416\t76.8443\n+chrom_4\t1416\t1431\t0\n+chrom_4\t1431\t1441\t25.6148\n+chrom_4\t1441\t1456\t51.2295\n+chrom_4\t1456\t1467\t25.6148\n+chrom_4\t1467\t1543\t0\n+chrom_4\t1543\t1566\t25.6148\n+chrom_4\t1566\t1587\t0\n+chrom_4\t1587\t1605\t25.6148\n+chrom_4\t1605\t1733\t0\n+chrom_4\t1733\t1754\t25.6148\n+chrom_4\t1754\t2000\t0\n+chrom_5\t0\t619\t0\n+chrom_5\t619\t640\t25.6148\n+chrom_5\t640\t674\t0\n+chrom_5\t674\t692\t25.6148\n+chrom_5\t692\t695\t51.2295\n+chrom_5\t695\t709\t25.6148\n+chrom_5\t709\t712\t51.2295\n+chrom_5\t712\t730\t25.6148\n+chrom_5\t730\t733\t0\n+chrom_5\t733\t737\t25.6148\n+chrom_5\t737\t752\t51.2295\n+chrom_5\t752\t754\t153.689\n+chrom_5\t754\t755\t128.074\n+chrom_5\t755\t765\t102.459\n+chrom_5\t765\t773\t128.074\n+chrom_5\t773\t774\t102.459\n+chrom_5\t774\t786\t25.6148\n+chrom_5\t786\t1414\t0\n+chrom_5\t1414\t1425\t76.8443\n+chrom_5\t1425\t1426\t102.459\n+chrom_5\t1426\t1438\t128.074\n+chrom_5\t1438\t1440\t76.8443\n+chrom_5\t1440\t1444\t51.2295\n+chrom_5\t1444\t1452\t25.6148\n+chrom_5\t1452\t1454\t0\n+chrom_5\t1454\t1457\t25.6148\n+chrom_5\t1457\t1462\t51.2295\n+chrom_5\t1462\t1463\t76.8443\n+chrom_5\t1463\t1465\t102.459\n+chrom_5\t1465\t1475\t128.074\n+chrom_5\t1475\t1482\t102.459\n+chrom_5\t1482\t1487\t76.8443\n+chrom_5\t1487\t1488\t51.2295\n+chrom_5\t1488\t1493\t25.6148\n+chrom_5\t1493\t1503\t0\n+chrom_5\t1503\t1504\t128.074\n+chrom_5\t1504\t1505\t307.377\n+chrom_5\t1505\t1523\t384.221\n+chrom_5\t1523\t1526\t51.2295\n+chrom_5\t1526\t1528\t25.6148\n+chrom_5\t1528\t1648\t0\n+chrom_5\t1648\t1669\t25.6148\n+chrom_5\t1669\t1782\t0\n+chrom_5\t1782\t1803\t25.6148\n+chrom_5\t1803\t1999\t0\n+chrom_6\t0\t440\t0\n+chrom_6\t440\t464\t25.6148\n+chrom_6\t464\t819\t0\n+chrom_6\t819\t845\t25.6148\n+chrom_6\t845\t854\t0\n+chrom_6\t854\t873\t25.6148\n+chrom_6\t873\t885\t0\n+chrom_6\t885\t905\t51.2295\n+chrom_6\t905\t906\t25.6148\n+chrom_6\t906\t1038\t0\n+chrom_6\t1038\t1043\t25.6148\n+chrom_6\t1043\t1046\t128.074\n+chrom_6\t1046\t1060\t153.689\n+chrom_6\t1060\t1061\t128.074\n+chrom_6\t1061\t1068\t102.459\n+chrom_6\t1068\t1071\t25.6148\n+chrom_6\t1071\t1086\t51.2295\n+chrom_6\t1086\t1095\t25.6148\n+chrom_6\t1095\t1109\t0\n+chrom_6\t1109\t1110\t25.6148\n+chrom_6\t1110\t1115\t51.2295\n+chrom_6\t1115\t1117\t102.459\n+chrom_6\t1117\t1125\t128.074\n+chrom_6\t1125\t1130\t153.689\n+chrom_6\t1130\t1133\t102.459\n+chrom_6\t1133\t1136\t76.8443\n+chrom_6\t1136\t1142\t51.2295\n+chrom_6\t1142\t1143\t25.6148\n+chrom_6\t1143\t1443\t0\n+chrom_6\t1443\t1445\t230.533\n+chrom_6\t1445\t1461\t256.148\n+chrom_6\t1461\t1467\t153.689\n+chrom_6\t1467\t1468\t102.459\n+chrom_6\t1468\t1497\t0\n+chrom_6\t1497\t1515\t51.2295\n+chrom_6\t1515\t2214\t0\n+chrom_6\t2214\t2232\t25.6148\n+chrom_6\t2232\t2244\t0\n+chrom_6\t2244\t2264\t25.6148\n+chrom_6\t2264\t2839\t0\n+chrom_6\t2839\t2859\t25.6148\n+chrom_6\t2859\t3002\t0\n+chrom_6\t3002\t3027\t25.6148\n+chrom_6\t3027\t3053\t0\n+chrom_6\t3053\t3072\t25.6148\n+chrom_6\t3072\t3242\t0\n+chrom_6\t3242\t3250\t25.6148\n+chrom_6\t3250\t3252\t51.2295\n+chrom_6\t3252\t3253\t76.8443\n+chrom_6\t3253\t3263\t102.459\n+chrom_6\t3263\t3271\t76.8443\n+chrom_6\t3271\t3273\t51.2295\n+chrom_6\t3273\t3999\t0\n' |
| b |
| diff -r 9645d995fb3c -r 9185ca0a7b43 test-data/res_files/reads-sample-small.fastq/genome/reads-sample-small.fastq_18-29_sorted.bam |
| b |
| Binary file test-data/res_files/reads-sample-small.fastq/genome/reads-sample-small.fastq_18-29_sorted.bam has changed |
| b |
| diff -r 9645d995fb3c -r 9185ca0a7b43 test-data/res_files/reads-sample-small.fastq/genome/reads-sample-small.fastq_18-29_unique_minus.bedgraph --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/res_files/reads-sample-small.fastq/genome/reads-sample-small.fastq_18-29_unique_minus.bedgraph Wed Jan 16 08:18:13 2019 -0500 |
| b |
| b'@@ -0,0 +1,4787 @@\n+chrom_1\t0\t3964\t0\n+chrom_1\t3964\t3988\t25.6148\n+chrom_1\t3988\t8675\t0\n+chrom_1\t8675\t8700\t25.6148\n+chrom_1\t8700\t9636\t0\n+chrom_1\t9636\t9661\t25.6148\n+chrom_1\t9661\t10201\t0\n+chrom_1\t10201\t10226\t25.6148\n+chrom_1\t10226\t11637\t0\n+chrom_1\t11637\t11661\t25.6148\n+chrom_1\t11661\t12140\t0\n+chrom_1\t12140\t12161\t25.6148\n+chrom_1\t12161\t12187\t0\n+chrom_1\t12187\t12211\t25.6148\n+chrom_1\t12211\t12214\t0\n+chrom_1\t12214\t12215\t25.6148\n+chrom_1\t12215\t12238\t51.2295\n+chrom_1\t12238\t13134\t0\n+chrom_1\t13134\t13159\t25.6148\n+chrom_1\t13159\t13465\t0\n+chrom_1\t13465\t13470\t25.6148\n+chrom_1\t13470\t13491\t51.2295\n+chrom_1\t13491\t13493\t25.6148\n+chrom_1\t13493\t14233\t0\n+chrom_1\t14233\t14258\t25.6148\n+chrom_1\t14258\t14318\t0\n+chrom_1\t14318\t14321\t25.6148\n+chrom_1\t14321\t14344\t51.2295\n+chrom_1\t14344\t14438\t0\n+chrom_1\t14438\t14463\t25.6148\n+chrom_1\t14463\t14500\t0\n+chrom_1\t14500\t14523\t25.6148\n+chrom_1\t14523\t14778\t0\n+chrom_1\t14778\t14790\t51.2295\n+chrom_1\t14790\t14803\t76.8443\n+chrom_1\t14803\t14804\t51.2295\n+chrom_1\t14804\t14814\t25.6148\n+chrom_1\t14814\t14840\t0\n+chrom_1\t14840\t14860\t51.2295\n+chrom_1\t14860\t14865\t25.6148\n+chrom_1\t14865\t14968\t0\n+chrom_1\t14968\t14973\t25.6148\n+chrom_1\t14973\t14977\t51.2295\n+chrom_1\t14977\t14985\t76.8443\n+chrom_1\t14985\t14992\t128.074\n+chrom_1\t14992\t14999\t102.459\n+chrom_1\t14999\t15002\t76.8443\n+chrom_1\t15002\t15005\t51.2295\n+chrom_1\t15005\t15009\t76.8443\n+chrom_1\t15009\t15025\t25.6148\n+chrom_1\t15025\t15089\t0\n+chrom_1\t15089\t15112\t25.6148\n+chrom_1\t15112\t15114\t51.2295\n+chrom_1\t15114\t15130\t25.6148\n+chrom_1\t15130\t15132\t76.8443\n+chrom_1\t15132\t15134\t128.074\n+chrom_1\t15134\t15137\t102.459\n+chrom_1\t15137\t15155\t128.074\n+chrom_1\t15155\t15157\t76.8443\n+chrom_1\t15157\t15160\t0\n+chrom_1\t15160\t15161\t51.2295\n+chrom_1\t15161\t15164\t102.459\n+chrom_1\t15164\t15184\t128.074\n+chrom_1\t15184\t15185\t76.8443\n+chrom_1\t15185\t15201\t0\n+chrom_1\t15201\t15225\t25.6148\n+chrom_1\t15225\t15250\t0\n+chrom_1\t15250\t15251\t25.6148\n+chrom_1\t15251\t15255\t76.8443\n+chrom_1\t15255\t15260\t102.459\n+chrom_1\t15260\t15274\t128.074\n+chrom_1\t15274\t15287\t25.6148\n+chrom_1\t15287\t15288\t51.2295\n+chrom_1\t15288\t15289\t76.8443\n+chrom_1\t15289\t15290\t204.918\n+chrom_1\t15290\t15291\t281.762\n+chrom_1\t15291\t15306\t307.377\n+chrom_1\t15306\t15313\t281.762\n+chrom_1\t15313\t15315\t128.074\n+chrom_1\t15315\t15348\t0\n+chrom_1\t15348\t15349\t25.6148\n+chrom_1\t15349\t15350\t51.2295\n+chrom_1\t15350\t15366\t76.8443\n+chrom_1\t15366\t15370\t102.459\n+chrom_1\t15370\t15372\t76.8443\n+chrom_1\t15372\t15390\t25.6148\n+chrom_1\t15390\t15444\t0\n+chrom_1\t15444\t15445\t51.2295\n+chrom_1\t15445\t15446\t76.8443\n+chrom_1\t15446\t15469\t128.074\n+chrom_1\t15469\t15470\t51.2295\n+chrom_1\t15470\t15471\t25.6148\n+chrom_1\t15471\t15476\t0\n+chrom_1\t15476\t15477\t25.6148\n+chrom_1\t15477\t15478\t51.2295\n+chrom_1\t15478\t15482\t102.459\n+chrom_1\t15482\t15499\t128.074\n+chrom_1\t15499\t15500\t153.689\n+chrom_1\t15500\t15504\t102.459\n+chrom_1\t15504\t15506\t51.2295\n+chrom_1\t15506\t15523\t25.6148\n+chrom_1\t15523\t15534\t0\n+chrom_1\t15534\t15535\t51.2295\n+chrom_1\t15535\t15536\t76.8443\n+chrom_1\t15536\t15558\t102.459\n+chrom_1\t15558\t15559\t51.2295\n+chrom_1\t15559\t15560\t128.074\n+chrom_1\t15560\t15580\t76.8443\n+chrom_1\t15580\t15584\t51.2295\n+chrom_1\t15584\t15586\t25.6148\n+chrom_1\t15586\t15587\t281.762\n+chrom_1\t15587\t15594\t307.377\n+chrom_1\t15594\t15598\t358.607\n+chrom_1\t15598\t15609\t461.066\n+chrom_1\t15609\t15620\t153.689\n+chrom_1\t15620\t15622\t102.459\n+chrom_1\t15622\t15623\t25.6148\n+chrom_1\t15623\t15688\t0\n+chrom_1\t15688\t15700\t25.6148\n+chrom_1\t15700\t15714\t76.8443\n+chrom_1\t15714\t15722\t51.2295\n+chrom_1\t15722\t15726\t76.8443\n+chrom_1\t15726\t15727\t51.2295\n+chrom_1\t15727\t15728\t102.459\n+chrom_1\t15728\t15730\t128.074\n+chrom_1\t15730\t15745\t204.918\n+chrom_1\t15745\t15750\t179.303\n+chrom_1\t15750\t15752\t76.8443\n+chrom_1\t15752\t15754\t51.2295\n+chrom_1\t15754\t15791\t0\n+chrom_1\t15791\t15793\t51.2295\n+chrom_1\t15793\t15794\t76.8443\n+chrom_1\t15794\t15796\t153.689\n+chrom_1\t15796\t15805\t179.303\n+chrom_1\t15805\t15806\t281.762\n+chrom_1\t15806\t15815\t307.377\n+chrom_1\t15815\t15816\t256.148\n+chrom_1\t15816\t15817\t230.533\n+chrom_1\t15817\t15819\t153.689\n+chrom_1\t15819\t15825\t128.074\n+chrom_1\t15825\t15828\t76.8443\n+chrom_1\t15828\t15925\t0\n+chrom_1\t15925\t15926\t128.074\n+chrom_1\t15926\t15'..b'_1\t83991\t84014\t25.6148\n+chrom_1\t84014\t85181\t0\n+chrom_1\t85181\t85202\t51.2295\n+chrom_1\t85202\t85205\t25.6148\n+chrom_1\t85205\t85252\t0\n+chrom_1\t85252\t85273\t25.6148\n+chrom_1\t85273\t85366\t0\n+chrom_1\t85366\t85390\t25.6148\n+chrom_1\t85390\t85640\t0\n+chrom_1\t85640\t85662\t25.6148\n+chrom_1\t85662\t85759\t0\n+chrom_1\t85759\t85783\t25.6148\n+chrom_1\t85783\t86402\t0\n+chrom_1\t86402\t86424\t25.6148\n+chrom_1\t86424\t86453\t0\n+chrom_1\t86453\t86474\t25.6148\n+chrom_1\t86474\t86632\t0\n+chrom_1\t86632\t86658\t25.6148\n+chrom_1\t86658\t86941\t0\n+chrom_1\t86941\t86967\t25.6148\n+chrom_1\t86967\t87002\t0\n+chrom_1\t87002\t87022\t25.6148\n+chrom_1\t87022\t87066\t0\n+chrom_1\t87066\t87087\t25.6148\n+chrom_1\t87087\t87142\t0\n+chrom_1\t87142\t87163\t25.6148\n+chrom_1\t87163\t87223\t0\n+chrom_1\t87223\t87244\t25.6148\n+chrom_1\t87244\t87446\t0\n+chrom_1\t87446\t87467\t25.6148\n+chrom_1\t87467\t87524\t0\n+chrom_1\t87524\t87546\t25.6148\n+chrom_1\t87546\t87581\t0\n+chrom_1\t87581\t87582\t25.6148\n+chrom_1\t87582\t87602\t51.2295\n+chrom_1\t87602\t87665\t0\n+chrom_1\t87665\t87683\t25.6148\n+chrom_1\t87683\t87819\t0\n+chrom_1\t87819\t87839\t25.6148\n+chrom_1\t87839\t87853\t0\n+chrom_1\t87853\t87878\t25.6148\n+chrom_1\t87878\t88309\t0\n+chrom_1\t88309\t88330\t25.6148\n+chrom_1\t88330\t88443\t0\n+chrom_1\t88443\t88464\t25.6148\n+chrom_1\t88464\t88710\t0\n+chrom_1\t88710\t88731\t25.6148\n+chrom_1\t88731\t89102\t0\n+chrom_1\t89102\t89120\t25.6148\n+chrom_1\t89120\t89812\t0\n+chrom_1\t89812\t89833\t25.6148\n+chrom_1\t89833\t89999\t0\n+chrom_2\t0\t22924\t0\n+chrom_2\t22924\t22934\t25.6148\n+chrom_2\t22934\t22936\t76.8443\n+chrom_2\t22936\t22940\t102.459\n+chrom_2\t22940\t22942\t128.074\n+chrom_2\t22942\t22946\t102.459\n+chrom_2\t22946\t22956\t153.689\n+chrom_2\t22956\t22958\t537.91\n+chrom_2\t22958\t22961\t563.525\n+chrom_2\t22961\t22962\t614.754\n+chrom_2\t22962\t22963\t691.598\n+chrom_2\t22963\t22964\t1306.35\n+chrom_2\t22964\t22965\t1511.27\n+chrom_2\t22965\t22968\t1664.96\n+chrom_2\t22968\t22970\t2638.32\n+chrom_2\t22970\t22971\t2663.93\n+chrom_2\t22971\t22972\t3586.07\n+chrom_2\t22972\t22973\t3944.67\n+chrom_2\t22973\t22974\t3995.9\n+chrom_2\t22974\t22977\t4021.52\n+chrom_2\t22977\t22980\t4047.13\n+chrom_2\t22980\t22981\t4021.52\n+chrom_2\t22981\t22982\t3381.15\n+chrom_2\t22982\t22983\t2996.93\n+chrom_2\t22983\t22984\t2715.16\n+chrom_2\t22984\t22985\t2689.55\n+chrom_2\t22985\t22986\t2612.7\n+chrom_2\t22986\t22989\t2561.48\n+chrom_2\t22989\t22991\t2382.17\n+chrom_2\t22991\t22992\t2202.87\n+chrom_2\t22992\t22993\t1997.95\n+chrom_2\t22993\t22994\t1203.89\n+chrom_2\t22994\t22995\t76.8443\n+chrom_2\t22995\t22996\t51.2295\n+chrom_2\t22996\t32272\t0\n+chrom_2\t32272\t32289\t25.6148\n+chrom_2\t32289\t32292\t51.2295\n+chrom_2\t32292\t32296\t76.8443\n+chrom_2\t32296\t32310\t51.2295\n+chrom_2\t32310\t39255\t0\n+chrom_2\t39255\t39276\t25.6148\n+chrom_2\t39276\t44459\t0\n+chrom_2\t44459\t44485\t25.6148\n+chrom_2\t44485\t49999\t0\n+chrom_4\t0\t575\t0\n+chrom_4\t575\t596\t25.6148\n+chrom_4\t596\t876\t0\n+chrom_4\t876\t901\t128.074\n+chrom_4\t901\t919\t0\n+chrom_4\t919\t944\t51.2295\n+chrom_4\t944\t1149\t0\n+chrom_4\t1149\t1158\t25.6148\n+chrom_4\t1158\t1174\t51.2295\n+chrom_4\t1174\t1184\t25.6148\n+chrom_4\t1184\t2000\t0\n+chrom_5\t0\t450\t0\n+chrom_5\t450\t468\t51.2295\n+chrom_5\t468\t613\t0\n+chrom_5\t613\t615\t25.6148\n+chrom_5\t615\t616\t102.459\n+chrom_5\t616\t632\t179.303\n+chrom_5\t632\t635\t204.918\n+chrom_5\t635\t638\t51.2295\n+chrom_5\t638\t644\t25.6148\n+chrom_5\t644\t646\t51.2295\n+chrom_5\t646\t649\t76.8443\n+chrom_5\t649\t652\t102.459\n+chrom_5\t652\t654\t76.8443\n+chrom_5\t654\t659\t102.459\n+chrom_5\t659\t665\t128.074\n+chrom_5\t665\t667\t102.459\n+chrom_5\t667\t673\t153.689\n+chrom_5\t673\t675\t204.918\n+chrom_5\t675\t679\t179.303\n+chrom_5\t679\t682\t307.377\n+chrom_5\t682\t688\t281.762\n+chrom_5\t688\t692\t230.533\n+chrom_5\t692\t693\t204.918\n+chrom_5\t693\t695\t179.303\n+chrom_5\t695\t699\t153.689\n+chrom_5\t699\t700\t179.303\n+chrom_5\t700\t712\t51.2295\n+chrom_5\t712\t715\t76.8443\n+chrom_5\t715\t716\t102.459\n+chrom_5\t716\t721\t76.8443\n+chrom_5\t721\t723\t51.2295\n+chrom_5\t723\t739\t102.459\n+chrom_5\t739\t744\t153.689\n+chrom_5\t744\t750\t76.8443\n+chrom_5\t750\t751\t179.303\n+chrom_5\t751\t753\t153.689\n+chrom_5\t753\t756\t179.303\n+chrom_5\t756\t762\t230.533\n+chrom_5\t762\t765\t256.148\n+chrom_5\t765\t771\t230.533\n+chrom_5\t771\t772\t204.918\n+chrom_5\t772\t774\t128.074\n+chrom_5\t774\t778\t102.459\n+chrom_5\t778\t783\t51.2295\n+chrom_5\t783\t786\t76.8443\n+chrom_5\t786\t804\t51.2295\n+chrom_5\t804\t1999\t0\n' |
| b |
| diff -r 9645d995fb3c -r 9185ca0a7b43 test-data/res_files/reads-sample-small.fastq/genome/reads-sample-small.fastq_18-29_unique_plus.bedgraph --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/res_files/reads-sample-small.fastq/genome/reads-sample-small.fastq_18-29_unique_plus.bedgraph Wed Jan 16 08:18:13 2019 -0500 |
| b |
| b'@@ -0,0 +1,6072 @@\n+chrom_1\t0\t1967\t0\n+chrom_1\t1967\t1991\t25.6148\n+chrom_1\t1991\t2932\t0\n+chrom_1\t2932\t2954\t25.6148\n+chrom_1\t2954\t3456\t0\n+chrom_1\t3456\t3481\t25.6148\n+chrom_1\t3481\t7648\t0\n+chrom_1\t7648\t7671\t25.6148\n+chrom_1\t7671\t7953\t0\n+chrom_1\t7953\t7978\t25.6148\n+chrom_1\t7978\t8721\t0\n+chrom_1\t8721\t8742\t25.6148\n+chrom_1\t8742\t8747\t51.2295\n+chrom_1\t8747\t8758\t25.6148\n+chrom_1\t8758\t8767\t51.2295\n+chrom_1\t8767\t8783\t25.6148\n+chrom_1\t8783\t9642\t0\n+chrom_1\t9642\t9668\t25.6148\n+chrom_1\t9668\t10407\t0\n+chrom_1\t10407\t10428\t25.6148\n+chrom_1\t10428\t14236\t0\n+chrom_1\t14236\t14261\t25.6148\n+chrom_1\t14261\t14309\t0\n+chrom_1\t14309\t14336\t25.6148\n+chrom_1\t14336\t14439\t0\n+chrom_1\t14439\t14463\t25.6148\n+chrom_1\t14463\t14523\t0\n+chrom_1\t14523\t14544\t25.6148\n+chrom_1\t14544\t14551\t0\n+chrom_1\t14551\t14552\t25.6148\n+chrom_1\t14552\t14554\t76.8443\n+chrom_1\t14554\t14578\t179.303\n+chrom_1\t14578\t14580\t25.6148\n+chrom_1\t14580\t14592\t0\n+chrom_1\t14592\t14616\t25.6148\n+chrom_1\t14616\t14979\t0\n+chrom_1\t14979\t15004\t25.6148\n+chrom_1\t15004\t15062\t0\n+chrom_1\t15062\t15087\t25.6148\n+chrom_1\t15087\t15089\t0\n+chrom_1\t15089\t15092\t25.6148\n+chrom_1\t15092\t15115\t128.074\n+chrom_1\t15115\t15117\t102.459\n+chrom_1\t15117\t15139\t0\n+chrom_1\t15139\t15164\t25.6148\n+chrom_1\t15164\t15258\t0\n+chrom_1\t15258\t15260\t25.6148\n+chrom_1\t15260\t15264\t76.8443\n+chrom_1\t15264\t15269\t102.459\n+chrom_1\t15269\t15283\t128.074\n+chrom_1\t15283\t15284\t102.459\n+chrom_1\t15284\t15290\t51.2295\n+chrom_1\t15290\t15293\t25.6148\n+chrom_1\t15293\t15395\t0\n+chrom_1\t15395\t15399\t25.6148\n+chrom_1\t15399\t15400\t76.8443\n+chrom_1\t15400\t15407\t281.762\n+chrom_1\t15407\t15420\t307.377\n+chrom_1\t15420\t15421\t281.762\n+chrom_1\t15421\t15422\t204.918\n+chrom_1\t15422\t15423\t102.459\n+chrom_1\t15423\t15424\t51.2295\n+chrom_1\t15424\t15433\t25.6148\n+chrom_1\t15433\t15460\t0\n+chrom_1\t15460\t15484\t25.6148\n+chrom_1\t15484\t15528\t0\n+chrom_1\t15528\t15529\t25.6148\n+chrom_1\t15529\t15530\t51.2295\n+chrom_1\t15530\t15545\t76.8443\n+chrom_1\t15545\t15546\t102.459\n+chrom_1\t15546\t15548\t486.68\n+chrom_1\t15548\t15550\t461.066\n+chrom_1\t15550\t15555\t435.451\n+chrom_1\t15555\t15567\t409.836\n+chrom_1\t15567\t15569\t384.221\n+chrom_1\t15569\t15570\t204.918\n+chrom_1\t15570\t15572\t25.6148\n+chrom_1\t15572\t15716\t0\n+chrom_1\t15716\t15739\t25.6148\n+chrom_1\t15739\t15801\t0\n+chrom_1\t15801\t15824\t25.6148\n+chrom_1\t15824\t15970\t0\n+chrom_1\t15970\t15993\t76.8443\n+chrom_1\t15993\t16004\t0\n+chrom_1\t16004\t16027\t76.8443\n+chrom_1\t16027\t16028\t25.6148\n+chrom_1\t16028\t16229\t0\n+chrom_1\t16229\t16232\t25.6148\n+chrom_1\t16232\t16237\t51.2295\n+chrom_1\t16237\t16239\t76.8443\n+chrom_1\t16239\t16250\t128.074\n+chrom_1\t16250\t16256\t102.459\n+chrom_1\t16256\t16262\t76.8443\n+chrom_1\t16262\t16336\t0\n+chrom_1\t16336\t16338\t256.148\n+chrom_1\t16338\t16339\t281.762\n+chrom_1\t16339\t16342\t307.377\n+chrom_1\t16342\t16359\t332.992\n+chrom_1\t16359\t16360\t128.074\n+chrom_1\t16360\t16363\t76.8443\n+chrom_1\t16363\t16364\t51.2295\n+chrom_1\t16364\t16365\t25.6148\n+chrom_1\t16365\t16380\t0\n+chrom_1\t16380\t16402\t25.6148\n+chrom_1\t16402\t16496\t0\n+chrom_1\t16496\t16521\t25.6148\n+chrom_1\t16521\t16619\t0\n+chrom_1\t16619\t16628\t25.6148\n+chrom_1\t16628\t16630\t76.8443\n+chrom_1\t16630\t16643\t256.148\n+chrom_1\t16643\t16653\t230.533\n+chrom_1\t16653\t16654\t153.689\n+chrom_1\t16654\t16655\t76.8443\n+chrom_1\t16655\t16656\t25.6148\n+chrom_1\t16656\t16661\t0\n+chrom_1\t16661\t16685\t25.6148\n+chrom_1\t16685\t16772\t0\n+chrom_1\t16772\t16798\t25.6148\n+chrom_1\t16798\t16800\t51.2295\n+chrom_1\t16800\t16801\t179.303\n+chrom_1\t16801\t16808\t461.066\n+chrom_1\t16808\t16810\t486.68\n+chrom_1\t16810\t16811\t512.295\n+chrom_1\t16811\t16819\t537.91\n+chrom_1\t16819\t16823\t512.295\n+chrom_1\t16823\t16825\t461.066\n+chrom_1\t16825\t16829\t128.074\n+chrom_1\t16829\t16835\t102.459\n+chrom_1\t16835\t16849\t51.2295\n+chrom_1\t16849\t16850\t25.6148\n+chrom_1\t16850\t16864\t0\n+chrom_1\t16864\t16866\t25.6148\n+chrom_1\t16866\t16867\t76.8443\n+chrom_1\t16867\t16868\t179.303\n+chrom_1\t16868\t16869\t307.377\n+chrom_1\t16869\t16870\t332.992\n+chrom_1\t16870\t16875\t358.607\n+chrom_1\t16875\t16881\t384.221\n+chrom_1\t16881\t16883\t435.451\n+chrom_1\t16883\t16884\t461.066\n+chrom_1\t16884\t16885\t537.91\n+chrom_1\t16885\t16886\t589.139\n+chrom_1\t16886\t16887\t640.369\n+chrom_1\t16887\t16892\t614.754\n+chrom_1\t16892\t16893\t435.451\n+chrom_1\t16893\t16894\t33'..b'4\t1140\t1141\t896.516\n+chrom_4\t1141\t1143\t870.902\n+chrom_4\t1143\t1144\t589.139\n+chrom_4\t1144\t1145\t665.984\n+chrom_4\t1145\t1146\t1075.82\n+chrom_4\t1146\t1147\t1306.35\n+chrom_4\t1147\t1148\t2843.24\n+chrom_4\t1148\t1149\t7479.51\n+chrom_4\t1149\t1150\t7914.96\n+chrom_4\t1150\t1151\t8247.95\n+chrom_4\t1151\t1152\t11091.2\n+chrom_4\t1152\t1153\t11782.8\n+chrom_4\t1153\t1154\t17879.1\n+chrom_4\t1154\t1155\t17827.9\n+chrom_4\t1155\t1156\t17879.1\n+chrom_4\t1156\t1160\t17776.6\n+chrom_4\t1160\t1161\t17751\n+chrom_4\t1161\t1163\t17725.4\n+chrom_4\t1163\t1169\t17674.2\n+chrom_4\t1169\t1170\t17520.5\n+chrom_4\t1170\t1171\t17494.9\n+chrom_4\t1171\t1172\t486.68\n+chrom_4\t1172\t1173\t409.836\n+chrom_4\t1173\t1174\t25.6148\n+chrom_4\t1174\t1194\t0\n+chrom_4\t1194\t1196\t25.6148\n+chrom_4\t1196\t1197\t128.074\n+chrom_4\t1197\t1198\t179.303\n+chrom_4\t1198\t1199\t6557.38\n+chrom_4\t1199\t1200\t134042\n+chrom_4\t1200\t1201\t137218\n+chrom_4\t1201\t1202\t137602\n+chrom_4\t1202\t1203\t138192\n+chrom_4\t1203\t1204\t138268\n+chrom_4\t1204\t1205\t142828\n+chrom_4\t1205\t1206\t145056\n+chrom_4\t1206\t1207\t149027\n+chrom_4\t1207\t1208\t150615\n+chrom_4\t1208\t1209\t153381\n+chrom_4\t1209\t1210\t155200\n+chrom_4\t1210\t1211\t155712\n+chrom_4\t1211\t1212\t156250\n+chrom_4\t1212\t1215\t156378\n+chrom_4\t1215\t1216\t156506\n+chrom_4\t1216\t1217\t156481\n+chrom_4\t1217\t1218\t156327\n+chrom_4\t1218\t1219\t155891\n+chrom_4\t1219\t1220\t155686\n+chrom_4\t1220\t1221\t153356\n+chrom_4\t1221\t1222\t150768\n+chrom_4\t1222\t1223\t123207\n+chrom_4\t1223\t1224\t67751\n+chrom_4\t1224\t1225\t32786.9\n+chrom_4\t1225\t1226\t24564.5\n+chrom_4\t1226\t1227\t24154.7\n+chrom_4\t1227\t1228\t18032.8\n+chrom_4\t1228\t1229\t17494.9\n+chrom_4\t1229\t1230\t1460.04\n+chrom_4\t1230\t1231\t435.451\n+chrom_4\t1231\t1232\t358.607\n+chrom_4\t1232\t1233\t332.992\n+chrom_4\t1233\t1234\t128.074\n+chrom_4\t1234\t1235\t102.459\n+chrom_4\t1235\t1239\t51.2295\n+chrom_4\t1239\t1242\t25.6148\n+chrom_4\t1242\t1300\t0\n+chrom_4\t1300\t1319\t25.6148\n+chrom_4\t1319\t1376\t0\n+chrom_4\t1376\t1385\t25.6148\n+chrom_4\t1385\t1386\t51.2295\n+chrom_4\t1386\t1387\t102.459\n+chrom_4\t1387\t1388\t332.992\n+chrom_4\t1388\t1389\t537.91\n+chrom_4\t1389\t1390\t1639.34\n+chrom_4\t1390\t1391\t3457.99\n+chrom_4\t1391\t1392\t3509.22\n+chrom_4\t1392\t1396\t3534.84\n+chrom_4\t1396\t1408\t3509.22\n+chrom_4\t1408\t1409\t3483.61\n+chrom_4\t1409\t1410\t3406.76\n+chrom_4\t1410\t1411\t3227.46\n+chrom_4\t1411\t1412\t3125\n+chrom_4\t1412\t1413\t2945.7\n+chrom_4\t1413\t1414\t1946.72\n+chrom_4\t1414\t1415\t819.672\n+chrom_4\t1415\t1416\t76.8443\n+chrom_4\t1416\t1431\t0\n+chrom_4\t1431\t1441\t25.6148\n+chrom_4\t1441\t1456\t51.2295\n+chrom_4\t1456\t1467\t25.6148\n+chrom_4\t1467\t2000\t0\n+chrom_5\t0\t619\t0\n+chrom_5\t619\t640\t25.6148\n+chrom_5\t640\t674\t0\n+chrom_5\t674\t692\t25.6148\n+chrom_5\t692\t695\t51.2295\n+chrom_5\t695\t709\t25.6148\n+chrom_5\t709\t712\t51.2295\n+chrom_5\t712\t730\t25.6148\n+chrom_5\t730\t733\t0\n+chrom_5\t733\t737\t25.6148\n+chrom_5\t737\t752\t51.2295\n+chrom_5\t752\t754\t153.689\n+chrom_5\t754\t755\t128.074\n+chrom_5\t755\t765\t102.459\n+chrom_5\t765\t773\t128.074\n+chrom_5\t773\t774\t102.459\n+chrom_5\t774\t786\t25.6148\n+chrom_5\t786\t1414\t0\n+chrom_5\t1414\t1425\t76.8443\n+chrom_5\t1425\t1426\t102.459\n+chrom_5\t1426\t1438\t128.074\n+chrom_5\t1438\t1440\t76.8443\n+chrom_5\t1440\t1444\t51.2295\n+chrom_5\t1444\t1452\t25.6148\n+chrom_5\t1452\t1454\t0\n+chrom_5\t1454\t1457\t25.6148\n+chrom_5\t1457\t1462\t51.2295\n+chrom_5\t1462\t1463\t76.8443\n+chrom_5\t1463\t1465\t102.459\n+chrom_5\t1465\t1475\t128.074\n+chrom_5\t1475\t1482\t102.459\n+chrom_5\t1482\t1487\t76.8443\n+chrom_5\t1487\t1488\t51.2295\n+chrom_5\t1488\t1493\t25.6148\n+chrom_5\t1493\t1503\t0\n+chrom_5\t1503\t1504\t128.074\n+chrom_5\t1504\t1505\t307.377\n+chrom_5\t1505\t1523\t384.221\n+chrom_5\t1523\t1526\t51.2295\n+chrom_5\t1526\t1528\t25.6148\n+chrom_5\t1528\t1648\t0\n+chrom_5\t1648\t1669\t25.6148\n+chrom_5\t1669\t1782\t0\n+chrom_5\t1782\t1803\t25.6148\n+chrom_5\t1803\t1999\t0\n+chrom_6\t0\t440\t0\n+chrom_6\t440\t464\t25.6148\n+chrom_6\t464\t819\t0\n+chrom_6\t819\t845\t25.6148\n+chrom_6\t845\t885\t0\n+chrom_6\t885\t905\t51.2295\n+chrom_6\t905\t906\t25.6148\n+chrom_6\t906\t1038\t0\n+chrom_6\t1038\t1060\t25.6148\n+chrom_6\t1060\t1109\t0\n+chrom_6\t1109\t1110\t25.6148\n+chrom_6\t1110\t1115\t51.2295\n+chrom_6\t1115\t1117\t102.459\n+chrom_6\t1117\t1125\t128.074\n+chrom_6\t1125\t1130\t153.689\n+chrom_6\t1130\t1133\t102.459\n+chrom_6\t1133\t1136\t76.8443\n+chrom_6\t1136\t1142\t51.2295\n+chrom_6\t1142\t1143\t25.6148\n+chrom_6\t1143\t3999\t0\n' |
| b |
| diff -r 9645d995fb3c -r 9185ca0a7b43 test-data/res_files/reads-sample-small.fastq/genome/reads-sample-small.fastq_18-29_unique_sorted.bam |
| b |
| Binary file test-data/res_files/reads-sample-small.fastq/genome/reads-sample-small.fastq_18-29_unique_sorted.bam has changed |
| b |
| diff -r 9645d995fb3c -r 9185ca0a7b43 test-data/res_files/reads-sample-small.fastq/size/duplicates.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/res_files/reads-sample-small.fastq/size/duplicates.txt Wed Jan 16 08:18:13 2019 -0500 |
| b |
| b'@@ -0,0 +1,14717 @@\n+size\tnumber\n+TGCTTGGACTACATATGGTTGAGG\t1985\n+TGCTTGGACTACATATGGTTGAGGG\t1319\n+TGCTTGGACTACATATGGTTGAG\t943\n+TATAGAATTGTAGAGCAAGACCT\t498\n+TGCTTGGACTACATATGGTTGAGGGT\t300\n+TTGATTAAGATAGCTGCTCCGCCT\t297\n+TATTGGCAAGCCTTTCGTCGAACC\t267\n+ATATCGCAGTCCATGCTG\t240\n+TTTACGGGATAGGACGGTAGCGC\t231\n+TATTGACTGGCGACGCTTTTGAGG\t229\n+TGCTTGGACTACATATGGTTGAGGGTTG\t226\n+TGAAAGACGCAGGATGGTCCGCCT\t226\n+TGAAAGACGCAGGATGGTCCGCCTG\t223\n+TATGTTTAGCGTTGTAGTCGCCT\t193\n+GATTGGACAGCCTCTGTAGTTTGC\t182\n+AACGCATATCGCAGTCCATGCTG\t173\n+TTCGATCTGCCGCGGGCTGCCGAGA\t168\n+TTTCTTCGGTTCGATATCAACGGA\t163\n+GGACTACATATGGTTGAGGGTTGTA\t160\n+TATTGCACTTGAGCCGGCCTGA\t156\n+TATAGAATTGTAGAGCAAGACCTTG\t144\n+CCATATCTAGGTTCTGTAGCCGAAG\t136\n+TATTTGATTGTTGGGCTACAAGCA\t130\n+TCAGAATCTTTGATTGTGCTCGCT\t128\n+ACTACATATGGTTGAGGGTTGTA\t125\n+TTCAGATGGTGCTCGACTATGGCCT\t117\n+CTGCTTGGACTACATATGGTTGAG\t115\n+TAACTGCGAAGTCGATCAGGTCT\t113\n+TCTTTGGTATTCTCGCTGTAGA\t112\n+GCATATCGCAGTCCATGCTG\t107\n+TTTTTGATCAATTGGCACCATGCGAA\t105\n+TTTTTGATCAATTGGCACCATGCGA\t105\n+TCAGATGAGAGACAAATTAGAATTA\t103\n+TGTAGAGGATCGCTTGTCTGGGC\t99\n+AACTCTAAGCGGTGGATCACTCGGC\t94\n+TGAGATCATTTTGCAAGCTGATT\t93\n+TAGATGTGGCCTGAAGATGATTTTC\t91\n+TGCTTGGACTACATATGGTTGA\t90\n+TTAGTGTTGAATGTAGGCCAGGGA\t90\n+CTGCTTGGACTACATATGGTTGAGG\t86\n+GACTACATATGGTTGAGGGTTGTA\t83\n+TCATGAGACGTCTGCTTGTTTGGC\t83\n+TGCGTTTGGGATTGTCGGTGAGAC\t82\n+GCTTGGACTACATATGGTTGAGG\t81\n+TAATACATCGATTTCGTGACGTCGC\t81\n+TATTTGATTGTTGGGCTACAAGCATT\t81\n+AAATGAGAGTCAGTAACTGCC\t80\n+TGCTTGGACTACATATGGTTG\t80\n+TACATATGGTTGAGGGTTGTA\t78\n+TTTCTTCGGTTCGATATCAACGGAT\t76\n+TATTGGCAAGCCTTTCGTCGAAC\t76\n+TCTTGTAAATACTTTGATTGGCCT\t74\n+TTCGATCGCCGACGTGTGAAGACGT\t73\n+TTTTCCGGGCTGAGCTTTCGCTTT\t73\n+TGCGTTTGGGATTGTCGGTGAGA\t71\n+ACATTTCCGTTTCTCGCGACT\t71\n+AACTCTAAGCGGTGGATCACTC\t70\n+TGCGTTTGGGATTGTCGGTGAGACG\t70\n+CCATGTCCCGTTGCTATCGACTAGA\t69\n+TATTGAAGGAATTGATATATGCC\t68\n+ACATATGGTTGAGGGTTGTA\t67\n+TACGAGTAGGATATCGATCTGGT\t65\n+TTGGGTGTTGCAGTAAGAGCTG\t65\n+TGAATGGTTGAAATCGCTCGGCGA\t63\n+TAATGAGATCCCTCGGTTGCCTT\t63\n+TAGAAGACGATTTTCGGGCCGAAAT\t63\n+TCCGAAAACAAGGCCCGTCGCTA\t62\n+TGTGCTAGAAGACGATTTTCGGGC\t61\n+TTCATCAGCGACTTGTGGGATTCC\t61\n+TTTTTGATCAATTGGCACCATGCG\t59\n+GAACGCATATCGCAGTCCATGCTG\t58\n+TTTACGGGATAGGACGGTAGCGCG\t58\n+CTACATATGGTTGAGGGTTGTA\t58\n+TCTGATGTTACGCCCGAAGAGA\t58\n+CCGTAAAGGCTTACATCTGGCT\t56\n+TGTATGAACAGTGGAAGTGG\t56\n+TAATTTGACACTGTTTGGAG\t54\n+TTAGGACGAAACACAATTGGGGTG\t54\n+TGCTAGAAGACGATTTTCGGGC\t54\n+TAAGTTGTTGGCTTTGAGTTTAAG\t53\n+CAAAGTCCTGGATACCATCGGCT\t52\n+TTGTAATGTAGCGGTCCATTCC\t51\n+TAATAGTCAGGGCGCGAATTTTTAA\t51\n+CAGTATGTAGGACTCCCGGGG\t50\n+TATTGGCAAGCCTTTCGTCGAACCA\t50\n+TTTGGTTAAAGCTGAATGTCTGCC\t50\n+TAGTTCTACAGTCCGACGATC\t50\n+TAATGAGATCCCTCGGTTGCCT\t49\n+TTTGACAAAATATGCCCTTCACCT\t49\n+TTTTCCGGGCTGAGCTTTCGC\t49\n+TGATTGCGTTGGTAACTGATGGGA\t48\n+TGAGATCATTTTGCAAGCTGAT\t48\n+TTTTAAACATTAGGCCGTCGAGCCAGA\t47\n+TGGACGGAGAACTGATAAGGGCA\t47\n+TGATTACGCATCATGTCTTGAATG\t46\n+TAGGACGGTAGCGCGAATGTGCTAGT\t46\n+TTTTAAACATTAGGCCGTCGAGCCAG\t45\n+TTTCTGTTTGGGTTTGGACT\t44\n+CAAGCATTCGACAAAGTCTGGC\t44\n+TAGGACTCCCGGGGGAAACATGGTC\t44\n+TATCCAGAAAGGACTTCAGCCCTC\t44\n+TACGAGTAGGATATCGATCTGGTG\t43\n+TATTGACTGGCGACGCTTTTGAG\t43\n+TTAAGTCTCTTTGGATGTTTTCACT\t43\n+TAGGACTCCCGGGGGAAACATGGT\t42\n+TAAAGAGGACAGGCCTTACAGGGTA\t42\n+CCATATCTAGGTTCTGTAGCCGAAGG\t41\n+TTTAAGCTGGTAGGTGTAGAAGCCT\t41\n+TTCAGTATTGAGTTTTGGGCTTAGC\t41\n+CGCTGATGAAATCTCCAGGCTCAG\t41\n+TATGTTTAGCGTTGTAGTCGCCTGC\t41\n+TTTTTGATCAATTGGCACCATGC\t41\n+TTGTAATGTAGCGGTCCATTCCA\t41\n+TATTGCACTTGAGACGGCCTGAA\t41\n+TCTGATGTTACGCCCGAAGAGATAAC\t40\n+TCAGATGAGAGACAAATTAGAAT\t40\n+AACTCTAAGCGGTGGATCACTCG\t40\n+TTTCTGTTTGGGTTTGGAC\t40\n+TCCGGGCTGAGCTTTCGCTTT\t40\n+TATTGCACTTGAGCCGGCCTG\t39\n+TCATACTCTTCGATCTCGAGCCAG\t39\n+TTATTGAATCTTCTTGTATAAGAACT\t39\n+CAAATGTGGATACCGTTAAGCGAC\t38\n+TCAAAGTATTTACAAGACGGCTT\t38\n+TAGAATAACAAGATGCGTAACGGCC\t38\n+TATTGAAGGAATTGATATATGC\t38\n+TTGTAATGTAGCGGTCCATTCCAG\t38\n+TTGCGTTGGTAACTGATGGGAT\t38\n+TAATGAGATCCCTCGGTTGCCTTCT\t37\n+CACAGAGGCCAAGTCATTGAGCGCC\t37\n+TTGATTAAGATAGCTGCTCCGCC\t36\n+TCTCGGTGGGCAGTAGACCGC\t35\n+TAGGACGGTAGCGCGAATGTGCTAG\t35\n+AAGATTCTGAGAACCATCACTGGGG\t35\n+CTAAGGAAATAGTCGCCGTGAT\t35\n+TCATACTCTTCGATCTCGAGCCA\t35\n+TTTGGGTGTTGCAGTAAGAGCTG\t34\n+TTAAAGAGGACAGGCCTTACAGGG'..b'AGTCGTTGCGA\t1\n+TATTGCACTTGAGACGTCCTGA\t1\n+TTTGTAATGATCACATCTGATGTTG\t1\n+TGCTTGGACTACATATGGTTGGGGG\t1\n+TCACAGCGAATTGATCGGATTG\t1\n+TTAAGTTTCTCGAACTGGGGCTCC\t1\n+TTTGGCGTAGCTAGAGATTGTTTCCA\t1\n+GACGAGATAAAGCGAAAACCGGCAC\t1\n+CATTGCAGAATTTCCAGGACGGCA\t1\n+TACTTGCAGGCCCTTGCTG\t1\n+GAGAGAATGGGTCCAAGGCTGA\t1\n+GAACATCGCTTCTATCTGACCGGA\t1\n+TATTAAGAAGGCTTTAGAGGG\t1\n+AGACTTGGGACTCCAATCGATGGA\t1\n+TAATTGTGTTGACTGGAAGGGCCT\t1\n+TGTCTGCGTTTGGGATTGTCGG\t1\n+GAAGAACGCAGCAAACTGTG\t1\n+TCAGCCGCGTAAAGCCTTAGGAC\t1\n+CAATATCACATACACTATGTACTAC\t1\n+AAAGTCCTGGATACCATCGGCT\t1\n+TAGCCGGCCTGCTGCAAAAA\t1\n+GAAACAAGAAGAGGACGACGATC\t1\n+TCATAGACTTCGGCTTCTCGGCCGCGT\t1\n+TCCTTGGTTTAATAAAGAGTTGAC\t1\n+CGATAGAGAACCTGGAGGACT\t1\n+TGTACACTTCGCCCGGTGTGCGTAGT\t1\n+TCACTGGGCTCTGTTTATCTCA\t1\n+TCCGAGAAGTGAGATACGTTGGT\t1\n+TTTGTTGACGATGAGCCATGCT\t1\n+TACGCATCATGTCTTGAATGGTGGTC\t1\n+TTAGGAGGGAAGTTTAATGAC\t1\n+GAGCGAGAGAGCGGAGAG\t1\n+TTCTGGGAATTCCGAAGATGG\t1\n+TGAATGGTCTAAGTGTACGGA\t1\n+TGGATTGCAATGCACACGTGCAGC\t1\n+TAACGAACAGGACCGTTGTTATTGA\t1\n+TAGGAGTACACCTTGACAG\t1\n+GAAGTTCATTGTTGCAGGCGATT\t1\n+AGAAAAATCAAGAGTGACGAG\t1\n+TCCAGCTGAATGTTGATAGAT\t1\n+TTTATTTTGTAGATCGCAAGC\t1\n+TTTGCTAAGGACTGGCTGAGAA\t1\n+CATTCCTGAGATCGGTTTTACTC\t1\n+TTATAAGGTCGCAGCCGGGGGT\t1\n+TGGGCGAAGAGTTGAGTGGGCT\t1\n+TCTAGGGGTACACTCCAGCGCTCGA\t1\n+AACTGGCCAACGCTCTGAAACA\t1\n+ACCGCCCGTCGCTACTACCGC\t1\n+CAGGTCTCTGTGCAGGGTGGTGT\t1\n+GAGTCGAACAAATGATCCGTCGTT\t1\n+TAAGCTCGAATCTGTTACGGCCC\t1\n+TACCGGTAACTAGCGGCTGCCCGCA\t1\n+TTTTTACGCAATTTAGAGATAATG\t1\n+GTCAACTAGTCCGTCAGGGGT\t1\n+TGAGTAAATTGGACGATGAGGCGT\t1\n+TAAGGGACTATTTTAGGAGAA\t1\n+CGCTGGGTTGGTAGGTCCTTTCG\t1\n+ACTGATCGGCCGGTAGGAGG\t1\n+GTCGATATGCTTCTCATGTAGGAAT\t1\n+TCCGTCGTTTGACTAAGA\t1\n+TAGAGATGGTGAGCTAGACGTT\t1\n+TATTGTTGTGGAAGATCGAGA\t1\n+AGGAGAGAAGGAGAGCGCGAGC\t1\n+AACATCAACATTGGACCTATGCCT\t1\n+GATGTCGGCTGTATAGATGA\t1\n+CCAACGCTGGACGCATTGACCAAAGCT\t1\n+TGAGGCATCTGGGGAGCATTGGA\t1\n+TCAATTGGGTGTAGCTACA\t1\n+TGGACGGAGAACTGATAAGGGTA\t1\n+GCAGCCGATGGTATCCAGGACTT\t1\n+ACAAGCGCGGAACCTTTTGATCGC\t1\n+CATTGCAGCAGTTCCAGGACGGCA\t1\n+TGATGCTATCGAACTGCT\t1\n+TTCGGCGGGTCGTCGCACCCT\t1\n+TGTCAATATTGCTGTTGCTGGCATT\t1\n+ATACACGCGACAACTCTACCT\t1\n+TATTCATAATATTAAAAAA\t1\n+TTTCTGACGAGATTGCGGTCTCCCA\t1\n+GACGAAACACAATTGGGGTGT\t1\n+TGTTTGTCAGCTGTGAGA\t1\n+ACTGGGGATCGCGACTTGTGAAC\t1\n+GGTACTTTGCTGCGTTCGGCT\t1\n+TTAACGAACGAGACCCCCGCC\t1\n+TGCGTTTGGGATTGTCGGTGAGACAT\t1\n+AAGCAGCCAAAGCTCCAGGGC\t1\n+CGCCTTGTTAGCATTAGCGACGG\t1\n+GCATGCACAGAACATAACGTA\t1\n+ACCCATAAAAAGATTGAACGCCT\t1\n+TCGGCTGGCACTCGGTCCGC\t1\n+TTCGAGCCTTTTCAGGTATCTCTCGC\t1\n+TTGGGTTTGGACTGGGGTTGTGG\t1\n+TTATTAAAGTCGTTTTACACC\t1\n+AAGACGTTTTTATCGTGCTCCGCACA\t1\n+ATGACACCGTTGGAAGAA\t1\n+TTACATCATGGATCAGTAACGAGAA\t1\n+TTTTCTTGGGCGTTTGGAG\t1\n+TGTTTGTGCGATCGCGTGGCAGC\t1\n+AGACTCATCACCGGCTGCGAG\t1\n+GAGGACAGCATCCCGAGTGTGAACT\t1\n+ATAGGACCCGGCTCTGCTTAGT\t1\n+TCTCCGCCGCGTAGCCGCTGACGA\t1\n+ATTTCGAGTCGAATAAATGATCCT\t1\n+TGTATTAGCGTCAGCCGCGTAAAGCC\t1\n+ATTGAGAAGTGGCTCTCTGACT\t1\n+TTTATCGAACCGCAGGAACCTCTTG\t1\n+GTTCGGCTTTCTGACGGGAACTCGA\t1\n+CATCACAGTCTGAGTTCTTGCC\t1\n+AGTGGAAGCAGCACGCTTTGTCGT\t1\n+TACCTGTGTGTAACTTCTTTGGCCT\t1\n+TGTTTAATCCAGAGTTGGCCGAACA\t1\n+AAATTGCCAAATGGTTCGACCCTG\t1\n+TTTCTCTGTTGCGATTGAACTTGATT\t1\n+TCTCCGGCGAAAGGACCTACCAA\t1\n+AAAACTAATTGATCTTCGGCT\t1\n+TTTCCGAATAACTTGTGATCTGGCA\t1\n+TACATAAACAGAACTCGGCT\t1\n+TCTATTGCCCCAGCAAGTCTGACTG\t1\n+TAGTCTGTTAGAATCCTACGC\t1\n+GAGTATTCAGAGCAACCATA\t1\n+GGTAGGTCCTTTCGCCGGAGACGG\t1\n+ATATTCTGAATTACCACTTTTAAAAAA\t1\n+TAATAAGGCAATGATTGT\t1\n+TTCTTACCAGGCTTTGGAATC\t1\n+TCTATATTGAAACCAATCTGGACC\t1\n+TTCAATGCCATCGTCGTCAGCGG\t1\n+CACTGTTGCAGCGGCAATTAAGACT\t1\n+AAGGGTCCGCAGAAGCTGACGCT\t1\n+TTATTACTTACTCTGCCAGACCACATC\t1\n+GCCTTCCACAGCGAATGCGTCGC\t1\n+ATCCGTCGAGCGCTGGAGTGTACCC\t1\n+TAACTTAAAGGTAGTGTTAACGGA\t1\n+TTTGTCGAATGCTTGGGATACGTCT\t1\n+AGAGACGAGAACGCGTATATGTG\t1\n+TTTGATACAAATGCTTGTAGCCC\t1\n+CTAGTCGGCTGGACGGATC\t1\n+AACACAAATTCAACTATCGCCGGCC\t1\n+CTTAAGTTCCGTGATTGCGTTGGTA\t1\n+GAGACGGGAACGGCTGCTGAGCT\t1\n+TAACGGATCAAATATTTTTGCTCGC\t1\n+TTGAACCCTGCGAGGTAGCCG\t1\n+TAACGATCAGGGCCTCTGCACC\t1\n+TCGCGACTTGTGAACCCAA\t1\n+AGAGAACCAGAAAAAGATAATCCT\t1\n+TCAAGGACTCAAGGGCTGTTCCT\t1\n+CAAAGGAGCCGCAGCCGGACAAGGGC\t1\n+TCTCGCGGATGTATATTGGCGGA\t1\n+ACAACCTCAACTCATATGGCA\t1\n+ACGGGGTTTGGACTGTCACCC\t1\n+TTTGTAAATTGTCAGCTTGTTGGA\t1\n+GATGAAAATGTAGTGCACGCCA\t1\n' |
| b |
| diff -r 9645d995fb3c -r 9185ca0a7b43 test-data/res_files/reads-sample-small.fastq/size/histogram.png |
| b |
| Binary file test-data/res_files/reads-sample-small.fastq/size/histogram.png has changed |
| b |
| diff -r 9645d995fb3c -r 9185ca0a7b43 test-data/res_files/reads-sample-small.fastq/size/reads_size.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/res_files/reads-sample-small.fastq/size/reads_size.txt Wed Jan 16 08:18:13 2019 -0500 |
| b |
| @@ -0,0 +1,13 @@ +size number percentage +18 859 1.89 +19 895 1.96 +20 1611 3.54 +21 3934 8.63 +22 4498 9.87 +23 7700 16.90 +24 11572 25.39 +25 10297 22.60 +26 3341 7.33 +27 531 1.17 +28 304 0.67 +29 28 0.06 |
| b |
| diff -r 9645d995fb3c -r 9185ca0a7b43 test-data/res_files/reads-sample-small.fastq/subgroups/PPPartners/BATUMI_I.html --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/res_files/reads-sample-small.fastq/subgroups/PPPartners/BATUMI_I.html Wed Jan 16 08:18:13 2019 -0500 |
| b |
| b'@@ -0,0 +1,295 @@\n+\n+ <!DOCTYPE html>\n+ <html lang="en">\n+ <head>\n+ <meta charset="utf-8">\n+ <title>pipeline</title>\n+ <meta name="viewport" content="width=device-width, initial-scale=1.0">\n+ <meta name="description" content="">\n+ <meta name="author" content="">\n+ <!-- Le styles -->\n+ <link href="css/bootstrap.css" rel="stylesheet">\n+ <link href="css/bootstrap-table.css" rel="stylesheet">\n+ <style type="text/css">\n+ body {\n+ padding-top: 60px;\n+ padding-bottom: 40px;\n+ }\n+ div#page {\n+ width: 940px;\n+ background-color: #fff;\n+ margin: 0 auto;\n+ text-align: left;\n+ border-color: #fff;\n+ border-style: none solid solid;\n+ border-width: medium 1px 1px;\n+ }\n+\n+ div.content {\n+ \tdisplay: none;\n+\t float: right;\n+\t width: 550px;\n+ }\n+ div.content a, div.navigation a {\n+ text-decoration: none;\n+ \tcolor: #777;\n+ }\n+ div.content a:focus, div.content a:hover, div.content a:active {\n+ text-decoration: underline;\n+ }\n+ \n+ div.controls {\n+ margin-top: 5px;\n+\t height: 23px;\n+ }\n+ \n+ div.controls a {\n+\t padding: 5px;\n+ }\n+ div.ss-controls {\n+\t float: left;\n+ }\n+ div.nav-controls {\n+\t float: right;\n+ }\n+ div.slideshow-container {\n+\t position: relative;\n+\t clear: both;\n+\t height: 502px; /* This should be set to be at least the height of the largest image in the slideshow */\n+ }\n+ div.loader {\n+ \tposition: absolute;\n+ \ttop: 0;\n+ \tleft: 0;\n+ background-image: url(\'loader.gif\');\n+ background-repeat: no-repeat;\n+ background-position: center;\n+ \twidth: 550px;\n+ \theight: 502px; /* This should be set to be at least the height of the largest image in the slideshow */\n+ }\n+ div.slideshow {\n+ \n+ }\n+ \n+ div.slideshow span.image-wrapper {\n+\t display: block;\n+\t position: absolute;\n+\t top: 0;\n+\t left: 0;\n+ }\n+ div.slideshow a.advance-link {\n+\t display: block;\n+ \t width: 550px;\n+ height: 502px; /* This should be set to be at least the height of the largest image in the slideshow */\n+ line-height: 502px; /* This should be set to be at least the height of the largest image in the slideshow */\n+ text-align: center;\n+ }\n+ div.slideshow a.advance-link:hover, div.slideshow a.advance-link:active, div.slideshow a.advance-link:visited {\n+ text-decoration: none;\n+ }\n+ div.slideshow img {\n+ vertical-align: middle;\n+\tborder: 1px solid #ccc;\n+ }\n+\n+ div.image-title {\n+ font-weight: bold;\n+ font-size: 1.4em;\n+ }\n+\n+ div.image-desc {\n+ line-height: 1.3em;\n+ padding-top: 12px;\n+ }\n+ div.navigation {\n+\n+ }\n+ ul.thumbs {\n+\tclear: both;\n+\tmargin: 0;\n+\tpadding: 0;\n+ }\n+ ul.thumbs li {\n+\tfloat: none;\n+\tpadding: 0;\n+\tmargin: 0;\n+ list-style: none;\n+ }\n+ a.thumb {\n+\tpadding: 0;\n+\tdisplay: inline;\n+\tborder: none;\n+ }\n+ ul.thumbs li.selected a.thumb {\n+\tcolor: #000;\n+ font-weight: bold;\n+ }\n+ a.thumb:focus {\n+\toutline: none;\n+ }\n+ ul.thumbs img {\n+\tborder: none;\n+\tdisplay: block;\n+ }\n+ div.pagination {\n+\tclear: both;\n+ }\n+ div.navigation div.top {\n+ margin-bottom: 12px;\n+\theight: 11px;\n+ }\n+ div.navigation div.bottom {\n+ margin-top: 12px;\n+ }\n+ div.pagination a, div.pagination span.current, div.pagination span.ellipsis {\n+\tdisplay: block;\n+\tfloat: left;\n+ margin-right: 2px;\n+\tpadding: 4px 7px 2px 7px;\n+\tborder: 1px solid #ccc;\n+ }\n+ div.pagination a:hover {\n+ background-color: #eee;\n+ text-decoration: none;\n+ }\n+ div.pagination span.current {\n+ font-weight: bold;\n+ background-color: #000;\n+ border-color: #000;\n+\tcolor: #fff;\n+ }\n+ div.pagination span.ellipsis {\n+\tborder: none;\n+\tpadding: 5px 0 3px 2px;\n+ }\n+ \n+ div.download {\n+\tfloat: right;\n+ }\n+ \n+ div.caption-container {\n+\tposition: relative;\n+\tclear: left;\n+\theight: 75px;\n+ }\n+ span.image-caption {\n+\tdisplay: block;\n+\tposition: absolute;\n+\twidth: 550px;\n+\ttop: 0;\n+\tleft: 0;\n+ }\n+ div.caption {\n+\tpadding: 12px;\n+ }\n+\n+ /* Featurettes\n+ ------------------------- */\n+\n+ .featurette {\n+ padding-top: 20px; /* Vertica'..b'ter images part 2: clear their floats. */\n+ text-align: center;\n+ }\n+\n+ .featurette-p\n+ {\n+ text-align: left;\n+ }\n+\n+ .featurette-image {\n+ margin-top: 10px; /* Vertically center images part 3: negative margin up the image the same amount of the padding to center it. */\n+ width: 450px;\n+ height: auto;\n+ }\n+\n+ </style>\n+ <link href="css/bootstrap-responsive.css" rel="stylesheet">\n+ </head>\n+ <body>\n+ \n+\t\t\t\t\t<div align="center">\n+\t\t\t\t\t<h2>BATUMI_I</h2>\n+\t\t\t\t\t<p> <img class="featurette-image" src="BATUMI_I/histogram.png"/></p>\n+\t\t\t\t\t<p><a href="BATUMI_I/overlap_size.txt">ping pong signature</a></p>\n+\t\t\t\t\t<p><a href="BATUMI_I/sensPPP.txt">sense reads with PPP</a></p>\n+\t\t\t\t\t<p><a href="BATUMI_I/antisensPPP.txt">reverse reads with PPP</a></p>\n+\t\t\t\t\t<p><a href="BATUMI_I/sens.txt">sense reads without PPP</a></p>\n+\t\t\t\t\t<p><a href="BATUMI_I/antisens.txt">reverse reads without PPP</a></p>\n+\t\t\t\t\t</div>\n+ <!-- FOOTER -->\n+ <div class="container">\n+ <footer>\n+ \n+ </footer>\n+ </div>\n+ <!-- Le javascript\n+ ================================================== -->\n+ <!-- Placed at the end of the document so the pages load faster -->\n+ <script type="text/javascript" src="js/filter.js"></script>\n+ <script type="text/javascript" src="js/jquery.js"></script>\n+ <script type="text/javascript" src="js/jquery-1.3.2.js"></script>\n+ <script type="text/javascript" src="js/jquery.galleriffic.js"></script>\n+ <script type="text/javascript" src="js/jquery.opacityrollover.js"></script>\n+ <script type="text/javascript" src="js/bootstrap-table.js"></script>\n+ <script type="text/javascript" src="js/bootstrap.min.js"></script>\n+ <script type="text/javascript">\n+ jQuery(document).ready(function($) {\n+ // We only want these styles applied when javascript is enabled\n+ $(\'div.navigation\').css({\'width\' : \'300px\', \'float\' : \'left\'});\n+ $(\'div.content\').css(\'display\', \'block\');\n+ \n+ $(".each-gallery").each(function(i){\n+ // Initially set opacity on thumbs and add\n+ // additional styling for hover effect on thumbs\n+ var onMouseOutOpacity = 0.67;\n+ $(\'#thumbs + i + ul.thumbs li\').opacityrollover({\n+ mouseOutOpacity: onMouseOutOpacity,\n+ mouseOverOpacity: 1.0,\n+ fadeSpeed: \'fast\',\n+ exemptionSelector: \'.selected\'\n+ });\n+ \n+ // Initialize Advanced Galleriffic Gallery\n+ var gallery = $(\'#thumbs\'+i).galleriffic({\n+ delay: 2500,\n+ numThumbs: 22,\n+ preloadAhead: 10,\n+ enableTopPager: true,\n+ enableBottomPager: true,\n+ maxPagesToShow: 7,\n+ imageContainerSel: \'#slideshow\'+ i,\n+ controlsContainerSel: \'#controls\' + i,\n+ captionContainerSel: \'#caption\' + i,\n+ loadingContainerSel: \'#loading\' + i,\n+ renderSSControls: true,\n+ renderNavControls: true,\n+ playLinkText: \'Play\',\n+ pauseLinkText: \'Pause\',\n+ prevLinkText: \'‹ Previous\',\n+ nextLinkText: \'Next ›\',\n+ nextPageLinkText: \'Next ›\',\n+ prevPageLinkText: \'‹ Prev\',\n+ enableHistory: false,\n+ autoStart: false,\n+ syncTransitions: true,\n+ defaultTransitionDuration: 900,\n+ onSlideChange: function(prevIndex, nextIndex) {\n+ // \'this\' refers to the gallery, which is an extension of $(\'#thumbs\')\n+ this.find(\'ul.thumbs\').children()\n+ .eq(prevIndex).fadeTo(\'fast\', onMouseOutOpacity).end()\n+ .eq(nextIndex).fadeTo(\'fast\', 1.0);\n+ },\n+ onPageTransitionOut: function(callback) {\n+ this.fadeTo(\'fast\', 0.0, callback);\n+ },\n+ onPageTransitionIn: function() {\n+ this.fadeTo(\'fast\', 1.0);\n+ }\n+ });\n+ });\n+ });\n+ </script>\n+ </body>\n+ </html>\n+ \n\\ No newline at end of file\n' |
| b |
| diff -r 9645d995fb3c -r 9185ca0a7b43 test-data/res_files/reads-sample-small.fastq/subgroups/PPPartners/BATUMI_I/antisens.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/res_files/reads-sample-small.fastq/subgroups/PPPartners/BATUMI_I/antisens.txt Wed Jan 16 08:18:13 2019 -0500 |
| b |
| @@ -0,0 +1,116 @@ +>5|16|BATUMI_I|3 +CAGGTTATCCGGCTCGAAGGACC +>5|16|BATUMI_I|1 +TCCAGGTTATCCGGCTCGAAGGACC +>13|16|BATUMI_I|1 +TGAAAATCCAGGTTATCCGGCTC +>15|16|BATUMI_I|1 +ACTTGAAAATCCAGGTTATCCGGC +>23|16|BATUMI_I|1 +GGTGGACAAACTTGAAAATCCAGGT +>26|16|BATUMI_I|1 +TGGTGGACAAACTTGAAAATCCA +>54|16|BATUMI_I|1 +TTTCGTACTTATCTTATAATTTG +>94|16|BATUMI_I|1 +TTCGAAACTTTTGCTGCAGACCGGCA +>96|16|BATUMI_I|1 +TTTTCGAAACTTTTGCTGCAGACCGG +>97|16|BATUMI_I|1 +TTTTCGAAACTTTTGCTGCAGACCG +>98|16|BATUMI_I|1 +TTTCGAAACTTTTGCTGCAGACC +>120|16|BATUMI_I|1 +TACAGCAAATTGAACGAAATTGGATT +>124|16|BATUMI_I|1 +TCTTACAGCAAATTGAACGAAATTG +>161|16|BATUMI_I|3 +TTTTGTCGGAGAAATCCGTTAGA +>161|16|BATUMI_I|1 +CCTTTTGTCGGAGAAATCCGTTAGA +>161|16|BATUMI_I|1 +GCCTTTTGTCGGAGAAATCCGTTAGA +>165|16|BATUMI_I|1 +TGCCTTTTGTCGGAGAAATCCGT +>165|16|BATUMI_I|1 +TTGCCTTTTGTCGGAGAAATCCGT +>166|16|BATUMI_I|2 +TTGCCTTTTGTCGGAGAAATCCG +>166|16|BATUMI_I|1 +TAATTGCCTTTTGTCGGAGAAATCCG +>170|16|BATUMI_I|1 +TCTTTAATTGCCTTTTGTCGGAGAAA +>215|16|BATUMI_I|1 +CGGTGGGTAATATGGCGGCGCCCGT +>248|16|BATUMI_I|1 +TTCACGAATGAGGGTGAAAGGAG +>262|16|BATUMI_I|1 +TTGGACTTAGAAATTTTCACGAAT +>296|16|BATUMI_I|1 +TGGACTGGATGAATATTTAAATATA +>296|16|BATUMI_I|2 +TTGGACTGGATGAATATTTAAATATA +>298|16|BATUMI_I|1 +TTGGACTGGATGAATATTTAAATA +>349|16|BATUMI_I|2 +TCACTGAACTTGGCACAAATTATTTT +>350|16|BATUMI_I|4 +TCACTGAACTTGGCACAAATTATTT +>351|16|BATUMI_I|11 +TCACTGAACTTGGCACAAATTATT +>353|16|BATUMI_I|1 +TTTCACTGAACTTGGCACAAATTA +>354|16|BATUMI_I|2 +TTTTCACTGAACTTGGCACAAATT +>355|16|BATUMI_I|1 +ATTTTCACTGAACTTGGCACAAAT +>355|16|BATUMI_I|1 +AATTTTCACTGAACTTGGCACAAAT +>358|16|BATUMI_I|2 +TAGAAATTTTCACTGAACTTGGCACA +>359|16|BATUMI_I|3 +TAGAAATTTTCACTGAACTTGGCAC +>359|16|BATUMI_I|2 +TTAGAAATTTTCACTGAACTTGGCAC +>360|16|BATUMI_I|4 +TAGAAATTTTCACTGAACTTGGCA +>360|16|BATUMI_I|12 +TTAGAAATTTTCACTGAACTTGGCA +>361|16|BATUMI_I|5 +TTAGAAATTTTCACTGAACTTGGC +>370|16|BATUMI_I|1 +GCTTTGGACTTAGAAATTTTCACT +>370|16|BATUMI_I|1 +AGCTTTGGACTTAGAAATTTTCACT +>371|16|BATUMI_I|1 +GCTTTGGACTTAGAAATTTTCAC +>379|16|BATUMI_I|2 +TTTTGGCAGAGCTTTGGACTTAGAA +>380|16|BATUMI_I|1 +TTTGGCAGAGCTTTGGACTTAGA +>380|16|BATUMI_I|1 +TTTTGGCAGAGCTTTGGACTTAGA +>384|16|BATUMI_I|2 +TGCCACTTTTGGCAGAGCTTTGGACT +>385|16|BATUMI_I|1 +CCACTTTTGGCAGAGCTTTGGAC +>385|16|BATUMI_I|5 +TGCCACTTTTGGCAGAGCTTTGGAC +>385|16|BATUMI_I|5 +TTGCCACTTTTGGCAGAGCTTTGGAC +>385|16|BATUMI_I|2 +TTTGCCACTTTTGGCAGAGCTTTGGAC +>386|16|BATUMI_I|2 +TGCCACTTTTGGCAGAGCTTTGGA +>414|16|BATUMI_I|1 +TTGGACACAGTGAAACGAGAACACAA +>419|16|BATUMI_I|3 +TGCGTTGGACACAGTGAAACGAGAA +>420|16|BATUMI_I|4 +TGCGTTGGACACAGTGAAACGAGA +>421|16|BATUMI_I|1 +TTGCGTTGGACACAGTGAAACGAG +>485|16|BATUMI_I|1 +AAGCAAATTGTATTAAGTGGACTG +>7078|16|BATUMI_I|1 +TCCTTGGAGACTCTGTGGTGAAGA |
| b |
| diff -r 9645d995fb3c -r 9185ca0a7b43 test-data/res_files/reads-sample-small.fastq/subgroups/PPPartners/BATUMI_I/antisensPPP.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/res_files/reads-sample-small.fastq/subgroups/PPPartners/BATUMI_I/antisensPPP.txt Wed Jan 16 08:18:13 2019 -0500 |
| b |
| @@ -0,0 +1,4 @@ +>7005|16|BATUMI_I|3 +TGACAGTCCAAACCCCGTAACTTG +>7006|16|BATUMI_I|2 +TGACAGTCCAAACCCCGTAACTT |
| b |
| diff -r 9645d995fb3c -r 9185ca0a7b43 test-data/res_files/reads-sample-small.fastq/subgroups/PPPartners/BATUMI_I/histogram.png |
| b |
| Binary file test-data/res_files/reads-sample-small.fastq/subgroups/PPPartners/BATUMI_I/histogram.png has changed |
| b |
| diff -r 9645d995fb3c -r 9185ca0a7b43 test-data/res_files/reads-sample-small.fastq/subgroups/PPPartners/BATUMI_I/overlap_size.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/res_files/reads-sample-small.fastq/subgroups/PPPartners/BATUMI_I/overlap_size.txt Wed Jan 16 08:18:13 2019 -0500 |
| b |
| @@ -0,0 +1,24 @@ +size number percentage of the total overlap number +1 1 1.09 +2 2 2.17 +3 0 0.00 +4 0 0.00 +5 0 0.00 +6 0 0.00 +7 2 2.17 +8 1 1.09 +9 0 0.00 +10 22 23.91 +11 22 23.91 +12 11 11.96 +13 0 0.00 +14 0 0.00 +15 0 0.00 +16 1 1.09 +17 2 2.17 +18 0 0.00 +19 7 7.61 +20 6 6.52 +21 7 7.61 +22 3 3.26 +23 5 5.43 |
| b |
| diff -r 9645d995fb3c -r 9185ca0a7b43 test-data/res_files/reads-sample-small.fastq/subgroups/PPPartners/BATUMI_I/sens.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/res_files/reads-sample-small.fastq/subgroups/PPPartners/BATUMI_I/sens.txt Wed Jan 16 08:18:13 2019 -0500 |
| b |
| @@ -0,0 +1,52 @@ +>1|0|BATUMI_I|1 +TTTTTTGGTCCTTCGAGCCGGATA +>2|0|BATUMI_I|1 +TTTGGTCCTTCGAGCCGGATAACCT +>7|0|BATUMI_I|1 +TCCTTCGAGCCGGATAACCTGGATTT +>120|0|BATUMI_I|2 +AATCCAATTTCGTTCAATTTGCTGT +>151|0|BATUMI_I|1 +TATTGTCAAATCTAACGGATTTCTCC +>161|0|BATUMI_I|1 +TCTAACGGATTTCTCCGACAAAAGG +>387|0|BATUMI_I|1 +CCAAAGCTCTGCCAAAAGTGGCAAA +>418|0|BATUMI_I|1 +GTTCTCGTTTCACTGTGTCCAACGC +>419|0|BATUMI_I|1 +TTCTCGTTTCACTGTGTCCAACGC +>419|0|BATUMI_I|2 +TTCTCGTTTCACTGTGTCCAACGCA +>419|0|BATUMI_I|1 +TTCTCGTTTCACTGTGTCCAACGCAA +>420|0|BATUMI_I|1 +TCTCGTTTCACTGTGTCCAACGCA +>7007|0|BATUMI_I|1 +AGTTACGGGGTTTGGACTGTCACCC +>7008|0|BATUMI_I|1 +GTTACGGGGTTTGGACTGTCACCC +>7009|0|BATUMI_I|3 +TTACGGGGTTTGGACTGTCACCC +>7010|0|BATUMI_I|1 +TACGGGGTTTGGACTGTCACCCGC +>7010|0|BATUMI_I|5 +TACGGGGTTTGGACTGTCACCCGCT +>7017|0|BATUMI_I|1 +TTTGGACTGTCACCCGCTCTCCGC +>7017|0|BATUMI_I|11 +TTTGGACTGTCACCCGCTCTCCGCT +>7017|0|BATUMI_I|1 +TTTGGACTGTCACCCGCTCTCCGCTC +>7017|0|BATUMI_I|1 +TTTGGACTGTCACCCGCTCTCCGCTCC +>7018|0|BATUMI_I|7 +TTGGACTGTCACCCGCTCTCCGC +>7018|0|BATUMI_I|13 +TTGGACTGTCACCCGCTCTCCGCT +>7018|0|BATUMI_I|3 +TTGGACTGTCACCCGCTCTCCGCTC +>7018|0|BATUMI_I|16 +TTGGACTGTCACCCGCTCTCCGCTCC +>7018|0|BATUMI_I|1 +TTGGACTGTCACCCGCTCTCCGCTCCC |
| b |
| diff -r 9645d995fb3c -r 9185ca0a7b43 test-data/res_files/reads-sample-small.fastq/subgroups/PPPartners/BATUMI_I/sensPPP.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/res_files/reads-sample-small.fastq/subgroups/PPPartners/BATUMI_I/sensPPP.txt Wed Jan 16 08:18:13 2019 -0500 |
| b |
| @@ -0,0 +1,10 @@ +>7019|0|BATUMI_I|15 +TGGACTGTCACCCGCTCTCCGCT +>7019|0|BATUMI_I|4 +TGGACTGTCACCCGCTCTCCGCTC +>7019|0|BATUMI_I|31 +TGGACTGTCACCCGCTCTCCGCTCC +>7019|0|BATUMI_I|9 +TGGACTGTCACCCGCTCTCCGCTCCC +>7019|0|BATUMI_I|1 +TGGACTGTCACCCGCTCTCCGCTCCCT |
| b |
| diff -r 9645d995fb3c -r 9185ca0a7b43 test-data/res_files/reads-sample-small.fastq/subgroups/PPPartners/BATUMI_LTR.html --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/res_files/reads-sample-small.fastq/subgroups/PPPartners/BATUMI_LTR.html Wed Jan 16 08:18:13 2019 -0500 |
| b |
| b'@@ -0,0 +1,295 @@\n+\n+ <!DOCTYPE html>\n+ <html lang="en">\n+ <head>\n+ <meta charset="utf-8">\n+ <title>pipeline</title>\n+ <meta name="viewport" content="width=device-width, initial-scale=1.0">\n+ <meta name="description" content="">\n+ <meta name="author" content="">\n+ <!-- Le styles -->\n+ <link href="css/bootstrap.css" rel="stylesheet">\n+ <link href="css/bootstrap-table.css" rel="stylesheet">\n+ <style type="text/css">\n+ body {\n+ padding-top: 60px;\n+ padding-bottom: 40px;\n+ }\n+ div#page {\n+ width: 940px;\n+ background-color: #fff;\n+ margin: 0 auto;\n+ text-align: left;\n+ border-color: #fff;\n+ border-style: none solid solid;\n+ border-width: medium 1px 1px;\n+ }\n+\n+ div.content {\n+ \tdisplay: none;\n+\t float: right;\n+\t width: 550px;\n+ }\n+ div.content a, div.navigation a {\n+ text-decoration: none;\n+ \tcolor: #777;\n+ }\n+ div.content a:focus, div.content a:hover, div.content a:active {\n+ text-decoration: underline;\n+ }\n+ \n+ div.controls {\n+ margin-top: 5px;\n+\t height: 23px;\n+ }\n+ \n+ div.controls a {\n+\t padding: 5px;\n+ }\n+ div.ss-controls {\n+\t float: left;\n+ }\n+ div.nav-controls {\n+\t float: right;\n+ }\n+ div.slideshow-container {\n+\t position: relative;\n+\t clear: both;\n+\t height: 502px; /* This should be set to be at least the height of the largest image in the slideshow */\n+ }\n+ div.loader {\n+ \tposition: absolute;\n+ \ttop: 0;\n+ \tleft: 0;\n+ background-image: url(\'loader.gif\');\n+ background-repeat: no-repeat;\n+ background-position: center;\n+ \twidth: 550px;\n+ \theight: 502px; /* This should be set to be at least the height of the largest image in the slideshow */\n+ }\n+ div.slideshow {\n+ \n+ }\n+ \n+ div.slideshow span.image-wrapper {\n+\t display: block;\n+\t position: absolute;\n+\t top: 0;\n+\t left: 0;\n+ }\n+ div.slideshow a.advance-link {\n+\t display: block;\n+ \t width: 550px;\n+ height: 502px; /* This should be set to be at least the height of the largest image in the slideshow */\n+ line-height: 502px; /* This should be set to be at least the height of the largest image in the slideshow */\n+ text-align: center;\n+ }\n+ div.slideshow a.advance-link:hover, div.slideshow a.advance-link:active, div.slideshow a.advance-link:visited {\n+ text-decoration: none;\n+ }\n+ div.slideshow img {\n+ vertical-align: middle;\n+\tborder: 1px solid #ccc;\n+ }\n+\n+ div.image-title {\n+ font-weight: bold;\n+ font-size: 1.4em;\n+ }\n+\n+ div.image-desc {\n+ line-height: 1.3em;\n+ padding-top: 12px;\n+ }\n+ div.navigation {\n+\n+ }\n+ ul.thumbs {\n+\tclear: both;\n+\tmargin: 0;\n+\tpadding: 0;\n+ }\n+ ul.thumbs li {\n+\tfloat: none;\n+\tpadding: 0;\n+\tmargin: 0;\n+ list-style: none;\n+ }\n+ a.thumb {\n+\tpadding: 0;\n+\tdisplay: inline;\n+\tborder: none;\n+ }\n+ ul.thumbs li.selected a.thumb {\n+\tcolor: #000;\n+ font-weight: bold;\n+ }\n+ a.thumb:focus {\n+\toutline: none;\n+ }\n+ ul.thumbs img {\n+\tborder: none;\n+\tdisplay: block;\n+ }\n+ div.pagination {\n+\tclear: both;\n+ }\n+ div.navigation div.top {\n+ margin-bottom: 12px;\n+\theight: 11px;\n+ }\n+ div.navigation div.bottom {\n+ margin-top: 12px;\n+ }\n+ div.pagination a, div.pagination span.current, div.pagination span.ellipsis {\n+\tdisplay: block;\n+\tfloat: left;\n+ margin-right: 2px;\n+\tpadding: 4px 7px 2px 7px;\n+\tborder: 1px solid #ccc;\n+ }\n+ div.pagination a:hover {\n+ background-color: #eee;\n+ text-decoration: none;\n+ }\n+ div.pagination span.current {\n+ font-weight: bold;\n+ background-color: #000;\n+ border-color: #000;\n+\tcolor: #fff;\n+ }\n+ div.pagination span.ellipsis {\n+\tborder: none;\n+\tpadding: 5px 0 3px 2px;\n+ }\n+ \n+ div.download {\n+\tfloat: right;\n+ }\n+ \n+ div.caption-container {\n+\tposition: relative;\n+\tclear: left;\n+\theight: 75px;\n+ }\n+ span.image-caption {\n+\tdisplay: block;\n+\tposition: absolute;\n+\twidth: 550px;\n+\ttop: 0;\n+\tleft: 0;\n+ }\n+ div.caption {\n+\tpadding: 12px;\n+ }\n+\n+ /* Featurettes\n+ ------------------------- */\n+\n+ .featurette {\n+ padding-top: 20px; /* Vertica'..b't 2: clear their floats. */\n+ text-align: center;\n+ }\n+\n+ .featurette-p\n+ {\n+ text-align: left;\n+ }\n+\n+ .featurette-image {\n+ margin-top: 10px; /* Vertically center images part 3: negative margin up the image the same amount of the padding to center it. */\n+ width: 450px;\n+ height: auto;\n+ }\n+\n+ </style>\n+ <link href="css/bootstrap-responsive.css" rel="stylesheet">\n+ </head>\n+ <body>\n+ \n+\t\t\t\t\t<div align="center">\n+\t\t\t\t\t<h2>BATUMI_LTR</h2>\n+\t\t\t\t\t<p> <img class="featurette-image" src="BATUMI_LTR/histogram.png"/></p>\n+\t\t\t\t\t<p><a href="BATUMI_LTR/overlap_size.txt">ping pong signature</a></p>\n+\t\t\t\t\t<p><a href="BATUMI_LTR/sensPPP.txt">sense reads with PPP</a></p>\n+\t\t\t\t\t<p><a href="BATUMI_LTR/antisensPPP.txt">reverse reads with PPP</a></p>\n+\t\t\t\t\t<p><a href="BATUMI_LTR/sens.txt">sense reads without PPP</a></p>\n+\t\t\t\t\t<p><a href="BATUMI_LTR/antisens.txt">reverse reads without PPP</a></p>\n+\t\t\t\t\t</div>\n+ <!-- FOOTER -->\n+ <div class="container">\n+ <footer>\n+ \n+ </footer>\n+ </div>\n+ <!-- Le javascript\n+ ================================================== -->\n+ <!-- Placed at the end of the document so the pages load faster -->\n+ <script type="text/javascript" src="js/filter.js"></script>\n+ <script type="text/javascript" src="js/jquery.js"></script>\n+ <script type="text/javascript" src="js/jquery-1.3.2.js"></script>\n+ <script type="text/javascript" src="js/jquery.galleriffic.js"></script>\n+ <script type="text/javascript" src="js/jquery.opacityrollover.js"></script>\n+ <script type="text/javascript" src="js/bootstrap-table.js"></script>\n+ <script type="text/javascript" src="js/bootstrap.min.js"></script>\n+ <script type="text/javascript">\n+ jQuery(document).ready(function($) {\n+ // We only want these styles applied when javascript is enabled\n+ $(\'div.navigation\').css({\'width\' : \'300px\', \'float\' : \'left\'});\n+ $(\'div.content\').css(\'display\', \'block\');\n+ \n+ $(".each-gallery").each(function(i){\n+ // Initially set opacity on thumbs and add\n+ // additional styling for hover effect on thumbs\n+ var onMouseOutOpacity = 0.67;\n+ $(\'#thumbs + i + ul.thumbs li\').opacityrollover({\n+ mouseOutOpacity: onMouseOutOpacity,\n+ mouseOverOpacity: 1.0,\n+ fadeSpeed: \'fast\',\n+ exemptionSelector: \'.selected\'\n+ });\n+ \n+ // Initialize Advanced Galleriffic Gallery\n+ var gallery = $(\'#thumbs\'+i).galleriffic({\n+ delay: 2500,\n+ numThumbs: 22,\n+ preloadAhead: 10,\n+ enableTopPager: true,\n+ enableBottomPager: true,\n+ maxPagesToShow: 7,\n+ imageContainerSel: \'#slideshow\'+ i,\n+ controlsContainerSel: \'#controls\' + i,\n+ captionContainerSel: \'#caption\' + i,\n+ loadingContainerSel: \'#loading\' + i,\n+ renderSSControls: true,\n+ renderNavControls: true,\n+ playLinkText: \'Play\',\n+ pauseLinkText: \'Pause\',\n+ prevLinkText: \'‹ Previous\',\n+ nextLinkText: \'Next ›\',\n+ nextPageLinkText: \'Next ›\',\n+ prevPageLinkText: \'‹ Prev\',\n+ enableHistory: false,\n+ autoStart: false,\n+ syncTransitions: true,\n+ defaultTransitionDuration: 900,\n+ onSlideChange: function(prevIndex, nextIndex) {\n+ // \'this\' refers to the gallery, which is an extension of $(\'#thumbs\')\n+ this.find(\'ul.thumbs\').children()\n+ .eq(prevIndex).fadeTo(\'fast\', onMouseOutOpacity).end()\n+ .eq(nextIndex).fadeTo(\'fast\', 1.0);\n+ },\n+ onPageTransitionOut: function(callback) {\n+ this.fadeTo(\'fast\', 0.0, callback);\n+ },\n+ onPageTransitionIn: function() {\n+ this.fadeTo(\'fast\', 1.0);\n+ }\n+ });\n+ });\n+ });\n+ </script>\n+ </body>\n+ </html>\n+ \n\\ No newline at end of file\n' |
| b |
| diff -r 9645d995fb3c -r 9185ca0a7b43 test-data/res_files/reads-sample-small.fastq/subgroups/PPPartners/BATUMI_LTR/antisens.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/res_files/reads-sample-small.fastq/subgroups/PPPartners/BATUMI_LTR/antisens.txt Wed Jan 16 08:18:13 2019 -0500 |
| b |
| @@ -0,0 +1,38 @@ +>70|16|BATUMI_LTR|1 +TCCTTGGAGACTCTGTGGTGAAGA +>100|16|BATUMI_LTR|1 +TAATTAGTTAGGCTCTCCCAAGCGC +>103|16|BATUMI_LTR|1 +TTCTAATTAGTTAGGCTCTCCCAAG +>106|16|BATUMI_LTR|34 +TTATTCTAATTAGTTAGGCTCTCCC +>107|16|BATUMI_LTR|30 +TTATTCTAATTAGTTAGGCTCTCC +>108|16|BATUMI_LTR|1 +TTATTCTAATTAGTTAGGCTCTC +>112|16|BATUMI_LTR|1 +CTGGTGCTTATTCTAATTAGTTAGGC +>178|16|BATUMI_LTR|2 +CACTAGACTTTTCATAATTGCGCGG +>180|16|BATUMI_LTR|1 +CACTAGACTTTTCATAATTGCGC +>192|16|BATUMI_LTR|1 +GAAGAAAAGCGAACACTAGACTTT +>193|16|BATUMI_LTR|1 +CGAAGAAAAGCGAACACTAGACTT +>193|16|BATUMI_LTR|1 +TCGAAGAAAAGCGAACACTAGACTT +>193|16|BATUMI_LTR|1 +CTCGAAGAAAAGCGAACACTAGACTT +>194|16|BATUMI_LTR|4 +TCGAAGAAAAGCGAACACTAGACT +>194|16|BATUMI_LTR|1 +CTCGAAGAAAAGCGAACACTAGACT +>194|16|BATUMI_LTR|1 +ACTCGAAGAAAAGCGAACACTAGACT +>205|16|BATUMI_LTR|1 +AAAAGAAACACTCGAAGAAAAGCG +>208|16|BATUMI_LTR|1 +TGAAAAGAAACACTCGAAGAAAA +>218|16|BATUMI_LTR|1 +TTCCAAATATGCTGAAAAGAAACAC |
| b |
| diff -r 9645d995fb3c -r 9185ca0a7b43 test-data/res_files/reads-sample-small.fastq/subgroups/PPPartners/BATUMI_LTR/antisensPPP.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/res_files/reads-sample-small.fastq/subgroups/PPPartners/BATUMI_LTR/antisensPPP.txt Wed Jan 16 08:18:13 2019 -0500 |
| b |
| @@ -0,0 +1,2 @@ +>103|16|BATUMI_LTR|1 +ATTCTAATTAGTTAGGCTCTCCCAAG |
| b |
| diff -r 9645d995fb3c -r 9185ca0a7b43 test-data/res_files/reads-sample-small.fastq/subgroups/PPPartners/BATUMI_LTR/histogram.png |
| b |
| Binary file test-data/res_files/reads-sample-small.fastq/subgroups/PPPartners/BATUMI_LTR/histogram.png has changed |
| b |
| diff -r 9645d995fb3c -r 9185ca0a7b43 test-data/res_files/reads-sample-small.fastq/subgroups/PPPartners/BATUMI_LTR/overlap_size.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/res_files/reads-sample-small.fastq/subgroups/PPPartners/BATUMI_LTR/overlap_size.txt Wed Jan 16 08:18:13 2019 -0500 |
| b |
| @@ -0,0 +1,24 @@ +size number percentage of the total overlap number +1 0 0.00 +2 0 0.00 +3 0 0.00 +4 0 0.00 +5 0 0.00 +6 1 7.69 +7 2 15.38 +8 0 0.00 +9 1 7.69 +10 1 7.69 +11 0 0.00 +12 3 23.08 +13 0 0.00 +14 0 0.00 +15 0 0.00 +16 0 0.00 +17 0 0.00 +18 0 0.00 +19 1 7.69 +20 1 7.69 +21 1 7.69 +22 2 15.38 +23 0 0.00 |
| b |
| diff -r 9645d995fb3c -r 9185ca0a7b43 test-data/res_files/reads-sample-small.fastq/subgroups/PPPartners/BATUMI_LTR/sens.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/res_files/reads-sample-small.fastq/subgroups/PPPartners/BATUMI_LTR/sens.txt Wed Jan 16 08:18:13 2019 -0500 |
| b |
| @@ -0,0 +1,4 @@ +>33|0|BATUMI_LTR|1 +TGTCACCCGCTCTCCGCTCCCTCTT +>196|0|BATUMI_LTR|1 +TCTAGTGTTCGCTTTTCTTCGAG |
| b |
| diff -r 9645d995fb3c -r 9185ca0a7b43 test-data/res_files/reads-sample-small.fastq/subgroups/PPPartners/BATUMI_LTR/sensPPP.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/res_files/reads-sample-small.fastq/subgroups/PPPartners/BATUMI_LTR/sensPPP.txt Wed Jan 16 08:18:13 2019 -0500 |
| b |
| @@ -0,0 +1,2 @@ +>119|0|BATUMI_LTR|1 +TAATTAGAATAAGCACCAGTGTCA |
| b |
| diff -r 9645d995fb3c -r 9185ca0a7b43 test-data/res_files/reads-sample-small.fastq/subgroups/PPPartners/BS2.html --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/res_files/reads-sample-small.fastq/subgroups/PPPartners/BS2.html Wed Jan 16 08:18:13 2019 -0500 |
| b |
| b'@@ -0,0 +1,295 @@\n+\n+ <!DOCTYPE html>\n+ <html lang="en">\n+ <head>\n+ <meta charset="utf-8">\n+ <title>pipeline</title>\n+ <meta name="viewport" content="width=device-width, initial-scale=1.0">\n+ <meta name="description" content="">\n+ <meta name="author" content="">\n+ <!-- Le styles -->\n+ <link href="css/bootstrap.css" rel="stylesheet">\n+ <link href="css/bootstrap-table.css" rel="stylesheet">\n+ <style type="text/css">\n+ body {\n+ padding-top: 60px;\n+ padding-bottom: 40px;\n+ }\n+ div#page {\n+ width: 940px;\n+ background-color: #fff;\n+ margin: 0 auto;\n+ text-align: left;\n+ border-color: #fff;\n+ border-style: none solid solid;\n+ border-width: medium 1px 1px;\n+ }\n+\n+ div.content {\n+ \tdisplay: none;\n+\t float: right;\n+\t width: 550px;\n+ }\n+ div.content a, div.navigation a {\n+ text-decoration: none;\n+ \tcolor: #777;\n+ }\n+ div.content a:focus, div.content a:hover, div.content a:active {\n+ text-decoration: underline;\n+ }\n+ \n+ div.controls {\n+ margin-top: 5px;\n+\t height: 23px;\n+ }\n+ \n+ div.controls a {\n+\t padding: 5px;\n+ }\n+ div.ss-controls {\n+\t float: left;\n+ }\n+ div.nav-controls {\n+\t float: right;\n+ }\n+ div.slideshow-container {\n+\t position: relative;\n+\t clear: both;\n+\t height: 502px; /* This should be set to be at least the height of the largest image in the slideshow */\n+ }\n+ div.loader {\n+ \tposition: absolute;\n+ \ttop: 0;\n+ \tleft: 0;\n+ background-image: url(\'loader.gif\');\n+ background-repeat: no-repeat;\n+ background-position: center;\n+ \twidth: 550px;\n+ \theight: 502px; /* This should be set to be at least the height of the largest image in the slideshow */\n+ }\n+ div.slideshow {\n+ \n+ }\n+ \n+ div.slideshow span.image-wrapper {\n+\t display: block;\n+\t position: absolute;\n+\t top: 0;\n+\t left: 0;\n+ }\n+ div.slideshow a.advance-link {\n+\t display: block;\n+ \t width: 550px;\n+ height: 502px; /* This should be set to be at least the height of the largest image in the slideshow */\n+ line-height: 502px; /* This should be set to be at least the height of the largest image in the slideshow */\n+ text-align: center;\n+ }\n+ div.slideshow a.advance-link:hover, div.slideshow a.advance-link:active, div.slideshow a.advance-link:visited {\n+ text-decoration: none;\n+ }\n+ div.slideshow img {\n+ vertical-align: middle;\n+\tborder: 1px solid #ccc;\n+ }\n+\n+ div.image-title {\n+ font-weight: bold;\n+ font-size: 1.4em;\n+ }\n+\n+ div.image-desc {\n+ line-height: 1.3em;\n+ padding-top: 12px;\n+ }\n+ div.navigation {\n+\n+ }\n+ ul.thumbs {\n+\tclear: both;\n+\tmargin: 0;\n+\tpadding: 0;\n+ }\n+ ul.thumbs li {\n+\tfloat: none;\n+\tpadding: 0;\n+\tmargin: 0;\n+ list-style: none;\n+ }\n+ a.thumb {\n+\tpadding: 0;\n+\tdisplay: inline;\n+\tborder: none;\n+ }\n+ ul.thumbs li.selected a.thumb {\n+\tcolor: #000;\n+ font-weight: bold;\n+ }\n+ a.thumb:focus {\n+\toutline: none;\n+ }\n+ ul.thumbs img {\n+\tborder: none;\n+\tdisplay: block;\n+ }\n+ div.pagination {\n+\tclear: both;\n+ }\n+ div.navigation div.top {\n+ margin-bottom: 12px;\n+\theight: 11px;\n+ }\n+ div.navigation div.bottom {\n+ margin-top: 12px;\n+ }\n+ div.pagination a, div.pagination span.current, div.pagination span.ellipsis {\n+\tdisplay: block;\n+\tfloat: left;\n+ margin-right: 2px;\n+\tpadding: 4px 7px 2px 7px;\n+\tborder: 1px solid #ccc;\n+ }\n+ div.pagination a:hover {\n+ background-color: #eee;\n+ text-decoration: none;\n+ }\n+ div.pagination span.current {\n+ font-weight: bold;\n+ background-color: #000;\n+ border-color: #000;\n+\tcolor: #fff;\n+ }\n+ div.pagination span.ellipsis {\n+\tborder: none;\n+\tpadding: 5px 0 3px 2px;\n+ }\n+ \n+ div.download {\n+\tfloat: right;\n+ }\n+ \n+ div.caption-container {\n+\tposition: relative;\n+\tclear: left;\n+\theight: 75px;\n+ }\n+ span.image-caption {\n+\tdisplay: block;\n+\tposition: absolute;\n+\twidth: 550px;\n+\ttop: 0;\n+\tleft: 0;\n+ }\n+ div.caption {\n+\tpadding: 12px;\n+ }\n+\n+ /* Featurettes\n+ ------------------------- */\n+\n+ .featurette {\n+ padding-top: 20px; /* Vertica'..b'overflow: hidden; /* Vertically center images part 2: clear their floats. */\n+ text-align: center;\n+ }\n+\n+ .featurette-p\n+ {\n+ text-align: left;\n+ }\n+\n+ .featurette-image {\n+ margin-top: 10px; /* Vertically center images part 3: negative margin up the image the same amount of the padding to center it. */\n+ width: 450px;\n+ height: auto;\n+ }\n+\n+ </style>\n+ <link href="css/bootstrap-responsive.css" rel="stylesheet">\n+ </head>\n+ <body>\n+ \n+\t\t\t\t\t<div align="center">\n+\t\t\t\t\t<h2>BS2</h2>\n+\t\t\t\t\t<p> <img class="featurette-image" src="BS2/histogram.png"/></p>\n+\t\t\t\t\t<p><a href="BS2/overlap_size.txt">ping pong signature</a></p>\n+\t\t\t\t\t<p><a href="BS2/sensPPP.txt">sense reads with PPP</a></p>\n+\t\t\t\t\t<p><a href="BS2/antisensPPP.txt">reverse reads with PPP</a></p>\n+\t\t\t\t\t<p><a href="BS2/sens.txt">sense reads without PPP</a></p>\n+\t\t\t\t\t<p><a href="BS2/antisens.txt">reverse reads without PPP</a></p>\n+\t\t\t\t\t</div>\n+ <!-- FOOTER -->\n+ <div class="container">\n+ <footer>\n+ \n+ </footer>\n+ </div>\n+ <!-- Le javascript\n+ ================================================== -->\n+ <!-- Placed at the end of the document so the pages load faster -->\n+ <script type="text/javascript" src="js/filter.js"></script>\n+ <script type="text/javascript" src="js/jquery.js"></script>\n+ <script type="text/javascript" src="js/jquery-1.3.2.js"></script>\n+ <script type="text/javascript" src="js/jquery.galleriffic.js"></script>\n+ <script type="text/javascript" src="js/jquery.opacityrollover.js"></script>\n+ <script type="text/javascript" src="js/bootstrap-table.js"></script>\n+ <script type="text/javascript" src="js/bootstrap.min.js"></script>\n+ <script type="text/javascript">\n+ jQuery(document).ready(function($) {\n+ // We only want these styles applied when javascript is enabled\n+ $(\'div.navigation\').css({\'width\' : \'300px\', \'float\' : \'left\'});\n+ $(\'div.content\').css(\'display\', \'block\');\n+ \n+ $(".each-gallery").each(function(i){\n+ // Initially set opacity on thumbs and add\n+ // additional styling for hover effect on thumbs\n+ var onMouseOutOpacity = 0.67;\n+ $(\'#thumbs + i + ul.thumbs li\').opacityrollover({\n+ mouseOutOpacity: onMouseOutOpacity,\n+ mouseOverOpacity: 1.0,\n+ fadeSpeed: \'fast\',\n+ exemptionSelector: \'.selected\'\n+ });\n+ \n+ // Initialize Advanced Galleriffic Gallery\n+ var gallery = $(\'#thumbs\'+i).galleriffic({\n+ delay: 2500,\n+ numThumbs: 22,\n+ preloadAhead: 10,\n+ enableTopPager: true,\n+ enableBottomPager: true,\n+ maxPagesToShow: 7,\n+ imageContainerSel: \'#slideshow\'+ i,\n+ controlsContainerSel: \'#controls\' + i,\n+ captionContainerSel: \'#caption\' + i,\n+ loadingContainerSel: \'#loading\' + i,\n+ renderSSControls: true,\n+ renderNavControls: true,\n+ playLinkText: \'Play\',\n+ pauseLinkText: \'Pause\',\n+ prevLinkText: \'‹ Previous\',\n+ nextLinkText: \'Next ›\',\n+ nextPageLinkText: \'Next ›\',\n+ prevPageLinkText: \'‹ Prev\',\n+ enableHistory: false,\n+ autoStart: false,\n+ syncTransitions: true,\n+ defaultTransitionDuration: 900,\n+ onSlideChange: function(prevIndex, nextIndex) {\n+ // \'this\' refers to the gallery, which is an extension of $(\'#thumbs\')\n+ this.find(\'ul.thumbs\').children()\n+ .eq(prevIndex).fadeTo(\'fast\', onMouseOutOpacity).end()\n+ .eq(nextIndex).fadeTo(\'fast\', 1.0);\n+ },\n+ onPageTransitionOut: function(callback) {\n+ this.fadeTo(\'fast\', 0.0, callback);\n+ },\n+ onPageTransitionIn: function() {\n+ this.fadeTo(\'fast\', 1.0);\n+ }\n+ });\n+ });\n+ });\n+ </script>\n+ </body>\n+ </html>\n+ \n\\ No newline at end of file\n' |
| b |
| diff -r 9645d995fb3c -r 9185ca0a7b43 test-data/res_files/reads-sample-small.fastq/subgroups/PPPartners/BS2/antisens.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/res_files/reads-sample-small.fastq/subgroups/PPPartners/BS2/antisens.txt Wed Jan 16 08:18:13 2019 -0500 |
| b |
| b'@@ -0,0 +1,1770 @@\n+>13|16|BS2|2\n+TGCGTATTGTTAGACACGAACCT\n+>14|16|BS2|1\n+AGGTGCGTATTGTTAGACACGAACC\n+>120|16|BS2|1\n+TTCACTGTTAGTGACTTGGGGGGTCAC\n+>122|16|BS2|4\n+TTCACTGTTAGTGACTTGGGGGGTC\n+>122|16|BS2|1\n+CACTGTTAGTGACTTGGGGGGTC\n+>135|16|BS2|2\n+TTTCACTATTATTTCACTGTTAGT\n+>139|16|BS2|1\n+TTCGTTTCACTATTATTTCACTGT\n+>140|16|BS2|3\n+TTTCGTTTCACTATTATTTCACTG\n+>206|16|BS2|1\n+CGCGTGGCAGCTGGGCAGCGGAGCC\n+>215|16|BS2|1\n+TTTGTGCGATCGCGTGGCAGCTGGGC\n+>215|16|BS2|5\n+TTGTGCGATCGCGTGGCAGCTGGGC\n+>215|16|BS2|1\n+TGTGCGATCGCGTGGCAGCTGGGC\n+>216|16|BS2|1\n+TTTGTGCGATCGCGTGGCAGCTGGG\n+>216|16|BS2|1\n+TTGTGCGATCGCGTGGCAGCTGGG\n+>216|16|BS2|1\n+TGTGCGATCGCGTGGCAGCTGGG\n+>217|16|BS2|2\n+TTTGTGCGATCGCGTGGCAGCTGG\n+>217|16|BS2|1\n+TTGTGCGATCGCGTGGCAGCTGG\n+>218|16|BS2|2\n+TGTTTGTGCGATCGCGTGGCAGCTG\n+>218|16|BS2|16\n+TTTGTGCGATCGCGTGGCAGCTG\n+>219|16|BS2|1\n+TGTTTGTGCGATCGCGTGGCAGCT\n+>219|16|BS2|1\n+GTTTGTGCGATCGCGTGGCAGCT\n+>220|16|BS2|1\n+TGTTTGTGCGATCGCGTGGCAGC\n+>221|16|BS2|1\n+GCTGTTTGTGCGATCGCGTGGCAG\n+>222|16|BS2|1\n+ACAGCTGTTTGTGCGATCGCGTGGCA\n+>226|16|BS2|1\n+AACAGCTGTTTGTGCGATCGCGT\n+>237|16|BS2|1\n+TTTAAGCTCGCAAACAGCTGTTTG\n+>252|16|BS2|1\n+CCCTGGGATAGAAAGCTTTAAGCTC\n+>262|16|BS2|1\n+AACTTGAACCCTGGGATAGAAAG\n+>264|16|BS2|1\n+CAAAACTTGAACCCTGGGATAGAA\n+>264|16|BS2|1\n+AAAACTTGAACCCTGGGATAGAA\n+>268|16|BS2|1\n+TCTAGCCAAAACTTGAACCCTGGGAT\n+>268|16|BS2|1\n+TAGCCAAAACTTGAACCCTGGGAT\n+>269|16|BS2|11\n+TCTAGCCAAAACTTGAACCCTGGGA\n+>270|16|BS2|3\n+TCTAGCCAAAACTTGAACCCTGGG\n+>271|16|BS2|1\n+TCTAGCCAAAACTTGAACCCTGG\n+>357|16|BS2|1\n+AGAGAAACGCAGTATCCAACGAT\n+>368|16|BS2|1\n+TTGGGGGCTCGAGAGAAACGCAG\n+>381|16|BS2|2\n+TGCGGGGCAGCACATTGGGGGCTC\n+>381|16|BS2|3\n+GCGGGGCAGCACATTGGGGGCTC\n+>382|16|BS2|1\n+TGCGGGGCAGCACATTGGGGGCT\n+>395|16|BS2|1\n+TATTTTTTGAAAGCGCTGCGGGGCAG\n+>395|16|BS2|1\n+TTTTTTGAAAGCGCTGCGGGGCAG\n+>422|16|BS2|1\n+TCCGGAGAAGCACGAGACTTTCGCT\n+>425|16|BS2|1\n+TCTCCGGAGAAGCACGAGACTTTC\n+>439|16|BS2|1\n+TTTTTTCCTTTCAGTCTCCGGAGA\n+>444|16|BS2|3\n+TTTGGGTTTTTTCCTTTCAGTCTCC\n+>467|16|BS2|2\n+TCCCCTTGTTTGCCGATGGTTGATT\n+>468|16|BS2|1\n+TTTCCCCTTGTTTGCCGATGGTTGAT\n+>469|16|BS2|1\n+TTTCCCCTTGTTTGCCGATGGTTGA\n+>470|16|BS2|2\n+TTTCCCCTTGTTTGCCGATGGTTG\n+>484|16|BS2|1\n+TTCTGTAGCCGAAGGGTTTTCCCCTTG\n+>485|16|BS2|5\n+TTCTGTAGCCGAAGGGTTTTCCCCTT\n+>486|16|BS2|1\n+TTCTGTAGCCGAAGGGTTTTCCCCT\n+>487|16|BS2|1\n+TTCTGTAGCCGAAGGGTTTTCCCC\n+>492|16|BS2|1\n+TAGGTTCTGTAGCCGAAGGGTTT\n+>493|16|BS2|2\n+TATCTAGGTTCTGTAGCCGAAGGGTT\n+>496|16|BS2|5\n+TATCTAGGTTCTGTAGCCGAAGG\n+>497|16|BS2|2\n+GCCATATCTAGGTTCTGTAGCCGAAG\n+>499|16|BS2|1\n+CGCCATATCTAGGTTCTGTAGCCGA\n+>499|16|BS2|1\n+GCCATATCTAGGTTCTGTAGCCGA\n+>501|16|BS2|1\n+CGCCATATCTAGGTTCTGTAGCC\n+>504|16|BS2|1\n+TTGCCGCCATATCTAGGTTCTGTA\n+>520|16|BS2|1\n+TAAACCAAATCGGTTTGAATTGCCGCC\n+>523|16|BS2|1\n+AGTAAACCAAATCGGTTTGAATTGCC\n+>550|16|BS2|1\n+TTGTTTGTCAGCTGTGAGATGCGC\n+>551|16|BS2|1\n+TTGTTTGTCAGCTGTGAGATGCG\n+>552|16|BS2|4\n+ACTTGTTTGTCAGCTGTGAGATGC\n+>561|16|BS2|1\n+TTCATTGCCTACTTGTTTGTCAGCT\n+>562|16|BS2|1\n+TTCATTGCCTACTTGTTTGTCAGC\n+>574|16|BS2|1\n+TACAGATCGCCAATTTCATTGCCTAC\n+>576|16|BS2|1\n+TACAGATCGCCAATTTCATTGCCT\n+>577|16|BS2|1\n+TACAGATCGCCAATTTCATTGCC\n+>588|16|BS2|1\n+CTGGGCTGGTCATACAGATCGCCA\n+>589|16|BS2|31\n+TACTGGGCTGGTCATACAGATCGCC\n+>589|16|BS2|1\n+ACTGGGCTGGTCATACAGATCGCC\n+>590|16|BS2|8\n+TACTGGGCTGGTCATACAGATCGC\n+>592|16|BS2|5\n+TGGTACTGGGCTGGTCATACAGATC\n+>593|16|BS2|1\n+TGGTACTGGGCTGGTCATACAGAT\n+>600|16|BS2|1\n+TTGATGACTGGTACTGGGCTGGTCA\n+>601|16|BS2|1\n+TTGATGACTGGTACTGGGCTGGTC\n+>602|16|BS2|3\n+TTGATGACTGGTACTGGGCTGGT\n+>603|16|BS2|1\n+CTTGATGACTGGTACTGGGCTGG\n+>606|16|BS2|12\n+TGCAGCTTGATGACTGGTACTGGGC\n+>606|16|BS2|2\n+GCAGCTTGATGACTGGTACTGGGC\n+>610|16|BS2|2\n+AATTGCAGCTTGATGACTGGTACT\n+>613|16|BS2|1\n+GCAATTGCAGCTTGATGACTGGT\n+>617|16|BS2|1\n+GCGGCAGCAATTGCAGCTTGATGAC\n+>635|16|BS2|1\n+GGCTGCATCCCGCTTAGCGGCAG\n+>649|16|BS2|1\n+TAGTGGTACCAGCGGAGGCTGCATC\n+>649|16|BS2|1\n+AGTGGTACCAGCGGAGGCTGCATC\n+>651|16|BS2|1\n+TAGTGGTACCAGCGGAGGCTGCA\n+>653|16|BS2|2\n+TGAGCTAGTGGTACCAGCGGAGGCTG\n+>655|16|BS2|1\n+TGAGCTAGTGGTACCAGCGGAGGC\n+>661|16|BS2|3\n+TTTTTGGCTGAGCTAGTGGTACCAGC\n+>661|16|BS2|6\n+TTTTGGCTGAGCTAGTGGTACCAGC\n+>661|16|BS2|9\n+TTTGGCTGAGCTAGTGGTACCAGC\n+>662|16|BS2'..b'GTGGCTGTCGCAGGC\n+>4265|16|BS2|1\n+GATCCTTTTGATGTGGCTGTCGCAG\n+>4274|16|BS2|1\n+TAGCCTGGATCCTTTTGATGTGG\n+>4275|16|BS2|1\n+AATAGCCTGGATCCTTTTGATGTG\n+>4276|16|BS2|1\n+GAATAGCCTGGATCCTTTTGATGT\n+>4279|16|BS2|4\n+TTTTGAATAGCCTGGATCCTTTTGA\n+>4279|16|BS2|2\n+TTTGAATAGCCTGGATCCTTTTGA\n+>4284|16|BS2|1\n+TACCTTATTTTGAATAGCCTGGATCCT\n+>4285|16|BS2|1\n+TACCTTATTTTGAATAGCCTGGATCC\n+>4311|16|BS2|1\n+ACTCGCAGCCGGTGATGAGTCTTGC\n+>4311|16|BS2|1\n+CTCGCAGCCGGTGATGAGTCTTGC\n+>4317|16|BS2|1\n+CAAACCACTCGCAGCCGGTGATGAG\n+>4323|16|BS2|2\n+TTCGAACAAACCACTCGCAGCCGGT\n+>4323|16|BS2|1\n+TCGAACAAACCACTCGCAGCCGGT\n+>4325|16|BS2|1\n+TTCGAACAAACCACTCGCAGCCG\n+>4347|16|BS2|2\n+TCAGGTCTCTGTGCAGGGTGGTGTT\n+>4348|16|BS2|8\n+TCAGGTCTCTGTGCAGGGTGGTGT\n+>4348|16|BS2|1\n+CAGGTCTCTGTGCAGGGTGGTGT\n+>4349|16|BS2|8\n+TCAGGTCTCTGTGCAGGGTGGTG\n+>4352|16|BS2|1\n+GTTTCAGGTCTCTGTGCAGGGTG\n+>4353|16|BS2|1\n+TGCGAGTTTCAGGTCTCTGTGCAGGGT\n+>4357|16|BS2|1\n+TTGCGAGTTTCAGGTCTCTGTGCA\n+>4408|16|BS2|1\n+TCCAGCCTGTCATGGTATCTGCTCG\n+>4412|16|BS2|1\n+TGGCGCTCCAGCCTGTCATGGTATCTG\n+>4412|16|BS2|1\n+GGCGCTCCAGCCTGTCATGGTATCTG\n+>4418|16|BS2|2\n+TTCTGTGGCGCTCCAGCCTGTCATGG\n+>4419|16|BS2|1\n+TTTCTGTGGCGCTCCAGCCTGTCATG\n+>4419|16|BS2|4\n+TTCTGTGGCGCTCCAGCCTGTCATG\n+>4421|16|BS2|1\n+TTTCTGTGGCGCTCCAGCCTGTCA\n+>4421|16|BS2|2\n+TTCTGTGGCGCTCCAGCCTGTCA\n+>4422|16|BS2|1\n+TTTCTGTGGCGCTCCAGCCTGTC\n+>4424|16|BS2|3\n+AGCCGATTTCTGTGGCGCTCCAGCCTG\n+>4424|16|BS2|1\n+GCCGATTTCTGTGGCGCTCCAGCCTG\n+>4424|16|BS2|2\n+CCGATTTCTGTGGCGCTCCAGCCTG\n+>4424|16|BS2|1\n+CGATTTCTGTGGCGCTCCAGCCTG\n+>4425|16|BS2|1\n+CAGCCGATTTCTGTGGCGCTCCAGCCT\n+>4425|16|BS2|1\n+AGCCGATTTCTGTGGCGCTCCAGCCT\n+>4426|16|BS2|1\n+CAGCCGATTTCTGTGGCGCTCCAGCC\n+>4433|16|BS2|1\n+CGCTGGCCAGCCGATTTCTGTGGCGC\n+>4433|16|BS2|1\n+TGGCCAGCCGATTTCTGTGGCGC\n+>4436|16|BS2|1\n+AGCGCTGGCCAGCCGATTTCTGTGG\n+>4445|16|BS2|2\n+TGTTTAAAGCGCTGGCCAGCCGA\n+>4450|16|BS2|1\n+AGATCTGTTTAAAGCGCTGGCCA\n+>4456|16|BS2|1\n+TTGGTGGGCGAGATCTGTTTAAAGCGC\n+>4456|16|BS2|1\n+GTGGGCGAGATCTGTTTAAAGCGC\n+>4456|16|BS2|4\n+TGGGCGAGATCTGTTTAAAGCGC\n+>4458|16|BS2|1\n+TTGGTGGGCGAGATCTGTTTAAAGC\n+>4459|16|BS2|1\n+TTGGTGGGCGAGATCTGTTTAAAG\n+>4462|16|BS2|1\n+TCCTTGGTGGGCGAGATCTGTTTA\n+>4470|16|BS2|8\n+TATTGAGCCTCCTTGGTGGGCGAGA\n+>4477|16|BS2|1\n+TGCCTTCTATTGAGCCTCCTTGGTG\n+>4484|16|BS2|2\n+CCTCGGTTGCCTTCTATTGAGCCTC\n+>4485|16|BS2|1\n+TCCCTCGGTTGCCTTCTATTGAGCCT\n+>4485|16|BS2|1\n+CCCTCGGTTGCCTTCTATTGAGCCT\n+>4485|16|BS2|1\n+CCTCGGTTGCCTTCTATTGAGCCT\n+>4485|16|BS2|1\n+CTCGGTTGCCTTCTATTGAGCCT\n+>4486|16|BS2|3\n+TCCCTCGGTTGCCTTCTATTGAGCC\n+>4487|16|BS2|2\n+TCCCTCGGTTGCCTTCTATTGAGC\n+>4493|16|BS2|2\n+TAATGAGATCCCTCGGTTGCCTTCTA\n+>4494|16|BS2|37\n+TAATGAGATCCCTCGGTTGCCTTCT\n+>4495|16|BS2|23\n+TAATGAGATCCCTCGGTTGCCTTC\n+>4496|16|BS2|63\n+TAATGAGATCCCTCGGTTGCCTT\n+>4497|16|BS2|1\n+CGGGTAATGAGATCCCTCGGTTGCCT\n+>4497|16|BS2|1\n+GTAATGAGATCCCTCGGTTGCCT\n+>4498|16|BS2|4\n+TCGGGTAATGAGATCCCTCGGTTGCC\n+>4498|16|BS2|2\n+CGGGTAATGAGATCCCTCGGTTGCC\n+>4507|16|BS2|1\n+TCAAAGGAGATCGGGTAATGAGATCCC\n+>4507|16|BS2|1\n+AAAGGAGATCGGGTAATGAGATCCC\n+>4509|16|BS2|1\n+AAAGGAGATCGGGTAATGAGATC\n+>4511|16|BS2|1\n+TGTCAAAGGAGATCGGGTAATGAGA\n+>4517|16|BS2|1\n+CCCTTGTCAAAGGAGATCGGGTA\n+>4518|16|BS2|1\n+GACCCTTGTCAAAGGAGATCGGGT\n+>4522|16|BS2|3\n+TGCGGACCCTTGTCAAAGGAGATC\n+>4525|16|BS2|1\n+TTCTGCGGACCCTTGTCAAAGGAG\n+>4534|16|BS2|1\n+TAAGCGTCAGCTTCTGCGGACCCTTG\n+>4536|16|BS2|1\n+GATAAGCGTCAGCTTCTGCGGACCCT\n+>4536|16|BS2|1\n+TAAGCGTCAGCTTCTGCGGACCCT\n+>4537|16|BS2|1\n+GATAAGCGTCAGCTTCTGCGGACCC\n+>4537|16|BS2|1\n+TAAGCGTCAGCTTCTGCGGACCC\n+>4538|16|BS2|1\n+GATAAGCGTCAGCTTCTGCGGACC\n+>4539|16|BS2|3\n+TAAGATAAGCGTCAGCTTCTGCGGAC\n+>4540|16|BS2|1\n+TTTAAGATAAGCGTCAGCTTCTGCGGA\n+>4540|16|BS2|1\n+TTAAGATAAGCGTCAGCTTCTGCGGA\n+>4540|16|BS2|12\n+TAAGATAAGCGTCAGCTTCTGCGGA\n+>4540|16|BS2|1\n+AAGATAAGCGTCAGCTTCTGCGGA\n+>4541|16|BS2|1\n+TAAGATAAGCGTCAGCTTCTGCGG\n+>4546|16|BS2|10\n+TAGGATTTAAGATAAGCGTCAGCTTC\n+>4567|16|BS2|1\n+TAACAATCACATATAACAAATAGGA\n+>4629|16|BS2|1\n+TTGGGCTCGCCGGCTAACTATAGTTA\n+>4629|16|BS2|1\n+TGGGCTCGCCGGCTAACTATAGTTA\n+>4630|16|BS2|6\n+TTTGGGCTCGCCGGCTAACTATAGTT\n+>4630|16|BS2|5\n+TTGGGCTCGCCGGCTAACTATAGTT\n+>4631|16|BS2|19\n+TTTGGGCTCGCCGGCTAACTATAGT\n+>4631|16|BS2|4\n+TTGGGCTCGCCGGCTAACTATAGT\n' |
| b |
| diff -r 9645d995fb3c -r 9185ca0a7b43 test-data/res_files/reads-sample-small.fastq/subgroups/PPPartners/BS2/antisensPPP.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/res_files/reads-sample-small.fastq/subgroups/PPPartners/BS2/antisensPPP.txt Wed Jan 16 08:18:13 2019 -0500 |
| b |
| @@ -0,0 +1,324 @@ +>53|16|BS2|2 +TTATTACCGCGAAAACTAATTTCACT +>56|16|BS2|1 +TTATTACCGCGAAAACTAATTTC +>269|16|BS2|2 +TTCTAGCCAAAACTTGAACCCTGGGA +>271|16|BS2|1 +TTCTAGCCAAAACTTGAACCCTGG +>324|16|BS2|1 +CGCAGCGGTTTCATTTAAAGTGTTC +>443|16|BS2|1 +TGGGTTTTTTCCTTTCAGTCTCCG +>462|16|BS2|1 +TGTTTGCCGATGGTTGATTTGGGT +>493|16|BS2|4 +TCTAGGTTCTGTAGCCGAAGGGTT +>495|16|BS2|3 +CCATATCTAGGTTCTGTAGCCGAAGGG +>496|16|BS2|41 +CCATATCTAGGTTCTGTAGCCGAAGG +>497|16|BS2|136 +CCATATCTAGGTTCTGTAGCCGAAG +>498|16|BS2|5 +CCATATCTAGGTTCTGTAGCCGAA +>499|16|BS2|2 +CCATATCTAGGTTCTGTAGCCGA +>548|16|BS2|2 +TGTTTGTCAGCTGTGAGATGCGCAA +>549|16|BS2|6 +TGTTTGTCAGCTGTGAGATGCGCA +>550|16|BS2|7 +TGTTTGTCAGCTGTGAGATGCGC +>552|16|BS2|18 +TACTTGTTTGTCAGCTGTGAGATGC +>553|16|BS2|1 +TACTTGTTTGTCAGCTGTGAGATG +>562|16|BS2|1 +TTTCATTGCCTACTTGTTTGTCAGC +>577|16|BS2|1 +TCATACAGATCGCCAATTTCATTGCC +>578|16|BS2|1 +TCATACAGATCGCCAATTTCATTGC +>580|16|BS2|1 +TCATACAGATCGCCAATTTCATT +>635|16|BS2|2 +GGAGGCTGCATCCCGCTTAGCGGCAG +>856|16|BS2|1 +TCATACTCTTCGATCTCGAGCCAGCT +>857|16|BS2|8 +TCATACTCTTCGATCTCGAGCCAGC +>858|16|BS2|39 +TCATACTCTTCGATCTCGAGCCAG +>859|16|BS2|35 +TCATACTCTTCGATCTCGAGCCA +>1023|16|BS2|1 +TTTTGAGGTACCCGGTTCGTTTCGC +>1047|16|BS2|2 +GAAGAACATATTGACTGGCGACGCT +>1048|16|BS2|6 +GAAGAACATATTGACTGGCGACGC +>1123|16|BS2|1 +TCAATAACTACTCTCATATGGCATAG +>1124|16|BS2|8 +TCAATAACTACTCTCATATGGCATA +>1158|16|BS2|1 +GCACTGGACAATAGCGTTACGCTTG +>1237|16|BS2|1 +TGTTCGCCGGCACATTTCACACA +>1390|16|BS2|14 +TTACTTCTGTTCTTCCAGCCACTCC +>1391|16|BS2|2 +TTACTTCTGTTCTTCCAGCCACTC +>1392|16|BS2|1 +TTACTTCTGTTCTTCCAGCCACT +>1463|16|BS2|1 +TGCATAAGATATTCCGCCTCGAGAAG +>1464|16|BS2|1 +TGCATAAGATATTCCGCCTCGAGAA +>1500|16|BS2|1 +TGGTTGCTTGTGGTGAATGGACCCT +>1591|16|BS2|1 +GACGCCCTTGTCCGGCTGCGGCTCCT +>1593|16|BS2|2 +GACGCCCTTGTCCGGCTGCGGCTC +>1599|16|BS2|1 +TACCCCTAGACGCCCTTGTCCGGCTG +>1615|16|BS2|1 +CGAGCGCTGGAGTGTACCCCTAGA +>1615|16|BS2|1 +GAGCGCTGGAGTGTACCCCTAGA +>1872|16|BS2|6 +GCACTCTACTTCAGGCAACTTCGT +>1899|16|BS2|1 +TAATACATCGATTTCGTGACGTCGCAC +>1900|16|BS2|5 +TAATACATCGATTTCGTGACGTCGCA +>1901|16|BS2|81 +TAATACATCGATTTCGTGACGTCGC +>1901|16|BS2|1 +ATACATCGATTTCGTGACGTCGC +>1902|16|BS2|4 +TAATACATCGATTTCGTGACGTCG +>1903|16|BS2|1 +TAATACATCGATTTCGTGACGTC +>1948|16|BS2|1 +TAGCTTAGGCGTCTCTGCCCCCT +>1966|16|BS2|2 +TGTAGGCTACAAATCCGAATAGCT +>1967|16|BS2|1 +TGTAGGCTACAAATCCGAATAGC +>2020|16|BS2|20 +TTGATTAAGATAGCTGCTCCGCCTT +>2021|16|BS2|297 +TTGATTAAGATAGCTGCTCCGCCT +>2022|16|BS2|36 +TTGATTAAGATAGCTGCTCCGCC +>2087|16|BS2|12 +TAACCGCCGGCGCAAGTTGCACCTTG +>2089|16|BS2|2 +TAACCGCCGGCGCAAGTTGCACCT +>2090|16|BS2|7 +TAACCGCCGGCGCAAGTTGCACC +>2108|16|BS2|1 +TAGGACCAAGTGCCGTTTCAATAACC +>2113|16|BS2|5 +TTATAGGACCAAGTGCCGTTTCAA +>2142|16|BS2|8 +AATCTCGGTGGGCAGTAGACCGCTCC +>2143|16|BS2|3 +AATCTCGGTGGGCAGTAGACCGCTC +>2144|16|BS2|6 +AATCTCGGTGGGCAGTAGACCGCT +>2145|16|BS2|14 +AATCTCGGTGGGCAGTAGACCGC +>2169|16|BS2|1 +TCCTTAAACTCTTCCGTAGTCCATGC +>2170|16|BS2|4 +TCCTTAAACTCTTCCGTAGTCCATG +>2288|16|BS2|1 +TTAGGACGAGATTCGCTAATGCAATG +>2289|16|BS2|30 +TTAGGACGAGATTCGCTAATGCAAT +>2290|16|BS2|19 +TTAGGACGAGATTCGCTAATGCAA +>2291|16|BS2|6 +TTAGGACGAGATTCGCTAATGCA +>2331|16|BS2|1 +TCTTGTTGGTCCTCCTGTTGCTAG +>2333|16|BS2|2 +TATCTTGTTGGTCCTCCTGTTGCT +>2338|16|BS2|1 +CGGGTATCTTGTTGGTCCTCCTG +>2339|16|BS2|1 +TACGGGTATCTTGTTGGTCCTCCT +>2367|16|BS2|5 +TCGATGTACCCTGGTGAGCCTCTACA +>2368|16|BS2|25 +TCGATGTACCCTGGTGAGCCTCTAC +>2369|16|BS2|2 +TCGATGTACCCTGGTGAGCCTCTA +>2435|16|BS2|1 +TCGGAGCTAAGCTCAACAACCGCACTT +>2436|16|BS2|14 +TCGGAGCTAAGCTCAACAACCGCACT +>2437|16|BS2|1 +TCGGAGCTAAGCTCAACAACCGCAC +>2438|16|BS2|1 +TCGGAGCTAAGCTCAACAACCGCA +>2457|16|BS2|1 +TAATTACCAGAGGCAGGTGGTCGGA +>2600|16|BS2|1 +TAGCATCATCAACGTCCTGTCCAGAG +>2601|16|BS2|12 +TAGCATCATCAACGTCCTGTCCAGA +>2602|16|BS2|1 +TAGCATCATCAACGTCCTGTCCAG +>2681|16|BS2|1 +TCGATCTGCCGCGGGCTGCCGAGAT +>2682|16|BS2|3 +TCGATCTGCCGCGGGCTGCCGAGA +>2809|16|BS2|1 +GCGCATCGGAGCCTACTCAGAGCTC +>2813|16|BS2|1 +CCAACGCGCATCGGAGCCTACTCAGA +>2856|16|BS2|50 +TATTGGCAAGCCTTTCGTCGAACCA +>2857|16|BS2|267 +TATTGGCAAGCCTTTCGTCGAACC +>2858|16|BS2|76 +TATTGGCAAGCCTTTCGTCGAAC +>2917|16|BS2|1 +CGCCTTTTGATTGCGCGCGTGGCCT +>2957|16|BS2|1 +CCATGTCCCGTTGCTATCGACTAGAGGC +>2959|16|BS2|7 +CCATGTCCCGTTGCTATCGACTAGAG +>2960|16|BS2|69 +CCATGTCCCGTTGCTATCGACTAGA +>2961|16|BS2|7 +CCATGTCCCGTTGCTATCGACTAG +>2962|16|BS2|4 +CCATGTCCCGTTGCTATCGACTA +>2983|16|BS2|1 +CTTGTCCCAAGTCGGTCCGACACC +>3026|16|BS2|4 +TGAATGGTTGAAATCGCTCGGCGAGG +>3027|16|BS2|13 +TGAATGGTTGAAATCGCTCGGCGAG +>3028|16|BS2|63 +TGAATGGTTGAAATCGCTCGGCGA +>3028|16|BS2|1 +GAATGGTTGAAATCGCTCGGCGA +>3029|16|BS2|1 +TGAATGGTTGAAATCGCTCGGCG +>3082|16|BS2|1 +AGCGCTTGGTTCAGCTGGTCCTGAG +>3114|16|BS2|1 +TTCAAACGGCGTGATTGGCATATC +>3161|16|BS2|8 +TGCTTTGTTGTTACTCTGGCGCACA +>3162|16|BS2|14 +TGCTTTGTTGTTACTCTGGCGCAC +>3163|16|BS2|4 +TGCTTTGTTGTTACTCTGGCGCA +>3275|16|BS2|2 +TGATAAGGGAAGTATTGCAACCTC +>3348|16|BS2|6 +TCGGCCGGTAGGAGGCGGGCTCCCT +>3349|16|BS2|2 +TCGGCCGGTAGGAGGCGGGCTCCC +>3350|16|BS2|3 +TCGGCCGGTAGGAGGCGGGCTCC +>3374|16|BS2|1 +TTCGAAATTGAAGGGAGGAGACTG +>3830|16|BS2|1 +ATCGGCAAATGTGGCCAACATAGAT +>3879|16|BS2|1 +TCGGCTGCGTCGTGCTCGCATCG +>3880|16|BS2|1 +CCATCGGCTGCGTCGTGCTCGCATC +>3880|16|BS2|3 +CATCGGCTGCGTCGTGCTCGCATC +>3880|16|BS2|1 +ATCGGCTGCGTCGTGCTCGCATC +>3881|16|BS2|1 +TACCATCGGCTGCGTCGTGCTCGCAT +>3882|16|BS2|2 +TACCATCGGCTGCGTCGTGCTCGCA +>3883|16|BS2|9 +TACCATCGGCTGCGTCGTGCTCGC +>3884|16|BS2|3 +TACCATCGGCTGCGTCGTGCTCG +>3894|16|BS2|1 +CAAAGTCCTGGATACCATCGGCTGC +>3896|16|BS2|3 +TGCAAAGTCCTGGATACCATCGGCT +>3896|16|BS2|52 +CAAAGTCCTGGATACCATCGGCT +>3897|16|BS2|8 +TATGCAAAGTCCTGGATACCATCGGC +>3897|16|BS2|4 +TGCAAAGTCCTGGATACCATCGGC +>3958|16|BS2|1 +TTGTTGGATTTACTGCTATTGATGC +>4048|16|BS2|2 +TCCAAGGTACTTTGCTGCGTTCGGCT +>4049|16|BS2|1 +TCCAAGGTACTTTGCTGCGTTCGGC +>4073|16|BS2|1 +TGTGAGTCTGCGATCCAGAAGCACT +>4101|16|BS2|10 +TTCTGATGTCGGTCACATGCTTGGA +>4102|16|BS2|13 +TTCTGATGTCGGTCACATGCTTGG +>4262|16|BS2|1 +TTTTGATGTGGCTGTCGCAGGCT +>4348|16|BS2|1 +TTTCAGGTCTCTGTGCAGGGTGGTGT +>4348|16|BS2|3 +TTCAGGTCTCTGTGCAGGGTGGTGT +>4349|16|BS2|1 +TTTCAGGTCTCTGTGCAGGGTGGTG +>4349|16|BS2|4 +TTCAGGTCTCTGTGCAGGGTGGTG +>4350|16|BS2|6 +TTTCAGGTCTCTGTGCAGGGTGGT +>4350|16|BS2|6 +TTCAGGTCTCTGTGCAGGGTGGT +>4351|16|BS2|3 +TTTCAGGTCTCTGTGCAGGGTGG +>4374|16|BS2|5 +TTATTTCGTCAAATACCGTTGCGAG +>4375|16|BS2|4 +TTATTTCGTCAAATACCGTTGCGA +>4403|16|BS2|1 +TGTCATGGTATCTGCTCGAGTGC +>4424|16|BS2|2 +GATTTCTGTGGCGCTCCAGCCTG +>4429|16|BS2|1 +CCAGCCGATTTCTGTGGCGCTCCA +>4430|16|BS2|1 +CCAGCCGATTTCTGTGGCGCTCC +>4431|16|BS2|1 +GGCCAGCCGATTTCTGTGGCGCTC +>4445|16|BS2|20 +TCTGTTTAAAGCGCTGGCCAGCCGA +>4446|16|BS2|1 +TCTGTTTAAAGCGCTGGCCAGCCG +>4447|16|BS2|2 +GATCTGTTTAAAGCGCTGGCCAGCC +>4447|16|BS2|2 +TCTGTTTAAAGCGCTGGCCAGCC +>4449|16|BS2|6 +GAGATCTGTTTAAAGCGCTGGCCAG +>4450|16|BS2|4 +CGAGATCTGTTTAAAGCGCTGGCCA +>4450|16|BS2|1 +GAGATCTGTTTAAAGCGCTGGCCA +>4451|16|BS2|14 +CGAGATCTGTTTAAAGCGCTGGCC +>4451|16|BS2|12 +GAGATCTGTTTAAAGCGCTGGCC +>4452|16|BS2|4 +CGAGATCTGTTTAAAGCGCTGGC |
| b |
| diff -r 9645d995fb3c -r 9185ca0a7b43 test-data/res_files/reads-sample-small.fastq/subgroups/PPPartners/BS2/histogram.png |
| b |
| Binary file test-data/res_files/reads-sample-small.fastq/subgroups/PPPartners/BS2/histogram.png has changed |
| b |
| diff -r 9645d995fb3c -r 9185ca0a7b43 test-data/res_files/reads-sample-small.fastq/subgroups/PPPartners/BS2/overlap_size.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/res_files/reads-sample-small.fastq/subgroups/PPPartners/BS2/overlap_size.txt Wed Jan 16 08:18:13 2019 -0500 |
| b |
| @@ -0,0 +1,24 @@ +size number percentage of the total overlap number +1 109 2.47 +2 179 4.05 +3 117 2.65 +4 134 3.03 +5 162 3.67 +6 214 4.84 +7 194 4.39 +8 192 4.35 +9 171 3.87 +10 610 13.81 +11 199 4.50 +12 201 4.55 +13 149 3.37 +14 176 3.98 +15 194 4.39 +16 154 3.49 +17 195 4.41 +18 208 4.71 +19 217 4.91 +20 143 3.24 +21 207 4.69 +22 179 4.05 +23 114 2.58 |
| b |
| diff -r 9645d995fb3c -r 9185ca0a7b43 test-data/res_files/reads-sample-small.fastq/subgroups/PPPartners/BS2/sens.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/res_files/reads-sample-small.fastq/subgroups/PPPartners/BS2/sens.txt Wed Jan 16 08:18:13 2019 -0500 |
| b |
| b'@@ -0,0 +1,822 @@\n+>22|0|BS2|2\n+TCTAACAATACGCACCTGACAAAG\n+>43|0|BS2|1\n+AAGTGGATTAAGTGAAATTAGTTTTC\n+>70|0|BS2|1\n+CGGTAATAAACTTATGGACAAGACC\n+>70|0|BS2|1\n+CGGTAATAAACTTATGGACAAGAC\n+>73|0|BS2|1\n+TAATAAACTTATGGACAAGACCAGAA\n+>73|0|BS2|1\n+TAATAAACTTATGGACAAGACCAGA\n+>78|0|BS2|1\n+AACTTATGGACAAGACCAGAATACT\n+>80|0|BS2|1\n+CTTATGGACAAGACCAGAATACTGGCA\n+>81|0|BS2|1\n+TTATGGACAAGACCAGAATACTGGCA\n+>82|0|BS2|2\n+TATGGACAAGACCAGAATACTGGCACA\n+>82|0|BS2|1\n+TATGGACAAGACCAGAATACTGGCAC\n+>82|0|BS2|3\n+TATGGACAAGACCAGAATACTGGCA\n+>83|0|BS2|1\n+ATGGACAAGACCAGAATACTGGCAC\n+>187|0|BS2|1\n+GTTAAGTTTCTCGAACTGGGGCTCC\n+>188|0|BS2|1\n+TTAAGTTTCTCGAACTGGGGCTCC\n+>189|0|BS2|1\n+TAAGTTTCTCGAACTGGGGCTCCGCT\n+>189|0|BS2|1\n+TAAGTTTCTCGAACTGGGGCTCCGC\n+>193|0|BS2|1\n+TTTCTCGAACTGGGGCTCCGCTG\n+>194|0|BS2|1\n+TTCTCGAACTGGGGCTCCGCTGCCCAGC\n+>195|0|BS2|2\n+TCTCGAACTGGGGCTCCGCTGCCCAGC\n+>195|0|BS2|2\n+TCTCGAACTGGGGCTCCGCTGCCCA\n+>197|0|BS2|1\n+TCGAACTGGGGCTCCGCTGCCCAG\n+>212|0|BS2|1\n+GCTGCCCAGCTGCCACGCGATCGC\n+>215|0|BS2|1\n+GCCCAGCTGCCACGCGATCGCACAAAC\n+>215|0|BS2|1\n+GCCCAGCTGCCACGCGATCGCACA\n+>215|0|BS2|2\n+GCCCAGCTGCCACGCGATCGCAC\n+>222|0|BS2|2\n+TGCCACGCGATCGCACAAACAGCTG\n+>223|0|BS2|1\n+GCCACGCGATCGCACAAACAGCTGTT\n+>223|0|BS2|1\n+GCCACGCGATCGCACAAACAGCTG\n+>224|0|BS2|1\n+CCACGCGATCGCACAAACAGCTGTT\n+>225|0|BS2|11\n+CACGCGATCGCACAAACAGCTGTT\n+>286|0|BS2|2\n+TGGCTAGAACCCTGGTGATTTGG\n+>304|0|BS2|1\n+TTTGGTGCACACTTCAATATGAACAC\n+>305|0|BS2|1\n+TTGGTGCACACTTCAATATGAACACT\n+>331|0|BS2|1\n+TTAAATGAAACCGCTGCGGCTGA\n+>336|0|BS2|1\n+TGAAACCGCTGCGGCTGATGAATCG\n+>340|0|BS2|2\n+ACCGCTGCGGCTGATGAATCGTTGG\n+>340|0|BS2|3\n+ACCGCTGCGGCTGATGAATCGTTG\n+>342|0|BS2|1\n+CGCTGCGGCTGATGAATCGTTGG\n+>345|0|BS2|2\n+TGCGGCTGATGAATCGTTGGATAC\n+>345|0|BS2|1\n+TGCGGCTGATGAATCGTTGGATA\n+>351|0|BS2|1\n+TGATGAATCGTTGGATACTGCGTT\n+>361|0|BS2|1\n+TTGGATACTGCGTTTCTCTCGAGCCC\n+>366|0|BS2|1\n+TACTGCGTTTCTCTCGAGCCCCCAA\n+>431|0|BS2|1\n+CTCGTGCTTCTCCGGAGACTGAAA\n+>441|0|BS2|1\n+TCCGGAGACTGAAAGGAAAAAACCC\n+>441|0|BS2|1\n+TCCGGAGACTGAAAGGAAAAAAC\n+>456|0|BS2|1\n+GAAAAAACCCAAATCAACCATCGGC\n+>458|0|BS2|1\n+AAAAACCCAAATCAACCATCGGCAAA\n+>472|0|BS2|1\n+ACCATCGGCAAACAAGGGGAAAACCC\n+>485|0|BS2|1\n+AAGGGGAAAACCCTTCGGCTACAGAAC\n+>493|0|BS2|1\n+AACCCTTCGGCTACAGAACCTAGA\n+>494|0|BS2|1\n+ACCCTTCGGCTACAGAACCTAGATA\n+>496|0|BS2|1\n+CCTTCGGCTACAGAACCTAGATAT\n+>498|0|BS2|1\n+TTCGGCTACAGAACCTAGATATGGC\n+>500|0|BS2|2\n+CGGCTACAGAACCTAGATATGGC\n+>504|0|BS2|2\n+TACAGAACCTAGATATGGCGGCAAT\n+>510|0|BS2|1\n+ACCTAGATATGGCGGCAATTCAAAC\n+>583|0|BS2|1\n+GAAATTGGCGATCTGTATGACCAGCC\n+>588|0|BS2|2\n+TGGCGATCTGTATGACCAGCCCAGT\n+>592|0|BS2|1\n+GATCTGTATGACCAGCCCAGTACCAG\n+>594|0|BS2|1\n+TCTGTATGACCAGCCCAGTACCAGT\n+>627|0|BS2|1\n+TGCAATTGCTGCCGCTAAGCGGGATG\n+>639|0|BS2|1\n+CGCTAAGCGGGATGCAGCCTCCGCT\n+>747|0|BS2|1\n+GCAGAGCATCGAAAATATAGTGGA\n+>764|0|BS2|1\n+TAGTGGACCTAGAAAAGATTGAGGC\n+>771|0|BS2|1\n+CCTAGAAAAGATTGAGGCTAGGGC\n+>772|0|BS2|5\n+CTAGAAAAGATTGAGGCTAGGGC\n+>773|0|BS2|1\n+TAGAAAAGATTGAGGCTAGGGCGTC\n+>796|0|BS2|2\n+TCAATGAGCGGTGTCCTAAGGCTT\n+>796|0|BS2|1\n+TCAATGAGCGGTGTCCTAAGGCT\n+>797|0|BS2|1\n+CAATGAGCGGTGTCCTAAGGCTTT\n+>860|0|BS2|1\n+GGCTCGAGATCGAAGAGTATGAGTT\n+>863|0|BS2|1\n+TCGAGATCGAAGAGTATGAGTTC\n+>899|0|BS2|34\n+TTAAAGAGGACAGGCCTTACAGGGTA\n+>899|0|BS2|2\n+TTAAAGAGGACAGGCCTTACAGGGT\n+>899|0|BS2|4\n+TTAAAGAGGACAGGCCTTACAGGG\n+>899|0|BS2|1\n+TTAAAGAGGACAGGCCTTACAGG\n+>900|0|BS2|1\n+TAAAGAGGACAGGCCTTACAGGGTATG\n+>900|0|BS2|42\n+TAAAGAGGACAGGCCTTACAGGGTA\n+>900|0|BS2|1\n+TAAAGAGGACAGGCCTTACAGGGT\n+>900|0|BS2|2\n+TAAAGAGGACAGGCCTTACAGGG\n+>902|0|BS2|3\n+AAGAGGACAGGCCTTACAGGGTATG\n+>903|0|BS2|1\n+AGAGGACAGGCCTTACAGGGTATG\n+>925|0|BS2|1\n+TGCGTGAAAGGCCTGCACCACAGTA\n+>1011|0|BS2|1\n+CACACCGCTTAGGCGAAACGAACC\n+>1020|0|BS2|1\n+TAGGCGAAACGAACCGGGTACCT\n+>1032|0|BS2|2\n+ACCGGGTACCTCAAAAGCGTCGCCAG\n+>1067|0|BS2|1\n+TCTTCCTAAATATTGCTGCTGCGGC\n+>1071|0|BS2|1\n+CCTAAATATTGCTGCTGCGGCAAA\n+>1090|0|BS2|1\n+GCAAACAATAAGGAGATCCTGGCG\n+>1090|0|BS2|4\n+GCAAACAATAAGGAGATCCTGGC\n+>1091|0|BS2|1\n+CAAACAATAAGGAGATCCTGGCGGT\n+>1095|0|BS2|1\n+CAATAAGGAGATCCTGGCGGTAAAG\n+>1098|0|BS2|1\n+TAAGGAGATCCTGGCGGTAAAGGCAC\n+>1098|0|BS2|1\n+TAAGGAGATCCTGGCGGTAAAGG\n+>1129|0|BS2|1\n+CATATGAGAGTAGTTATTGAGCCT\n+>1164|0|BS2|1\n+TAACGCTATTG'..b'TGGAAGCTCGGGATAATCTCCA\n+>3313|0|BS2|1\n+TAATCTCCATGATCCACAAACCTG\n+>3316|0|BS2|1\n+TCTCCATGATCCACAAACCTGGCAAG\n+>3318|0|BS2|1\n+TCCATGATCCACAAACCTGGCAAGCC\n+>3320|0|BS2|1\n+CATGATCCACAAACCTGGCAAGCCGGA\n+>3320|0|BS2|2\n+CATGATCCACAAACCTGGCAAGCC\n+>3322|0|BS2|3\n+TGATCCACAAACCTGGCAAGCCGGA\n+>3346|0|BS2|2\n+AAAGGGAGCCCGCCTCCTACCGGCC\n+>3347|0|BS2|2\n+AAGGGAGCCCGCCTCCTACCGGCCGA\n+>3347|0|BS2|5\n+AAGGGAGCCCGCCTCCTACCGGCCG\n+>3347|0|BS2|5\n+AAGGGAGCCCGCCTCCTACCGGCC\n+>3353|0|BS2|1\n+GCCCGCCTCCTACCGGCCGATCAGTC\n+>3356|0|BS2|1\n+CGCCTCCTACCGGCCGATCAGTC\n+>3360|0|BS2|1\n+TCCTACCGGCCGATCAGTCTCCTCCCT\n+>3360|0|BS2|1\n+TCCTACCGGCCGATCAGTCTCCT\n+>3427|0|BS2|1\n+TTGTAAGGATTATGGAAGCCCAGGG\n+>3427|0|BS2|1\n+TTGTAAGGATTATGGAAGCCCAG\n+>3430|0|BS2|17\n+TAAGGATTATGGAAGCCCAGGGGAT\n+>3430|0|BS2|4\n+TAAGGATTATGGAAGCCCAGGGGA\n+>3861|0|BS2|1\n+TGCGTCACCTACAGGTCCCGATG\n+>3882|0|BS2|1\n+TGCGAGCACGACGCAGCCGATGGTA\n+>3890|0|BS2|1\n+CGACGCAGCCGATGGTATCCAGGAC\n+>3891|0|BS2|1\n+GACGCAGCCGATGGTATCCAGGAC\n+>3900|0|BS2|1\n+GATGGTATCCAGGACTTTGCATAC\n+>3906|0|BS2|1\n+ATCCAGGACTTTGCATACCGGTTC\n+>3915|0|BS2|1\n+TTTGCATACCGGTTCTCGGAATGGGC\n+>3921|0|BS2|3\n+TACCGGTTCTCGGAATGGGCAAGAC\n+>3934|0|BS2|1\n+AATGGGCAAGACGATGGAATATTG\n+>3936|0|BS2|1\n+TGGGCAAGACGATGGAATATTGGCA\n+>3969|0|BS2|3\n+AGTAAATCCAACAACGTCTGCTTC\n+>3969|0|BS2|1\n+AGTAAATCCAACAACGTCTGCTT\n+>3992|0|BS2|1\n+CACTTTAAAGCGGAGAACGCCACC\n+>3995|0|BS2|1\n+TTTAAAGCGGAGAACGCCACCGCCCG\n+>3995|0|BS2|1\n+TTTAAAGCGGAGAACGCCACCGCCC\n+>3996|0|BS2|1\n+TTAAAGCGGAGAACGCCACCGCCCG\n+>3997|0|BS2|1\n+TAAAGCGGAGAACGCCACCGCCCGTCT\n+>3997|0|BS2|2\n+TAAAGCGGAGAACGCCACCGCCCGTC\n+>3997|0|BS2|1\n+TAAAGCGGAGAACGCCACCGCCCG\n+>4057|0|BS2|1\n+CAGCAAAGTACCTTGGAGTGCTTC\n+>4065|0|BS2|1\n+TACCTTGGAGTGCTTCTGGATCGCAGA\n+>4065|0|BS2|3\n+TACCTTGGAGTGCTTCTGGATCGCA\n+>4065|0|BS2|2\n+TACCTTGGAGTGCTTCTGGATCGC\n+>4068|0|BS2|1\n+CTTGGAGTGCTTCTGGATCGCAGAC\n+>4069|0|BS2|1\n+TTGGAGTGCTTCTGGATCGCAGACTC\n+>4069|0|BS2|6\n+TTGGAGTGCTTCTGGATCGCAGACT\n+>4069|0|BS2|2\n+TTGGAGTGCTTCTGGATCGCAGA\n+>4107|0|BS2|3\n+CATGTGACCGACATCAGAACGCGCC\n+>4108|0|BS2|2\n+ATGTGACCGACATCAGAACGCGCC\n+>4111|0|BS2|1\n+TGACCGACATCAGAACGCGCCTACG\n+>4112|0|BS2|1\n+GACCGACATCAGAACGCGCCTACG\n+>4113|0|BS2|1\n+ACCGACATCAGAACGCGCCTACGTGCT\n+>4113|0|BS2|1\n+ACCGACATCAGAACGCGCCTACGTGC\n+>4139|0|BS2|2\n+TAAGGTGGCGAAGCACTACTGGCT\n+>4139|0|BS2|1\n+TAAGGTGGCGAAGCACTACTGGC\n+>4245|0|BS2|1\n+TGCCAAATCTGGGGCTTAGCCTGCGA\n+>4245|0|BS2|1\n+TGCCAAATCTGGGGCTTAGCCTGC\n+>4246|0|BS2|1\n+GCCAAATCTGGGGCTTAGCCTGCGA\n+>4251|0|BS2|1\n+ATCTGGGGCTTAGCCTGCGACAGCC\n+>4252|0|BS2|2\n+TCTGGGGCTTAGCCTGCGACAGCCA\n+>4252|0|BS2|2\n+TCTGGGGCTTAGCCTGCGACAGCC\n+>4279|0|BS2|2\n+TCAAAAGGATCCAGGCTATTCAAAA\n+>4314|0|BS2|2\n+AGACTCATCACCGGCTGCGAGTGG\n+>4347|0|BS2|1\n+AACACCACCCTGCACAGAGACCTGAA\n+>4349|0|BS2|1\n+CACCACCCTGCACAGAGACCTGAAAC\n+>4351|0|BS2|2\n+CCACCCTGCACAGAGACCTGAAACT\n+>4357|0|BS2|1\n+TGCACAGAGACCTGAAACTCGCAACGG\n+>4357|0|BS2|1\n+TGCACAGAGACCTGAAACTCGCA\n+>4360|0|BS2|1\n+ACAGAGACCTGAAACTCGCAACGG\n+>4368|0|BS2|1\n+CTGAAACTCGCAACGGTATTTGACGA\n+>4386|0|BS2|1\n+TTTGACGAAATAAACAAGCACTCGA\n+>4419|0|BS2|1\n+CATGACAGGCTGGAGCGCCACAGAAA\n+>4425|0|BS2|1\n+AGGCTGGAGCGCCACAGAAATCGGC\n+>4444|0|BS2|1\n+ATCGGCTGGCCAGCGCTTTAAACAGA\n+>4444|0|BS2|5\n+ATCGGCTGGCCAGCGCTTTAAACAG\n+>4478|0|BS2|1\n+ACCAAGGAGGCTCAATAGAAGGC\n+>4484|0|BS2|1\n+GAGGCTCAATAGAAGGCAACCGAGG\n+>4527|0|BS2|1\n+CCTTTGACAAGGGTCCGCAGAAGCTG\n+>4529|0|BS2|4\n+TTTGACAAGGGTCCGCAGAAGCTGA\n+>4529|0|BS2|1\n+TTTGACAAGGGTCCGCAGAAGCTG\n+>4531|0|BS2|1\n+TGACAAGGGTCCGCAGAAGCTGA\n+>4534|0|BS2|1\n+CAAGGGTCCGCAGAAGCTGACGCTT\n+>4534|0|BS2|2\n+CAAGGGTCCGCAGAAGCTGACGCT\n+>4535|0|BS2|1\n+AAGGGTCCGCAGAAGCTGACGCT\n+>4565|0|BS2|1\n+AATCCTATTTGTTATATGTGATTGT\n+>4597|0|BS2|1\n+TTGTAGTTAAATTACTGTAAATTT\n+>4607|0|BS2|1\n+ATTACTGTAAATTTGAAAAAGCTAAC\n+>4609|0|BS2|1\n+TACTGTAAATTTGAAAAAGCTAAC\n+>4637|0|BS2|3\n+GTTAGCCGGCGAGCCCAAATGGGCTGA\n+>4638|0|BS2|2\n+TTAGCCGGCGAGCCCAAATGGGCTGA\n+>4638|0|BS2|1\n+TTAGCCGGCGAGCCCAAATGGGCTG\n+>4639|0|BS2|6\n+TAGCCGGCGAGCCCAAATGGGCTGA\n+>4639|0|BS2|1\n+TAGCCGGCGAGCCCAAATGGGCTG\n+>4666|0|BS2|1\n+TAATAGATAAGAAGGACACAAAGGGGC\n+>4669|0|BS2|1\n+TAGATAAGAAGGACACAAAGGGGCT\n+>4669|0|BS2|2\n+TAGATAAGAAGGACACAAAGGGGC\n+>4678|0|BS2|1\n+AGGACACAAAGGGGCTTCAAGACT\n' |
| b |
| diff -r 9645d995fb3c -r 9185ca0a7b43 test-data/res_files/reads-sample-small.fastq/subgroups/PPPartners/BS2/sensPPP.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/res_files/reads-sample-small.fastq/subgroups/PPPartners/BS2/sensPPP.txt Wed Jan 16 08:18:13 2019 -0500 |
| b |
| @@ -0,0 +1,274 @@ +>69|0|BS2|2 +GCGGTAATAAACTTATGGACAAGACC +>69|0|BS2|12 +GCGGTAATAAACTTATGGACAAGAC +>69|0|BS2|1 +GCGGTAATAAACTTATGGACAAG +>285|0|BS2|1 +TTGGCTAGAACCCTGGTGATTTGG +>339|0|BS2|4 +AACCGCTGCGGCTGATGAATCGTTG +>339|0|BS2|5 +AACCGCTGCGGCTGATGAATCGTT +>457|0|BS2|6 +AAAAAACCCAAATCAACCATCGGC +>476|0|BS2|1 +TCGGCAAACAAGGGGAAAACCCTTCG +>507|0|BS2|1 +AGAACCTAGATATGGCGGCAATTC +>512|0|BS2|1 +CTAGATATGGCGGCAATTCAAACCGA +>512|0|BS2|2 +CTAGATATGGCGGCAATTCAAACC +>512|0|BS2|5 +CTAGATATGGCGGCAATTCAAAC +>563|0|BS2|1 +CTGACAAACAAGTAGGCAATGAAATT +>563|0|BS2|2 +CTGACAAACAAGTAGGCAATGAAAT +>563|0|BS2|1 +CTGACAAACAAGTAGGCAATGAAA +>567|0|BS2|2 +CAAACAAGTAGGCAATGAAATTGGC +>577|0|BS2|1 +GGCAATGAAATTGGCGATCTGTATG +>593|0|BS2|2 +ATCTGTATGACCAGCCCAGTACC +>651|0|BS2|1 +TGCAGCCTCCGCTGGTACCACTAGCTC +>872|0|BS2|2 +AAGAGTATGAGTTCCACTGCTACC +>1038|0|BS2|1 +TACCTCAAAAGCGTCGCCAGTCAA +>1038|0|BS2|1 +TACCTCAAAAGCGTCGCCAGTCA +>1062|0|BS2|1 +TATGTTCTTCCTAAATATTGCTGC +>1139|0|BS2|1 +TAGTTATTGAGCCTCTCCGCAAGC +>1173|0|BS2|2 +TGTCCAGTGCCATCGTTGTCAGCAG +>1173|0|BS2|1 +TGTCCAGTGCCATCGTTGTCAGCA +>1250|0|BS2|1 +CCGGCGAACACCCAGCCAAGGACT +>1405|0|BS2|3 +ACAGAAGTAAGCGAGCGACCAACTC +>1479|0|BS2|1 +ATCTTATGCAGATGTGGCTAGAG +>1515|0|BS2|1 +CAAGCAACCAATGAGCCTGACGCACC +>1515|0|BS2|1 +CAAGCAACCAATGAGCCTGACGCAC +>1607|0|BS2|1 +CAAGGGCGTCTAGGGGTACACTC +>1615|0|BS2|1 +TCTAGGGGTACACTCCAGCGCTCGA +>1628|0|BS2|1 +TCCAGCGCTCGACGGATGCTAGCAG +>1628|0|BS2|2 +TCCAGCGCTCGACGGATGCTAGC +>1629|0|BS2|1 +CCAGCGCTCGACGGATGCTAGCAGC +>1886|0|BS2|1 +AGTAGAGTGCTTCGTGCGACGTCAC +>1914|0|BS2|1 +ATCGATGTATTACTGCTCAGCGA +>1916|0|BS2|7 +CGATGTATTACTGCTCAGCGAGACA +>1916|0|BS2|5 +CGATGTATTACTGCTCAGCGAGAC +>1916|0|BS2|11 +CGATGTATTACTGCTCAGCGAGA +>1961|0|BS2|2 +GCCTAAGCTATTCGGATTTGTAGCC +>1980|0|BS2|1 +GTAGCCTACACTGCCAATGATCCGA +>2035|0|BS2|1 +TCTTAATCAAAAATAGCCTTGCCC +>2103|0|BS2|1 +CCGGCGGTTATTGAAACGGCACT +>2124|0|BS2|1 +CTTGGTCCTATAAGCTTTGGAGC +>2127|0|BS2|1 +GGTCCTATAAGCTTTGGAGCGGTCT +>2127|0|BS2|1 +GGTCCTATAAGCTTTGGAGCGGTC +>2158|0|BS2|1 +CACCGAGATTTGCATGGACTACGGA +>2158|0|BS2|1 +CACCGAGATTTGCATGGACTACG +>2185|0|BS2|1 +AGTTTAAGGACATTTTGGAAGAGTTC +>2185|0|BS2|16 +AGTTTAAGGACATTTTGGAAGAGT +>2185|0|BS2|8 +AGTTTAAGGACATTTTGGAAGAG +>2304|0|BS2|4 +CTCGTCCTAAATTCGGAGGTGGACT +>2304|0|BS2|2 +CTCGTCCTAAATTCGGAGGTGGAC +>2304|0|BS2|1 +CTCGTCCTAAATTCGGAGGTGGA +>2345|0|BS2|4 +ACCAACAAGATACCCGTACGGCTGTA +>2345|0|BS2|3 +ACCAACAAGATACCCGTACGGCTGT +>2345|0|BS2|2 +ACCAACAAGATACCCGTACGGCT +>2347|0|BS2|4 +CAACAAGATACCCGTACGGCTGTA +>2347|0|BS2|1 +CAACAAGATACCCGTACGGCTGT +>2351|0|BS2|1 +AAGATACCCGTACGGCTGTAGAGGC +>2353|0|BS2|1 +GATACCCGTACGGCTGTAGAGGCTC +>2353|0|BS2|2 +GATACCCGTACGGCTGTAGAGGCT +>2353|0|BS2|3 +GATACCCGTACGGCTGTAGAGGC +>2383|0|BS2|1 +GGTACATCGATTTTGCACTGACAAAG +>2452|0|BS2|1 +TTAGCTCCGACCACCTGCCTCTGGTAAT +>2452|0|BS2|2 +TTAGCTCCGACCACCTGCCTCTGGTA +>2472|0|BS2|1 +CTGGTAATTACGCTGGATGCGGG +>2616|0|BS2|2 +GATGATGCTATCGAACTGCTCACC +>2696|0|BS2|1 +GGCAGATCGAATCCCAATACCCAGGG +>2824|0|BS2|1 +TCCGATGCGCGTTGGTGCTGCACAAA +>2824|0|BS2|1 +TCCGATGCGCGTTGGTGCTGCAC +>2829|0|BS2|1 +TGCGCGTTGGTGCTGCACAAAGCCGC +>2829|0|BS2|1 +TGCGCGTTGGTGCTGCACAAAGCCG +>2871|0|BS2|28 +CTTGCCAATACCGGAGTCGAAAGC +>2871|0|BS2|15 +CTTGCCAATACCGGAGTCGAAAG +>2932|0|BS2|2 +TCAAAAGGCGTTGCACGAGGAAGGC +>2975|0|BS2|12 +CGGGACATGGTGTCGGACCGACT +>2997|0|BS2|1 +TTGGGACAAGCGGAGGTATTCGCTG +>2997|0|BS2|1 +TTGGGACAAGCGGAGGTATTCGCT +>3041|0|BS2|2 +TCAACCATTCAAGCTTGCCAGCCTG +>3042|0|BS2|17 +CAACCATTCAAGCTTGCCAGCCTG +>3097|0|BS2|1 +ACCAAGCGCTTCAAATGGATATGC +>3128|0|BS2|1 +GCCGTTTGAACCCTGCGAGGTAGC +>3176|0|BS2|1 +CAACAAAGCACCTGGACATGACGTCA +>3176|0|BS2|2 +CAACAAAGCACCTGGACATGACGT +>3176|0|BS2|1 +CAACAAAGCACCTGGACATGACG +>3289|0|BS2|1 +TCCCTTATCAGTGGAAGCTCGGGAT +>3363|0|BS2|6 +TACCGGCCGATCAGTCTCCTCCCT +>3363|0|BS2|3 +TACCGGCCGATCAGTCTCCTCCC +>3388|0|BS2|1 +CAATTTCGAAGGTGTTTGAGAGACT +>3845|0|BS2|1 +ATTTGCCGATGACGTGTGCGTCACC +>3892|0|BS2|1 +ACGCAGCCGATGGTATCCAGGACTT +>3893|0|BS2|1 +CGCAGCCGATGGTATCCAGGACTTT +>3893|0|BS2|10 +CGCAGCCGATGGTATCCAGGACTT +>3894|0|BS2|1 +GCAGCCGATGGTATCCAGGACTTTG +>3894|0|BS2|1 +GCAGCCGATGGTATCCAGGACTT +>3895|0|BS2|1 +CAGCCGATGGTATCCAGGACTTTGC +>3897|0|BS2|1 +GCCGATGGTATCCAGGACTTTGCAT +>3897|0|BS2|4 +GCCGATGGTATCCAGGACTTTGCA +>3909|0|BS2|1 +CAGGACTTTGCATACCGGTTCTCGGA +>3909|0|BS2|4 +CAGGACTTTGCATACCGGTTCTCGG +>3909|0|BS2|1 +CAGGACTTTGCATACCGGTTCTC +>3911|0|BS2|1 +GGACTTTGCATACCGGTTCTCGGA +>3913|0|BS2|1 +ACTTTGCATACCGGTTCTCGGAAT +>3973|0|BS2|1 +AATCCAACAACGTCTGCTTCACT +>4064|0|BS2|1 +GTACCTTGGAGTGCTTCTGGATCGC +>4064|0|BS2|2 +GTACCTTGGAGTGCTTCTGGATC +>4088|0|BS2|1 +CAGACTCACATTTTCCAAGCATG +>4116|0|BS2|1 +GACATCAGAACGCGCCTACGTGCT +>4275|0|BS2|1 +CACATCAAAAGGATCCAGGCTATT +>4363|0|BS2|1 +GAGACCTGAAACTCGCAACGGTATT +>4364|0|BS2|1 +AGACCTGAAACTCGCAACGGTATT +>4389|0|BS2|2 +GACGAAATAAACAAGCACTCGAGCA +>4389|0|BS2|1 +GACGAAATAAACAAGCACTCGAGC +>4416|0|BS2|9 +TACCATGACAGGCTGGAGCGCCACA +>4416|0|BS2|1 +TACCATGACAGGCTGGAGCGCCAC +>4416|0|BS2|6 +TACCATGACAGGCTGGAGCGCCA +>4437|0|BS2|2 +CACAGAAATCGGCTGGCCAGCGCT +>4437|0|BS2|3 +CACAGAAATCGGCTGGCCAGCGC +>4443|0|BS2|1 +AATCGGCTGGCCAGCGCTTTAAACAG +>4443|0|BS2|1 +AATCGGCTGGCCAGCGCTTTAAAC +>4445|0|BS2|18 +TCGGCTGGCCAGCGCTTTAAACAGA +>4445|0|BS2|6 +TCGGCTGGCCAGCGCTTTAAACAG +>4460|0|BS2|1 +TTTAAACAGATCTCGCCCACCAAGGA +>4460|0|BS2|2 +TTTAAACAGATCTCGCCCACCAAGG +>4462|0|BS2|9 +TAAACAGATCTCGCCCACCAAGGAGGC +>4462|0|BS2|1 +TAAACAGATCTCGCCCACCAAGGAG +>4462|0|BS2|1 +TAAACAGATCTCGCCCACCAAGGA +>4462|0|BS2|1 +TAAACAGATCTCGCCCACCAAGG +>4464|0|BS2|3 +AACAGATCTCGCCCACCAAGGAGGC +>4464|0|BS2|4 +AACAGATCTCGCCCACCAAGGAGG +>4464|0|BS2|2 +AACAGATCTCGCCCACCAAGGAG +>4465|0|BS2|4 +ACAGATCTCGCCCACCAAGGAGGCTC +>4465|0|BS2|3 +ACAGATCTCGCCCACCAAGGAGGC +>4465|0|BS2|1 +ACAGATCTCGCCCACCAAGGAGG |
| b |
| diff -r 9645d995fb3c -r 9185ca0a7b43 test-data/res_files/reads-sample-small.fastq/subgroups/PPPartners/DMCR1A.html --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/res_files/reads-sample-small.fastq/subgroups/PPPartners/DMCR1A.html Wed Jan 16 08:18:13 2019 -0500 |
| b |
| b'@@ -0,0 +1,295 @@\n+\n+ <!DOCTYPE html>\n+ <html lang="en">\n+ <head>\n+ <meta charset="utf-8">\n+ <title>pipeline</title>\n+ <meta name="viewport" content="width=device-width, initial-scale=1.0">\n+ <meta name="description" content="">\n+ <meta name="author" content="">\n+ <!-- Le styles -->\n+ <link href="css/bootstrap.css" rel="stylesheet">\n+ <link href="css/bootstrap-table.css" rel="stylesheet">\n+ <style type="text/css">\n+ body {\n+ padding-top: 60px;\n+ padding-bottom: 40px;\n+ }\n+ div#page {\n+ width: 940px;\n+ background-color: #fff;\n+ margin: 0 auto;\n+ text-align: left;\n+ border-color: #fff;\n+ border-style: none solid solid;\n+ border-width: medium 1px 1px;\n+ }\n+\n+ div.content {\n+ \tdisplay: none;\n+\t float: right;\n+\t width: 550px;\n+ }\n+ div.content a, div.navigation a {\n+ text-decoration: none;\n+ \tcolor: #777;\n+ }\n+ div.content a:focus, div.content a:hover, div.content a:active {\n+ text-decoration: underline;\n+ }\n+ \n+ div.controls {\n+ margin-top: 5px;\n+\t height: 23px;\n+ }\n+ \n+ div.controls a {\n+\t padding: 5px;\n+ }\n+ div.ss-controls {\n+\t float: left;\n+ }\n+ div.nav-controls {\n+\t float: right;\n+ }\n+ div.slideshow-container {\n+\t position: relative;\n+\t clear: both;\n+\t height: 502px; /* This should be set to be at least the height of the largest image in the slideshow */\n+ }\n+ div.loader {\n+ \tposition: absolute;\n+ \ttop: 0;\n+ \tleft: 0;\n+ background-image: url(\'loader.gif\');\n+ background-repeat: no-repeat;\n+ background-position: center;\n+ \twidth: 550px;\n+ \theight: 502px; /* This should be set to be at least the height of the largest image in the slideshow */\n+ }\n+ div.slideshow {\n+ \n+ }\n+ \n+ div.slideshow span.image-wrapper {\n+\t display: block;\n+\t position: absolute;\n+\t top: 0;\n+\t left: 0;\n+ }\n+ div.slideshow a.advance-link {\n+\t display: block;\n+ \t width: 550px;\n+ height: 502px; /* This should be set to be at least the height of the largest image in the slideshow */\n+ line-height: 502px; /* This should be set to be at least the height of the largest image in the slideshow */\n+ text-align: center;\n+ }\n+ div.slideshow a.advance-link:hover, div.slideshow a.advance-link:active, div.slideshow a.advance-link:visited {\n+ text-decoration: none;\n+ }\n+ div.slideshow img {\n+ vertical-align: middle;\n+\tborder: 1px solid #ccc;\n+ }\n+\n+ div.image-title {\n+ font-weight: bold;\n+ font-size: 1.4em;\n+ }\n+\n+ div.image-desc {\n+ line-height: 1.3em;\n+ padding-top: 12px;\n+ }\n+ div.navigation {\n+\n+ }\n+ ul.thumbs {\n+\tclear: both;\n+\tmargin: 0;\n+\tpadding: 0;\n+ }\n+ ul.thumbs li {\n+\tfloat: none;\n+\tpadding: 0;\n+\tmargin: 0;\n+ list-style: none;\n+ }\n+ a.thumb {\n+\tpadding: 0;\n+\tdisplay: inline;\n+\tborder: none;\n+ }\n+ ul.thumbs li.selected a.thumb {\n+\tcolor: #000;\n+ font-weight: bold;\n+ }\n+ a.thumb:focus {\n+\toutline: none;\n+ }\n+ ul.thumbs img {\n+\tborder: none;\n+\tdisplay: block;\n+ }\n+ div.pagination {\n+\tclear: both;\n+ }\n+ div.navigation div.top {\n+ margin-bottom: 12px;\n+\theight: 11px;\n+ }\n+ div.navigation div.bottom {\n+ margin-top: 12px;\n+ }\n+ div.pagination a, div.pagination span.current, div.pagination span.ellipsis {\n+\tdisplay: block;\n+\tfloat: left;\n+ margin-right: 2px;\n+\tpadding: 4px 7px 2px 7px;\n+\tborder: 1px solid #ccc;\n+ }\n+ div.pagination a:hover {\n+ background-color: #eee;\n+ text-decoration: none;\n+ }\n+ div.pagination span.current {\n+ font-weight: bold;\n+ background-color: #000;\n+ border-color: #000;\n+\tcolor: #fff;\n+ }\n+ div.pagination span.ellipsis {\n+\tborder: none;\n+\tpadding: 5px 0 3px 2px;\n+ }\n+ \n+ div.download {\n+\tfloat: right;\n+ }\n+ \n+ div.caption-container {\n+\tposition: relative;\n+\tclear: left;\n+\theight: 75px;\n+ }\n+ span.image-caption {\n+\tdisplay: block;\n+\tposition: absolute;\n+\twidth: 550px;\n+\ttop: 0;\n+\tleft: 0;\n+ }\n+ div.caption {\n+\tpadding: 12px;\n+ }\n+\n+ /* Featurettes\n+ ------------------------- */\n+\n+ .featurette {\n+ padding-top: 20px; /* Vertica'..b'Vertically center images part 2: clear their floats. */\n+ text-align: center;\n+ }\n+\n+ .featurette-p\n+ {\n+ text-align: left;\n+ }\n+\n+ .featurette-image {\n+ margin-top: 10px; /* Vertically center images part 3: negative margin up the image the same amount of the padding to center it. */\n+ width: 450px;\n+ height: auto;\n+ }\n+\n+ </style>\n+ <link href="css/bootstrap-responsive.css" rel="stylesheet">\n+ </head>\n+ <body>\n+ \n+\t\t\t\t\t<div align="center">\n+\t\t\t\t\t<h2>DMCR1A</h2>\n+\t\t\t\t\t<p> <img class="featurette-image" src="DMCR1A/histogram.png"/></p>\n+\t\t\t\t\t<p><a href="DMCR1A/overlap_size.txt">ping pong signature</a></p>\n+\t\t\t\t\t<p><a href="DMCR1A/sensPPP.txt">sense reads with PPP</a></p>\n+\t\t\t\t\t<p><a href="DMCR1A/antisensPPP.txt">reverse reads with PPP</a></p>\n+\t\t\t\t\t<p><a href="DMCR1A/sens.txt">sense reads without PPP</a></p>\n+\t\t\t\t\t<p><a href="DMCR1A/antisens.txt">reverse reads without PPP</a></p>\n+\t\t\t\t\t</div>\n+ <!-- FOOTER -->\n+ <div class="container">\n+ <footer>\n+ \n+ </footer>\n+ </div>\n+ <!-- Le javascript\n+ ================================================== -->\n+ <!-- Placed at the end of the document so the pages load faster -->\n+ <script type="text/javascript" src="js/filter.js"></script>\n+ <script type="text/javascript" src="js/jquery.js"></script>\n+ <script type="text/javascript" src="js/jquery-1.3.2.js"></script>\n+ <script type="text/javascript" src="js/jquery.galleriffic.js"></script>\n+ <script type="text/javascript" src="js/jquery.opacityrollover.js"></script>\n+ <script type="text/javascript" src="js/bootstrap-table.js"></script>\n+ <script type="text/javascript" src="js/bootstrap.min.js"></script>\n+ <script type="text/javascript">\n+ jQuery(document).ready(function($) {\n+ // We only want these styles applied when javascript is enabled\n+ $(\'div.navigation\').css({\'width\' : \'300px\', \'float\' : \'left\'});\n+ $(\'div.content\').css(\'display\', \'block\');\n+ \n+ $(".each-gallery").each(function(i){\n+ // Initially set opacity on thumbs and add\n+ // additional styling for hover effect on thumbs\n+ var onMouseOutOpacity = 0.67;\n+ $(\'#thumbs + i + ul.thumbs li\').opacityrollover({\n+ mouseOutOpacity: onMouseOutOpacity,\n+ mouseOverOpacity: 1.0,\n+ fadeSpeed: \'fast\',\n+ exemptionSelector: \'.selected\'\n+ });\n+ \n+ // Initialize Advanced Galleriffic Gallery\n+ var gallery = $(\'#thumbs\'+i).galleriffic({\n+ delay: 2500,\n+ numThumbs: 22,\n+ preloadAhead: 10,\n+ enableTopPager: true,\n+ enableBottomPager: true,\n+ maxPagesToShow: 7,\n+ imageContainerSel: \'#slideshow\'+ i,\n+ controlsContainerSel: \'#controls\' + i,\n+ captionContainerSel: \'#caption\' + i,\n+ loadingContainerSel: \'#loading\' + i,\n+ renderSSControls: true,\n+ renderNavControls: true,\n+ playLinkText: \'Play\',\n+ pauseLinkText: \'Pause\',\n+ prevLinkText: \'‹ Previous\',\n+ nextLinkText: \'Next ›\',\n+ nextPageLinkText: \'Next ›\',\n+ prevPageLinkText: \'‹ Prev\',\n+ enableHistory: false,\n+ autoStart: false,\n+ syncTransitions: true,\n+ defaultTransitionDuration: 900,\n+ onSlideChange: function(prevIndex, nextIndex) {\n+ // \'this\' refers to the gallery, which is an extension of $(\'#thumbs\')\n+ this.find(\'ul.thumbs\').children()\n+ .eq(prevIndex).fadeTo(\'fast\', onMouseOutOpacity).end()\n+ .eq(nextIndex).fadeTo(\'fast\', 1.0);\n+ },\n+ onPageTransitionOut: function(callback) {\n+ this.fadeTo(\'fast\', 0.0, callback);\n+ },\n+ onPageTransitionIn: function() {\n+ this.fadeTo(\'fast\', 1.0);\n+ }\n+ });\n+ });\n+ });\n+ </script>\n+ </body>\n+ </html>\n+ \n\\ No newline at end of file\n' |
| b |
| diff -r 9645d995fb3c -r 9185ca0a7b43 test-data/res_files/reads-sample-small.fastq/subgroups/PPPartners/DMCR1A/antisens.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/res_files/reads-sample-small.fastq/subgroups/PPPartners/DMCR1A/antisens.txt Wed Jan 16 08:18:13 2019 -0500 |
| b |
| @@ -0,0 +1,230 @@ +>6|16|DMCR1A|1 +AAAAACACGACCGTTCGCTTTGAAA +>65|16|DMCR1A|1 +AAGATTATTAAAAACCACTGCTG +>341|16|DMCR1A|1 +ACCGCACGAGAGCAGTCTGCACGCT +>341|16|DMCR1A|1 +AACCGCACGAGAGCAGTCTGCACGCT +>541|16|DMCR1A|1 +TTCGGCCATTAAAACCAGCGCACT +>546|16|DMCR1A|1 +TCACTCGTTCGGCCATTAAAACCAGC +>550|16|DMCR1A|1 +TCATCACTCGTTCGGCCATTAAAAC +>558|16|DMCR1A|2 +TGCTAGGTCATCACTCGTTCGGCC +>662|16|DMCR1A|1 +GTTGATCAGTTCTTTCAAGCCACCT +>703|16|DMCR1A|2 +TCATCGGCTCGACGGAAACAATCTC +>705|16|DMCR1A|2 +TATCATCGGCTCGACGGAAACAATC +>733|16|DMCR1A|2 +TAAACTGTGAATTAAGCGCGCACA +>734|16|DMCR1A|2 +TTAAACTGTGAATTAAGCGCGCAC +>774|16|DMCR1A|1 +TTTTTTGATCTTTGGAGATTTATC +>861|16|DMCR1A|1 +TTGCTGCGATTGACAGCTGATCAGT +>867|16|DMCR1A|1 +TGCGGATTTGCTGCGATTGACAGCTG +>868|16|DMCR1A|1 +TGCGGATTTGCTGCGATTGACAGCT +>869|16|DMCR1A|1 +TGCGGATTTGCTGCGATTGACAGC +>869|16|DMCR1A|4 +TATGCGGATTTGCTGCGATTGACAGC +>870|16|DMCR1A|2 +TGCGGATTTGCTGCGATTGACAG +>870|16|DMCR1A|1 +TATGCGGATTTGCTGCGATTGACAG +>928|16|DMCR1A|1 +TCACAGCGAATTGATCGGATTGCT +>1024|16|DMCR1A|2 +CCTTGTGGTTGTAAACTATTCGGGA +>1025|16|DMCR1A|1 +CCTTGTGGTTGTAAACTATTCGGG +>1026|16|DMCR1A|1 +TCCCTTGTGGTTGTAAACTATTCGG +>1056|16|DMCR1A|1 +TGCCCACTTGTGCCGGTAGACCGGACTC +>1057|16|DMCR1A|1 +CACTTGTGCCGGTAGACCGGACT +>1058|16|DMCR1A|1 +TGCCCACTTGTGCCGGTAGACCGGAC +>1058|16|DMCR1A|1 +AGTGCCCACTTGTGCCGGTAGACCGGAC +>1150|16|DMCR1A|2 +TTTGATCAGGGGAAAGCCGAGAAA +>1151|16|DMCR1A|1 +TGTTTGATCAGGGGAAAGCCGAGAA +>1152|16|DMCR1A|1 +TGTTTGATCAGGGGAAAGCCGAGA +>1175|16|DMCR1A|2 +TATATAATACAATACATCAGACGAT +>1200|16|DMCR1A|1 +TATTATCGGCTTTTGTTTTGTCTTG +>1202|16|DMCR1A|10 +TATTATCGGCTTTTGTTTTGTCT +>1210|16|DMCR1A|2 +TTCCACTTTTATATTATCGGCTTTTG +>1214|16|DMCR1A|3 +TTTTCCACTTTTATATTATCGGCT +>1214|16|DMCR1A|1 +TTTTTCCACTTTTATATTATCGGCT +>1343|16|DMCR1A|1 +TCTTAGCTTCGAACTCTTTTACC +>1347|16|DMCR1A|1 +TTTGATCTTAGCTTCGAACTCTTT +>1348|16|DMCR1A|1 +TTTGATCTTAGCTTCGAACTCTT +>1348|16|DMCR1A|1 +TTTTTGATCTTAGCTTCGAACTCTT +>1351|16|DMCR1A|2 +TATTTTTGATCTTAGCTTCGAACT +>1411|16|DMCR1A|2 +CGGATGGTGCAGTGGTCTGGCCAC +>1413|16|DMCR1A|1 +GCGGATGGTGCAGTGGTCTGGCC +>1414|16|DMCR1A|3 +GGCGGATGGTGCAGTGGTCTGGC +>1416|16|DMCR1A|1 +GAGGCGGATGGTGCAGTGGTCTG +>1425|16|DMCR1A|2 +GAAGATGAAGAGGCGGATGGTGC +>1538|16|DMCR1A|5 +TTATATGGGATGCAAATGAAAGACT +>1539|16|DMCR1A|1 +TTATATGGGATGCAAATGAAAGAC +>1555|16|DMCR1A|1 +TCGCTGTGAACACTATTATATGG +>1576|16|DMCR1A|3 +TAAGTATCTCCGGCTTTAACCAAGTC +>1578|16|DMCR1A|7 +TAAGTATCTCCGGCTTTAACCAAG +>1592|16|DMCR1A|1 +GAAGACTTCGGAGTTAAGTATCTC +>1681|16|DMCR1A|1 +TCCTCCGGCGCGAGGGTAGATCTAACC +>1753|16|DMCR1A|1 +TAAACTGAACTGTCGGAAAAAGACAGC +>1755|16|DMCR1A|1 +TAAACTGAACTGTCGGAAAAAGACA +>1756|16|DMCR1A|2 +TATAAACTGAACTGTCGGAAAAAGAC +>1757|16|DMCR1A|3 +TATAAACTGAACTGTCGGAAAAAGA +>1770|16|DMCR1A|1 +TACGAGAACGTAATATAAACTGAAC +>1773|16|DMCR1A|1 +TATACGAGAACGTAATATAAACTG +>1783|16|DMCR1A|1 +GATGGCGGAATATACGAGAACGTA +>1800|16|DMCR1A|2 +TATTCTGGGAATTCCGAAGATGGCG +>1802|16|DMCR1A|1 +TATTCTGGGAATTCCGAAGATGG +>1805|16|DMCR1A|1 +TCTGATATTCTGGGAATTCCGAAGA +>1807|16|DMCR1A|1 +TTCTGATATTCTGGGAATTCCGAA +>1813|16|DMCR1A|5 +GATGATTCTGATATTCTGGGAAT +>1820|16|DMCR1A|2 +TAGAGGACAGATGATTCTGATATTC +>1838|16|DMCR1A|1 +TATTCAAGGTGGACTGGATAGAGGA +>1863|16|DMCR1A|3 +TACCAATTGGTCCCTGTCAGACAGTT +>1864|16|DMCR1A|1 +TACCAATTGGTCCCTGTCAGACAGT +>1864|16|DMCR1A|1 +CTACCAATTGGTCCCTGTCAGACAGT +>1865|16|DMCR1A|2 +TACCAATTGGTCCCTGTCAGACAG +>1865|16|DMCR1A|1 +CTACCAATTGGTCCCTGTCAGACAG +>1865|16|DMCR1A|2 +ACTACCAATTGGTCCCTGTCAGACAG +>1872|16|DMCR1A|6 +CCTAGAACTACCAATTGGTCCCTGT +>1873|16|DMCR1A|1 +TCACCTAGAACTACCAATTGGTCCCTG +>1874|16|DMCR1A|1 +CCTAGAACTACCAATTGGTCCCT +>1874|16|DMCR1A|6 +TCACCTAGAACTACCAATTGGTCCCT +>1875|16|DMCR1A|1 +CACCTAGAACTACCAATTGGTCCC +>1875|16|DMCR1A|16 +TCACCTAGAACTACCAATTGGTCCC +>1876|16|DMCR1A|1 +TCACCTAGAACTACCAATTGGTCC +>1879|16|DMCR1A|3 +TAAAATCACCTAGAACTACCAATTGG +>1882|16|DMCR1A|1 +TAAAATCACCTAGAACTACCAAT +>1883|16|DMCR1A|1 +TTAAAATCACCTAGAACTACCAA +>1884|16|DMCR1A|1 +TATATTAAAATCACCTAGAACTACCA +>1895|16|DMCR1A|2 +TTGTGCCAGGTATATTAAAATCACC +>1925|16|DMCR1A|1 +TATATTCGATTGTTTTTCTGGGGA +>1971|16|DMCR1A|1 +TAAGTCGAGCAAGCCGTCAATAAAGT +>1981|16|DMCR1A|1 +ACAACGATAAGTCGAGCAAGCCG +>1988|16|DMCR1A|1 +TTAACTTGCGACAACGATAAGTCGAG +>2100|16|DMCR1A|1 +TGATATGGATATTCAGGTTGAGTTC +>2126|16|DMCR1A|1 +TATGTCGATTGCCACCTCGAAAGTAGG +>2130|16|DMCR1A|1 +CCTATGTCGATTGCCACCTCGAAAG +>2131|16|DMCR1A|1 +TACCTATGTCGATTGCCACCTCGAAA +>2132|16|DMCR1A|1 +TACCTATGTCGATTGCCACCTCGAA +>2133|16|DMCR1A|1 +TACCTATGTCGATTGCCACCTCGA +>2153|16|DMCR1A|2 +TCTGAATTTACTTTTAATACCGTACC +>2160|16|DMCR1A|1 +ACTTCTCTGAATTTACTTTTAATA +>2161|16|DMCR1A|1 +TGACTTCTCTGAATTTACTTTTAAT +>2211|16|DMCR1A|2 +TGTTTAGCCTCCGAAAATTTGCCT +>2211|16|DMCR1A|3 +TTGTTTAGCCTCCGAAAATTTGCCT +>2335|16|DMCR1A|1 +TTGACGGATAGTACATCGGAACACAA +>2343|16|DMCR1A|1 +TTTCGAGATTGACGGATAGTACATCG +>2346|16|DMCR1A|1 +TTTCGAGATTGACGGATAGTACA +>2350|16|DMCR1A|1 +GAGGTTTCGAGATTGACGGATAG +>2350|16|DMCR1A|1 +GGAGGTTTCGAGATTGACGGATAG +>2386|16|DMCR1A|1 +TACATTTCTTAGGTGTGTCAACTCT +>2413|16|DMCR1A|1 +TTTTTAAATTTTATATAGAGTCTGGAC +>2436|16|DMCR1A|1 +GGATGGACTGAGAACCGGTATTTT +>2437|16|DMCR1A|1 +GGATGGACTGAGAACCGGTATTT +>2442|16|DMCR1A|5 +TTACAAAGGATGGACTGAGAACCGG +>2444|16|DMCR1A|5 +TTACAAAGGATGGACTGAGAACC +>2446|16|DMCR1A|6 +TATTTACAAAGGATGGACTGAGAA +>2447|16|DMCR1A|2 +TATTTACAAAGGATGGACTGAGA |
| b |
| diff -r 9645d995fb3c -r 9185ca0a7b43 test-data/res_files/reads-sample-small.fastq/subgroups/PPPartners/DMCR1A/antisensPPP.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/res_files/reads-sample-small.fastq/subgroups/PPPartners/DMCR1A/antisensPPP.txt Wed Jan 16 08:18:13 2019 -0500 |
| b |
| @@ -0,0 +1,32 @@ +>830|16|DMCR1A|1 +TCCTGTTGATCATTTGGCCGTGGT +>831|16|DMCR1A|2 +TCCTGTTGATCATTTGGCCGTGG +>1026|16|DMCR1A|1 +CCCTTGTGGTTGTAAACTATTCGG +>1321|16|DMCR1A|2 +TACCAACATACTATCCGGCAAAAAAC +>1602|16|DMCR1A|8 +TACATACCTGGGAAGACTTCGGAGT +>1603|16|DMCR1A|9 +TACATACCTGGGAAGACTTCGGAG +>1604|16|DMCR1A|1 +TACATACCTGGGAAGACTTCGGA +>1953|16|DMCR1A|1 +TAAAGTCATGTTGTGCTAAAGGGA +>2323|16|DMCR1A|1 +CATCGGAACACAAGAGTCAAAAAAT +>2324|16|DMCR1A|2 +TACATCGGAACACAAGAGTCAAAAAA +>2327|16|DMCR1A|1 +TACATCGGAACACAAGAGTCAAA +>2430|16|DMCR1A|1 +TGGACTGAGAACCGGTATTTTTAAATT +>2431|16|DMCR1A|3 +TGGACTGAGAACCGGTATTTTTAAAT +>2432|16|DMCR1A|9 +TGGACTGAGAACCGGTATTTTTAAA +>2433|16|DMCR1A|8 +TGGACTGAGAACCGGTATTTTTAA +>2434|16|DMCR1A|1 +TGGACTGAGAACCGGTATTTTTA |
| b |
| diff -r 9645d995fb3c -r 9185ca0a7b43 test-data/res_files/reads-sample-small.fastq/subgroups/PPPartners/DMCR1A/histogram.png |
| b |
| Binary file test-data/res_files/reads-sample-small.fastq/subgroups/PPPartners/DMCR1A/histogram.png has changed |
| b |
| diff -r 9645d995fb3c -r 9185ca0a7b43 test-data/res_files/reads-sample-small.fastq/subgroups/PPPartners/DMCR1A/overlap_size.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/res_files/reads-sample-small.fastq/subgroups/PPPartners/DMCR1A/overlap_size.txt Wed Jan 16 08:18:13 2019 -0500 |
| b |
| @@ -0,0 +1,24 @@ +size number percentage of the total overlap number +1 0 0.00 +2 1 0.92 +3 1 0.92 +4 1 0.92 +5 2 1.83 +6 0 0.00 +7 1 0.92 +8 5 4.59 +9 2 1.83 +10 30 27.52 +11 1 0.92 +12 8 7.34 +13 4 3.67 +14 10 9.17 +15 3 2.75 +16 3 2.75 +17 0 0.00 +18 1 0.92 +19 12 11.01 +20 5 4.59 +21 11 10.09 +22 3 2.75 +23 5 4.59 |
| b |
| diff -r 9645d995fb3c -r 9185ca0a7b43 test-data/res_files/reads-sample-small.fastq/subgroups/PPPartners/DMCR1A/sens.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/res_files/reads-sample-small.fastq/subgroups/PPPartners/DMCR1A/sens.txt Wed Jan 16 08:18:13 2019 -0500 |
| b |
| @@ -0,0 +1,66 @@ +>7|0|DMCR1A|1 +TTCAAAGCGAACGGTCGTGTTTTT +>116|0|DMCR1A|1 +TTATTAAAGATCCGTTCGCTTCGCGAG +>117|0|DMCR1A|2 +TATTAAAGATCCGTTCGCTTCGCGAG +>119|0|DMCR1A|3 +TTAAAGATCCGTTCGCTTCGCGAG +>119|0|DMCR1A|1 +TTAAAGATCCGTTCGCTTCGCGAGTG +>153|0|DMCR1A|1 +TGATTTGTGCAGTAGTTTAAACAA +>552|0|DMCR1A|1 +TTTAATGGCCGAACGAGTGATGACC +>635|0|DMCR1A|1 +GATGAAATCGTTTATGCGCCAAACT +>662|0|DMCR1A|1 +AGGTGGCTTGAAAGAACTGATCAACA +>665|0|DMCR1A|4 +TGGCTTGAAAGAACTGATCAACAGT +>838|0|DMCR1A|1 +CAAATGATCAACAGGACTCCACAAC +>840|0|DMCR1A|2 +AATGATCAACAGGACTCCACAACT +>849|0|DMCR1A|1 +CAGGACTCCACAACTGATCAGCTG +>975|0|DMCR1A|1 +AAAGATTCCGAATTGTCTGCACTGG +>979|0|DMCR1A|2 +ATTCCGAATTGTCTGCACTGGTTT +>980|0|DMCR1A|1 +TTCCGAATTGTCTGCACTGGTTTT +>987|0|DMCR1A|1 +TTGTCTGCACTGGTTTTTCAACCAGT +>1145|0|DMCR1A|1 +TTTCGTTTCTCGGCTTTCCCCTGATC +>1161|0|DMCR1A|1 +TCCCCTGATCAAACATCGTCTGATG +>1162|0|DMCR1A|7 +CCCCTGATCAAACATCGTCTGAT +>1162|0|DMCR1A|6 +CCCCTGATCAAACATCGTCTGATG +>1162|0|DMCR1A|1 +CCCCTGATCAAACATCGTCTGATGTA +>1421|0|DMCR1A|1 +CACTGCACCATCCGCCTCTTCAT +>1583|0|DMCR1A|3 +TTAAAGCCGGAGATACTTAACTC +>1863|0|DMCR1A|1 +AACTGTCTGACAGGGACCAATTGG +>1868|0|DMCR1A|1 +TCTGACAGGGACCAATTGGTAGTTC +>1870|0|DMCR1A|2 +TGACAGGGACCAATTGGTAGTTC +>1969|0|DMCR1A|1 +TGACTTTATTGACGGCTTGCTCGAC +>1970|0|DMCR1A|1 +GACTTTATTGACGGCTTGCTCGACT +>1973|0|DMCR1A|1 +TTTATTGACGGCTTGCTCGACTT +>2205|0|DMCR1A|1 +TTCGCAAGGCAAATTTTCGGAGGCT +>2329|0|DMCR1A|1 +TGACTCTTGTGTTCCGATGTACTA +>2371|0|DMCR1A|1 +TCCTTGGTTTAATAAAGAGTTGAC |
| b |
| diff -r 9645d995fb3c -r 9185ca0a7b43 test-data/res_files/reads-sample-small.fastq/subgroups/PPPartners/DMCR1A/sensPPP.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/res_files/reads-sample-small.fastq/subgroups/PPPartners/DMCR1A/sensPPP.txt Wed Jan 16 08:18:13 2019 -0500 |
| b |
| @@ -0,0 +1,26 @@ +>844|0|DMCR1A|1 +ATCAACAGGACTCCACAACTGATCAG +>1040|0|DMCR1A|1 +ACCACAAGGGAACATTGAGTCCGG +>1337|0|DMCR1A|1 +TATGTTGGTAAAAGAGTTCGAAG +>1617|0|DMCR1A|2 +CAGGTATGTACACTATATATAGG +>1617|0|DMCR1A|1 +CAGGTATGTACACTATATATAGGT +>1967|0|DMCR1A|8 +CATGACTTTATTGACGGCTTGCT +>1967|0|DMCR1A|2 +CATGACTTTATTGACGGCTTGCTC +>2338|0|DMCR1A|2 +TGTTCCGATGTACTATCCGTCAATC +>2340|0|DMCR1A|1 +TTCCGATGTACTATCCGTCAATC +>2340|0|DMCR1A|3 +TTCCGATGTACTATCCGTCAATCT +>2340|0|DMCR1A|2 +TTCCGATGTACTATCCGTCAATCTC +>2340|0|DMCR1A|1 +TTCCGATGTACTATCCGTCAATCTCG +>2447|0|DMCR1A|1 +TCTCAGTCCATCCTTTGTAAATAT |
| b |
| diff -r 9645d995fb3c -r 9185ca0a7b43 test-data/res_files/reads-sample-small.fastq/subgroups/PPPartners/DMRT1B.html --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/res_files/reads-sample-small.fastq/subgroups/PPPartners/DMRT1B.html Wed Jan 16 08:18:13 2019 -0500 |
| b |
| b'@@ -0,0 +1,295 @@\n+\n+ <!DOCTYPE html>\n+ <html lang="en">\n+ <head>\n+ <meta charset="utf-8">\n+ <title>pipeline</title>\n+ <meta name="viewport" content="width=device-width, initial-scale=1.0">\n+ <meta name="description" content="">\n+ <meta name="author" content="">\n+ <!-- Le styles -->\n+ <link href="css/bootstrap.css" rel="stylesheet">\n+ <link href="css/bootstrap-table.css" rel="stylesheet">\n+ <style type="text/css">\n+ body {\n+ padding-top: 60px;\n+ padding-bottom: 40px;\n+ }\n+ div#page {\n+ width: 940px;\n+ background-color: #fff;\n+ margin: 0 auto;\n+ text-align: left;\n+ border-color: #fff;\n+ border-style: none solid solid;\n+ border-width: medium 1px 1px;\n+ }\n+\n+ div.content {\n+ \tdisplay: none;\n+\t float: right;\n+\t width: 550px;\n+ }\n+ div.content a, div.navigation a {\n+ text-decoration: none;\n+ \tcolor: #777;\n+ }\n+ div.content a:focus, div.content a:hover, div.content a:active {\n+ text-decoration: underline;\n+ }\n+ \n+ div.controls {\n+ margin-top: 5px;\n+\t height: 23px;\n+ }\n+ \n+ div.controls a {\n+\t padding: 5px;\n+ }\n+ div.ss-controls {\n+\t float: left;\n+ }\n+ div.nav-controls {\n+\t float: right;\n+ }\n+ div.slideshow-container {\n+\t position: relative;\n+\t clear: both;\n+\t height: 502px; /* This should be set to be at least the height of the largest image in the slideshow */\n+ }\n+ div.loader {\n+ \tposition: absolute;\n+ \ttop: 0;\n+ \tleft: 0;\n+ background-image: url(\'loader.gif\');\n+ background-repeat: no-repeat;\n+ background-position: center;\n+ \twidth: 550px;\n+ \theight: 502px; /* This should be set to be at least the height of the largest image in the slideshow */\n+ }\n+ div.slideshow {\n+ \n+ }\n+ \n+ div.slideshow span.image-wrapper {\n+\t display: block;\n+\t position: absolute;\n+\t top: 0;\n+\t left: 0;\n+ }\n+ div.slideshow a.advance-link {\n+\t display: block;\n+ \t width: 550px;\n+ height: 502px; /* This should be set to be at least the height of the largest image in the slideshow */\n+ line-height: 502px; /* This should be set to be at least the height of the largest image in the slideshow */\n+ text-align: center;\n+ }\n+ div.slideshow a.advance-link:hover, div.slideshow a.advance-link:active, div.slideshow a.advance-link:visited {\n+ text-decoration: none;\n+ }\n+ div.slideshow img {\n+ vertical-align: middle;\n+\tborder: 1px solid #ccc;\n+ }\n+\n+ div.image-title {\n+ font-weight: bold;\n+ font-size: 1.4em;\n+ }\n+\n+ div.image-desc {\n+ line-height: 1.3em;\n+ padding-top: 12px;\n+ }\n+ div.navigation {\n+\n+ }\n+ ul.thumbs {\n+\tclear: both;\n+\tmargin: 0;\n+\tpadding: 0;\n+ }\n+ ul.thumbs li {\n+\tfloat: none;\n+\tpadding: 0;\n+\tmargin: 0;\n+ list-style: none;\n+ }\n+ a.thumb {\n+\tpadding: 0;\n+\tdisplay: inline;\n+\tborder: none;\n+ }\n+ ul.thumbs li.selected a.thumb {\n+\tcolor: #000;\n+ font-weight: bold;\n+ }\n+ a.thumb:focus {\n+\toutline: none;\n+ }\n+ ul.thumbs img {\n+\tborder: none;\n+\tdisplay: block;\n+ }\n+ div.pagination {\n+\tclear: both;\n+ }\n+ div.navigation div.top {\n+ margin-bottom: 12px;\n+\theight: 11px;\n+ }\n+ div.navigation div.bottom {\n+ margin-top: 12px;\n+ }\n+ div.pagination a, div.pagination span.current, div.pagination span.ellipsis {\n+\tdisplay: block;\n+\tfloat: left;\n+ margin-right: 2px;\n+\tpadding: 4px 7px 2px 7px;\n+\tborder: 1px solid #ccc;\n+ }\n+ div.pagination a:hover {\n+ background-color: #eee;\n+ text-decoration: none;\n+ }\n+ div.pagination span.current {\n+ font-weight: bold;\n+ background-color: #000;\n+ border-color: #000;\n+\tcolor: #fff;\n+ }\n+ div.pagination span.ellipsis {\n+\tborder: none;\n+\tpadding: 5px 0 3px 2px;\n+ }\n+ \n+ div.download {\n+\tfloat: right;\n+ }\n+ \n+ div.caption-container {\n+\tposition: relative;\n+\tclear: left;\n+\theight: 75px;\n+ }\n+ span.image-caption {\n+\tdisplay: block;\n+\tposition: absolute;\n+\twidth: 550px;\n+\ttop: 0;\n+\tleft: 0;\n+ }\n+ div.caption {\n+\tpadding: 12px;\n+ }\n+\n+ /* Featurettes\n+ ------------------------- */\n+\n+ .featurette {\n+ padding-top: 20px; /* Vertica'..b'Vertically center images part 2: clear their floats. */\n+ text-align: center;\n+ }\n+\n+ .featurette-p\n+ {\n+ text-align: left;\n+ }\n+\n+ .featurette-image {\n+ margin-top: 10px; /* Vertically center images part 3: negative margin up the image the same amount of the padding to center it. */\n+ width: 450px;\n+ height: auto;\n+ }\n+\n+ </style>\n+ <link href="css/bootstrap-responsive.css" rel="stylesheet">\n+ </head>\n+ <body>\n+ \n+\t\t\t\t\t<div align="center">\n+\t\t\t\t\t<h2>DMRT1B</h2>\n+\t\t\t\t\t<p> <img class="featurette-image" src="DMRT1B/histogram.png"/></p>\n+\t\t\t\t\t<p><a href="DMRT1B/overlap_size.txt">ping pong signature</a></p>\n+\t\t\t\t\t<p><a href="DMRT1B/sensPPP.txt">sense reads with PPP</a></p>\n+\t\t\t\t\t<p><a href="DMRT1B/antisensPPP.txt">reverse reads with PPP</a></p>\n+\t\t\t\t\t<p><a href="DMRT1B/sens.txt">sense reads without PPP</a></p>\n+\t\t\t\t\t<p><a href="DMRT1B/antisens.txt">reverse reads without PPP</a></p>\n+\t\t\t\t\t</div>\n+ <!-- FOOTER -->\n+ <div class="container">\n+ <footer>\n+ \n+ </footer>\n+ </div>\n+ <!-- Le javascript\n+ ================================================== -->\n+ <!-- Placed at the end of the document so the pages load faster -->\n+ <script type="text/javascript" src="js/filter.js"></script>\n+ <script type="text/javascript" src="js/jquery.js"></script>\n+ <script type="text/javascript" src="js/jquery-1.3.2.js"></script>\n+ <script type="text/javascript" src="js/jquery.galleriffic.js"></script>\n+ <script type="text/javascript" src="js/jquery.opacityrollover.js"></script>\n+ <script type="text/javascript" src="js/bootstrap-table.js"></script>\n+ <script type="text/javascript" src="js/bootstrap.min.js"></script>\n+ <script type="text/javascript">\n+ jQuery(document).ready(function($) {\n+ // We only want these styles applied when javascript is enabled\n+ $(\'div.navigation\').css({\'width\' : \'300px\', \'float\' : \'left\'});\n+ $(\'div.content\').css(\'display\', \'block\');\n+ \n+ $(".each-gallery").each(function(i){\n+ // Initially set opacity on thumbs and add\n+ // additional styling for hover effect on thumbs\n+ var onMouseOutOpacity = 0.67;\n+ $(\'#thumbs + i + ul.thumbs li\').opacityrollover({\n+ mouseOutOpacity: onMouseOutOpacity,\n+ mouseOverOpacity: 1.0,\n+ fadeSpeed: \'fast\',\n+ exemptionSelector: \'.selected\'\n+ });\n+ \n+ // Initialize Advanced Galleriffic Gallery\n+ var gallery = $(\'#thumbs\'+i).galleriffic({\n+ delay: 2500,\n+ numThumbs: 22,\n+ preloadAhead: 10,\n+ enableTopPager: true,\n+ enableBottomPager: true,\n+ maxPagesToShow: 7,\n+ imageContainerSel: \'#slideshow\'+ i,\n+ controlsContainerSel: \'#controls\' + i,\n+ captionContainerSel: \'#caption\' + i,\n+ loadingContainerSel: \'#loading\' + i,\n+ renderSSControls: true,\n+ renderNavControls: true,\n+ playLinkText: \'Play\',\n+ pauseLinkText: \'Pause\',\n+ prevLinkText: \'‹ Previous\',\n+ nextLinkText: \'Next ›\',\n+ nextPageLinkText: \'Next ›\',\n+ prevPageLinkText: \'‹ Prev\',\n+ enableHistory: false,\n+ autoStart: false,\n+ syncTransitions: true,\n+ defaultTransitionDuration: 900,\n+ onSlideChange: function(prevIndex, nextIndex) {\n+ // \'this\' refers to the gallery, which is an extension of $(\'#thumbs\')\n+ this.find(\'ul.thumbs\').children()\n+ .eq(prevIndex).fadeTo(\'fast\', onMouseOutOpacity).end()\n+ .eq(nextIndex).fadeTo(\'fast\', 1.0);\n+ },\n+ onPageTransitionOut: function(callback) {\n+ this.fadeTo(\'fast\', 0.0, callback);\n+ },\n+ onPageTransitionIn: function() {\n+ this.fadeTo(\'fast\', 1.0);\n+ }\n+ });\n+ });\n+ });\n+ </script>\n+ </body>\n+ </html>\n+ \n\\ No newline at end of file\n' |
| b |
| diff -r 9645d995fb3c -r 9185ca0a7b43 test-data/res_files/reads-sample-small.fastq/subgroups/PPPartners/DMRT1B/antisens.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/res_files/reads-sample-small.fastq/subgroups/PPPartners/DMRT1B/antisens.txt Wed Jan 16 08:18:13 2019 -0500 |
| b |
| @@ -0,0 +1,74 @@ +>58|16|DMRT1B|1 +TCTGATCGAACGGTTGATCTGGCAAC +>416|16|DMRT1B|1 +TCGTTGCGATCAGGGGGACTGCCCC +>417|16|DMRT1B|2 +TCGTTGCGATCAGGGGGACTGCCC +>429|16|DMRT1B|1 +TCCTGAACGGGTCGTTGCGATCA +>430|16|DMRT1B|5 +TCCTCCTGAACGGGTCGTTGCGATC +>430|16|DMRT1B|1 +CTCCTGAACGGGTCGTTGCGATC +>439|16|DMRT1B|1 +TCTGGAGCTCCTCCTGAACGGGTC +>491|16|DMRT1B|1 +TTCCGTCACCCTGAGTCGGGTTAC +>534|16|DMRT1B|1 +GCTGGGGGCCTGCTTGCTTACCCCTT +>547|16|DMRT1B|1 +TAGTCAACAGTGGCTGGGGGCCTGC +>593|16|DMRT1B|1 +TGCTGTAGGAGCCAAGTTCTCCACCT +>635|16|DMRT1B|1 +AATGTGGTCCATCGTTTTCTGAC +>1076|16|DMRT1B|2 +GATGCGTAGCTGCCTGGCTTGGACT +>1076|16|DMRT1B|3 +TGCGTAGCTGCCTGGCTTGGACT +>1077|16|DMRT1B|9 +GATGCGTAGCTGCCTGGCTTGGAC +>1089|16|DMRT1B|1 +TTCTTGGCAACAGATGCGTAGCTG +>1105|16|DMRT1B|1 +TCTGCACCCGTGCTAGCATTCTTGGC +>1106|16|DMRT1B|5 +TCTGCACCCGTGCTAGCATTCTTGG +>1191|16|DMRT1B|1 +TCTGCGTACGAAGCCTCACCCGTC +>1234|16|DMRT1B|1 +CCAGTTCGCTAAGGCTCGTGTCCGA +>1241|16|DMRT1B|4 +TGGCTGCCCAGTTCGCTAAGGCTCG +>1242|16|DMRT1B|3 +CGTGGCTGCCCAGTTCGCTAAGGCTC +>1242|16|DMRT1B|4 +TGGCTGCCCAGTTCGCTAAGGCTC +>1243|16|DMRT1B|2 +CGTGGCTGCCCAGTTCGCTAAGGCT +>1254|16|DMRT1B|3 +TTTTGCGTACGTGGCTGCCCAGT +>1332|16|DMRT1B|2 +TCGCTCTTAAACTTGGGAACGCTT +>1333|16|DMRT1B|2 +TCGCTCTTAAACTTGGGAACGCT +>1336|16|DMRT1B|2 +TCCAGGTCGCTCTTAAACTTGGGAAC +>1336|16|DMRT1B|2 +CAGGTCGCTCTTAAACTTGGGAAC +>1341|16|DMRT1B|1 +CGCTTCCAGGTCGCTCTTAAACTTG +>1364|16|DMRT1B|1 +CACAGAGGCCAAGTCATTGAGCGCCG +>1365|16|DMRT1B|37 +CACAGAGGCCAAGTCATTGAGCGCC +>1369|16|DMRT1B|1 +TGCGCACAGAGGCCAAGTCATTGAG +>1381|16|DMRT1B|1 +TTGCGCTCCCGTGCGCACAGAGGC +>1410|16|DMRT1B|1 +TCCAGTCCGCTGCAGGATAGCGCT +>1413|16|DMRT1B|1 +TCGTCCAGTCCGCTGCAGGATAGC +>1422|16|DMRT1B|3 +TCGTAGCCTCGTCCAGTCCGCTG |
| b |
| diff -r 9645d995fb3c -r 9185ca0a7b43 test-data/res_files/reads-sample-small.fastq/subgroups/PPPartners/DMRT1B/antisensPPP.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/res_files/reads-sample-small.fastq/subgroups/PPPartners/DMRT1B/antisensPPP.txt Wed Jan 16 08:18:13 2019 -0500 |
| b |
| @@ -0,0 +1,12 @@ +>619|16|DMRT1B|5 +TTCTGACTTGTCGCGGTGGTAGC +>1220|16|DMRT1B|1 +TCGTGTCCGATCTTAGCTTCCTAA +>1328|16|DMRT1B|1 +TCTTAAACTTGGGAACGCTTTCCG +>1353|16|DMRT1B|1 +TCATTGAGCGCCGCTTCCAGGTCG +>1365|16|DMRT1B|9 +CAGAGGCCAAGTCATTGAGCGCC +>1366|16|DMRT1B|1 +ACAGAGGCCAAGTCATTGAGCGC |
| b |
| diff -r 9645d995fb3c -r 9185ca0a7b43 test-data/res_files/reads-sample-small.fastq/subgroups/PPPartners/DMRT1B/histogram.png |
| b |
| Binary file test-data/res_files/reads-sample-small.fastq/subgroups/PPPartners/DMRT1B/histogram.png has changed |
| b |
| diff -r 9645d995fb3c -r 9185ca0a7b43 test-data/res_files/reads-sample-small.fastq/subgroups/PPPartners/DMRT1B/overlap_size.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/res_files/reads-sample-small.fastq/subgroups/PPPartners/DMRT1B/overlap_size.txt Wed Jan 16 08:18:13 2019 -0500 |
| b |
| @@ -0,0 +1,24 @@ +size number percentage of the total overlap number +1 7 2.34 +2 3 1.00 +3 8 2.68 +4 4 1.34 +5 6 2.01 +6 5 1.67 +7 8 2.68 +8 3 1.00 +9 6 2.01 +10 13 4.35 +11 5 1.67 +12 6 2.01 +13 2 0.67 +14 23 7.69 +15 12 4.01 +16 30 10.03 +17 16 5.35 +18 30 10.03 +19 26 8.70 +20 43 14.38 +21 9 3.01 +22 25 8.36 +23 9 3.01 |
| b |
| diff -r 9645d995fb3c -r 9185ca0a7b43 test-data/res_files/reads-sample-small.fastq/subgroups/PPPartners/DMRT1B/sens.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/res_files/reads-sample-small.fastq/subgroups/PPPartners/DMRT1B/sens.txt Wed Jan 16 08:18:13 2019 -0500 |
| b |
| @@ -0,0 +1,96 @@ +>414|0|DMRT1B|1 +GGGGGGCAGTCCCCCTGATCGCAACGA +>419|0|DMRT1B|1 +GCAGTCCCCCTGATCGCAACGACCC +>422|0|DMRT1B|1 +GTCCCCCTGATCGCAACGACCCGTT +>422|0|DMRT1B|1 +GTCCCCCTGATCGCAACGACCCGT +>423|0|DMRT1B|1 +TCCCCCTGATCGCAACGACCCGT +>433|0|DMRT1B|1 +CGCAACGACCCGTTCAGGAGGAG +>438|0|DMRT1B|1 +CGACCCGTTCAGGAGGAGCTCCAGAC +>553|0|DMRT1B|1 +CCCCAGCCACTGTTGACTAGCGAC +>796|0|DMRT1B|1 +TCCACATTCGAGACTCAACGGCGC +>796|0|DMRT1B|1 +TCCACATTCGAGACTCAACGGCG +>799|0|DMRT1B|1 +ACATTCGAGACTCAACGGCGCGT +>824|0|DMRT1B|1 +CAAGAGAGACACAGGGCGTAGCT +>1224|0|DMRT1B|22 +GAAGCTAAGATCGGACACGAGCCT +>1229|0|DMRT1B|1 +TAAGATCGGACACGAGCCTTAGCG +>1229|0|DMRT1B|20 +TAAGATCGGACACGAGCCTTAGC +>1232|0|DMRT1B|3 +GATCGGACACGAGCCTTAGCGAAC +>1232|0|DMRT1B|1 +GATCGGACACGAGCCTTAGCGAA +>1323|0|DMRT1B|1 +AGTTTCGGAAAGCGTTCCCAAGTT +>1337|0|DMRT1B|1 +TTCCCAAGTTTAAGAGCGACCTG +>1353|0|DMRT1B|1 +CGACCTGGAAGCGGCGCTCAATGAC +>1355|0|DMRT1B|1 +ACCTGGAAGCGGCGCTCAATGACTT +>1355|0|DMRT1B|1 +ACCTGGAAGCGGCGCTCAATGAC +>1357|0|DMRT1B|1 +CTGGAAGCGGCGCTCAATGACTTG +>1360|0|DMRT1B|4 +GAAGCGGCGCTCAATGACTTGGCC +>1360|0|DMRT1B|1 +GAAGCGGCGCTCAATGACTTGGC +>1361|0|DMRT1B|4 +AAGCGGCGCTCAATGACTTGGCCT +>1362|0|DMRT1B|1 +AGCGGCGCTCAATGACTTGGCCTCT +>1362|0|DMRT1B|2 +AGCGGCGCTCAATGACTTGGCCTC +>1362|0|DMRT1B|2 +AGCGGCGCTCAATGACTTGGCCT +>1368|0|DMRT1B|8 +GCTCAATGACTTGGCCTCTGTGCGCA +>1368|0|DMRT1B|4 +GCTCAATGACTTGGCCTCTGTGCGC +>1369|0|DMRT1B|1 +CTCAATGACTTGGCCTCTGTGCGCA +>1370|0|DMRT1B|7 +TCAATGACTTGGCCTCTGTGCGCACG +>1370|0|DMRT1B|4 +TCAATGACTTGGCCTCTGTGCGCAC +>1370|0|DMRT1B|3 +TCAATGACTTGGCCTCTGTGCGCA +>1370|0|DMRT1B|4 +TCAATGACTTGGCCTCTGTGCGC +>1371|0|DMRT1B|5 +CAATGACTTGGCCTCTGTGCGCACG +>1371|0|DMRT1B|3 +CAATGACTTGGCCTCTGTGCGCAC +>1371|0|DMRT1B|1 +CAATGACTTGGCCTCTGTGCGCA +>1372|0|DMRT1B|2 +AATGACTTGGCCTCTGTGCGCACGG +>1372|0|DMRT1B|1 +AATGACTTGGCCTCTGTGCGCACG +>1373|0|DMRT1B|1 +ATGACTTGGCCTCTGTGCGCACGG +>1374|0|DMRT1B|12 +TGACTTGGCCTCTGTGCGCACGGGA +>1374|0|DMRT1B|4 +TGACTTGGCCTCTGTGCGCACGGG +>1374|0|DMRT1B|5 +TGACTTGGCCTCTGTGCGCACGG +>1376|0|DMRT1B|1 +ACTTGGCCTCTGTGCGCACGGGA +>1415|0|DMRT1B|1 +TATCCTGCAGCGGACTGGACGAGGC +>1425|0|DMRT1B|1 +CGGACTGGACGAGGCTACGACAG |
| b |
| diff -r 9645d995fb3c -r 9185ca0a7b43 test-data/res_files/reads-sample-small.fastq/subgroups/PPPartners/DMRT1B/sensPPP.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/res_files/reads-sample-small.fastq/subgroups/PPPartners/DMRT1B/sensPPP.txt Wed Jan 16 08:18:13 2019 -0500 |
| b |
| @@ -0,0 +1,18 @@ +>632|0|DMRT1B|7 +CAAGTCAGAAAACGATGGACCACAT +>632|0|DMRT1B|1 +CAAGTCAGAAAACGATGGACCACA +>1234|0|DMRT1B|1 +TCGGACACGAGCCTTAGCGAACTGG +>1342|0|DMRT1B|1 +AAGTTTAAGAGCGACCTGGAAGC +>1367|0|DMRT1B|1 +CGCTCAATGACTTGGCCTCTGTGCGCA +>1367|0|DMRT1B|2 +CGCTCAATGACTTGGCCTCTGTGCG +>1367|0|DMRT1B|1 +CGCTCAATGACTTGGCCTCTGTGC +>1378|0|DMRT1B|1 +TTGGCCTCTGTGCGCACGGGAGCGCA +>1379|0|DMRT1B|1 +TGGCCTCTGTGCGCACGGGAGCGC |
| b |
| diff -r 9645d995fb3c -r 9185ca0a7b43 test-data/res_files/reads-sample-small.fastq/subgroups/PPPartners/FW.html --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/res_files/reads-sample-small.fastq/subgroups/PPPartners/FW.html Wed Jan 16 08:18:13 2019 -0500 |
| b |
| b'@@ -0,0 +1,295 @@\n+\n+ <!DOCTYPE html>\n+ <html lang="en">\n+ <head>\n+ <meta charset="utf-8">\n+ <title>pipeline</title>\n+ <meta name="viewport" content="width=device-width, initial-scale=1.0">\n+ <meta name="description" content="">\n+ <meta name="author" content="">\n+ <!-- Le styles -->\n+ <link href="css/bootstrap.css" rel="stylesheet">\n+ <link href="css/bootstrap-table.css" rel="stylesheet">\n+ <style type="text/css">\n+ body {\n+ padding-top: 60px;\n+ padding-bottom: 40px;\n+ }\n+ div#page {\n+ width: 940px;\n+ background-color: #fff;\n+ margin: 0 auto;\n+ text-align: left;\n+ border-color: #fff;\n+ border-style: none solid solid;\n+ border-width: medium 1px 1px;\n+ }\n+\n+ div.content {\n+ \tdisplay: none;\n+\t float: right;\n+\t width: 550px;\n+ }\n+ div.content a, div.navigation a {\n+ text-decoration: none;\n+ \tcolor: #777;\n+ }\n+ div.content a:focus, div.content a:hover, div.content a:active {\n+ text-decoration: underline;\n+ }\n+ \n+ div.controls {\n+ margin-top: 5px;\n+\t height: 23px;\n+ }\n+ \n+ div.controls a {\n+\t padding: 5px;\n+ }\n+ div.ss-controls {\n+\t float: left;\n+ }\n+ div.nav-controls {\n+\t float: right;\n+ }\n+ div.slideshow-container {\n+\t position: relative;\n+\t clear: both;\n+\t height: 502px; /* This should be set to be at least the height of the largest image in the slideshow */\n+ }\n+ div.loader {\n+ \tposition: absolute;\n+ \ttop: 0;\n+ \tleft: 0;\n+ background-image: url(\'loader.gif\');\n+ background-repeat: no-repeat;\n+ background-position: center;\n+ \twidth: 550px;\n+ \theight: 502px; /* This should be set to be at least the height of the largest image in the slideshow */\n+ }\n+ div.slideshow {\n+ \n+ }\n+ \n+ div.slideshow span.image-wrapper {\n+\t display: block;\n+\t position: absolute;\n+\t top: 0;\n+\t left: 0;\n+ }\n+ div.slideshow a.advance-link {\n+\t display: block;\n+ \t width: 550px;\n+ height: 502px; /* This should be set to be at least the height of the largest image in the slideshow */\n+ line-height: 502px; /* This should be set to be at least the height of the largest image in the slideshow */\n+ text-align: center;\n+ }\n+ div.slideshow a.advance-link:hover, div.slideshow a.advance-link:active, div.slideshow a.advance-link:visited {\n+ text-decoration: none;\n+ }\n+ div.slideshow img {\n+ vertical-align: middle;\n+\tborder: 1px solid #ccc;\n+ }\n+\n+ div.image-title {\n+ font-weight: bold;\n+ font-size: 1.4em;\n+ }\n+\n+ div.image-desc {\n+ line-height: 1.3em;\n+ padding-top: 12px;\n+ }\n+ div.navigation {\n+\n+ }\n+ ul.thumbs {\n+\tclear: both;\n+\tmargin: 0;\n+\tpadding: 0;\n+ }\n+ ul.thumbs li {\n+\tfloat: none;\n+\tpadding: 0;\n+\tmargin: 0;\n+ list-style: none;\n+ }\n+ a.thumb {\n+\tpadding: 0;\n+\tdisplay: inline;\n+\tborder: none;\n+ }\n+ ul.thumbs li.selected a.thumb {\n+\tcolor: #000;\n+ font-weight: bold;\n+ }\n+ a.thumb:focus {\n+\toutline: none;\n+ }\n+ ul.thumbs img {\n+\tborder: none;\n+\tdisplay: block;\n+ }\n+ div.pagination {\n+\tclear: both;\n+ }\n+ div.navigation div.top {\n+ margin-bottom: 12px;\n+\theight: 11px;\n+ }\n+ div.navigation div.bottom {\n+ margin-top: 12px;\n+ }\n+ div.pagination a, div.pagination span.current, div.pagination span.ellipsis {\n+\tdisplay: block;\n+\tfloat: left;\n+ margin-right: 2px;\n+\tpadding: 4px 7px 2px 7px;\n+\tborder: 1px solid #ccc;\n+ }\n+ div.pagination a:hover {\n+ background-color: #eee;\n+ text-decoration: none;\n+ }\n+ div.pagination span.current {\n+ font-weight: bold;\n+ background-color: #000;\n+ border-color: #000;\n+\tcolor: #fff;\n+ }\n+ div.pagination span.ellipsis {\n+\tborder: none;\n+\tpadding: 5px 0 3px 2px;\n+ }\n+ \n+ div.download {\n+\tfloat: right;\n+ }\n+ \n+ div.caption-container {\n+\tposition: relative;\n+\tclear: left;\n+\theight: 75px;\n+ }\n+ span.image-caption {\n+\tdisplay: block;\n+\tposition: absolute;\n+\twidth: 550px;\n+\ttop: 0;\n+\tleft: 0;\n+ }\n+ div.caption {\n+\tpadding: 12px;\n+ }\n+\n+ /* Featurettes\n+ ------------------------- */\n+\n+ .featurette {\n+ padding-top: 20px; /* Vertica'..b' */\n+ overflow: hidden; /* Vertically center images part 2: clear their floats. */\n+ text-align: center;\n+ }\n+\n+ .featurette-p\n+ {\n+ text-align: left;\n+ }\n+\n+ .featurette-image {\n+ margin-top: 10px; /* Vertically center images part 3: negative margin up the image the same amount of the padding to center it. */\n+ width: 450px;\n+ height: auto;\n+ }\n+\n+ </style>\n+ <link href="css/bootstrap-responsive.css" rel="stylesheet">\n+ </head>\n+ <body>\n+ \n+\t\t\t\t\t<div align="center">\n+\t\t\t\t\t<h2>FW</h2>\n+\t\t\t\t\t<p> <img class="featurette-image" src="FW/histogram.png"/></p>\n+\t\t\t\t\t<p><a href="FW/overlap_size.txt">ping pong signature</a></p>\n+\t\t\t\t\t<p><a href="FW/sensPPP.txt">sense reads with PPP</a></p>\n+\t\t\t\t\t<p><a href="FW/antisensPPP.txt">reverse reads with PPP</a></p>\n+\t\t\t\t\t<p><a href="FW/sens.txt">sense reads without PPP</a></p>\n+\t\t\t\t\t<p><a href="FW/antisens.txt">reverse reads without PPP</a></p>\n+\t\t\t\t\t</div>\n+ <!-- FOOTER -->\n+ <div class="container">\n+ <footer>\n+ \n+ </footer>\n+ </div>\n+ <!-- Le javascript\n+ ================================================== -->\n+ <!-- Placed at the end of the document so the pages load faster -->\n+ <script type="text/javascript" src="js/filter.js"></script>\n+ <script type="text/javascript" src="js/jquery.js"></script>\n+ <script type="text/javascript" src="js/jquery-1.3.2.js"></script>\n+ <script type="text/javascript" src="js/jquery.galleriffic.js"></script>\n+ <script type="text/javascript" src="js/jquery.opacityrollover.js"></script>\n+ <script type="text/javascript" src="js/bootstrap-table.js"></script>\n+ <script type="text/javascript" src="js/bootstrap.min.js"></script>\n+ <script type="text/javascript">\n+ jQuery(document).ready(function($) {\n+ // We only want these styles applied when javascript is enabled\n+ $(\'div.navigation\').css({\'width\' : \'300px\', \'float\' : \'left\'});\n+ $(\'div.content\').css(\'display\', \'block\');\n+ \n+ $(".each-gallery").each(function(i){\n+ // Initially set opacity on thumbs and add\n+ // additional styling for hover effect on thumbs\n+ var onMouseOutOpacity = 0.67;\n+ $(\'#thumbs + i + ul.thumbs li\').opacityrollover({\n+ mouseOutOpacity: onMouseOutOpacity,\n+ mouseOverOpacity: 1.0,\n+ fadeSpeed: \'fast\',\n+ exemptionSelector: \'.selected\'\n+ });\n+ \n+ // Initialize Advanced Galleriffic Gallery\n+ var gallery = $(\'#thumbs\'+i).galleriffic({\n+ delay: 2500,\n+ numThumbs: 22,\n+ preloadAhead: 10,\n+ enableTopPager: true,\n+ enableBottomPager: true,\n+ maxPagesToShow: 7,\n+ imageContainerSel: \'#slideshow\'+ i,\n+ controlsContainerSel: \'#controls\' + i,\n+ captionContainerSel: \'#caption\' + i,\n+ loadingContainerSel: \'#loading\' + i,\n+ renderSSControls: true,\n+ renderNavControls: true,\n+ playLinkText: \'Play\',\n+ pauseLinkText: \'Pause\',\n+ prevLinkText: \'‹ Previous\',\n+ nextLinkText: \'Next ›\',\n+ nextPageLinkText: \'Next ›\',\n+ prevPageLinkText: \'‹ Prev\',\n+ enableHistory: false,\n+ autoStart: false,\n+ syncTransitions: true,\n+ defaultTransitionDuration: 900,\n+ onSlideChange: function(prevIndex, nextIndex) {\n+ // \'this\' refers to the gallery, which is an extension of $(\'#thumbs\')\n+ this.find(\'ul.thumbs\').children()\n+ .eq(prevIndex).fadeTo(\'fast\', onMouseOutOpacity).end()\n+ .eq(nextIndex).fadeTo(\'fast\', 1.0);\n+ },\n+ onPageTransitionOut: function(callback) {\n+ this.fadeTo(\'fast\', 0.0, callback);\n+ },\n+ onPageTransitionIn: function() {\n+ this.fadeTo(\'fast\', 1.0);\n+ }\n+ });\n+ });\n+ });\n+ </script>\n+ </body>\n+ </html>\n+ \n\\ No newline at end of file\n' |
| b |
| diff -r 9645d995fb3c -r 9185ca0a7b43 test-data/res_files/reads-sample-small.fastq/subgroups/PPPartners/FW/antisens.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/res_files/reads-sample-small.fastq/subgroups/PPPartners/FW/antisens.txt Wed Jan 16 08:18:13 2019 -0500 |
| b |
| b'@@ -0,0 +1,2902 @@\n+>218|16|FW|1\n+TGAATTGAGAGTCGGCGTTCGTCAT\n+>219|16|FW|34\n+TGAATTGAGAGTCGGCGTTCGTCA\n+>220|16|FW|17\n+TGAATTGAGAGTCGGCGTTCGTC\n+>223|16|FW|1\n+CGCTGAATTGAGAGTCGGCGTTC\n+>224|16|FW|1\n+GTTGCGCTGAATTGAGAGTCGGCGTT\n+>224|16|FW|1\n+TGCGCTGAATTGAGAGTCGGCGTT\n+>226|16|FW|2\n+TGTTGCGCTGAATTGAGAGTCGGCG\n+>226|16|FW|5\n+GTTGCGCTGAATTGAGAGTCGGCG\n+>227|16|FW|1\n+TGTTGCGCTGAATTGAGAGTCGGC\n+>228|16|FW|1\n+GTTGTTGCGCTGAATTGAGAGTCGG\n+>228|16|FW|2\n+TTGTTGCGCTGAATTGAGAGTCGG\n+>228|16|FW|4\n+TGTTGCGCTGAATTGAGAGTCGG\n+>230|16|FW|1\n+CGTTGTTGCGCTGAATTGAGAGTC\n+>233|16|FW|1\n+TACGCGTTGTTGCGCTGAATTGAGA\n+>237|16|FW|14\n+GAAGTACGCGTTGTTGCGCTGAATT\n+>238|16|FW|2\n+AGAAGTACGCGTTGTTGCGCTGAAT\n+>238|16|FW|2\n+GAAGTACGCGTTGTTGCGCTGAAT\n+>239|16|FW|1\n+GAAGTACGCGTTGTTGCGCTGAA\n+>240|16|FW|3\n+GGAGAAGTACGCGTTGTTGCGCTGA\n+>241|16|FW|8\n+TAGGAGAAGTACGCGTTGTTGCGCTG\n+>241|16|FW|3\n+GGAGAAGTACGCGTTGTTGCGCTG\n+>242|16|FW|6\n+TAGGAGAAGTACGCGTTGTTGCGCT\n+>243|16|FW|3\n+CGTAGGAGAAGTACGCGTTGTTGCGC\n+>243|16|FW|1\n+TAGGAGAAGTACGCGTTGTTGCGC\n+>245|16|FW|9\n+CGTAGGAGAAGTACGCGTTGTTGC\n+>246|16|FW|2\n+CGTAGGAGAAGTACGCGTTGTTG\n+>250|16|FW|1\n+TGAGACGTAGGAGAAGTACGCGTT\n+>256|16|FW|1\n+TTGTCGGTGAGACGTAGGAGAAGTA\n+>257|16|FW|1\n+TTGTCGGTGAGACGTAGGAGAAGT\n+>258|16|FW|2\n+TTGTCGGTGAGACGTAGGAGAAG\n+>259|16|FW|1\n+GATTGTCGGTGAGACGTAGGAGAA\n+>259|16|FW|1\n+ATTGTCGGTGAGACGTAGGAGAA\n+>268|16|FW|1\n+TCTGCGTTTGGGATTGTCGGTGAGAC\n+>269|16|FW|6\n+TCTGCGTTTGGGATTGTCGGTGAGA\n+>272|16|FW|1\n+TGTCTGCGTTTGGGATTGTCGGTG\n+>273|16|FW|1\n+TGTCTGCGTTTGGGATTGTCGGT\n+>276|16|FW|1\n+CGATGTCTGCGTTTGGGATTGTC\n+>286|16|FW|1\n+TTATTGACCGCTCGATGTCTGCGTT\n+>286|16|FW|7\n+TATTGACCGCTCGATGTCTGCGTT\n+>287|16|FW|1\n+TATTGACCGCTCGATGTCTGCGT\n+>291|16|FW|3\n+TATGGGTTATTGACCGCTCGATGTCT\n+>292|16|FW|1\n+TATGGGTTATTGACCGCTCGATGTC\n+>292|16|FW|1\n+ATGGGTTATTGACCGCTCGATGTC\n+>293|16|FW|1\n+TATGGGTTATTGACCGCTCGATGT\n+>294|16|FW|1\n+GCTATGGGTTATTGACCGCTCGATG\n+>294|16|FW|1\n+TATGGGTTATTGACCGCTCGATG\n+>298|16|FW|5\n+CCTGGGCTATGGGTTATTGACCGCTC\n+>298|16|FW|2\n+CTGGGCTATGGGTTATTGACCGCTC\n+>298|16|FW|2\n+TGGGCTATGGGTTATTGACCGCTC\n+>299|16|FW|27\n+TCCTGGGCTATGGGTTATTGACCGCT\n+>299|16|FW|24\n+CCTGGGCTATGGGTTATTGACCGCT\n+>299|16|FW|3\n+CTGGGCTATGGGTTATTGACCGCT\n+>300|16|FW|2\n+TTCCTGGGCTATGGGTTATTGACCGC\n+>300|16|FW|5\n+TCCTGGGCTATGGGTTATTGACCGC\n+>300|16|FW|1\n+CCTGGGCTATGGGTTATTGACCGC\n+>300|16|FW|2\n+CTGGGCTATGGGTTATTGACCGC\n+>301|16|FW|6\n+TCCTGGGCTATGGGTTATTGACCG\n+>301|16|FW|2\n+CCTGGGCTATGGGTTATTGACCG\n+>302|16|FW|2\n+TTTCCTGGGCTATGGGTTATTGACC\n+>302|16|FW|4\n+TTCCTGGGCTATGGGTTATTGACC\n+>302|16|FW|9\n+TCCTGGGCTATGGGTTATTGACC\n+>303|16|FW|2\n+TTTCCTGGGCTATGGGTTATTGAC\n+>303|16|FW|1\n+TTCCTGGGCTATGGGTTATTGAC\n+>315|16|FW|1\n+GTAGAAGAAGGTTTCCTGGGCTA\n+>319|16|FW|1\n+TGTTGGTAGAAGAAGGTTTCCTGG\n+>323|16|FW|6\n+TGATTTGTTGGTAGAAGAAGGTTTC\n+>324|16|FW|7\n+TGATTTGTTGGTAGAAGAAGGTTT\n+>325|16|FW|1\n+TTGATTTGTTGGTAGAAGAAGGTT\n+>325|16|FW|22\n+TGATTTGTTGGTAGAAGAAGGTT\n+>327|16|FW|1\n+TTCTTGATTTGTTGGTAGAAGAAGG\n+>330|16|FW|1\n+TTTCTTGATTTGTTGGTAGAAGA\n+>365|16|FW|1\n+CGGAGCCAATAGAGCGGGAGAGC\n+>367|16|FW|1\n+CTGTCGGAGCCAATAGAGCGGGAGA\n+>369|16|FW|24\n+TTCTGTCGGAGCCAATAGAGCGGGA\n+>371|16|FW|1\n+TTCTGTCGGAGCCAATAGAGCGG\n+>376|16|FW|1\n+TAGCGGGGCTTCTGTCGGAGCCAATAG\n+>378|16|FW|1\n+AGCGGGGCTTCTGTCGGAGCCAAT\n+>379|16|FW|1\n+TAGCGGGGCTTCTGTCGGAGCCAA\n+>381|16|FW|2\n+GGTAGCGGGGCTTCTGTCGGAGCC\n+>382|16|FW|1\n+GGTAGCGGGGCTTCTGTCGGAGC\n+>390|16|FW|1\n+TTGTTGGAGGTAGCGGGGCTTCT\n+>391|16|FW|6\n+TGTTGTTGGAGGTAGCGGGGCTTC\n+>392|16|FW|1\n+TTGTTGTTGGAGGTAGCGGGGCTT\n+>392|16|FW|4\n+TGTTGTTGGAGGTAGCGGGGCTT\n+>398|16|FW|1\n+TCCAGCTGTTGTTGTTGGAGGTAGCG\n+>407|16|FW|2\n+TCCCTCTCCAGCTGTTGTTGTTG\n+>410|16|FW|1\n+CGGTCCCTCTCCAGCTGTTGTTG\n+>416|16|FW|3\n+GCGGGCTGCCGGTCCCTCTCCAGCTG\n+>416|16|FW|1\n+CGGGCTGCCGGTCCCTCTCCAGCTG\n+>417|16|FW|1\n+GCGGGCTGCCGGTCCCTCTCCAGCT\n+>418|16|FW|3\n+GCGGGCTGCCGGTCCCTCTCCAGC\n+>419|16|FW|1\n+GCGGGCTGCCGGTCCCTCTCCAG\n+>433|16|FW|5\n+GCCGATGACGAGGCAGAGCGGGCTGC\n+>433|16|FW|8\n+GATGACGAGGCAGAGCGGGCTGC\n+>435|16|FW|1\n+GCAGCCGATGACGAGGCAGAGCGGGCT\n+>435|16|FW|1\n+GCCGATGACGAGGCAGAGCGGGCT\n+>436|16|FW|1\n+GCAGCCGATGACGAGGCAGAGCGGGC\n+>436|16|FW|4\n+GCCGATGACGAGGCAGAGCGGGC\n+>444|16|FW|1\n+GAGCGGGTGCAGC'..b'ATTGCTGTTGCTGGC\n+>4283|16|FW|1\n+TGATGTCAATATTGCTGTTGCTG\n+>4284|16|FW|2\n+TGAATGATGTCAATATTGCTGTTGCT\n+>4284|16|FW|1\n+GAATGATGTCAATATTGCTGTTGCT\n+>4284|16|FW|3\n+AATGATGTCAATATTGCTGTTGCT\n+>4285|16|FW|19\n+TGAATGATGTCAATATTGCTGTTGC\n+>4285|16|FW|2\n+GAATGATGTCAATATTGCTGTTGC\n+>4285|16|FW|1\n+AATGATGTCAATATTGCTGTTGC\n+>4286|16|FW|7\n+TGAATGATGTCAATATTGCTGTTG\n+>4286|16|FW|2\n+GAATGATGTCAATATTGCTGTTG\n+>4288|16|FW|2\n+TCGCTGAATGATGTCAATATTGCTGT\n+>4289|16|FW|1\n+TCGCTGAATGATGTCAATATTGCTG\n+>4291|16|FW|1\n+TGCTCGCTGAATGATGTCAATATTGC\n+>4291|16|FW|1\n+CTCGCTGAATGATGTCAATATTGC\n+>4291|16|FW|1\n+TCGCTGAATGATGTCAATATTGC\n+>4292|16|FW|1\n+GCTCGCTGAATGATGTCAATATTG\n+>4299|16|FW|2\n+TGATTGTGCTCGCTGAATGATGTC\n+>4300|16|FW|1\n+TTTGATTGTGCTCGCTGAATGATGT\n+>4301|16|FW|1\n+TTTGATTGTGCTCGCTGAATGATG\n+>4318|16|FW|2\n+TGATGGTTCTCAGAATCTTTGATT\n+>4345|16|FW|1\n+TTCACTCCGAACGTACCACGGTGCCC\n+>4345|16|FW|3\n+TCACTCCGAACGTACCACGGTGCCC\n+>4354|16|FW|1\n+TTTGGATGTTTTCACTCCGAACGTACC\n+>4354|16|FW|1\n+TGGATGTTTTCACTCCGAACGTACC\n+>4360|16|FW|1\n+GTCTCTTTGGATGTTTTCACTCCGAA\n+>4360|16|FW|1\n+TCTCTTTGGATGTTTTCACTCCGAA\n+>4365|16|FW|2\n+TAAGTCTCTTTGGATGTTTTCACT\n+>4381|16|FW|3\n+TAACTGATGGGATATTTAAGTCTC\n+>4384|16|FW|3\n+TTGGTAACTGATGGGATATTTAAGT\n+>4386|16|FW|1\n+GTTGGTAACTGATGGGATATTTAA\n+>4389|16|FW|8\n+TTGCGTTGGTAACTGATGGGATATT\n+>4389|16|FW|8\n+TGCGTTGGTAACTGATGGGATATT\n+>4390|16|FW|1\n+ATTGCGTTGGTAACTGATGGGATAT\n+>4390|16|FW|12\n+TTGCGTTGGTAACTGATGGGATAT\n+>4390|16|FW|3\n+TGCGTTGGTAACTGATGGGATAT\n+>4391|16|FW|2\n+GATTGCGTTGGTAACTGATGGGATA\n+>4391|16|FW|1\n+ATTGCGTTGGTAACTGATGGGATA\n+>4391|16|FW|13\n+TTGCGTTGGTAACTGATGGGATA\n+>4392|16|FW|3\n+TGATTGCGTTGGTAACTGATGGGAT\n+>4392|16|FW|12\n+GATTGCGTTGGTAACTGATGGGAT\n+>4392|16|FW|3\n+ATTGCGTTGGTAACTGATGGGAT\n+>4393|16|FW|48\n+TGATTGCGTTGGTAACTGATGGGA\n+>4393|16|FW|32\n+GATTGCGTTGGTAACTGATGGGA\n+>4396|16|FW|1\n+TCCGTGATTGCGTTGGTAACTGATG\n+>4397|16|FW|2\n+TCCGTGATTGCGTTGGTAACTGAT\n+>4397|16|FW|1\n+CCGTGATTGCGTTGGTAACTGAT\n+>4398|16|FW|7\n+TTCCGTGATTGCGTTGGTAACTGA\n+>4398|16|FW|3\n+TCCGTGATTGCGTTGGTAACTGA\n+>4402|16|FW|1\n+TTCCTTAAGTTCCGTGATTGCGTTGGTAA\n+>4403|16|FW|1\n+CTTAAGTTCCGTGATTGCGTTGGTA\n+>4407|16|FW|1\n+TTCCTTAAGTTCCGTGATTGCGTT\n+>4408|16|FW|1\n+TTTCCTTAAGTTCCGTGATTGCGT\n+>4416|16|FW|8\n+TATGGTATTTTTCCTTAAGTTCCGT\n+>4417|16|FW|6\n+TATGGTATTTTTCCTTAAGTTCCG\n+>4457|16|FW|1\n+TAGACCTCGCGCTAGGTGGTTGGGG\n+>4463|16|FW|1\n+GCTGGATTAGACCTCGCGCTAGGTGG\n+>4465|16|FW|2\n+GCTGGATTAGACCTCGCGCTAGGT\n+>4466|16|FW|4\n+AGCTGGATTAGACCTCGCGCTAGG\n+>4466|16|FW|2\n+GCTGGATTAGACCTCGCGCTAGG\n+>4468|16|FW|1\n+CTGAGCTGGATTAGACCTCGCGCTA\n+>4468|16|FW|5\n+TGAGCTGGATTAGACCTCGCGCTA\n+>4469|16|FW|1\n+CTGAGCTGGATTAGACCTCGCGCT\n+>4472|16|FW|4\n+GCTGCTGAGCTGGATTAGACCTCGC\n+>4475|16|FW|6\n+AACGGCTGCTGAGCTGGATTAGACCT\n+>4475|16|FW|5\n+ACGGCTGCTGAGCTGGATTAGACCT\n+>4476|16|FW|2\n+GAACGGCTGCTGAGCTGGATTAGACC\n+>4476|16|FW|6\n+AACGGCTGCTGAGCTGGATTAGACC\n+>4476|16|FW|4\n+ACGGCTGCTGAGCTGGATTAGACC\n+>4486|16|FW|3\n+CGGAGACGGGAACGGCTGCTGAGCT\n+>4489|16|FW|1\n+CGCCGGAGACGGGAACGGCTGCTGA\n+>4494|16|FW|1\n+TCCTTTCGCCGGAGACGGGAACGGCT\n+>4494|16|FW|1\n+CCTTTCGCCGGAGACGGGAACGGCT\n+>4498|16|FW|3\n+TAGGTCCTTTCGCCGGAGACGGGAAC\n+>4498|16|FW|1\n+GGTCCTTTCGCCGGAGACGGGAAC\n+>4500|16|FW|1\n+GTAGGTCCTTTCGCCGGAGACGGGA\n+>4500|16|FW|1\n+TAGGTCCTTTCGCCGGAGACGGGA\n+>4502|16|FW|4\n+TTGGTAGGTCCTTTCGCCGGAGACGG\n+>4503|16|FW|1\n+TTGGTAGGTCCTTTCGCCGGAGACG\n+>4504|16|FW|4\n+TTGGTAGGTCCTTTCGCCGGAGAC\n+>4505|16|FW|3\n+GTTGGTAGGTCCTTTCGCCGGAGA\n+>4505|16|FW|1\n+TTGGTAGGTCCTTTCGCCGGAGA\n+>4506|16|FW|1\n+GTTGGTAGGTCCTTTCGCCGGAG\n+>4509|16|FW|1\n+GCTGGGTTGGTAGGTCCTTTCGCCG\n+>4510|16|FW|4\n+GCTGGGTTGGTAGGTCCTTTCGCC\n+>4510|16|FW|1\n+CTGGGTTGGTAGGTCCTTTCGCC\n+>4511|16|FW|6\n+CGCTGGGTTGGTAGGTCCTTTCGC\n+>4511|16|FW|2\n+GCTGGGTTGGTAGGTCCTTTCGC\n+>4512|16|FW|1\n+TCGCTGGGTTGGTAGGTCCTTTCG\n+>4512|16|FW|1\n+CGCTGGGTTGGTAGGTCCTTTCG\n+>4513|16|FW|4\n+TTCGCTGGGTTGGTAGGTCCTTTC\n+>4515|16|FW|5\n+TATTCGCTGGGTTGGTAGGTCCTT\n+>4515|16|FW|1\n+ATTCGCTGGGTTGGTAGGTCCTT\n+>4516|16|FW|4\n+TATTCGCTGGGTTGGTAGGTCCT\n+>4517|16|FW|2\n+TTTATTCGCTGGGTTGGTAGGTCC\n+>4522|16|FW|1\n+TAATAATTTATTCGCTGGGTTGGTA\n+>4547|16|FW|1\n+CAACTGTTCTATGTTTAAACGGCCC\n+>4558|16|FW|1\n+TATTATTTTTCCAACTGTTCTATGT\n' |
| b |
| diff -r 9645d995fb3c -r 9185ca0a7b43 test-data/res_files/reads-sample-small.fastq/subgroups/PPPartners/FW/antisensPPP.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/res_files/reads-sample-small.fastq/subgroups/PPPartners/FW/antisensPPP.txt Wed Jan 16 08:18:13 2019 -0500 |
| b |
| b'@@ -0,0 +1,720 @@\n+>237|16|FW|1\n+GAGAAGTACGCGTTGTTGCGCTGAATT\n+>240|16|FW|2\n+GAGAAGTACGCGTTGTTGCGCTGA\n+>241|16|FW|7\n+GAGAAGTACGCGTTGTTGCGCTG\n+>265|16|FW|3\n+TGCGTTTGGGATTGTCGGTGAGACGTA\n+>267|16|FW|70\n+TGCGTTTGGGATTGTCGGTGAGACG\n+>267|16|FW|1\n+GCGTTTGGGATTGTCGGTGAGACG\n+>268|16|FW|82\n+TGCGTTTGGGATTGTCGGTGAGAC\n+>269|16|FW|71\n+TGCGTTTGGGATTGTCGGTGAGA\n+>276|16|FW|6\n+TCGATGTCTGCGTTTGGGATTGTC\n+>277|16|FW|1\n+TCGATGTCTGCGTTTGGGATTGT\n+>367|16|FW|1\n+TCTGTCGGAGCCAATAGAGCGGGAGA\n+>369|16|FW|22\n+TCTGTCGGAGCCAATAGAGCGGGA\n+>370|16|FW|1\n+TCTGTCGGAGCCAATAGAGCGGG\n+>422|16|FW|1\n+CAGAGCGGGCTGCCGGTCCCTCTC\n+>434|16|FW|1\n+CGATGACGAGGCAGAGCGGGCTG\n+>436|16|FW|3\n+TGCAGCCGATGACGAGGCAGAGCGGGC\n+>447|16|FW|1\n+TGAGCGGGTGCAGCCGATGACGAG\n+>448|16|FW|1\n+TGAGCGGGTGCAGCCGATGACGA\n+>487|16|FW|1\n+TATTGCTAGCGGTTTTGCTTTCGC\n+>531|16|FW|1\n+TGTTTACGTTTTCGTTTTGTTTTGCT\n+>532|16|FW|3\n+TGTTTACGTTTTCGTTTTGTTTTGC\n+>613|16|FW|6\n+ATCTGAATTTTCCGGGCTGAGCTT\n+>614|16|FW|6\n+ATCTGAATTTTCCGGGCTGAGCT\n+>660|16|FW|1\n+TTGATCAAGGTAGAGTTGTCGCGT\n+>660|16|FW|1\n+TGATCAAGGTAGAGTTGTCGCGT\n+>663|16|FW|4\n+TTTTTGATCAAGGTAGAGTTGTCG\n+>664|16|FW|11\n+TTTTTGATCAAGGTAGAGTTGTC\n+>687|16|FW|4\n+TCTGTTGGTATTTGCAGGGGCTACA\n+>688|16|FW|9\n+TCTGTTGGTATTTGCAGGGGCTAC\n+>689|16|FW|1\n+TCTGTTGGTATTTGCAGGGGCTA\n+>698|16|FW|1\n+GCAAGGCAAATCTGTTGGTATTTG\n+>706|16|FW|1\n+TATCTACCAGCAAGGCAAATCTGTT\n+>707|16|FW|1\n+TATCTACCAGCAAGGCAAATCTGT\n+>740|16|FW|8\n+TATCAACGGATCCCAGCGGCACGT\n+>814|16|FW|4\n+TCAAAGTATTTACAAGACGGCTTGT\n+>815|16|FW|14\n+TCAAAGTATTTACAAGACGGCTTG\n+>816|16|FW|38\n+TCAAAGTATTTACAAGACGGCTT\n+>886|16|FW|25\n+TGAAGTTTGATTTCGTTGATAGTACC\n+>888|16|FW|1\n+TGAAGTTTGATTTCGTTGATAGTA\n+>893|16|FW|3\n+TTCGTCTGAAGTTTGATTTCGTTGA\n+>900|16|FW|1\n+CTCCGTTTTCGTCTGAAGTTTGATT\n+>943|16|FW|1\n+TTTTTGTGCGGTAAAATAGTTTGT\n+>966|16|FW|2\n+TAAGCTGGTAGGTGTAGAAGCCTATT\n+>967|16|FW|3\n+TAAGCTGGTAGGTGTAGAAGCCTAT\n+>968|16|FW|1\n+TTTTAAGCTGGTAGGTGTAGAAGCCTA\n+>968|16|FW|3\n+TTTAAGCTGGTAGGTGTAGAAGCCTA\n+>968|16|FW|4\n+TAAGCTGGTAGGTGTAGAAGCCTA\n+>969|16|FW|14\n+TTTTAAGCTGGTAGGTGTAGAAGCCT\n+>969|16|FW|41\n+TTTAAGCTGGTAGGTGTAGAAGCCT\n+>969|16|FW|7\n+TAAGCTGGTAGGTGTAGAAGCCT\n+>970|16|FW|21\n+TTTTAAGCTGGTAGGTGTAGAAGCC\n+>970|16|FW|16\n+TTTAAGCTGGTAGGTGTAGAAGCC\n+>971|16|FW|7\n+TTTTAAGCTGGTAGGTGTAGAAGC\n+>971|16|FW|3\n+TTTAAGCTGGTAGGTGTAGAAGC\n+>1014|16|FW|5\n+TCAGACTCAATGCCCTTCAGGACT\n+>1015|16|FW|1\n+TCAGACTCAATGCCCTTCAGGAC\n+>1017|16|FW|5\n+TAACATCAGACTCAATGCCCTTCAGG\n+>1018|16|FW|2\n+TAACATCAGACTCAATGCCCTTCAG\n+>1019|16|FW|2\n+TAACATCAGACTCAATGCCCTTCA\n+>1020|16|FW|1\n+TAACATCAGACTCAATGCCCTTC\n+>1137|16|FW|11\n+TTCTGGTTCAAGCTCAATCTTGAAG\n+>1138|16|FW|9\n+TTCTGGTTCAAGCTCAATCTTGAA\n+>1139|16|FW|8\n+TTCTGGTTCAAGCTCAATCTTGA\n+>1179|16|FW|1\n+TTGTAAATTGGGTGAACCTCGTTT\n+>1179|16|FW|1\n+TGTAAATTGGGTGAACCTCGTTT\n+>1180|16|FW|1\n+TTGTAAATTGGGTGAACCTCGTT\n+>1183|16|FW|5\n+GAGTTTGTAAATTGGGTGAACCTC\n+>1184|16|FW|4\n+GAGTTTGTAAATTGGGTGAACCT\n+>1202|16|FW|1\n+TACGGTGCAAAAGGAGCTGGAGTT\n+>1203|16|FW|3\n+TACGGTGCAAAAGGAGCTGGAGT\n+>1204|16|FW|1\n+TCCTACGGTGCAAAAGGAGCTGGAG\n+>1229|16|FW|4\n+CGTTTGTGCGGCTCTTCTACCGTGA\n+>1230|16|FW|2\n+CGTTTGTGCGGCTCTTCTACCGTG\n+>1231|16|FW|1\n+CGTTTGTGCGGCTCTTCTACCGT\n+>1278|16|FW|1\n+TGACCTCGTGTGGCCATACTCTTGGCAG\n+>1278|16|FW|1\n+CCTCGTGTGGCCATACTCTTGGCAG\n+>1279|16|FW|5\n+TGACCTCGTGTGGCCATACTCTTGGCA\n+>1280|16|FW|2\n+TGACCTCGTGTGGCCATACTCTTGGC\n+>1281|16|FW|3\n+TGACCTCGTGTGGCCATACTCTTGG\n+>1282|16|FW|5\n+TGACCTCGTGTGGCCATACTCTTG\n+>1283|16|FW|1\n+TGACCTCGTGTGGCCATACTCTT\n+>1411|16|FW|4\n+TGTAGTTTGCTGTGTGATTGCCCCC\n+>1412|16|FW|12\n+TGTAGTTTGCTGTGTGATTGCCCC\n+>1413|16|FW|11\n+TGTAGTTTGCTGTGTGATTGCCC\n+>1537|16|FW|7\n+TTTCGAGAAAATTACTTCAGGATT\n+>1599|16|FW|6\n+TAAAACGTTAGCAAATGTTGTCTTG\n+>1673|16|FW|1\n+TTGTTGTGTGTCTAATTTTGTGTGCA\n+>1676|16|FW|2\n+TTGTTGTGTGTCTAATTTTGTGT\n+>1836|16|FW|81\n+TATTTGATTGTTGGGCTACAAGCATT\n+>1837|16|FW|13\n+TATTTGATTGTTGGGCTACAAGCAT\n+>1838|16|FW|130\n+TATTTGATTGTTGGGCTACAAGCA\n+>1839|16|FW|34\n+TATTTGATTGTTGGGCTACAAGC\n+>1890|16|FW|1\n+TGCGCTGTGAAACGCCATTGGCGTTCCA\n+>1893|16|FW|5\n+TGCGCTGTGAAACGCCATTGGCGTT\n+>1894|16|FW|2\n+TGCGCTGTGAAACGCCATTGGCGT\n+>1936|16|FW|2\n+TACGTCGATATGCTTCTCATGTAGGA\n+>1937|16|FW|15\n+TACGTCGATATGCTTCTCATGT'..b'AGACTTATTGGTCTGTAAG\n+>3395|16|FW|10\n+TGAGAGTAGACTTATTGGTCTGTAA\n+>3396|16|FW|12\n+TGAGAGTAGACTTATTGGTCTGTA\n+>3397|16|FW|1\n+TGAGAGTAGACTTATTGGTCTGT\n+>3455|16|FW|1\n+GTATATCAGATGTTGATTAAGTCGG\n+>3456|16|FW|3\n+GTATATCAGATGTTGATTAAGTCG\n+>3521|16|FW|1\n+TTCACCTGTTCAATGGTTCCGTGG\n+>3524|16|FW|1\n+TACGATTCACCTGTTCAATGGTTCCG\n+>3525|16|FW|1\n+TACGATTCACCTGTTCAATGGTTCC\n+>3526|16|FW|1\n+TACGATTCACCTGTTCAATGGTTC\n+>3554|16|FW|2\n+TTCAAATGCAGTTCTTATTTCCGTT\n+>3555|16|FW|4\n+TTCAAATGCAGTTCTTATTTCCGT\n+>3556|16|FW|1\n+TTCAAATGCAGTTCTTATTTCCG\n+>3599|16|FW|1\n+TGCTTGGGATACGTCTAAAAATACT\n+>3600|16|FW|1\n+TGCTTGGGATACGTCTAAAAATAC\n+>3603|16|FW|9\n+CGAATGCTTGGGATACGTCTAAAAA\n+>3604|16|FW|1\n+CGAATGCTTGGGATACGTCTAAAA\n+>3605|16|FW|2\n+CGAATGCTTGGGATACGTCTAAA\n+>3608|16|FW|1\n+TTTGTCGAATGCTTGGGATACGTCT\n+>3609|16|FW|8\n+TTTGTCGAATGCTTGGGATACGTC\n+>3688|16|FW|1\n+TAGAGGTAAGACTTTAGAAGTTTGT\n+>3689|16|FW|2\n+TAGAGGTAAGACTTTAGAAGTTTG\n+>3690|16|FW|23\n+TAGAGGTAAGACTTTAGAAGTTT\n+>3744|16|FW|5\n+AATTGTATGAACAGTGGAAGTGGC\n+>3745|16|FW|7\n+AATTGTATGAACAGTGGAAGTGG\n+>3799|16|FW|5\n+TGTATAGATGAGGTATAAGGTTGGCC\n+>3800|16|FW|5\n+TGTATAGATGAGGTATAAGGTTGGC\n+>3801|16|FW|2\n+TGTATAGATGAGGTATAAGGTTGG\n+>3802|16|FW|6\n+TGTATAGATGAGGTATAAGGTTG\n+>3843|16|FW|1\n+AAATGTGGATACCGTTAAGCGACT\n+>3844|16|FW|1\n+AAATGTGGATACCGTTAAGCGAC\n+>3900|16|FW|2\n+CTGTGCTGTAGCTTGGATAGGGGA\n+>3900|16|FW|26\n+TGTGCTGTAGCTTGGATAGGGGA\n+>3949|16|FW|4\n+TATTCGCCAGTCAGAGAGCCACTTCT\n+>3950|16|FW|15\n+TATTCGCCAGTCAGAGAGCCACTTC\n+>3952|16|FW|24\n+TATTCGCCAGTCAGAGAGCCACT\n+>3967|16|FW|1\n+TTTTTGCTCGTTTACTTTTATTCGCC\n+>3996|16|FW|5\n+TGTTTAGCGTAAACGTCACGTGCTT\n+>3997|16|FW|14\n+TGTTTAGCGTAAACGTCACGTGCT\n+>4023|16|FW|1\n+TTCAACAAGAGCGGAGGACAGTCTTG\n+>4023|16|FW|2\n+TCAACAAGAGCGGAGGACAGTCTTG\n+>4023|16|FW|1\n+AACAAGAGCGGAGGACAGTCTTG\n+>4024|16|FW|1\n+TTCAACAAGAGCGGAGGACAGTCTT\n+>4025|16|FW|30\n+TTCAACAAGAGCGGAGGACAGTCT\n+>4025|16|FW|11\n+TCAACAAGAGCGGAGGACAGTCT\n+>4027|16|FW|1\n+CTGTTCAACAAGAGCGGAGGACAGT\n+>4030|16|FW|1\n+TGCTGTTCAACAAGAGCGGAGGAC\n+>4083|16|FW|1\n+TTCTGTCAAGGTGTACTCCTAGGTA\n+>4085|16|FW|5\n+TCTTCTGTCAAGGTGTACTCCTAGG\n+>4085|16|FW|4\n+TTCTGTCAAGGTGTACTCCTAGG\n+>4086|16|FW|1\n+TCTTCTGTCAAGGTGTACTCCTAG\n+>4090|16|FW|3\n+TGAGTCTTCTGTCAAGGTGTACTC\n+>4091|16|FW|1\n+TGTGAGTCTTCTGTCAAGGTGTACT\n+>4134|16|FW|3\n+GAGTTTAAGTTGGGTTTTTTTGGC\n+>4148|16|FW|27\n+TAAGTTGTTGGCTTTGAGTTTAAGT\n+>4149|16|FW|53\n+TAAGTTGTTGGCTTTGAGTTTAAG\n+>4150|16|FW|3\n+TAAGTTGTTGGCTTTGAGTTTAA\n+>4183|16|FW|2\n+TAGGCTGAGCGGAGAACCAGAGTTGA\n+>4185|16|FW|4\n+TAGGCTGAGCGGAGAACCAGAGTT\n+>4186|16|FW|4\n+TAGGCTGAGCGGAGAACCAGAGT\n+>4216|16|FW|1\n+CAATATAGAATTGTAGAGCAAGACCT\n+>4218|16|FW|1\n+CAATATAGAATTGTAGAGCAAGAC\n+>4227|16|FW|1\n+GATTGGTTTCAATATAGAATTGTA\n+>4308|16|FW|4\n+TCAGAATCTTTGATTGTGCTCGCTG\n+>4309|16|FW|3\n+TCTCAGAATCTTTGATTGTGCTCGCT\n+>4309|16|FW|7\n+CTCAGAATCTTTGATTGTGCTCGCT\n+>4309|16|FW|128\n+TCAGAATCTTTGATTGTGCTCGCT\n+>4310|16|FW|1\n+TCTCAGAATCTTTGATTGTGCTCGC\n+>4310|16|FW|1\n+CTCAGAATCTTTGATTGTGCTCGC\n+>4310|16|FW|6\n+TCAGAATCTTTGATTGTGCTCGC\n+>4311|16|FW|1\n+CTCAGAATCTTTGATTGTGCTCG\n+>4312|16|FW|1\n+GTTCTCAGAATCTTTGATTGTGCTC\n+>4312|16|FW|4\n+TTCTCAGAATCTTTGATTGTGCTC\n+>4313|16|FW|1\n+GGTTCTCAGAATCTTTGATTGTGCT\n+>4313|16|FW|1\n+GTTCTCAGAATCTTTGATTGTGCT\n+>4315|16|FW|4\n+TGGTTCTCAGAATCTTTGATTGTG\n+>4339|16|FW|1\n+TCCGAACGTACCACGGTGCCCCAGTGA\n+>4341|16|FW|2\n+TCCGAACGTACCACGGTGCCCCAGT\n+>4342|16|FW|1\n+TCCGAACGTACCACGGTGCCCCAG\n+>4365|16|FW|43\n+TTAAGTCTCTTTGGATGTTTTCACT\n+>4366|16|FW|5\n+TTAAGTCTCTTTGGATGTTTTCAC\n+>4457|16|FW|1\n+TTAGACCTCGCGCTAGGTGGTTGGGG\n+>4470|16|FW|1\n+TGCTGAGCTGGATTAGACCTCGCGC\n+>4471|16|FW|1\n+TGCTGAGCTGGATTAGACCTCGCG\n+>4476|16|FW|1\n+CGGCTGCTGAGCTGGATTAGACC\n+>4484|16|FW|1\n+GAGACGGGAACGGCTGCTGAGCTGG\n+>4484|16|FW|2\n+GACGGGAACGGCTGCTGAGCTGG\n+>4486|16|FW|1\n+GAGACGGGAACGGCTGCTGAGCT\n+>4487|16|FW|1\n+GGAGACGGGAACGGCTGCTGAGC\n+>4491|16|FW|1\n+TTTCGCCGGAGACGGGAACGGCTGCT\n+>4491|16|FW|1\n+TCGCCGGAGACGGGAACGGCTGCT\n+>4492|16|FW|1\n+TTCGCCGGAGACGGGAACGGCTGC\n+>4493|16|FW|2\n+TTCGCCGGAGACGGGAACGGCTG\n+>4494|16|FW|1\n+CTTTCGCCGGAGACGGGAACGGCT\n+>4502|16|FW|1\n+GGTAGGTCCTTTCGCCGGAGACGG\n+>4515|16|FW|1\n+TTATTCGCTGGGTTGGTAGGTCCTT\n+>4517|16|FW|1\n+TTATTCGCTGGGTTGGTAGGTCC\n' |
| b |
| diff -r 9645d995fb3c -r 9185ca0a7b43 test-data/res_files/reads-sample-small.fastq/subgroups/PPPartners/FW/histogram.png |
| b |
| Binary file test-data/res_files/reads-sample-small.fastq/subgroups/PPPartners/FW/histogram.png has changed |
| b |
| diff -r 9645d995fb3c -r 9185ca0a7b43 test-data/res_files/reads-sample-small.fastq/subgroups/PPPartners/FW/overlap_size.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/res_files/reads-sample-small.fastq/subgroups/PPPartners/FW/overlap_size.txt Wed Jan 16 08:18:13 2019 -0500 |
| b |
| @@ -0,0 +1,24 @@ +size number percentage of the total overlap number +1 324 3.24 +2 377 3.77 +3 320 3.20 +4 399 3.99 +5 421 4.21 +6 442 4.42 +7 449 4.49 +8 323 3.23 +9 367 3.67 +10 1042 10.43 +11 442 4.42 +12 465 4.65 +13 442 4.42 +14 351 3.51 +15 399 3.99 +16 364 3.64 +17 539 5.39 +18 374 3.74 +19 432 4.32 +20 415 4.15 +21 445 4.45 +22 516 5.16 +23 347 3.47 |
| b |
| diff -r 9645d995fb3c -r 9185ca0a7b43 test-data/res_files/reads-sample-small.fastq/subgroups/PPPartners/FW/sens.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/res_files/reads-sample-small.fastq/subgroups/PPPartners/FW/sens.txt Wed Jan 16 08:18:13 2019 -0500 |
| b |
| b'@@ -0,0 +1,720 @@\n+>220|0|FW|1\n+GACGAACGCCGACTCTCAATTCAG\n+>283|0|FW|1\n+CCAAACGCAGACATCGAGCGGTCAA\n+>288|0|FW|1\n+CGCAGACATCGAGCGGTCAATAACC\n+>291|0|FW|1\n+AGACATCGAGCGGTCAATAACCC\n+>294|0|FW|1\n+CATCGAGCGGTCAATAACCCATAGC\n+>296|0|FW|1\n+TCGAGCGGTCAATAACCCATAGCCC\n+>361|0|FW|2\n+TCCTGCTCTCCCGCTCTATTGGCTCC\n+>362|0|FW|9\n+CCTGCTCTCCCGCTCTATTGGCTCC\n+>362|0|FW|1\n+CCTGCTCTCCCGCTCTATTGGCTC\n+>367|0|FW|1\n+TCTCCCGCTCTATTGGCTCCGACAGA\n+>370|0|FW|1\n+CCCGCTCTATTGGCTCCGACAGAA\n+>409|0|FW|1\n+ACAACAACAGCTGGAGAGGGACC\n+>424|0|FW|1\n+GAGGGACCGGCAGCCCGCTCTGCCT\n+>429|0|FW|1\n+ACCGGCAGCCCGCTCTGCCTCGTCATC\n+>433|0|FW|1\n+GCAGCCCGCTCTGCCTCGTCATCGGC\n+>435|0|FW|1\n+AGCCCGCTCTGCCTCGTCATCGGCT\n+>435|0|FW|1\n+AGCCCGCTCTGCCTCGTCATCGGC\n+>437|0|FW|1\n+CCCGCTCTGCCTCGTCATCGGCTG\n+>439|0|FW|3\n+CGCTCTGCCTCGTCATCGGCTGC\n+>441|0|FW|1\n+CTCTGCCTCGTCATCGGCTGCACCCG\n+>442|0|FW|10\n+TCTGCCTCGTCATCGGCTGCACCCGC\n+>442|0|FW|1\n+TCTGCCTCGTCATCGGCTGCACCCG\n+>442|0|FW|2\n+TCTGCCTCGTCATCGGCTGCACCC\n+>442|0|FW|2\n+TCTGCCTCGTCATCGGCTGCACC\n+>448|0|FW|1\n+TCGTCATCGGCTGCACCCGCTCAC\n+>451|0|FW|1\n+TCATCGGCTGCACCCGCTCACGGTC\n+>451|0|FW|1\n+TCATCGGCTGCACCCGCTCACGGT\n+>451|0|FW|1\n+TCATCGGCTGCACCCGCTCACGG\n+>454|0|FW|1\n+TCGGCTGCACCCGCTCACGGTCTGAC\n+>455|0|FW|1\n+CGGCTGCACCCGCTCACGGTCTG\n+>456|0|FW|2\n+GGCTGCACCCGCTCACGGTCTGAC\n+>500|0|FW|1\n+CGCTAGCAATAAACGGTACTGCT\n+>509|0|FW|1\n+TAAACGGTACTGCTGCACTGCCAG\n+>511|0|FW|1\n+AACGGTACTGCTGCACTGCCAGCA\n+>568|0|FW|1\n+TCGACCTGGCAGACTGGAATGGACC\n+>568|0|FW|1\n+TCGACCTGGCAGACTGGAATGGAC\n+>571|0|FW|3\n+ACCTGGCAGACTGGAATGGACCGC\n+>571|0|FW|1\n+ACCTGGCAGACTGGAATGGACCG\n+>572|0|FW|1\n+CCTGGCAGACTGGAATGGACCGCT\n+>572|0|FW|2\n+CCTGGCAGACTGGAATGGACCGC\n+>574|0|FW|1\n+TGGCAGACTGGAATGGACCGCTAC\n+>631|0|FW|1\n+TCAGATTTGGGAAACAAGCCGAAA\n+>651|0|FW|1\n+GAAAAATACACGCGACAACTCTACC\n+>653|0|FW|1\n+AAAATACACGCGACAACTCTACCTT\n+>657|0|FW|1\n+TACACGCGACAACTCTACCTTGA\n+>672|0|FW|1\n+TACCTTGATCAAAAATGTAGCCCC\n+>713|0|FW|1\n+TTGCCTTGCTGGTAGATACCGCTGA\n+>718|0|FW|1\n+TTGCTGGTAGATACCGCTGAGGA\n+>719|0|FW|1\n+TGCTGGTAGATACCGCTGAGGACG\n+>725|0|FW|2\n+TAGATACCGCTGAGGACGTGCCGCT\n+>725|0|FW|1\n+TAGATACCGCTGAGGACGTGCCGC\n+>729|0|FW|1\n+TACCGCTGAGGACGTGCCGCTGGGA\n+>729|0|FW|2\n+TACCGCTGAGGACGTGCCGCTGGG\n+>729|0|FW|1\n+TACCGCTGAGGACGTGCCGCTGG\n+>744|0|FW|1\n+GCCGCTGGGATCCGTTGATATCGA\n+>762|0|FW|2\n+TATCGAACCGAAGAAAACAAAGCC\n+>821|0|FW|6\n+GTCTTGTAAATACTTTGATTGGCCT\n+>821|0|FW|1\n+GTCTTGTAAATACTTTGATTGGCC\n+>822|0|FW|74\n+TCTTGTAAATACTTTGATTGGCCT\n+>822|0|FW|4\n+TCTTGTAAATACTTTGATTGGCC\n+>823|0|FW|3\n+CTTGTAAATACTTTGATTGGCCT\n+>824|0|FW|1\n+TTGTAAATACTTTGATTGGCCTTAT\n+>824|0|FW|1\n+TTGTAAATACTTTGATTGGCCTT\n+>918|0|FW|1\n+AACGGAGGACGACTACAGAAAAGT\n+>1007|0|FW|1\n+TGCAAGTAGTCCTGAAGGGCATTG\n+>1027|0|FW|1\n+ATTGAGTCTGATGTTACGCCCGA\n+>1048|0|FW|3\n+GAAGAGATAACTGAGGCGCTAAAG\n+>1064|0|FW|2\n+CGCTAAAGGAAAAGGGATTTTACGCC\n+>1067|0|FW|1\n+TAAAGGAAAAGGGATTTTACGCC\n+>1141|0|FW|1\n+AAGATTGAGCTTGAACCAGAAAACA\n+>1189|0|FW|1\n+CACCCAATTTACAAACTCCAGCTC\n+>1214|0|FW|2\n+TTTTGCACCGTAGGATCACGGTAGAA\n+>1214|0|FW|1\n+TTTTGCACCGTAGGATCACGGTAGA\n+>1217|0|FW|2\n+TGCACCGTAGGATCACGGTAGAAGAG\n+>1221|0|FW|4\n+CCGTAGGATCACGGTAGAAGAGCC\n+>1221|0|FW|1\n+CCGTAGGATCACGGTAGAAGAGC\n+>1223|0|FW|1\n+GTAGGATCACGGTAGAAGAGCCGC\n+>1224|0|FW|1\n+TAGGATCACGGTAGAAGAGCCGC\n+>1235|0|FW|1\n+TAGAAGAGCCGCACAAACGCAACGCT\n+>1242|0|FW|1\n+GCCGCACAAACGCAACGCTCCTGT\n+>1272|0|FW|1\n+TACAAACTGCCAAGAGTATGGCC\n+>1303|0|FW|1\n+TCATATTGTACACTTCGCCCGGT\n+>1309|0|FW|1\n+TGTACACTTCGCCCGGTGTGCGTAGT\n+>1322|0|FW|1\n+CGGTGTGCGTAGTCTGTGGAGATC\n+>1323|0|FW|1\n+GGTGTGCGTAGTCTGTGGAGATCTC\n+>1323|0|FW|1\n+GGTGTGCGTAGTCTGTGGAGATCT\n+>1325|0|FW|1\n+TGTGCGTAGTCTGTGGAGATCTCCACGA\n+>1325|0|FW|1\n+TGTGCGTAGTCTGTGGAGATCTCCACG\n+>1325|0|FW|1\n+TGTGCGTAGTCTGTGGAGATCTCCAC\n+>1325|0|FW|5\n+TGTGCGTAGTCTGTGGAGATCTCCA\n+>1325|0|FW|1\n+TGTGCGTAGTCTGTGGAGATCTCC\n+>1325|0|FW|1\n+TGTGCGTAGTCTGTGGAGATCTC\n+>1327|0|FW|3\n+TGCGTAGTCTGTGGAGATCTCCACGA\n+>1327|0|FW|2\n+TGCGTAGTCTGTGGAGATCTCCA\n+>1328|0|FW|1\n+GCGTAGTCTGTGGAGATCTCCACGA\n+>1385|0|FW|1\n+CATGCGAGAAAAAATGCAATAACTG\n+>1386|0|FW|1\n+ATGCGAGAAAAAATGCAATAACTGT\n+>1386|0|FW|2\n+ATGCGAGAAAAAATGCAATAACTG\n+>1387|0|FW|1\n+TGCGAGAAAAAATGCAATAACTGT\n+>1431|0|FW|1\n+CTACAGAGGCTGTCCAATCTACAA\n+>1432'..b'3579|0|FW|1\n+CATCGCGAATACTGTACAGCAGT\n+>3604|0|FW|1\n+TTTTAGACGTATCCCAAGCATTCGAC\n+>3621|0|FW|1\n+GCATTCGACAAAGTCTGGCTCGACG\n+>3621|0|FW|3\n+GCATTCGACAAAGTCTGGCTCGAC\n+>3621|0|FW|9\n+GCATTCGACAAAGTCTGGCTCGA\n+>3624|0|FW|1\n+TTCGACAAAGTCTGGCTCGACGGCCT\n+>3624|0|FW|1\n+TTCGACAAAGTCTGGCTCGACGGCC\n+>3626|0|FW|1\n+CGACAAAGTCTGGCTCGACGGCCT\n+>3656|0|FW|1\n+TAAAATTAAAACATCCCTACCCGAA\n+>3750|0|FW|1\n+TCCACTGTTCATACAATTGAGGCTG\n+>3751|0|FW|10\n+CCACTGTTCATACAATTGAGGCTG\n+>3751|0|FW|8\n+CCACTGTTCATACAATTGAGGCT\n+>3754|0|FW|1\n+CTGTTCATACAATTGAGGCTGGA\n+>3755|0|FW|3\n+TGTTCATACAATTGAGGCTGGAGTC\n+>3755|0|FW|7\n+TGTTCATACAATTGAGGCTGGAGT\n+>3755|0|FW|5\n+TGTTCATACAATTGAGGCTGGAG\n+>3757|0|FW|3\n+TTCATACAATTGAGGCTGGAGTCCC\n+>3759|0|FW|1\n+CATACAATTGAGGCTGGAGTCCC\n+>3836|0|FW|1\n+TACAAATAGTCGCTTAACGGTATC\n+>3901|0|FW|1\n+CCCCTATCCAAGCTACAGCACAGT\n+>3901|0|FW|1\n+CCCCTATCCAAGCTACAGCACAG\n+>3907|0|FW|1\n+TCCAAGCTACAGCACAGTTGGCACTG\n+>3909|0|FW|1\n+CAAGCTACAGCACAGTTGGCACTG\n+>3910|0|FW|2\n+AAGCTACAGCACAGTTGGCACTG\n+>3912|0|FW|1\n+GCTACAGCACAGTTGGCACTGTACCT\n+>3912|0|FW|1\n+GCTACAGCACAGTTGGCACTGTACC\n+>3912|0|FW|1\n+GCTACAGCACAGTTGGCACTGTAC\n+>3925|0|FW|9\n+TGGCACTGTACCTCACCGACATTGA\n+>3927|0|FW|1\n+GCACTGTACCTCACCGACATTGA\n+>3943|0|FW|1\n+ACATTGAGAAGTGGCTCTCTGACT\n+>3960|0|FW|1\n+TCTGACTGGCGAATAAAAGTAAAC\n+>3962|0|FW|1\n+TGACTGGCGAATAAAAGTAAACGAGC\n+>4008|0|FW|1\n+TTTACGCTAAACAGACAAGACTGTC\n+>4010|0|FW|2\n+TACGCTAAACAGACAAGACTGTCCT\n+>4012|0|FW|1\n+CGCTAAACAGACAAGACTGTCCT\n+>4015|0|FW|1\n+TAAACAGACAAGACTGTCCTCCGCT\n+>4016|0|FW|1\n+AAACAGACAAGACTGTCCTCCGCTCT\n+>4018|0|FW|1\n+ACAGACAAGACTGTCCTCCGCTCT\n+>4040|0|FW|1\n+CTTGTTGAACAGCATACCACTCCCGA\n+>4045|0|FW|1\n+TGAACAGCATACCACTCCCGAAAGC\n+>4045|0|FW|1\n+TGAACAGCATACCACTCCCGAAA\n+>4046|0|FW|1\n+GAACAGCATACCACTCCCGAAAG\n+>4049|0|FW|1\n+CAGCATACCACTCCCGAAAGCAGAC\n+>4093|0|FW|1\n+TACACCTTGACAGAAGACTCACATGG\n+>4099|0|FW|1\n+TTGACAGAAGACTCACATGGCGC\n+>4103|0|FW|1\n+CAGAAGACTCACATGGCGCAGGCACA\n+>4103|0|FW|1\n+CAGAAGACTCACATGGCGCAGGCAC\n+>4103|0|FW|1\n+CAGAAGACTCACATGGCGCAGGCA\n+>4105|0|FW|1\n+GAAGACTCACATGGCGCAGGCACA\n+>4164|0|FW|1\n+AACAACTTACACTGGCTCATCAACTC\n+>4166|0|FW|1\n+CAACTTACACTGGCTCATCAACTC\n+>4169|0|FW|1\n+CTTACACTGGCTCATCAACTCTGGT\n+>4170|0|FW|1\n+TTACACTGGCTCATCAACTCTGG\n+>4183|0|FW|1\n+TCAACTCTGGTTCTCCGCTCAGCCTA\n+>4188|0|FW|1\n+TCTGGTTCTCCGCTCAGCCTAGAT\n+>4196|0|FW|2\n+TCCGCTCAGCCTAGATCACAAGGTC\n+>4233|0|FW|1\n+TCTATATTGAAACCAATCTGGACC\n+>4234|0|FW|1\n+CTATATTGAAACCAATCTGGACCT\n+>4235|0|FW|1\n+TATATTGAAACCAATCTGGACCT\n+>4239|0|FW|1\n+TTGAAACCAATCTGGACCTATGGCTC\n+>4240|0|FW|1\n+TGAAACCAATCTGGACCTATGGCT\n+>4240|0|FW|1\n+TGAAACCAATCTGGACCTATGGC\n+>4242|0|FW|3\n+AAACCAATCTGGACCTATGGCTC\n+>4244|0|FW|1\n+ACCAATCTGGACCTATGGCTCACAGT\n+>4246|0|FW|1\n+CAATCTGGACCTATGGCTCACAGT\n+>4295|0|FW|1\n+TATTGACATCATTCAGCGAGCAC\n+>4309|0|FW|1\n+AGCGAGCACAATCAAAGATTCTG\n+>4314|0|FW|1\n+GCACAATCAAAGATTCTGAGAACCA\n+>4319|0|FW|2\n+ATCAAAGATTCTGAGAACCATCACT\n+>4320|0|FW|1\n+TCAAAGATTCTGAGAACCATCACTGG\n+>4320|0|FW|3\n+TCAAAGATTCTGAGAACCATCACT\n+>4321|0|FW|2\n+CAAAGATTCTGAGAACCATCACTGG\n+>4321|0|FW|1\n+CAAAGATTCTGAGAACCATCACT\n+>4322|0|FW|1\n+AAAGATTCTGAGAACCATCACTGGGG\n+>4322|0|FW|5\n+AAAGATTCTGAGAACCATCACTGG\n+>4347|0|FW|1\n+GCACCGTGGTACGTTCGGAGTGA\n+>4348|0|FW|1\n+CACCGTGGTACGTTCGGAGTGAAAAC\n+>4348|0|FW|4\n+CACCGTGGTACGTTCGGAGTGAAAA\n+>4348|0|FW|8\n+CACCGTGGTACGTTCGGAGTGAAA\n+>4348|0|FW|6\n+CACCGTGGTACGTTCGGAGTGAA\n+>4349|0|FW|2\n+ACCGTGGTACGTTCGGAGTGAAAACA\n+>4349|0|FW|9\n+ACCGTGGTACGTTCGGAGTGAAAAC\n+>4349|0|FW|3\n+ACCGTGGTACGTTCGGAGTGAAAA\n+>4349|0|FW|1\n+ACCGTGGTACGTTCGGAGTGAAA\n+>4352|0|FW|2\n+GTGGTACGTTCGGAGTGAAAACATC\n+>4352|0|FW|1\n+GTGGTACGTTCGGAGTGAAAACA\n+>4353|0|FW|2\n+TGGTACGTTCGGAGTGAAAACATC\n+>4396|0|FW|1\n+CATCAGTTACCAACGCAATCACGGA\n+>4414|0|FW|1\n+TCACGGAACTTAAGGAAAAATACC\n+>4415|0|FW|1\n+CACGGAACTTAAGGAAAAATACC\n+>4434|0|FW|1\n+TACCATAGCAAGCTTCACACGCACCC\n+>4464|0|FW|1\n+CACCTAGCGCGAGGTCTAATCCAGC\n+>4468|0|FW|1\n+TAGCGCGAGGTCTAATCCAGCTC\n+>4495|0|FW|4\n+GCCGTTCCCGTCTCCGGCGAAAGGACC\n+>4496|0|FW|1\n+CCGTTCCCGTCTCCGGCGAAAGGAC\n+>4498|0|FW|5\n+GTTCCCGTCTCCGGCGAAAGGAC\n+>4541|0|FW|1\n+TTATTAGGGCCGTTTAAACATAGAA\n+>4545|0|FW|1\n+TAGGGCCGTTTAAACATAGAACAGT\n+>4551|0|FW|13\n+CGTTTAAACATAGAACAGTTGGAA\n' |
| b |
| diff -r 9645d995fb3c -r 9185ca0a7b43 test-data/res_files/reads-sample-small.fastq/subgroups/PPPartners/FW/sensPPP.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/res_files/reads-sample-small.fastq/subgroups/PPPartners/FW/sensPPP.txt Wed Jan 16 08:18:13 2019 -0500 |
| b |
| b'@@ -0,0 +1,578 @@\n+>254|0|FW|1\n+CGTACTTCTCCTACGTCTCACCG\n+>281|0|FW|2\n+TCCCAAACGCAGACATCGAGCGGTC\n+>281|0|FW|1\n+TCCCAAACGCAGACATCGAGCGGT\n+>281|0|FW|1\n+TCCCAAACGCAGACATCGAGCGG\n+>282|0|FW|1\n+CCCAAACGCAGACATCGAGCGGTCAA\n+>282|0|FW|1\n+CCCAAACGCAGACATCGAGCGGTCA\n+>282|0|FW|7\n+CCCAAACGCAGACATCGAGCGGTC\n+>290|0|FW|1\n+CAGACATCGAGCGGTCAATAACCCA\n+>290|0|FW|2\n+CAGACATCGAGCGGTCAATAACC\n+>383|0|FW|1\n+CTCCGACAGAAGCCCCGCTACCTC\n+>436|0|FW|1\n+GCCCGCTCTGCCTCGTCATCGGCTGC\n+>436|0|FW|5\n+GCCCGCTCTGCCTCGTCATCGGCTG\n+>436|0|FW|1\n+GCCCGCTCTGCCTCGTCATCGGC\n+>447|0|FW|1\n+CTCGTCATCGGCTGCACCCGCTCAC\n+>453|0|FW|1\n+ATCGGCTGCACCCGCTCACGGTCT\n+>461|0|FW|1\n+CACCCGCTCACGGTCTGACTAAGTC\n+>501|0|FW|5\n+GCTAGCAATAAACGGTACTGCTGC\n+>501|0|FW|2\n+GCTAGCAATAAACGGTACTGCTG\n+>547|0|FW|1\n+AACGTAAACAAAAAAGCTGGGTCGAC\n+>547|0|FW|9\n+AACGTAAACAAAAAAGCTGGGTCG\n+>547|0|FW|6\n+AACGTAAACAAAAAAGCTGGGTC\n+>627|0|FW|1\n+AAATTCAGATTTGGGAAACAAGC\n+>673|0|FW|1\n+ACCTTGATCAAAAATGTAGCCCCTGC\n+>673|0|FW|1\n+ACCTTGATCAAAAATGTAGCCCCTG\n+>673|0|FW|3\n+ACCTTGATCAAAAATGTAGCCCCT\n+>673|0|FW|5\n+ACCTTGATCAAAAATGTAGCCCC\n+>674|0|FW|1\n+CCTTGATCAAAAATGTAGCCCCTGC\n+>677|0|FW|2\n+TGATCAAAAATGTAGCCCCTGCAAA\n+>702|0|FW|1\n+TACCAACAGATTTGCCTTGCTGG\n+>712|0|FW|1\n+TTTGCCTTGCTGGTAGATACCGCTG\n+>721|0|FW|2\n+CTGGTAGATACCGCTGAGGACGTGC\n+>721|0|FW|1\n+CTGGTAGATACCGCTGAGGACGTG\n+>754|0|FW|1\n+TCCGTTGATATCGAACCGAAGAAAA\n+>829|0|FW|1\n+AATACTTTGATTGGCCTTATTGGGA\n+>829|0|FW|2\n+AATACTTTGATTGGCCTTATTGGG\n+>829|0|FW|1\n+AATACTTTGATTGGCCTTATTGG\n+>902|0|FW|3\n+TCAAACTTCAGACGAAAACGGAG\n+>908|0|FW|1\n+TTCAGACGAAAACGGAGGACGACT\n+>908|0|FW|1\n+TTCAGACGAAAACGGAGGACGAC\n+>915|0|FW|1\n+GAAAACGGAGGACGACTACAGAAAAG\n+>957|0|FW|1\n+CGCACAAAAAATAGGCTTCTACACCT\n+>957|0|FW|13\n+CGCACAAAAAATAGGCTTCTACACC\n+>982|0|FW|7\n+TACCAGCTTAAAAGCAGCAAGGGC\n+>984|0|FW|1\n+CCAGCTTAAAAGCAGCAAGGGCCTG\n+>985|0|FW|1\n+CAGCTTAAAAGCAGCAAGGGCCT\n+>1028|0|FW|1\n+TTGAGTCTGATGTTACGCCCGAAGA\n+>1033|0|FW|3\n+TCTGATGTTACGCCCGAAGAGATAACT\n+>1033|0|FW|40\n+TCTGATGTTACGCCCGAAGAGATAAC\n+>1033|0|FW|20\n+TCTGATGTTACGCCCGAAGAGATAA\n+>1033|0|FW|15\n+TCTGATGTTACGCCCGAAGAGATA\n+>1033|0|FW|22\n+TCTGATGTTACGCCCGAAGAGAT\n+>1152|0|FW|3\n+TGAACCAGAAAACAAGCCTCCTAGAA\n+>1152|0|FW|9\n+TGAACCAGAAAACAAGCCTCCTAGA\n+>1152|0|FW|2\n+TGAACCAGAAAACAAGCCTCCTAG\n+>1192|0|FW|4\n+CCAATTTACAAACTCCAGCTCCT\n+>1193|0|FW|1\n+CAATTTACAAACTCCAGCTCCTTT\n+>1197|0|FW|2\n+TTACAAACTCCAGCTCCTTTTGCACC\n+>1216|0|FW|3\n+TTGCACCGTAGGATCACGGTAGAAGA\n+>1219|0|FW|1\n+CACCGTAGGATCACGGTAGAAGAGC\n+>1244|0|FW|1\n+CGCACAAACGCAACGCTCCTGTA\n+>1293|0|FW|1\n+CCACACGAGGTCATATTGTACACTT\n+>1296|0|FW|1\n+CACGAGGTCATATTGTACACTTCGCC\n+>1296|0|FW|8\n+CACGAGGTCATATTGTACACTTC\n+>1426|0|FW|1\n+GCAAACTACAGAGGCTGTCCAATCTAC\n+>1426|0|FW|1\n+GCAAACTACAGAGGCTGTCCAATCT\n+>1426|0|FW|1\n+GCAAACTACAGAGGCTGTCCAATC\n+>1551|0|FW|1\n+TTTCTCGAAAGCAGCTAGTTTCGCTC\n+>1614|0|FW|9\n+TAACGTTTTAAAATCAGGTATGACG\n+>1614|0|FW|3\n+TAACGTTTTAAAATCAGGTATGAC\n+>1689|0|FW|2\n+CACACAACAAAACTATCACCCAGCTG\n+>1852|0|FW|1\n+CAATCAAATAAATAATGGCTACC\n+>1908|0|FW|1\n+TCACAGCGCAAACTTGAGCTAGCTC\n+>1952|0|FW|4\n+TATCGACGTAATGCTTCTTTCGGA\n+>1967|0|FW|1\n+TCTTTCGGAAACTCATCTCACAAGC\n+>2000|0|FW|1\n+TTTTCAAATAAGAGACTACCATTTC\n+>2000|0|FW|1\n+TTTTCAAATAAGAGACTACCATT\n+>2024|0|FW|1\n+CTACGGTACAAATCATCCCGACGGA\n+>2025|0|FW|3\n+TACGGTACAAATCATCCCGACGGA\n+>2029|0|FW|1\n+GTACAAATCATCCCGACGGAAAAGC\n+>2040|0|FW|1\n+CCCGACGGAAAAGCACACGGTGG\n+>2041|0|FW|1\n+CCGACGGAAAAGCACACGGTGGCACC\n+>2042|0|FW|1\n+CGACGGAAAAGCACACGGTGGCAC\n+>2045|0|FW|1\n+CGGAAAAGCACACGGTGGCACCGC\n+>2097|0|FW|2\n+CACTTTTACAAAGAATTTGCGGAAA\n+>2097|0|FW|2\n+CACTTTTACAAAGAATTTGCGGA\n+>2133|0|FW|3\n+GCCACATCTATCAACATTCAGCTG\n+>2167|0|FW|1\n+CTCTCCTTACACTAGCGGCCGTATAC\n+>2167|0|FW|3\n+CTCTCCTTACACTAGCGGCCGTA\n+>2171|0|FW|1\n+CCTTACACTAGCGGCCGTATACTGCC\n+>2171|0|FW|1\n+CCTTACACTAGCGGCCGTATACTG\n+>2281|0|FW|1\n+ACGCTAAACATACTCACTGGGGA\n+>2286|0|FW|1\n+AAACATACTCACTGGGGATCGCGAC\n+>2287|0|FW|2\n+AACATACTCACTGGGGATCGCGACT\n+>2287|0|FW|2\n+AACATACTCACTGGGGATCGCGAC\n+>2389|0|FW|1\n+GTCCTACATACTGGCCATCAGACCT\n+>2389|0|FW|1\n+GTCCTACATACTGGCCATCAGACC\n+>2393|0|FW|1\n+TACATACTGGCCATCAGACCTCAATAA\n+>2398|0|FW|1\n+ACTGGCCATCAGACCTCAATAAGCTG\n+>2403|0|FW|1\n+CCATCAGACCTCAATAAGCTGCCAG\n+>2409|0|'..b'3|0|FW|1\n+GAAATGATCATCCAGCTGCCACAT\n+>3243|0|FW|1\n+GAAATGATCATCCAGCTGCCACA\n+>3367|0|FW|1\n+CTGGTAAGAACCACACAGTCGCTTCA\n+>3367|0|FW|1\n+CTGGTAAGAACCACACAGTCGCTTC\n+>3367|0|FW|3\n+CTGGTAAGAACCACACAGTCGCTT\n+>3367|0|FW|4\n+CTGGTAAGAACCACACAGTCGCT\n+>3410|0|FW|3\n+TCTACTCTCATGCATTTCGAAACT\n+>3470|0|FW|2\n+TCTGATATACCACAATATAATCCCAG\n+>3470|0|FW|1\n+TCTGATATACCACAATATAATCCCA\n+>3470|0|FW|4\n+TCTGATATACCACAATATAATCCC\n+>3470|0|FW|1\n+TCTGATATACCACAATATAATCC\n+>3535|0|FW|1\n+AACAGGTGAATCGTATTACAACGGA\n+>3540|0|FW|1\n+GTGAATCGTATTACAACGGAAATAA\n+>3540|0|FW|7\n+GTGAATCGTATTACAACGGAAATA\n+>3569|0|FW|3\n+TGCATTTGAACATCGCGAATACT\n+>3614|0|FW|1\n+ATCCCAAGCATTCGACAAAGTCTG\n+>3618|0|FW|6\n+CAAGCATTCGACAAAGTCTGGCTC\n+>3618|0|FW|21\n+CAAGCATTCGACAAAGTCTGGCT\n+>3623|0|FW|2\n+ATTCGACAAAGTCTGGCTCGACGG\n+>3703|0|FW|2\n+CTTACCTCTATGACAGAAAGTTTG\n+>3758|0|FW|1\n+TCATACAATTGAGGCTGGAGTCCCGC\n+>3815|0|FW|1\n+CATCTATACAGCCGACATCCCTAC\n+>3857|0|FW|1\n+ATCCACATTTGCCGACGATACAG\n+>3913|0|FW|3\n+CTACAGCACAGTTGGCACTGTACCT\n+>3913|0|FW|8\n+CTACAGCACAGTTGGCACTGTACC\n+>3913|0|FW|9\n+CTACAGCACAGTTGGCACTGTAC\n+>3914|0|FW|1\n+TACAGCACAGTTGGCACTGTACCT\n+>3914|0|FW|1\n+TACAGCACAGTTGGCACTGTACC\n+>3965|0|FW|4\n+CTGGCGAATAAAAGTAAACGAGC\n+>3983|0|FW|1\n+CGAGCAAAAATGCAAGCACGTGA\n+>4011|0|FW|1\n+ACGCTAAACAGACAAGACTGTCCTCCG\n+>4011|0|FW|6\n+ACGCTAAACAGACAAGACTGTCCTCC\n+>4011|0|FW|4\n+ACGCTAAACAGACAAGACTGTCCTC\n+>4011|0|FW|25\n+ACGCTAAACAGACAAGACTGTCCT\n+>4011|0|FW|15\n+ACGCTAAACAGACAAGACTGTCC\n+>4036|0|FW|1\n+CGCTCTTGTTGAACAGCATACCACT\n+>4038|0|FW|1\n+CTCTTGTTGAACAGCATACCACTCC\n+>4039|0|FW|1\n+TCTTGTTGAACAGCATACCACTCCCGA\n+>4039|0|FW|1\n+TCTTGTTGAACAGCATACCACTCCCG\n+>4039|0|FW|1\n+TCTTGTTGAACAGCATACCACTCCC\n+>4039|0|FW|2\n+TCTTGTTGAACAGCATACCACTCC\n+>4042|0|FW|6\n+TGTTGAACAGCATACCACTCCCGAAA\n+>4044|0|FW|1\n+TTGAACAGCATACCACTCCCGAAAGC\n+>4098|0|FW|1\n+CTTGACAGAAGACTCACATGGCGCA\n+>4098|0|FW|2\n+CTTGACAGAAGACTCACATGGCGC\n+>4100|0|FW|1\n+TGACAGAAGACTCACATGGCGCAG\n+>4104|0|FW|1\n+AGAAGACTCACATGGCGCAGGCACAT\n+>4104|0|FW|8\n+AGAAGACTCACATGGCGCAGGCACA\n+>4104|0|FW|10\n+AGAAGACTCACATGGCGCAGGCAC\n+>4104|0|FW|1\n+AGAAGACTCACATGGCGCAGGCA\n+>4106|0|FW|2\n+AAGACTCACATGGCGCAGGCACATT\n+>4106|0|FW|4\n+AAGACTCACATGGCGCAGGCACAT\n+>4106|0|FW|20\n+AAGACTCACATGGCGCAGGCACA\n+>4148|0|FW|1\n+ACTTAAACTCAAAGCCAACAACT\n+>4163|0|FW|4\n+CAACAACTTACACTGGCTCATCAAC\n+>4199|0|FW|1\n+GCTCAGCCTAGATCACAAGGTCT\n+>4232|0|FW|1\n+TTCTATATTGAAACCAATCTGGACC\n+>4241|0|FW|4\n+GAAACCAATCTGGACCTATGGCTC\n+>4323|0|FW|6\n+AAGATTCTGAGAACCATCACTGGGGC\n+>4323|0|FW|35\n+AAGATTCTGAGAACCATCACTGGGG\n+>4323|0|FW|5\n+AAGATTCTGAGAACCATCACTGGG\n+>4323|0|FW|17\n+AAGATTCTGAGAACCATCACTGG\n+>4324|0|FW|2\n+AGATTCTGAGAACCATCACTGGGGC\n+>4324|0|FW|1\n+AGATTCTGAGAACCATCACTGGG\n+>4325|0|FW|1\n+GATTCTGAGAACCATCACTGGGGC\n+>4326|0|FW|2\n+ATTCTGAGAACCATCACTGGGGCAC\n+>4326|0|FW|1\n+ATTCTGAGAACCATCACTGGGGCA\n+>4326|0|FW|3\n+ATTCTGAGAACCATCACTGGGGC\n+>4327|0|FW|1\n+TTCTGAGAACCATCACTGGGGCACC\n+>4328|0|FW|1\n+TCTGAGAACCATCACTGGGGCACC\n+>4329|0|FW|1\n+CTGAGAACCATCACTGGGGCACCGT\n+>4356|0|FW|3\n+TACGTTCGGAGTGAAAACATCCAAA\n+>4356|0|FW|4\n+TACGTTCGGAGTGAAAACATCCAA\n+>4380|0|FW|1\n+AGAGACTTAAATATCCCATCAGTTACC\n+>4380|0|FW|4\n+AGAGACTTAAATATCCCATCAGT\n+>4473|0|FW|1\n+CGAGGTCTAATCCAGCTCAGCAGC\n+>4485|0|FW|2\n+CAGCTCAGCAGCCGTTCCCGTCTC\n+>4485|0|FW|1\n+CAGCTCAGCAGCCGTTCCCGTCT\n+>4489|0|FW|1\n+TCAGCAGCCGTTCCCGTCTCCGG\n+>4497|0|FW|6\n+CGTTCCCGTCTCCGGCGAAAGGACC\n+>4497|0|FW|7\n+CGTTCCCGTCTCCGGCGAAAGGAC\n+>4497|0|FW|1\n+CGTTCCCGTCTCCGGCGAAAGGA\n+>4499|0|FW|1\n+TTCCCGTCTCCGGCGAAAGGACC\n+>4500|0|FW|8\n+TCCCGTCTCCGGCGAAAGGACCTACC\n+>4505|0|FW|1\n+TCTCCGGCGAAAGGACCTACCAACCC\n+>4505|0|FW|10\n+TCTCCGGCGAAAGGACCTACCAACC\n+>4505|0|FW|7\n+TCTCCGGCGAAAGGACCTACCAAC\n+>4505|0|FW|1\n+TCTCCGGCGAAAGGACCTACCAA\n+>4506|0|FW|1\n+CTCCGGCGAAAGGACCTACCAACCC\n+>4506|0|FW|2\n+CTCCGGCGAAAGGACCTACCAACC\n+>4506|0|FW|1\n+CTCCGGCGAAAGGACCTACCAAC\n+>4507|0|FW|20\n+TCCGGCGAAAGGACCTACCAACCCAGC\n+>4507|0|FW|4\n+TCCGGCGAAAGGACCTACCAACCCA\n+>4507|0|FW|4\n+TCCGGCGAAAGGACCTACCAACCC\n+>4507|0|FW|3\n+TCCGGCGAAAGGACCTACCAACC\n+>4508|0|FW|2\n+CCGGCGAAAGGACCTACCAACCCAGC\n+>4508|0|FW|2\n+CCGGCGAAAGGACCTACCAACCC\n+>4516|0|FW|1\n+AGGACCTACCAACCCAGCGAATAAAT\n+>4530|0|FW|1\n+CAGCGAATAAATTATTAGGGCCGT\n' |
| b |
| diff -r 9645d995fb3c -r 9185ca0a7b43 test-data/res_files/reads-sample-small.fastq/subgroups/PPPartners/G6_DM.html --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/res_files/reads-sample-small.fastq/subgroups/PPPartners/G6_DM.html Wed Jan 16 08:18:13 2019 -0500 |
| b |
| b'@@ -0,0 +1,295 @@\n+\n+ <!DOCTYPE html>\n+ <html lang="en">\n+ <head>\n+ <meta charset="utf-8">\n+ <title>pipeline</title>\n+ <meta name="viewport" content="width=device-width, initial-scale=1.0">\n+ <meta name="description" content="">\n+ <meta name="author" content="">\n+ <!-- Le styles -->\n+ <link href="css/bootstrap.css" rel="stylesheet">\n+ <link href="css/bootstrap-table.css" rel="stylesheet">\n+ <style type="text/css">\n+ body {\n+ padding-top: 60px;\n+ padding-bottom: 40px;\n+ }\n+ div#page {\n+ width: 940px;\n+ background-color: #fff;\n+ margin: 0 auto;\n+ text-align: left;\n+ border-color: #fff;\n+ border-style: none solid solid;\n+ border-width: medium 1px 1px;\n+ }\n+\n+ div.content {\n+ \tdisplay: none;\n+\t float: right;\n+\t width: 550px;\n+ }\n+ div.content a, div.navigation a {\n+ text-decoration: none;\n+ \tcolor: #777;\n+ }\n+ div.content a:focus, div.content a:hover, div.content a:active {\n+ text-decoration: underline;\n+ }\n+ \n+ div.controls {\n+ margin-top: 5px;\n+\t height: 23px;\n+ }\n+ \n+ div.controls a {\n+\t padding: 5px;\n+ }\n+ div.ss-controls {\n+\t float: left;\n+ }\n+ div.nav-controls {\n+\t float: right;\n+ }\n+ div.slideshow-container {\n+\t position: relative;\n+\t clear: both;\n+\t height: 502px; /* This should be set to be at least the height of the largest image in the slideshow */\n+ }\n+ div.loader {\n+ \tposition: absolute;\n+ \ttop: 0;\n+ \tleft: 0;\n+ background-image: url(\'loader.gif\');\n+ background-repeat: no-repeat;\n+ background-position: center;\n+ \twidth: 550px;\n+ \theight: 502px; /* This should be set to be at least the height of the largest image in the slideshow */\n+ }\n+ div.slideshow {\n+ \n+ }\n+ \n+ div.slideshow span.image-wrapper {\n+\t display: block;\n+\t position: absolute;\n+\t top: 0;\n+\t left: 0;\n+ }\n+ div.slideshow a.advance-link {\n+\t display: block;\n+ \t width: 550px;\n+ height: 502px; /* This should be set to be at least the height of the largest image in the slideshow */\n+ line-height: 502px; /* This should be set to be at least the height of the largest image in the slideshow */\n+ text-align: center;\n+ }\n+ div.slideshow a.advance-link:hover, div.slideshow a.advance-link:active, div.slideshow a.advance-link:visited {\n+ text-decoration: none;\n+ }\n+ div.slideshow img {\n+ vertical-align: middle;\n+\tborder: 1px solid #ccc;\n+ }\n+\n+ div.image-title {\n+ font-weight: bold;\n+ font-size: 1.4em;\n+ }\n+\n+ div.image-desc {\n+ line-height: 1.3em;\n+ padding-top: 12px;\n+ }\n+ div.navigation {\n+\n+ }\n+ ul.thumbs {\n+\tclear: both;\n+\tmargin: 0;\n+\tpadding: 0;\n+ }\n+ ul.thumbs li {\n+\tfloat: none;\n+\tpadding: 0;\n+\tmargin: 0;\n+ list-style: none;\n+ }\n+ a.thumb {\n+\tpadding: 0;\n+\tdisplay: inline;\n+\tborder: none;\n+ }\n+ ul.thumbs li.selected a.thumb {\n+\tcolor: #000;\n+ font-weight: bold;\n+ }\n+ a.thumb:focus {\n+\toutline: none;\n+ }\n+ ul.thumbs img {\n+\tborder: none;\n+\tdisplay: block;\n+ }\n+ div.pagination {\n+\tclear: both;\n+ }\n+ div.navigation div.top {\n+ margin-bottom: 12px;\n+\theight: 11px;\n+ }\n+ div.navigation div.bottom {\n+ margin-top: 12px;\n+ }\n+ div.pagination a, div.pagination span.current, div.pagination span.ellipsis {\n+\tdisplay: block;\n+\tfloat: left;\n+ margin-right: 2px;\n+\tpadding: 4px 7px 2px 7px;\n+\tborder: 1px solid #ccc;\n+ }\n+ div.pagination a:hover {\n+ background-color: #eee;\n+ text-decoration: none;\n+ }\n+ div.pagination span.current {\n+ font-weight: bold;\n+ background-color: #000;\n+ border-color: #000;\n+\tcolor: #fff;\n+ }\n+ div.pagination span.ellipsis {\n+\tborder: none;\n+\tpadding: 5px 0 3px 2px;\n+ }\n+ \n+ div.download {\n+\tfloat: right;\n+ }\n+ \n+ div.caption-container {\n+\tposition: relative;\n+\tclear: left;\n+\theight: 75px;\n+ }\n+ span.image-caption {\n+\tdisplay: block;\n+\tposition: absolute;\n+\twidth: 550px;\n+\ttop: 0;\n+\tleft: 0;\n+ }\n+ div.caption {\n+\tpadding: 12px;\n+ }\n+\n+ /* Featurettes\n+ ------------------------- */\n+\n+ .featurette {\n+ padding-top: 20px; /* Vertica'..b'en; /* Vertically center images part 2: clear their floats. */\n+ text-align: center;\n+ }\n+\n+ .featurette-p\n+ {\n+ text-align: left;\n+ }\n+\n+ .featurette-image {\n+ margin-top: 10px; /* Vertically center images part 3: negative margin up the image the same amount of the padding to center it. */\n+ width: 450px;\n+ height: auto;\n+ }\n+\n+ </style>\n+ <link href="css/bootstrap-responsive.css" rel="stylesheet">\n+ </head>\n+ <body>\n+ \n+\t\t\t\t\t<div align="center">\n+\t\t\t\t\t<h2>G6_DM</h2>\n+\t\t\t\t\t<p> <img class="featurette-image" src="G6_DM/histogram.png"/></p>\n+\t\t\t\t\t<p><a href="G6_DM/overlap_size.txt">ping pong signature</a></p>\n+\t\t\t\t\t<p><a href="G6_DM/sensPPP.txt">sense reads with PPP</a></p>\n+\t\t\t\t\t<p><a href="G6_DM/antisensPPP.txt">reverse reads with PPP</a></p>\n+\t\t\t\t\t<p><a href="G6_DM/sens.txt">sense reads without PPP</a></p>\n+\t\t\t\t\t<p><a href="G6_DM/antisens.txt">reverse reads without PPP</a></p>\n+\t\t\t\t\t</div>\n+ <!-- FOOTER -->\n+ <div class="container">\n+ <footer>\n+ \n+ </footer>\n+ </div>\n+ <!-- Le javascript\n+ ================================================== -->\n+ <!-- Placed at the end of the document so the pages load faster -->\n+ <script type="text/javascript" src="js/filter.js"></script>\n+ <script type="text/javascript" src="js/jquery.js"></script>\n+ <script type="text/javascript" src="js/jquery-1.3.2.js"></script>\n+ <script type="text/javascript" src="js/jquery.galleriffic.js"></script>\n+ <script type="text/javascript" src="js/jquery.opacityrollover.js"></script>\n+ <script type="text/javascript" src="js/bootstrap-table.js"></script>\n+ <script type="text/javascript" src="js/bootstrap.min.js"></script>\n+ <script type="text/javascript">\n+ jQuery(document).ready(function($) {\n+ // We only want these styles applied when javascript is enabled\n+ $(\'div.navigation\').css({\'width\' : \'300px\', \'float\' : \'left\'});\n+ $(\'div.content\').css(\'display\', \'block\');\n+ \n+ $(".each-gallery").each(function(i){\n+ // Initially set opacity on thumbs and add\n+ // additional styling for hover effect on thumbs\n+ var onMouseOutOpacity = 0.67;\n+ $(\'#thumbs + i + ul.thumbs li\').opacityrollover({\n+ mouseOutOpacity: onMouseOutOpacity,\n+ mouseOverOpacity: 1.0,\n+ fadeSpeed: \'fast\',\n+ exemptionSelector: \'.selected\'\n+ });\n+ \n+ // Initialize Advanced Galleriffic Gallery\n+ var gallery = $(\'#thumbs\'+i).galleriffic({\n+ delay: 2500,\n+ numThumbs: 22,\n+ preloadAhead: 10,\n+ enableTopPager: true,\n+ enableBottomPager: true,\n+ maxPagesToShow: 7,\n+ imageContainerSel: \'#slideshow\'+ i,\n+ controlsContainerSel: \'#controls\' + i,\n+ captionContainerSel: \'#caption\' + i,\n+ loadingContainerSel: \'#loading\' + i,\n+ renderSSControls: true,\n+ renderNavControls: true,\n+ playLinkText: \'Play\',\n+ pauseLinkText: \'Pause\',\n+ prevLinkText: \'‹ Previous\',\n+ nextLinkText: \'Next ›\',\n+ nextPageLinkText: \'Next ›\',\n+ prevPageLinkText: \'‹ Prev\',\n+ enableHistory: false,\n+ autoStart: false,\n+ syncTransitions: true,\n+ defaultTransitionDuration: 900,\n+ onSlideChange: function(prevIndex, nextIndex) {\n+ // \'this\' refers to the gallery, which is an extension of $(\'#thumbs\')\n+ this.find(\'ul.thumbs\').children()\n+ .eq(prevIndex).fadeTo(\'fast\', onMouseOutOpacity).end()\n+ .eq(nextIndex).fadeTo(\'fast\', 1.0);\n+ },\n+ onPageTransitionOut: function(callback) {\n+ this.fadeTo(\'fast\', 0.0, callback);\n+ },\n+ onPageTransitionIn: function() {\n+ this.fadeTo(\'fast\', 1.0);\n+ }\n+ });\n+ });\n+ });\n+ </script>\n+ </body>\n+ </html>\n+ \n\\ No newline at end of file\n' |
| b |
| diff -r 9645d995fb3c -r 9185ca0a7b43 test-data/res_files/reads-sample-small.fastq/subgroups/PPPartners/G6_DM/antisens.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/res_files/reads-sample-small.fastq/subgroups/PPPartners/G6_DM/antisens.txt Wed Jan 16 08:18:13 2019 -0500 |
| b |
| @@ -0,0 +1,268 @@ +>1160|16|G6_DM|1 +TCCAGGAAGCAGTAACGCTGTGTAT +>1161|16|G6_DM|1 +TTCCAGGAAGCAGTAACGCTGTGTA +>1172|16|G6_DM|2 +TACACATCGGTATTCCAGGAAGCAGT +>1176|16|G6_DM|1 +TTACACATCGGTATTCCAGGAAG +>1213|16|G6_DM|1 +TCTTCTCACATGCCCTCGATTCGTG +>1227|16|G6_DM|1 +TTGTCGTCCTCCCTCTTCTCACAT +>1241|16|G6_DM|1 +GTGGAAGCAGCACGCTTTGTCGTCCT +>1242|16|G6_DM|2 +GTGGAAGCAGCACGCTTTGTCGTCC +>1242|16|G6_DM|2 +AGTGGAAGCAGCACGCTTTGTCGTCC +>1243|16|G6_DM|1 +GTGGAAGCAGCACGCTTTGTCGTC +>1243|16|G6_DM|3 +AGTGGAAGCAGCACGCTTTGTCGTC +>1243|16|G6_DM|3 +CAGTGGAAGCAGCACGCTTTGTCGTC +>1243|16|G6_DM|1 +GCAGTGGAAGCAGCACGCTTTGTCGTC +>1244|16|G6_DM|1 +AGTGGAAGCAGCACGCTTTGTCGT +>1248|16|G6_DM|2 +TGGCAGTGGAAGCAGCACGCTTTG +>1261|16|G6_DM|1 +CAGGATGGTCCGCCTGGCAGTGGAA +>1268|16|G6_DM|1 +TGAAAGACGCAGGATGGTCCGCCTGGC +>1270|16|G6_DM|1 +AAAGACGCAGGATGGTCCGCCTG +>1270|16|G6_DM|1 +GAAAGACGCAGGATGGTCCGCCTG +>1270|16|G6_DM|223 +TGAAAGACGCAGGATGGTCCGCCTG +>1271|16|G6_DM|226 +TGAAAGACGCAGGATGGTCCGCCT +>1272|16|G6_DM|20 +TGAAAGACGCAGGATGGTCCGCC +>1272|16|G6_DM|1 +CTTGAAAGACGCAGGATGGTCCGCC +>1272|16|G6_DM|4 +CCTTGAAAGACGCAGGATGGTCCGCC +>1315|16|G6_DM|30 +TCGGAGCAGCGAGTGCTTTGGCCCT +>1315|16|G6_DM|18 +TTCGGAGCAGCGAGTGCTTTGGCCCT +>1316|16|G6_DM|1 +TCGGAGCAGCGAGTGCTTTGGCCC +>1316|16|G6_DM|16 +TTCGGAGCAGCGAGTGCTTTGGCCC +>1331|16|G6_DM|3 +GACGGGCCTTGTTTTCGGAGCAG +>1333|16|G6_DM|1 +TAGCGACGGGCCTTGTTTTCGGAGC +>1334|16|G6_DM|1 +TAGCGACGGGCCTTGTTTTCGGAG +>1335|16|G6_DM|1 +TTAGCGACGGGCCTTGTTTTCGGA +>1343|16|G6_DM|2 +TGTTAGCATTAGCGACGGGCCTTG +>1343|16|G6_DM|3 +TTGTTAGCATTAGCGACGGGCCTTG +>1349|16|G6_DM|1 +CGCCTTGTTAGCATTAGCGACGG +>1357|16|G6_DM|1 +CACGGGCGGCGCCTTGTTAGCATT +>1385|16|G6_DM|1 +CTCCTGCCAGAGGTGACGTTTGGTG +>1393|16|G6_DM|3 +TCGGTAGCTCCTGCCAGAGGTGAC +>1393|16|G6_DM|1 +TCTCGGTAGCTCCTGCCAGAGGTGAC +>1394|16|G6_DM|1 +TCGGTAGCTCCTGCCAGAGGTGA +>1395|16|G6_DM|1 +TCTCGGTAGCTCCTGCCAGAGGTG +>1396|16|G6_DM|1 +TCTCGGTAGCTCCTGCCAGAGGT +>1401|16|G6_DM|1 +TGAGGGCGTCTCGGTAGCTCCTGCCA +>1402|16|G6_DM|1 +GAGGGCGTCTCGGTAGCTCCTGCC +>1402|16|G6_DM|4 +TGAGGGCGTCTCGGTAGCTCCTGCC +>1406|16|G6_DM|4 +TCCGTTGAGGGCGTCTCGGTAGCTCC +>1408|16|G6_DM|1 +TCCGTTGAGGGCGTCTCGGTAGCT +>1409|16|G6_DM|1 +CTCCGTTGAGGGCGTCTCGGTAGC +>1410|16|G6_DM|2 +CACTCCGTTGAGGGCGTCTCGGTAG +>1411|16|G6_DM|1 +TGCACTCCGTTGAGGGCGTCTCGGTA +>1418|16|G6_DM|1 +TGCTGCGTGCACTCCGTTGAGGGCGT +>1426|16|G6_DM|1 +TGCGGTGCTGCGTGCACTCCGTT +>1429|16|G6_DM|1 +TTCTGCGGTGCTGCGTGCACTCC +>1430|16|G6_DM|1 +GATTCTGCGGTGCTGCGTGCACTC +>1431|16|G6_DM|2 +TGTGGGATTCTGCGGTGCTGCGTGCACT +>1433|16|G6_DM|1 +GTGGGATTCTGCGGTGCTGCGTGCA +>1433|16|G6_DM|1 +TGTGGGATTCTGCGGTGCTGCGTGCA +>1435|16|G6_DM|22 +TGTGGGATTCTGCGGTGCTGCGTG +>1435|16|G6_DM|2 +TTGTGGGATTCTGCGGTGCTGCGTG +>1436|16|G6_DM|32 +TGTGGGATTCTGCGGTGCTGCGT +>1436|16|G6_DM|11 +TTGTGGGATTCTGCGGTGCTGCGT +>1437|16|G6_DM|5 +TTGTGGGATTCTGCGGTGCTGCG +>1453|16|G6_DM|1 +TTGGGTTTGGACTGGGGTTGTGGG +>1454|16|G6_DM|1 +TTGGGTTTGGACTGGGGTTGTGG +>1459|16|G6_DM|2 +TCTGTTTGGGTTTGGACTGGGGT +>1459|16|G6_DM|3 +TTCTGTTTGGGTTTGGACTGGGGT +>1460|16|G6_DM|2 +TTCTGTTTGGGTTTGGACTGGGG +>1484|16|G6_DM|1 +TTCTATCTGACCGGAGTGTGGGG +>1488|16|G6_DM|8 +CATCGCTTCTATCTGACCGGAGTGT +>1489|16|G6_DM|6 +CATCGCTTCTATCTGACCGGAGTG +>1489|16|G6_DM|1 +AACATCGCTTCTATCTGACCGGAGTG +>1490|16|G6_DM|2 +CATCGCTTCTATCTGACCGGAGT +>1492|16|G6_DM|1 +AACATCGCTTCTATCTGACCGGA +>1492|16|G6_DM|1 +GAACATCGCTTCTATCTGACCGGA +>1493|16|G6_DM|1 +GAACATCGCTTCTATCTGACCGG +>1550|16|G6_DM|6 +TGTGTCATCTGGGTGAACATGCGCT +>1551|16|G6_DM|1 +TGTGTCATCTGGGTGAACATGCGC +>1554|16|G6_DM|1 +GCTGTGTCATCTGGGTGAACATG +>1556|16|G6_DM|1 +CAGCTGTGTCATCTGGGTGAACA +>1564|16|G6_DM|6 +TGGTGGCCACCAGCTGTGTCATCTG +>1566|16|G6_DM|1 +TGGTGGCCACCAGCTGTGTCATC +>1573|16|G6_DM|6 +TGTTGAGAATGGTGGCCACCAGCTG +>1575|16|G6_DM|1 +TGCTGTTGAGAATGGTGGCCACCAGC +>1575|16|G6_DM|1 +TTGCTGTTGAGAATGGTGGCCACCAGC +>1576|16|G6_DM|1 +TGCTGTTGAGAATGGTGGCCACCAG +>1578|16|G6_DM|3 +TGCTGTTGAGAATGGTGGCCACC +>1578|16|G6_DM|1 +TTGCTGTTGAGAATGGTGGCCACC +>1587|16|G6_DM|2 +TGCATGACTTGCTGTTGAGAATG +>1587|16|G6_DM|1 +TTGCATGACTTGCTGTTGAGAATG +>1601|16|G6_DM|1 +TAGGTGGAGCTTTAATTGCATGACT +>1616|16|G6_DM|1 +CGCATTCCAGACGACTAGGTGGAGC +>1622|16|G6_DM|1 +CCGTTCGCATTCCAGACGACTAGG +>1627|16|G6_DM|1 +TGCAGGCCGTTCGCATTCCAGACGA +>1628|16|G6_DM|1 +TGCAGGCCGTTCGCATTCCAGACG +>1628|16|G6_DM|1 +TCTGCAGGCCGTTCGCATTCCAGACG +>1629|16|G6_DM|1 +TGCAGGCCGTTCGCATTCCAGAC +>1635|16|G6_DM|18 +TGCTGTTCTGCAGGCCGTTCGCATT +>1635|16|G6_DM|1 +TTGCTGTTCTGCAGGCCGTTCGCATT +>1636|16|G6_DM|4 +TGCTGTTCTGCAGGCCGTTCGCAT +>1654|16|G6_DM|1 +TGGTGCTCGACTATGGCCTTGCTGT +>1655|16|G6_DM|2 +TGGTGCTCGACTATGGCCTTGCTG +>1658|16|G6_DM|1 +GATGGTGCTCGACTATGGCCTTG +>1660|16|G6_DM|22 +TCAGATGGTGCTCGACTATGGCCT +>1660|16|G6_DM|117 +TTCAGATGGTGCTCGACTATGGCCT +>1660|16|G6_DM|17 +TCTTCAGATGGTGCTCGACTATGGCCT +>1661|16|G6_DM|3 +TCAGATGGTGCTCGACTATGGCC +>1661|16|G6_DM|8 +TTCAGATGGTGCTCGACTATGGCC +>1661|16|G6_DM|1 +TCTTCAGATGGTGCTCGACTATGGCC +>1662|16|G6_DM|1 +TCTTCAGATGGTGCTCGACTATGGC +>1663|16|G6_DM|1 +TCTTCAGATGGTGCTCGACTATGG +>1664|16|G6_DM|2 +TCTTCAGATGGTGCTCGACTATG +>1678|16|G6_DM|3 +TATCGATCTGGTGGGTCTTCAGAT +>1679|16|G6_DM|1 +TATCGATCTGGTGGGTCTTCAGA +>1693|16|G6_DM|1 +TCGGCTACGAGTAGGATATCGATCT +>1693|16|G6_DM|2 +TTCGGCTACGAGTAGGATATCGATCT +>1694|16|G6_DM|2 +TTCGGCTACGAGTAGGATATCGATC +>1694|16|G6_DM|3 +TTTCGGCTACGAGTAGGATATCGATC +>1696|16|G6_DM|1 +TTCGGCTACGAGTAGGATATCGA +>1696|16|G6_DM|5 +TTTCGGCTACGAGTAGGATATCGA +>1696|16|G6_DM|1 +GTTTCGGCTACGAGTAGGATATCGA +>1714|16|G6_DM|1 +TCTGGGGGAGAAGTGGGTTTCGG +>1885|16|G6_DM|2 +TTGTGGAAGATCGAGAGGGTGTCT +>1886|16|G6_DM|2 +TTGTGGAAGATCGAGAGGGTGTC +>1887|16|G6_DM|1 +TGTTGTGGAAGATCGAGAGGGTGT +>1888|16|G6_DM|4 +TGTTGTGGAAGATCGAGAGGGTG +>1890|16|G6_DM|1 +TATTGTTGTGGAAGATCGAGAGGG +>1892|16|G6_DM|1 +TCTATTGTTGTGGAAGATCGAGAG +>1893|16|G6_DM|2 +TGTCTATTGTTGTGGAAGATCGAGA +>1894|16|G6_DM|2 +TGTCTATTGTTGTGGAAGATCGAG +>1895|16|G6_DM|3 +TGTCTATTGTTGTGGAAGATCGA +>1897|16|G6_DM|1 +GTTGTCTATTGTTGTGGAAGATC +>1899|16|G6_DM|1 +TGTGTTGTCTATTGTTGTGGAAGA +>1901|16|G6_DM|1 +TATGTGTTGTCTATTGTTGTGGAA +>1905|16|G6_DM|1 +TTTTATATGTGTTGTCTATTGTTGT |
| b |
| diff -r 9645d995fb3c -r 9185ca0a7b43 test-data/res_files/reads-sample-small.fastq/subgroups/PPPartners/G6_DM/antisensPPP.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/res_files/reads-sample-small.fastq/subgroups/PPPartners/G6_DM/antisensPPP.txt Wed Jan 16 08:18:13 2019 -0500 |
| b |
| @@ -0,0 +1,48 @@ +>1164|16|G6_DM|3 +TATTCCAGGAAGCAGTAACGCTGT +>1165|16|G6_DM|11 +TATTCCAGGAAGCAGTAACGCTG +>1199|16|G6_DM|1 +TCGATTCGTGAGGGCCTCCACACT +>1316|16|G6_DM|5 +TTTCGGAGCAGCGAGTGCTTTGGCCC +>1316|16|G6_DM|5 +TTTTCGGAGCAGCGAGTGCTTTGGCCC +>1317|16|G6_DM|1 +TTTTCGGAGCAGCGAGTGCTTTGGCC +>1318|16|G6_DM|1 +TTTTCGGAGCAGCGAGTGCTTTGGC +>1321|16|G6_DM|7 +TGTTTTCGGAGCAGCGAGTGCTTT +>1322|16|G6_DM|12 +TGTTTTCGGAGCAGCGAGTGCTT +>1322|16|G6_DM|2 +TTGTTTTCGGAGCAGCGAGTGCTT +>1369|16|G6_DM|1 +TTTGGTGATGCCACGGGCGGCGC +>1459|16|G6_DM|3 +TTTCTGTTTGGGTTTGGACTGGGGT +>1460|16|G6_DM|25 +TTTCTGTTTGGGTTTGGACTGGGG +>1461|16|G6_DM|25 +TTTCTGTTTGGGTTTGGACTGGG +>1479|16|G6_DM|1 +ATCTGACCGGAGTGTGGGGTTTCT +>1489|16|G6_DM|1 +ATCGCTTCTATCTGACCGGAGTG +>1633|16|G6_DM|1 +TGTTCTGCAGGCCGTTCGCATTCC +>1652|16|G6_DM|1 +TGCTCGACTATGGCCTTGCTGTTC +>1688|16|G6_DM|13 +TACGAGTAGGATATCGATCTGGTGG +>1689|16|G6_DM|43 +TACGAGTAGGATATCGATCTGGTG +>1689|16|G6_DM|4 +CTACGAGTAGGATATCGATCTGGTG +>1690|16|G6_DM|65 +TACGAGTAGGATATCGATCTGGT +>1690|16|G6_DM|15 +CTACGAGTAGGATATCGATCTGGT +>1691|16|G6_DM|8 +CTACGAGTAGGATATCGATCTGG |
| b |
| diff -r 9645d995fb3c -r 9185ca0a7b43 test-data/res_files/reads-sample-small.fastq/subgroups/PPPartners/G6_DM/histogram.png |
| b |
| Binary file test-data/res_files/reads-sample-small.fastq/subgroups/PPPartners/G6_DM/histogram.png has changed |
| b |
| diff -r 9645d995fb3c -r 9185ca0a7b43 test-data/res_files/reads-sample-small.fastq/subgroups/PPPartners/G6_DM/overlap_size.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/res_files/reads-sample-small.fastq/subgroups/PPPartners/G6_DM/overlap_size.txt Wed Jan 16 08:18:13 2019 -0500 |
| b |
| @@ -0,0 +1,24 @@ +size number percentage of the total overlap number +1 1 0.09 +2 30 2.77 +3 17 1.57 +4 14 1.29 +5 69 6.37 +6 87 8.03 +7 27 2.49 +8 64 5.90 +9 27 2.49 +10 129 11.90 +11 81 7.47 +12 21 1.94 +13 44 4.06 +14 28 2.58 +15 36 3.32 +16 56 5.17 +17 56 5.17 +18 59 5.44 +19 49 4.52 +20 53 4.89 +21 80 7.38 +22 17 1.57 +23 39 3.60 |
| b |
| diff -r 9645d995fb3c -r 9185ca0a7b43 test-data/res_files/reads-sample-small.fastq/subgroups/PPPartners/G6_DM/sens.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/res_files/reads-sample-small.fastq/subgroups/PPPartners/G6_DM/sens.txt Wed Jan 16 08:18:13 2019 -0500 |
| b |
| @@ -0,0 +1,186 @@ +>1186|0|G6_DM|2 +TACCGATGTGTAAAGTGTGGAGGC +>1186|0|G6_DM|2 +TACCGATGTGTAAAGTGTGGAGGCC +>1190|0|G6_DM|1 +GATGTGTAAAGTGTGGAGGCCCTC +>1196|0|G6_DM|1 +TAAAGTGTGGAGGCCCTCACGAAT +>1212|0|G6_DM|1 +TCACGAATCGAGGGCATGTGAGAA +>1219|0|G6_DM|5 +TCGAGGGCATGTGAGAAGAGGGA +>1219|0|G6_DM|2 +TCGAGGGCATGTGAGAAGAGGGAG +>1221|0|G6_DM|1 +GAGGGCATGTGAGAAGAGGGAGGA +>1226|0|G6_DM|1 +CATGTGAGAAGAGGGAGGACGAC +>1251|0|G6_DM|1 +AGCGTGCTGCTTCCACTGCCAGGCG +>1255|0|G6_DM|5 +TGCTGCTTCCACTGCCAGGCGGACC +>1305|0|G6_DM|1 +TGCATACAAAAGGGCCAAAGCACTC +>1309|0|G6_DM|1 +TACAAAAGGGCCAAAGCACTCGC +>1309|0|G6_DM|3 +TACAAAAGGGCCAAAGCACTCGCT +>1309|0|G6_DM|1 +TACAAAAGGGCCAAAGCACTCGCTG +>1309|0|G6_DM|4 +TACAAAAGGGCCAAAGCACTCGCTGC +>1309|0|G6_DM|2 +TACAAAAGGGCCAAAGCACTCGCTGCT +>1311|0|G6_DM|1 +CAAAAGGGCCAAAGCACTCGCTG +>1311|0|G6_DM|1 +CAAAAGGGCCAAAGCACTCGCTGC +>1311|0|G6_DM|10 +CAAAAGGGCCAAAGCACTCGCTGCT +>1311|0|G6_DM|1 +CAAAAGGGCCAAAGCACTCGCTGCTC +>1312|0|G6_DM|1 +AAAAGGGCCAAAGCACTCGCTGCTCC +>1313|0|G6_DM|1 +AAAGGGCCAAAGCACTCGCTGCTC +>1315|0|G6_DM|1 +AGGGCCAAAGCACTCGCTGCTCCGA +>1324|0|G6_DM|1 +GCACTCGCTGCTCCGAAAACAAGGCCC +>1325|0|G6_DM|1 +CACTCGCTGCTCCGAAAACAAGGCCC +>1327|0|G6_DM|1 +CTCGCTGCTCCGAAAACAAGGCCC +>1327|0|G6_DM|1 +CTCGCTGCTCCGAAAACAAGGCCCG +>1329|0|G6_DM|1 +CGCTGCTCCGAAAACAAGGCCCGT +>1329|0|G6_DM|1 +CGCTGCTCCGAAAACAAGGCCCGTC +>1334|0|G6_DM|1 +CTCCGAAAACAAGGCCCGTCGCTAA +>1337|0|G6_DM|1 +CGAAAACAAGGCCCGTCGCTAATGC +>1338|0|G6_DM|1 +GAAAACAAGGCCCGTCGCTAATGC +>1384|0|G6_DM|1 +TCACCAAACGTCACCTCTGGCAGG +>1384|0|G6_DM|31 +TCACCAAACGTCACCTCTGGCAGGA +>1384|0|G6_DM|3 +TCACCAAACGTCACCTCTGGCAGGAG +>1384|0|G6_DM|5 +TCACCAAACGTCACCTCTGGCAGGAGC +>1385|0|G6_DM|3 +CACCAAACGTCACCTCTGGCAGGAGC +>1386|0|G6_DM|8 +ACCAAACGTCACCTCTGGCAGGA +>1386|0|G6_DM|1 +ACCAAACGTCACCTCTGGCAGGAG +>1386|0|G6_DM|6 +ACCAAACGTCACCTCTGGCAGGAGC +>1387|0|G6_DM|1 +CCAAACGTCACCTCTGGCAGGAGC +>1389|0|G6_DM|1 +AAACGTCACCTCTGGCAGGAGCT +>1389|0|G6_DM|1 +AAACGTCACCTCTGGCAGGAGCTAC +>1389|0|G6_DM|1 +AAACGTCACCTCTGGCAGGAGCTACC +>1393|0|G6_DM|1 +GTCACCTCTGGCAGGAGCTACCGAG +>1394|0|G6_DM|2 +TCACCTCTGGCAGGAGCTACCGAGA +>1398|0|G6_DM|1 +CTCTGGCAGGAGCTACCGAGACGCCCT +>1399|0|G6_DM|1 +TCTGGCAGGAGCTACCGAGACGC +>1399|0|G6_DM|3 +TCTGGCAGGAGCTACCGAGACGCC +>1399|0|G6_DM|7 +TCTGGCAGGAGCTACCGAGACGCCC +>1399|0|G6_DM|4 +TCTGGCAGGAGCTACCGAGACGCCCT +>1401|0|G6_DM|1 +TGGCAGGAGCTACCGAGACGCCCTC +>1411|0|G6_DM|4 +TACCGAGACGCCCTCAACGGAGTG +>1484|0|G6_DM|1 +CCCCACACTCCGGTCAGATAGAAG +>1487|0|G6_DM|1 +CACACTCCGGTCAGATAGAAGCGA +>1487|0|G6_DM|1 +CACACTCCGGTCAGATAGAAGCGAT +>1489|0|G6_DM|1 +CACTCCGGTCAGATAGAAGCGATG +>1492|0|G6_DM|6 +TCCGGTCAGATAGAAGCGATGTTCGC +>1532|0|G6_DM|1 +TGATGGAAAGGATGATGGAGCGCAT +>1534|0|G6_DM|9 +ATGGAAAGGATGATGGAGCGCAT +>1537|0|G6_DM|2 +GAAAGGATGATGGAGCGCATGTTCA +>1539|0|G6_DM|1 +AAGGATGATGGAGCGCATGTTCACC +>1540|0|G6_DM|1 +AGGATGATGGAGCGCATGTTCACCC +>1618|0|G6_DM|1 +TCCACCTAGTCGTCTGGAATGCGAACG +>1619|0|G6_DM|1 +CCACCTAGTCGTCTGGAATGCGAA +>1620|0|G6_DM|1 +CACCTAGTCGTCTGGAATGCGAAC +>1620|0|G6_DM|1 +CACCTAGTCGTCTGGAATGCGAACGG +>1621|0|G6_DM|1 +ACCTAGTCGTCTGGAATGCGAACGG +>1624|0|G6_DM|1 +TAGTCGTCTGGAATGCGAACGGC +>1624|0|G6_DM|8 +TAGTCGTCTGGAATGCGAACGGCCT +>1630|0|G6_DM|1 +TCTGGAATGCGAACGGCCTGCAGAAC +>1634|0|G6_DM|1 +GAATGCGAACGGCCTGCAGAACAGC +>1637|0|G6_DM|2 +TGCGAACGGCCTGCAGAACAGCA +>1637|0|G6_DM|1 +TGCGAACGGCCTGCAGAACAGCAAGG +>1637|0|G6_DM|1 +TGCGAACGGCCTGCAGAACAGCAAGGC +>1639|0|G6_DM|1 +CGAACGGCCTGCAGAACAGCAAGGC +>1649|0|G6_DM|1 +GCAGAACAGCAAGGCCATAGTCGAG +>1663|0|G6_DM|1 +CCATAGTCGAGCACCATCTGAAGAC +>1664|0|G6_DM|2 +CATAGTCGAGCACCATCTGAAGA +>1664|0|G6_DM|1 +CATAGTCGAGCACCATCTGAAGACC +>1668|0|G6_DM|1 +GTCGAGCACCATCTGAAGACCCACCA +>1670|0|G6_DM|1 +CGAGCACCATCTGAAGACCCACCA +>1679|0|G6_DM|4 +TCTGAAGACCCACCAGATCGATATC +>1679|0|G6_DM|3 +TCTGAAGACCCACCAGATCGATATCC +>1679|0|G6_DM|1 +TCTGAAGACCCACCAGATCGATATCCT +>1681|0|G6_DM|2 +TGAAGACCCACCAGATCGATATCC +>1685|0|G6_DM|3 +GACCCACCAGATCGATATCCTACTCG +>1689|0|G6_DM|1 +CACCAGATCGATATCCTACTCGTAG +>1700|0|G6_DM|1 +TATCCTACTCGTAGCCGAAACCCA +>1700|0|G6_DM|1 +TATCCTACTCGTAGCCGAAACCCAC +>1893|0|G6_DM|1 +TCTCGATCTTCCACAACAATAGAC +>1893|0|G6_DM|1 +TCTCGATCTTCCACAACAATAGACAA |
| b |
| diff -r 9645d995fb3c -r 9185ca0a7b43 test-data/res_files/reads-sample-small.fastq/subgroups/PPPartners/G6_DM/sensPPP.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/res_files/reads-sample-small.fastq/subgroups/PPPartners/G6_DM/sensPPP.txt Wed Jan 16 08:18:13 2019 -0500 |
| b |
| @@ -0,0 +1,50 @@ +>1178|0|G6_DM|2 +TCCTGGAATACCGATGTGTAAAGTG +>1213|0|G6_DM|3 +CACGAATCGAGGGCATGTGAGAA +>1332|0|G6_DM|1 +TGCTCCGAAAACAAGGCCCGTCGCT +>1333|0|G6_DM|1 +GCTCCGAAAACAAGGCCCGTCGCTAA +>1335|0|G6_DM|62 +TCCGAAAACAAGGCCCGTCGCTA +>1335|0|G6_DM|1 +TCCGAAAACAAGGCCCGTCGCTAA +>1335|0|G6_DM|5 +TCCGAAAACAAGGCCCGTCGCTAAT +>1335|0|G6_DM|1 +TCCGAAAACAAGGCCCGTCGCTAATG +>1336|0|G6_DM|1 +CCGAAAACAAGGCCCGTCGCTAA +>1382|0|G6_DM|1 +CATCACCAAACGTCACCTCTGGC +>1382|0|G6_DM|1 +CATCACCAAACGTCACCTCTGGCA +>1382|0|G6_DM|1 +CATCACCAAACGTCACCTCTGGCAGG +>1382|0|G6_DM|1 +CATCACCAAACGTCACCTCTGGCAGGA +>1474|0|G6_DM|3 +CAAACAGAAACCCCACACTCCGGTC +>1493|0|G6_DM|8 +CCGGTCAGATAGAAGCGATGTTCGC +>1502|0|G6_DM|1 +TAGAAGCGATGTTCGCTCGCATGGAAG +>1647|0|G6_DM|1 +CTGCAGAACAGCAAGGCCATAGT +>1666|0|G6_DM|1 +TAGTCGAGCACCATCTGAAGACCC +>1666|0|G6_DM|3 +TAGTCGAGCACCATCTGAAGACCCA +>1666|0|G6_DM|4 +TAGTCGAGCACCATCTGAAGACCCAC +>1666|0|G6_DM|1 +TAGTCGAGCACCATCTGAAGACCCACC +>1703|0|G6_DM|9 +CCTACTCGTAGCCGAAACCCACT +>1703|0|G6_DM|5 +CCTACTCGTAGCCGAAACCCACTT +>1703|0|G6_DM|6 +CCTACTCGTAGCCGAAACCCACTTC +>1704|0|G6_DM|2 +CTACTCGTAGCCGAAACCCACTTC |
| b |
| diff -r 9645d995fb3c -r 9185ca0a7b43 test-data/res_files/reads-sample-small.fastq/subgroups/PPPartners/Gypsy2-LTR_DM.html --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/res_files/reads-sample-small.fastq/subgroups/PPPartners/Gypsy2-LTR_DM.html Wed Jan 16 08:18:13 2019 -0500 |
| b |
| b'@@ -0,0 +1,295 @@\n+\n+ <!DOCTYPE html>\n+ <html lang="en">\n+ <head>\n+ <meta charset="utf-8">\n+ <title>pipeline</title>\n+ <meta name="viewport" content="width=device-width, initial-scale=1.0">\n+ <meta name="description" content="">\n+ <meta name="author" content="">\n+ <!-- Le styles -->\n+ <link href="css/bootstrap.css" rel="stylesheet">\n+ <link href="css/bootstrap-table.css" rel="stylesheet">\n+ <style type="text/css">\n+ body {\n+ padding-top: 60px;\n+ padding-bottom: 40px;\n+ }\n+ div#page {\n+ width: 940px;\n+ background-color: #fff;\n+ margin: 0 auto;\n+ text-align: left;\n+ border-color: #fff;\n+ border-style: none solid solid;\n+ border-width: medium 1px 1px;\n+ }\n+\n+ div.content {\n+ \tdisplay: none;\n+\t float: right;\n+\t width: 550px;\n+ }\n+ div.content a, div.navigation a {\n+ text-decoration: none;\n+ \tcolor: #777;\n+ }\n+ div.content a:focus, div.content a:hover, div.content a:active {\n+ text-decoration: underline;\n+ }\n+ \n+ div.controls {\n+ margin-top: 5px;\n+\t height: 23px;\n+ }\n+ \n+ div.controls a {\n+\t padding: 5px;\n+ }\n+ div.ss-controls {\n+\t float: left;\n+ }\n+ div.nav-controls {\n+\t float: right;\n+ }\n+ div.slideshow-container {\n+\t position: relative;\n+\t clear: both;\n+\t height: 502px; /* This should be set to be at least the height of the largest image in the slideshow */\n+ }\n+ div.loader {\n+ \tposition: absolute;\n+ \ttop: 0;\n+ \tleft: 0;\n+ background-image: url(\'loader.gif\');\n+ background-repeat: no-repeat;\n+ background-position: center;\n+ \twidth: 550px;\n+ \theight: 502px; /* This should be set to be at least the height of the largest image in the slideshow */\n+ }\n+ div.slideshow {\n+ \n+ }\n+ \n+ div.slideshow span.image-wrapper {\n+\t display: block;\n+\t position: absolute;\n+\t top: 0;\n+\t left: 0;\n+ }\n+ div.slideshow a.advance-link {\n+\t display: block;\n+ \t width: 550px;\n+ height: 502px; /* This should be set to be at least the height of the largest image in the slideshow */\n+ line-height: 502px; /* This should be set to be at least the height of the largest image in the slideshow */\n+ text-align: center;\n+ }\n+ div.slideshow a.advance-link:hover, div.slideshow a.advance-link:active, div.slideshow a.advance-link:visited {\n+ text-decoration: none;\n+ }\n+ div.slideshow img {\n+ vertical-align: middle;\n+\tborder: 1px solid #ccc;\n+ }\n+\n+ div.image-title {\n+ font-weight: bold;\n+ font-size: 1.4em;\n+ }\n+\n+ div.image-desc {\n+ line-height: 1.3em;\n+ padding-top: 12px;\n+ }\n+ div.navigation {\n+\n+ }\n+ ul.thumbs {\n+\tclear: both;\n+\tmargin: 0;\n+\tpadding: 0;\n+ }\n+ ul.thumbs li {\n+\tfloat: none;\n+\tpadding: 0;\n+\tmargin: 0;\n+ list-style: none;\n+ }\n+ a.thumb {\n+\tpadding: 0;\n+\tdisplay: inline;\n+\tborder: none;\n+ }\n+ ul.thumbs li.selected a.thumb {\n+\tcolor: #000;\n+ font-weight: bold;\n+ }\n+ a.thumb:focus {\n+\toutline: none;\n+ }\n+ ul.thumbs img {\n+\tborder: none;\n+\tdisplay: block;\n+ }\n+ div.pagination {\n+\tclear: both;\n+ }\n+ div.navigation div.top {\n+ margin-bottom: 12px;\n+\theight: 11px;\n+ }\n+ div.navigation div.bottom {\n+ margin-top: 12px;\n+ }\n+ div.pagination a, div.pagination span.current, div.pagination span.ellipsis {\n+\tdisplay: block;\n+\tfloat: left;\n+ margin-right: 2px;\n+\tpadding: 4px 7px 2px 7px;\n+\tborder: 1px solid #ccc;\n+ }\n+ div.pagination a:hover {\n+ background-color: #eee;\n+ text-decoration: none;\n+ }\n+ div.pagination span.current {\n+ font-weight: bold;\n+ background-color: #000;\n+ border-color: #000;\n+\tcolor: #fff;\n+ }\n+ div.pagination span.ellipsis {\n+\tborder: none;\n+\tpadding: 5px 0 3px 2px;\n+ }\n+ \n+ div.download {\n+\tfloat: right;\n+ }\n+ \n+ div.caption-container {\n+\tposition: relative;\n+\tclear: left;\n+\theight: 75px;\n+ }\n+ span.image-caption {\n+\tdisplay: block;\n+\tposition: absolute;\n+\twidth: 550px;\n+\ttop: 0;\n+\tleft: 0;\n+ }\n+ div.caption {\n+\tpadding: 12px;\n+ }\n+\n+ /* Featurettes\n+ ------------------------- */\n+\n+ .featurette {\n+ padding-top: 20px; /* Vertica'..b'ts. */\n+ text-align: center;\n+ }\n+\n+ .featurette-p\n+ {\n+ text-align: left;\n+ }\n+\n+ .featurette-image {\n+ margin-top: 10px; /* Vertically center images part 3: negative margin up the image the same amount of the padding to center it. */\n+ width: 450px;\n+ height: auto;\n+ }\n+\n+ </style>\n+ <link href="css/bootstrap-responsive.css" rel="stylesheet">\n+ </head>\n+ <body>\n+ \n+\t\t\t\t\t<div align="center">\n+\t\t\t\t\t<h2>Gypsy2-LTR_DM</h2>\n+\t\t\t\t\t<p> <img class="featurette-image" src="Gypsy2-LTR_DM/histogram.png"/></p>\n+\t\t\t\t\t<p><a href="Gypsy2-LTR_DM/overlap_size.txt">ping pong signature</a></p>\n+\t\t\t\t\t<p><a href="Gypsy2-LTR_DM/sensPPP.txt">sense reads with PPP</a></p>\n+\t\t\t\t\t<p><a href="Gypsy2-LTR_DM/antisensPPP.txt">reverse reads with PPP</a></p>\n+\t\t\t\t\t<p><a href="Gypsy2-LTR_DM/sens.txt">sense reads without PPP</a></p>\n+\t\t\t\t\t<p><a href="Gypsy2-LTR_DM/antisens.txt">reverse reads without PPP</a></p>\n+\t\t\t\t\t</div>\n+ <!-- FOOTER -->\n+ <div class="container">\n+ <footer>\n+ \n+ </footer>\n+ </div>\n+ <!-- Le javascript\n+ ================================================== -->\n+ <!-- Placed at the end of the document so the pages load faster -->\n+ <script type="text/javascript" src="js/filter.js"></script>\n+ <script type="text/javascript" src="js/jquery.js"></script>\n+ <script type="text/javascript" src="js/jquery-1.3.2.js"></script>\n+ <script type="text/javascript" src="js/jquery.galleriffic.js"></script>\n+ <script type="text/javascript" src="js/jquery.opacityrollover.js"></script>\n+ <script type="text/javascript" src="js/bootstrap-table.js"></script>\n+ <script type="text/javascript" src="js/bootstrap.min.js"></script>\n+ <script type="text/javascript">\n+ jQuery(document).ready(function($) {\n+ // We only want these styles applied when javascript is enabled\n+ $(\'div.navigation\').css({\'width\' : \'300px\', \'float\' : \'left\'});\n+ $(\'div.content\').css(\'display\', \'block\');\n+ \n+ $(".each-gallery").each(function(i){\n+ // Initially set opacity on thumbs and add\n+ // additional styling for hover effect on thumbs\n+ var onMouseOutOpacity = 0.67;\n+ $(\'#thumbs + i + ul.thumbs li\').opacityrollover({\n+ mouseOutOpacity: onMouseOutOpacity,\n+ mouseOverOpacity: 1.0,\n+ fadeSpeed: \'fast\',\n+ exemptionSelector: \'.selected\'\n+ });\n+ \n+ // Initialize Advanced Galleriffic Gallery\n+ var gallery = $(\'#thumbs\'+i).galleriffic({\n+ delay: 2500,\n+ numThumbs: 22,\n+ preloadAhead: 10,\n+ enableTopPager: true,\n+ enableBottomPager: true,\n+ maxPagesToShow: 7,\n+ imageContainerSel: \'#slideshow\'+ i,\n+ controlsContainerSel: \'#controls\' + i,\n+ captionContainerSel: \'#caption\' + i,\n+ loadingContainerSel: \'#loading\' + i,\n+ renderSSControls: true,\n+ renderNavControls: true,\n+ playLinkText: \'Play\',\n+ pauseLinkText: \'Pause\',\n+ prevLinkText: \'‹ Previous\',\n+ nextLinkText: \'Next ›\',\n+ nextPageLinkText: \'Next ›\',\n+ prevPageLinkText: \'‹ Prev\',\n+ enableHistory: false,\n+ autoStart: false,\n+ syncTransitions: true,\n+ defaultTransitionDuration: 900,\n+ onSlideChange: function(prevIndex, nextIndex) {\n+ // \'this\' refers to the gallery, which is an extension of $(\'#thumbs\')\n+ this.find(\'ul.thumbs\').children()\n+ .eq(prevIndex).fadeTo(\'fast\', onMouseOutOpacity).end()\n+ .eq(nextIndex).fadeTo(\'fast\', 1.0);\n+ },\n+ onPageTransitionOut: function(callback) {\n+ this.fadeTo(\'fast\', 0.0, callback);\n+ },\n+ onPageTransitionIn: function() {\n+ this.fadeTo(\'fast\', 1.0);\n+ }\n+ });\n+ });\n+ });\n+ </script>\n+ </body>\n+ </html>\n+ \n\\ No newline at end of file\n' |
| b |
| diff -r 9645d995fb3c -r 9185ca0a7b43 test-data/res_files/reads-sample-small.fastq/subgroups/PPPartners/Gypsy2-LTR_DM/antisens.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/res_files/reads-sample-small.fastq/subgroups/PPPartners/Gypsy2-LTR_DM/antisens.txt Wed Jan 16 08:18:13 2019 -0500 |
| b |
| @@ -0,0 +1,68 @@ +>55|16|Gypsy2-LTR_DM|1 +TTGGTCAGCATTTTGGGCACTCGTG +>62|16|Gypsy2-LTR_DM|1 +TGCAGACCTTTGGTCAGCATTTTGGGC +>75|16|Gypsy2-LTR_DM|1 +AGCGGAAAGAATGCAGACCTTTGGT +>80|16|Gypsy2-LTR_DM|2 +TTGACAGCGGAAAGAATGCAGACCT +>80|16|Gypsy2-LTR_DM|1 +TGACAGCGGAAAGAATGCAGACCT +>93|16|Gypsy2-LTR_DM|1 +TTTTAGCTGGTCGTTGACAGCGGAA +>94|16|Gypsy2-LTR_DM|1 +CACTTTTAGCTGGTCGTTGACAGCGGA +>94|16|Gypsy2-LTR_DM|2 +CTTTTAGCTGGTCGTTGACAGCGGA +>95|16|Gypsy2-LTR_DM|1 +CACTTTTAGCTGGTCGTTGACAGCGG +>97|16|Gypsy2-LTR_DM|4 +TCGCACTTTTAGCTGGTCGTTGACAGC +>97|16|Gypsy2-LTR_DM|1 +CGCACTTTTAGCTGGTCGTTGACAGC +>97|16|Gypsy2-LTR_DM|2 +GCACTTTTAGCTGGTCGTTGACAGC +>97|16|Gypsy2-LTR_DM|1 +CACTTTTAGCTGGTCGTTGACAGC +>98|16|Gypsy2-LTR_DM|1 +TCGCACTTTTAGCTGGTCGTTGACAG +>98|16|Gypsy2-LTR_DM|1 +CGCACTTTTAGCTGGTCGTTGACAG +>98|16|Gypsy2-LTR_DM|1 +GCACTTTTAGCTGGTCGTTGACAG +>108|16|Gypsy2-LTR_DM|2 +GCAGATGATCGCACTTTTAGCTGG +>109|16|Gypsy2-LTR_DM|1 +TGCAGATGATCGCACTTTTAGCTG +>109|16|Gypsy2-LTR_DM|1 +GCAGATGATCGCACTTTTAGCTG +>120|16|Gypsy2-LTR_DM|1 +CGGCGGAGAAGTGCAGATGATCGC +>146|16|Gypsy2-LTR_DM|1 +AGCGAATCAGTGGTCGTCAGCGGCTA +>148|16|Gypsy2-LTR_DM|4 +AGCGAATCAGTGGTCGTCAGCGGC +>151|16|Gypsy2-LTR_DM|1 +TCGGCAGCGAATCAGTGGTCGTCAGC +>151|16|Gypsy2-LTR_DM|7 +GGCAGCGAATCAGTGGTCGTCAGC +>154|16|Gypsy2-LTR_DM|1 +TCGGCAGCGAATCAGTGGTCGTC +>159|16|Gypsy2-LTR_DM|2 +GCAGGCGTCGGCAGCGAATCAGTGG +>161|16|Gypsy2-LTR_DM|2 +GCAGGCGTCGGCAGCGAATCAGT +>165|16|Gypsy2-LTR_DM|2 +TCGCAGCAGGCGTCGGCAGCGAAT +>167|16|Gypsy2-LTR_DM|1 +AGCGTCGCAGCAGGCGTCGGCAGCGA +>169|16|Gypsy2-LTR_DM|1 +AGCGTCGCAGCAGGCGTCGGCAGC +>172|16|Gypsy2-LTR_DM|1 +AGCAGCGTCGCAGCAGGCGTCGGC +>172|16|Gypsy2-LTR_DM|1 +GCAGCGTCGCAGCAGGCGTCGGC +>245|16|Gypsy2-LTR_DM|1 +TGTAATTGTTCATTTGAAACTAAAGC +>250|16|Gypsy2-LTR_DM|1 +TTATTGTAATTGTTCATTTGAAACT |
| b |
| diff -r 9645d995fb3c -r 9185ca0a7b43 test-data/res_files/reads-sample-small.fastq/subgroups/PPPartners/Gypsy2-LTR_DM/antisensPPP.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/res_files/reads-sample-small.fastq/subgroups/PPPartners/Gypsy2-LTR_DM/antisensPPP.txt Wed Jan 16 08:18:13 2019 -0500 |
| b |
| @@ -0,0 +1,28 @@ +>71|16|Gypsy2-LTR_DM|1 +GCGGAAAGAATGCAGACCTTTGGTCAGC +>73|16|Gypsy2-LTR_DM|1 +GCGGAAAGAATGCAGACCTTTGGTCA +>73|16|Gypsy2-LTR_DM|1 +CGGAAAGAATGCAGACCTTTGGTCA +>76|16|Gypsy2-LTR_DM|2 +GCGGAAAGAATGCAGACCTTTGG +>94|16|Gypsy2-LTR_DM|1 +ACTTTTAGCTGGTCGTTGACAGCGGA +>121|16|Gypsy2-LTR_DM|1 +GCGGCGGAGAAGTGCAGATGATCG +>123|16|Gypsy2-LTR_DM|1 +TACGCGGCGGAGAAGTGCAGATGAT +>140|16|Gypsy2-LTR_DM|20 +TCAGTGGTCGTCAGCGGCTACGCGGC +>141|16|Gypsy2-LTR_DM|1 +GAATCAGTGGTCGTCAGCGGCTACGCGG +>146|16|Gypsy2-LTR_DM|1 +GAATCAGTGGTCGTCAGCGGCTA +>193|16|Gypsy2-LTR_DM|1 +TAGCAATCAAGTGTGGGCGTCAGC +>250|16|Gypsy2-LTR_DM|1 +TTTATTGTAATTGTTCATTTGAAACT +>250|16|Gypsy2-LTR_DM|2 +TATTGTAATTGTTCATTTGAAACT +>274|16|Gypsy2-LTR_DM|1 +ATTTTGTAGATCGCAAGCGACCGTT |
| b |
| diff -r 9645d995fb3c -r 9185ca0a7b43 test-data/res_files/reads-sample-small.fastq/subgroups/PPPartners/Gypsy2-LTR_DM/histogram.png |
| b |
| Binary file test-data/res_files/reads-sample-small.fastq/subgroups/PPPartners/Gypsy2-LTR_DM/histogram.png has changed |
| b |
| diff -r 9645d995fb3c -r 9185ca0a7b43 test-data/res_files/reads-sample-small.fastq/subgroups/PPPartners/Gypsy2-LTR_DM/overlap_size.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/res_files/reads-sample-small.fastq/subgroups/PPPartners/Gypsy2-LTR_DM/overlap_size.txt Wed Jan 16 08:18:13 2019 -0500 |
| b |
| @@ -0,0 +1,24 @@ +size number percentage of the total overlap number +1 4 2.35 +2 3 1.76 +3 1 0.59 +4 5 2.94 +5 5 2.94 +6 3 1.76 +7 10 5.88 +8 11 6.47 +9 11 6.47 +10 20 11.76 +11 15 8.82 +12 7 4.12 +13 11 6.47 +14 9 5.29 +15 6 3.53 +16 12 7.06 +17 5 2.94 +18 4 2.35 +19 8 4.71 +20 5 2.94 +21 6 3.53 +22 4 2.35 +23 5 2.94 |
| b |
| diff -r 9645d995fb3c -r 9185ca0a7b43 test-data/res_files/reads-sample-small.fastq/subgroups/PPPartners/Gypsy2-LTR_DM/sens.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/res_files/reads-sample-small.fastq/subgroups/PPPartners/Gypsy2-LTR_DM/sens.txt Wed Jan 16 08:18:13 2019 -0500 |
| b |
| @@ -0,0 +1,48 @@ +>59|0|Gypsy2-LTR_DM|1 +AGTGCCCAAAATGCTGACCAAAGGTCT +>61|0|Gypsy2-LTR_DM|2 +TGCCCAAAATGCTGACCAAAGGTCTG +>62|0|Gypsy2-LTR_DM|2 +GCCCAAAATGCTGACCAAAGGTCTG +>85|0|Gypsy2-LTR_DM|1 +TGCATTCTTTCCGCTGTCAACGAC +>127|0|Gypsy2-LTR_DM|5 +TCTGCACTTCTCCGCCGCGTAGCCGC +>133|0|Gypsy2-LTR_DM|1 +CTTCTCCGCCGCGTAGCCGCTGACGA +>137|0|Gypsy2-LTR_DM|1 +TCCGCCGCGTAGCCGCTGACGACC +>145|0|Gypsy2-LTR_DM|1 +GTAGCCGCTGACGACCACTGATTCG +>146|0|Gypsy2-LTR_DM|2 +TAGCCGCTGACGACCACTGATTCGC +>146|0|Gypsy2-LTR_DM|1 +TAGCCGCTGACGACCACTGATTCG +>146|0|Gypsy2-LTR_DM|1 +TAGCCGCTGACGACCACTGATTC +>150|0|Gypsy2-LTR_DM|1 +CGCTGACGACCACTGATTCGCTG +>158|0|Gypsy2-LTR_DM|2 +ACCACTGATTCGCTGCCGACGCCTG +>168|0|Gypsy2-LTR_DM|1 +CGCTGCCGACGCCTGCTGCGACGC +>206|0|Gypsy2-LTR_DM|1 +CTTGATTGCTAGGGACTTAGGGAA +>208|0|Gypsy2-LTR_DM|1 +TGATTGCTAGGGACTTAGGGAAA +>223|0|Gypsy2-LTR_DM|1 +TAGGGAAATATTTTGTATCTTAGCTT +>259|0|Gypsy2-LTR_DM|2 +TGAACAATTACAATAAACGGTCGCT +>260|0|Gypsy2-LTR_DM|1 +GAACAATTACAATAAACGGTCGCT +>263|0|Gypsy2-LTR_DM|1 +CAATTACAATAAACGGTCGCTTGC +>267|0|Gypsy2-LTR_DM|6 +TACAATAAACGGTCGCTTGCGATC +>267|0|Gypsy2-LTR_DM|1 +TACAATAAACGGTCGCTTGCGAT +>291|0|Gypsy2-LTR_DM|1 +TACAAAATAAAAATCAATAAACTGT +>298|0|Gypsy2-LTR_DM|1 +TAAAAATCAATAAACTGTAATTAT |
| b |
| diff -r 9645d995fb3c -r 9185ca0a7b43 test-data/res_files/reads-sample-small.fastq/subgroups/PPPartners/Gypsy2-LTR_DM/sensPPP.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/res_files/reads-sample-small.fastq/subgroups/PPPartners/Gypsy2-LTR_DM/sensPPP.txt Wed Jan 16 08:18:13 2019 -0500 |
| b |
| @@ -0,0 +1,30 @@ +>88|0|Gypsy2-LTR_DM|1 +ATTCTTTCCGCTGTCAACGACCAG +>89|0|Gypsy2-LTR_DM|1 +TTCTTTCCGCTGTCAACGACCAG +>110|0|Gypsy2-LTR_DM|1 +AGCTAAAAGTGCGATCATCTGCACT +>135|0|Gypsy2-LTR_DM|1 +TCTCCGCCGCGTAGCCGCTGACGACC +>135|0|Gypsy2-LTR_DM|1 +TCTCCGCCGCGTAGCCGCTGACGA +>138|0|Gypsy2-LTR_DM|1 +CCGCCGCGTAGCCGCTGACGACCA +>138|0|Gypsy2-LTR_DM|1 +CCGCCGCGTAGCCGCTGACGACC +>156|0|Gypsy2-LTR_DM|2 +CGACCACTGATTCGCTGCCGACGCC +>159|0|Gypsy2-LTR_DM|2 +CCACTGATTCGCTGCCGACGCCTG +>207|0|Gypsy2-LTR_DM|1 +TTGATTGCTAGGGACTTAGGGAAAT +>207|0|Gypsy2-LTR_DM|1 +TTGATTGCTAGGGACTTAGGGAA +>264|0|Gypsy2-LTR_DM|2 +AATTACAATAAACGGTCGCTTGCGA +>266|0|Gypsy2-LTR_DM|4 +TTACAATAAACGGTCGCTTGCGATC +>266|0|Gypsy2-LTR_DM|1 +TTACAATAAACGGTCGCTTGCGA +>289|0|Gypsy2-LTR_DM|1 +TCTACAAAATAAAAATCAATAAACTG |
| b |
| diff -r 9645d995fb3c -r 9185ca0a7b43 test-data/res_files/reads-sample-small.fastq/subgroups/PPPartners/I_DM.html --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/res_files/reads-sample-small.fastq/subgroups/PPPartners/I_DM.html Wed Jan 16 08:18:13 2019 -0500 |
| b |
| b'@@ -0,0 +1,295 @@\n+\n+ <!DOCTYPE html>\n+ <html lang="en">\n+ <head>\n+ <meta charset="utf-8">\n+ <title>pipeline</title>\n+ <meta name="viewport" content="width=device-width, initial-scale=1.0">\n+ <meta name="description" content="">\n+ <meta name="author" content="">\n+ <!-- Le styles -->\n+ <link href="css/bootstrap.css" rel="stylesheet">\n+ <link href="css/bootstrap-table.css" rel="stylesheet">\n+ <style type="text/css">\n+ body {\n+ padding-top: 60px;\n+ padding-bottom: 40px;\n+ }\n+ div#page {\n+ width: 940px;\n+ background-color: #fff;\n+ margin: 0 auto;\n+ text-align: left;\n+ border-color: #fff;\n+ border-style: none solid solid;\n+ border-width: medium 1px 1px;\n+ }\n+\n+ div.content {\n+ \tdisplay: none;\n+\t float: right;\n+\t width: 550px;\n+ }\n+ div.content a, div.navigation a {\n+ text-decoration: none;\n+ \tcolor: #777;\n+ }\n+ div.content a:focus, div.content a:hover, div.content a:active {\n+ text-decoration: underline;\n+ }\n+ \n+ div.controls {\n+ margin-top: 5px;\n+\t height: 23px;\n+ }\n+ \n+ div.controls a {\n+\t padding: 5px;\n+ }\n+ div.ss-controls {\n+\t float: left;\n+ }\n+ div.nav-controls {\n+\t float: right;\n+ }\n+ div.slideshow-container {\n+\t position: relative;\n+\t clear: both;\n+\t height: 502px; /* This should be set to be at least the height of the largest image in the slideshow */\n+ }\n+ div.loader {\n+ \tposition: absolute;\n+ \ttop: 0;\n+ \tleft: 0;\n+ background-image: url(\'loader.gif\');\n+ background-repeat: no-repeat;\n+ background-position: center;\n+ \twidth: 550px;\n+ \theight: 502px; /* This should be set to be at least the height of the largest image in the slideshow */\n+ }\n+ div.slideshow {\n+ \n+ }\n+ \n+ div.slideshow span.image-wrapper {\n+\t display: block;\n+\t position: absolute;\n+\t top: 0;\n+\t left: 0;\n+ }\n+ div.slideshow a.advance-link {\n+\t display: block;\n+ \t width: 550px;\n+ height: 502px; /* This should be set to be at least the height of the largest image in the slideshow */\n+ line-height: 502px; /* This should be set to be at least the height of the largest image in the slideshow */\n+ text-align: center;\n+ }\n+ div.slideshow a.advance-link:hover, div.slideshow a.advance-link:active, div.slideshow a.advance-link:visited {\n+ text-decoration: none;\n+ }\n+ div.slideshow img {\n+ vertical-align: middle;\n+\tborder: 1px solid #ccc;\n+ }\n+\n+ div.image-title {\n+ font-weight: bold;\n+ font-size: 1.4em;\n+ }\n+\n+ div.image-desc {\n+ line-height: 1.3em;\n+ padding-top: 12px;\n+ }\n+ div.navigation {\n+\n+ }\n+ ul.thumbs {\n+\tclear: both;\n+\tmargin: 0;\n+\tpadding: 0;\n+ }\n+ ul.thumbs li {\n+\tfloat: none;\n+\tpadding: 0;\n+\tmargin: 0;\n+ list-style: none;\n+ }\n+ a.thumb {\n+\tpadding: 0;\n+\tdisplay: inline;\n+\tborder: none;\n+ }\n+ ul.thumbs li.selected a.thumb {\n+\tcolor: #000;\n+ font-weight: bold;\n+ }\n+ a.thumb:focus {\n+\toutline: none;\n+ }\n+ ul.thumbs img {\n+\tborder: none;\n+\tdisplay: block;\n+ }\n+ div.pagination {\n+\tclear: both;\n+ }\n+ div.navigation div.top {\n+ margin-bottom: 12px;\n+\theight: 11px;\n+ }\n+ div.navigation div.bottom {\n+ margin-top: 12px;\n+ }\n+ div.pagination a, div.pagination span.current, div.pagination span.ellipsis {\n+\tdisplay: block;\n+\tfloat: left;\n+ margin-right: 2px;\n+\tpadding: 4px 7px 2px 7px;\n+\tborder: 1px solid #ccc;\n+ }\n+ div.pagination a:hover {\n+ background-color: #eee;\n+ text-decoration: none;\n+ }\n+ div.pagination span.current {\n+ font-weight: bold;\n+ background-color: #000;\n+ border-color: #000;\n+\tcolor: #fff;\n+ }\n+ div.pagination span.ellipsis {\n+\tborder: none;\n+\tpadding: 5px 0 3px 2px;\n+ }\n+ \n+ div.download {\n+\tfloat: right;\n+ }\n+ \n+ div.caption-container {\n+\tposition: relative;\n+\tclear: left;\n+\theight: 75px;\n+ }\n+ span.image-caption {\n+\tdisplay: block;\n+\tposition: absolute;\n+\twidth: 550px;\n+\ttop: 0;\n+\tleft: 0;\n+ }\n+ div.caption {\n+\tpadding: 12px;\n+ }\n+\n+ /* Featurettes\n+ ------------------------- */\n+\n+ .featurette {\n+ padding-top: 20px; /* Vertica'..b'w: hidden; /* Vertically center images part 2: clear their floats. */\n+ text-align: center;\n+ }\n+\n+ .featurette-p\n+ {\n+ text-align: left;\n+ }\n+\n+ .featurette-image {\n+ margin-top: 10px; /* Vertically center images part 3: negative margin up the image the same amount of the padding to center it. */\n+ width: 450px;\n+ height: auto;\n+ }\n+\n+ </style>\n+ <link href="css/bootstrap-responsive.css" rel="stylesheet">\n+ </head>\n+ <body>\n+ \n+\t\t\t\t\t<div align="center">\n+\t\t\t\t\t<h2>I_DM</h2>\n+\t\t\t\t\t<p> <img class="featurette-image" src="I_DM/histogram.png"/></p>\n+\t\t\t\t\t<p><a href="I_DM/overlap_size.txt">ping pong signature</a></p>\n+\t\t\t\t\t<p><a href="I_DM/sensPPP.txt">sense reads with PPP</a></p>\n+\t\t\t\t\t<p><a href="I_DM/antisensPPP.txt">reverse reads with PPP</a></p>\n+\t\t\t\t\t<p><a href="I_DM/sens.txt">sense reads without PPP</a></p>\n+\t\t\t\t\t<p><a href="I_DM/antisens.txt">reverse reads without PPP</a></p>\n+\t\t\t\t\t</div>\n+ <!-- FOOTER -->\n+ <div class="container">\n+ <footer>\n+ \n+ </footer>\n+ </div>\n+ <!-- Le javascript\n+ ================================================== -->\n+ <!-- Placed at the end of the document so the pages load faster -->\n+ <script type="text/javascript" src="js/filter.js"></script>\n+ <script type="text/javascript" src="js/jquery.js"></script>\n+ <script type="text/javascript" src="js/jquery-1.3.2.js"></script>\n+ <script type="text/javascript" src="js/jquery.galleriffic.js"></script>\n+ <script type="text/javascript" src="js/jquery.opacityrollover.js"></script>\n+ <script type="text/javascript" src="js/bootstrap-table.js"></script>\n+ <script type="text/javascript" src="js/bootstrap.min.js"></script>\n+ <script type="text/javascript">\n+ jQuery(document).ready(function($) {\n+ // We only want these styles applied when javascript is enabled\n+ $(\'div.navigation\').css({\'width\' : \'300px\', \'float\' : \'left\'});\n+ $(\'div.content\').css(\'display\', \'block\');\n+ \n+ $(".each-gallery").each(function(i){\n+ // Initially set opacity on thumbs and add\n+ // additional styling for hover effect on thumbs\n+ var onMouseOutOpacity = 0.67;\n+ $(\'#thumbs + i + ul.thumbs li\').opacityrollover({\n+ mouseOutOpacity: onMouseOutOpacity,\n+ mouseOverOpacity: 1.0,\n+ fadeSpeed: \'fast\',\n+ exemptionSelector: \'.selected\'\n+ });\n+ \n+ // Initialize Advanced Galleriffic Gallery\n+ var gallery = $(\'#thumbs\'+i).galleriffic({\n+ delay: 2500,\n+ numThumbs: 22,\n+ preloadAhead: 10,\n+ enableTopPager: true,\n+ enableBottomPager: true,\n+ maxPagesToShow: 7,\n+ imageContainerSel: \'#slideshow\'+ i,\n+ controlsContainerSel: \'#controls\' + i,\n+ captionContainerSel: \'#caption\' + i,\n+ loadingContainerSel: \'#loading\' + i,\n+ renderSSControls: true,\n+ renderNavControls: true,\n+ playLinkText: \'Play\',\n+ pauseLinkText: \'Pause\',\n+ prevLinkText: \'‹ Previous\',\n+ nextLinkText: \'Next ›\',\n+ nextPageLinkText: \'Next ›\',\n+ prevPageLinkText: \'‹ Prev\',\n+ enableHistory: false,\n+ autoStart: false,\n+ syncTransitions: true,\n+ defaultTransitionDuration: 900,\n+ onSlideChange: function(prevIndex, nextIndex) {\n+ // \'this\' refers to the gallery, which is an extension of $(\'#thumbs\')\n+ this.find(\'ul.thumbs\').children()\n+ .eq(prevIndex).fadeTo(\'fast\', onMouseOutOpacity).end()\n+ .eq(nextIndex).fadeTo(\'fast\', 1.0);\n+ },\n+ onPageTransitionOut: function(callback) {\n+ this.fadeTo(\'fast\', 0.0, callback);\n+ },\n+ onPageTransitionIn: function() {\n+ this.fadeTo(\'fast\', 1.0);\n+ }\n+ });\n+ });\n+ });\n+ </script>\n+ </body>\n+ </html>\n+ \n\\ No newline at end of file\n' |
| b |
| diff -r 9645d995fb3c -r 9185ca0a7b43 test-data/res_files/reads-sample-small.fastq/subgroups/PPPartners/I_DM/antisens.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/res_files/reads-sample-small.fastq/subgroups/PPPartners/I_DM/antisens.txt Wed Jan 16 08:18:13 2019 -0500 |
| b |
| @@ -0,0 +1,32 @@ +>1256|16|I_DM|3 +TCCATGTCTTCAAGTTTGTCGTAGC +>1487|16|I_DM|1 +TAACTTAAAGGTAGTGTTAACGGA +>1659|16|I_DM|1 +TATTGAGGTTGGAATGTTATTAGT +>2966|16|I_DM|1 +TTGTGGTATGTGTCTATTGGATATT +>2980|16|I_DM|1 +TGTTTTGTAGGCTTGTGGTATGT +>2997|16|I_DM|1 +ATTGGGATGATTAGACTTGTTTT +>3007|16|I_DM|1 +TTCGGCTTGAGGATTGGGATGATTA +>4286|16|I_DM|1 +TTATGGATTCTGAGTGATGTGTCT +>4289|16|I_DM|1 +TCTTATGGATTCTGAGTGATGTG +>4425|16|I_DM|1 +TGTATGTTTCCGTTGTAATGGCGAA +>4748|16|I_DM|1 +TTTATGTTTGGGGTGAGGATAACT +>4985|16|I_DM|1 +GTTGGTATTGAATTTGGATTTAGG +>5007|16|I_DM|1 +TATCAACTTAGCAAAACGGACAAGT +>5103|16|I_DM|1 +TTTGCTAAGAAGGTCTAGAGGGTT +>5115|16|I_DM|1 +TTATTGGATTGGGTTTGCTAAGAAG +>5344|16|I_DM|1 +TATTTATTATGATAGATAGGATAGT |
| b |
| diff -r 9645d995fb3c -r 9185ca0a7b43 test-data/res_files/reads-sample-small.fastq/subgroups/PPPartners/I_DM/antisensPPP.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/res_files/reads-sample-small.fastq/subgroups/PPPartners/I_DM/antisensPPP.txt Wed Jan 16 08:18:13 2019 -0500 |
| b |
| @@ -0,0 +1,2 @@ +>3202|16|I_DM|2 +TTATGAGATAGTCTACATAGAGTA |
| b |
| diff -r 9645d995fb3c -r 9185ca0a7b43 test-data/res_files/reads-sample-small.fastq/subgroups/PPPartners/I_DM/histogram.png |
| b |
| Binary file test-data/res_files/reads-sample-small.fastq/subgroups/PPPartners/I_DM/histogram.png has changed |
| b |
| diff -r 9645d995fb3c -r 9185ca0a7b43 test-data/res_files/reads-sample-small.fastq/subgroups/PPPartners/I_DM/overlap_size.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/res_files/reads-sample-small.fastq/subgroups/PPPartners/I_DM/overlap_size.txt Wed Jan 16 08:18:13 2019 -0500 |
| b |
| @@ -0,0 +1,24 @@ +size number percentage of the total overlap number +1 0 0.00 +2 0 0.00 +3 0 0.00 +4 0 0.00 +5 0 0.00 +6 0 0.00 +7 0 0.00 +8 0 0.00 +9 0 0.00 +10 1 50.00 +11 0 0.00 +12 0 0.00 +13 0 0.00 +14 0 0.00 +15 0 0.00 +16 0 0.00 +17 0 0.00 +18 0 0.00 +19 0 0.00 +20 0 0.00 +21 0 0.00 +22 1 50.00 +23 0 0.00 |
| b |
| diff -r 9645d995fb3c -r 9185ca0a7b43 test-data/res_files/reads-sample-small.fastq/subgroups/PPPartners/I_DM/sens.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/res_files/reads-sample-small.fastq/subgroups/PPPartners/I_DM/sens.txt Wed Jan 16 08:18:13 2019 -0500 |
| b |
| @@ -0,0 +1,20 @@ +>903|0|I_DM|1 +CCAACAGAGCCCAATTGACCGCAAATG +>1428|0|I_DM|1 +AAACAAGCACACTAACTACAGCGAC +>1721|0|I_DM|1 +TGGGGGCGTAGCATTACTAGTGC +>3191|0|I_DM|3 +TTCGGACTTTCTACTCTATGTAGAC +>3236|0|I_DM|1 +AATGCACACCTCCCTCGTCACTCTTG +>3238|0|I_DM|1 +TGCACACCTCCCTCGTCACTCTTGA +>4624|0|I_DM|1 +TATGAATACGATCGCTAATAACG +>4826|0|I_DM|1 +AAACATAATAAACTGCAGTCAATG +>4913|0|I_DM|1 +TTGGACCAGACTCGACCAAATAAAAAT +>5105|0|I_DM|1 +CCCTCTAGACCTTCTTAGCAAACC |
| b |
| diff -r 9645d995fb3c -r 9185ca0a7b43 test-data/res_files/reads-sample-small.fastq/subgroups/PPPartners/I_DM/sensPPP.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/res_files/reads-sample-small.fastq/subgroups/PPPartners/I_DM/sensPPP.txt Wed Jan 16 08:18:13 2019 -0500 |
| b |
| @@ -0,0 +1,2 @@ +>3216|0|I_DM|1 +TATCTCATAACGAAGTCAAAAATG |
| b |
| diff -r 9645d995fb3c -r 9185ca0a7b43 test-data/res_files/reads-sample-small.fastq/subgroups/PPPartners/MAX_I.html --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/res_files/reads-sample-small.fastq/subgroups/PPPartners/MAX_I.html Wed Jan 16 08:18:13 2019 -0500 |
| b |
| b'@@ -0,0 +1,295 @@\n+\n+ <!DOCTYPE html>\n+ <html lang="en">\n+ <head>\n+ <meta charset="utf-8">\n+ <title>pipeline</title>\n+ <meta name="viewport" content="width=device-width, initial-scale=1.0">\n+ <meta name="description" content="">\n+ <meta name="author" content="">\n+ <!-- Le styles -->\n+ <link href="css/bootstrap.css" rel="stylesheet">\n+ <link href="css/bootstrap-table.css" rel="stylesheet">\n+ <style type="text/css">\n+ body {\n+ padding-top: 60px;\n+ padding-bottom: 40px;\n+ }\n+ div#page {\n+ width: 940px;\n+ background-color: #fff;\n+ margin: 0 auto;\n+ text-align: left;\n+ border-color: #fff;\n+ border-style: none solid solid;\n+ border-width: medium 1px 1px;\n+ }\n+\n+ div.content {\n+ \tdisplay: none;\n+\t float: right;\n+\t width: 550px;\n+ }\n+ div.content a, div.navigation a {\n+ text-decoration: none;\n+ \tcolor: #777;\n+ }\n+ div.content a:focus, div.content a:hover, div.content a:active {\n+ text-decoration: underline;\n+ }\n+ \n+ div.controls {\n+ margin-top: 5px;\n+\t height: 23px;\n+ }\n+ \n+ div.controls a {\n+\t padding: 5px;\n+ }\n+ div.ss-controls {\n+\t float: left;\n+ }\n+ div.nav-controls {\n+\t float: right;\n+ }\n+ div.slideshow-container {\n+\t position: relative;\n+\t clear: both;\n+\t height: 502px; /* This should be set to be at least the height of the largest image in the slideshow */\n+ }\n+ div.loader {\n+ \tposition: absolute;\n+ \ttop: 0;\n+ \tleft: 0;\n+ background-image: url(\'loader.gif\');\n+ background-repeat: no-repeat;\n+ background-position: center;\n+ \twidth: 550px;\n+ \theight: 502px; /* This should be set to be at least the height of the largest image in the slideshow */\n+ }\n+ div.slideshow {\n+ \n+ }\n+ \n+ div.slideshow span.image-wrapper {\n+\t display: block;\n+\t position: absolute;\n+\t top: 0;\n+\t left: 0;\n+ }\n+ div.slideshow a.advance-link {\n+\t display: block;\n+ \t width: 550px;\n+ height: 502px; /* This should be set to be at least the height of the largest image in the slideshow */\n+ line-height: 502px; /* This should be set to be at least the height of the largest image in the slideshow */\n+ text-align: center;\n+ }\n+ div.slideshow a.advance-link:hover, div.slideshow a.advance-link:active, div.slideshow a.advance-link:visited {\n+ text-decoration: none;\n+ }\n+ div.slideshow img {\n+ vertical-align: middle;\n+\tborder: 1px solid #ccc;\n+ }\n+\n+ div.image-title {\n+ font-weight: bold;\n+ font-size: 1.4em;\n+ }\n+\n+ div.image-desc {\n+ line-height: 1.3em;\n+ padding-top: 12px;\n+ }\n+ div.navigation {\n+\n+ }\n+ ul.thumbs {\n+\tclear: both;\n+\tmargin: 0;\n+\tpadding: 0;\n+ }\n+ ul.thumbs li {\n+\tfloat: none;\n+\tpadding: 0;\n+\tmargin: 0;\n+ list-style: none;\n+ }\n+ a.thumb {\n+\tpadding: 0;\n+\tdisplay: inline;\n+\tborder: none;\n+ }\n+ ul.thumbs li.selected a.thumb {\n+\tcolor: #000;\n+ font-weight: bold;\n+ }\n+ a.thumb:focus {\n+\toutline: none;\n+ }\n+ ul.thumbs img {\n+\tborder: none;\n+\tdisplay: block;\n+ }\n+ div.pagination {\n+\tclear: both;\n+ }\n+ div.navigation div.top {\n+ margin-bottom: 12px;\n+\theight: 11px;\n+ }\n+ div.navigation div.bottom {\n+ margin-top: 12px;\n+ }\n+ div.pagination a, div.pagination span.current, div.pagination span.ellipsis {\n+\tdisplay: block;\n+\tfloat: left;\n+ margin-right: 2px;\n+\tpadding: 4px 7px 2px 7px;\n+\tborder: 1px solid #ccc;\n+ }\n+ div.pagination a:hover {\n+ background-color: #eee;\n+ text-decoration: none;\n+ }\n+ div.pagination span.current {\n+ font-weight: bold;\n+ background-color: #000;\n+ border-color: #000;\n+\tcolor: #fff;\n+ }\n+ div.pagination span.ellipsis {\n+\tborder: none;\n+\tpadding: 5px 0 3px 2px;\n+ }\n+ \n+ div.download {\n+\tfloat: right;\n+ }\n+ \n+ div.caption-container {\n+\tposition: relative;\n+\tclear: left;\n+\theight: 75px;\n+ }\n+ span.image-caption {\n+\tdisplay: block;\n+\tposition: absolute;\n+\twidth: 550px;\n+\ttop: 0;\n+\tleft: 0;\n+ }\n+ div.caption {\n+\tpadding: 12px;\n+ }\n+\n+ /* Featurettes\n+ ------------------------- */\n+\n+ .featurette {\n+ padding-top: 20px; /* Vertica'..b'en; /* Vertically center images part 2: clear their floats. */\n+ text-align: center;\n+ }\n+\n+ .featurette-p\n+ {\n+ text-align: left;\n+ }\n+\n+ .featurette-image {\n+ margin-top: 10px; /* Vertically center images part 3: negative margin up the image the same amount of the padding to center it. */\n+ width: 450px;\n+ height: auto;\n+ }\n+\n+ </style>\n+ <link href="css/bootstrap-responsive.css" rel="stylesheet">\n+ </head>\n+ <body>\n+ \n+\t\t\t\t\t<div align="center">\n+\t\t\t\t\t<h2>MAX_I</h2>\n+\t\t\t\t\t<p> <img class="featurette-image" src="MAX_I/histogram.png"/></p>\n+\t\t\t\t\t<p><a href="MAX_I/overlap_size.txt">ping pong signature</a></p>\n+\t\t\t\t\t<p><a href="MAX_I/sensPPP.txt">sense reads with PPP</a></p>\n+\t\t\t\t\t<p><a href="MAX_I/antisensPPP.txt">reverse reads with PPP</a></p>\n+\t\t\t\t\t<p><a href="MAX_I/sens.txt">sense reads without PPP</a></p>\n+\t\t\t\t\t<p><a href="MAX_I/antisens.txt">reverse reads without PPP</a></p>\n+\t\t\t\t\t</div>\n+ <!-- FOOTER -->\n+ <div class="container">\n+ <footer>\n+ \n+ </footer>\n+ </div>\n+ <!-- Le javascript\n+ ================================================== -->\n+ <!-- Placed at the end of the document so the pages load faster -->\n+ <script type="text/javascript" src="js/filter.js"></script>\n+ <script type="text/javascript" src="js/jquery.js"></script>\n+ <script type="text/javascript" src="js/jquery-1.3.2.js"></script>\n+ <script type="text/javascript" src="js/jquery.galleriffic.js"></script>\n+ <script type="text/javascript" src="js/jquery.opacityrollover.js"></script>\n+ <script type="text/javascript" src="js/bootstrap-table.js"></script>\n+ <script type="text/javascript" src="js/bootstrap.min.js"></script>\n+ <script type="text/javascript">\n+ jQuery(document).ready(function($) {\n+ // We only want these styles applied when javascript is enabled\n+ $(\'div.navigation\').css({\'width\' : \'300px\', \'float\' : \'left\'});\n+ $(\'div.content\').css(\'display\', \'block\');\n+ \n+ $(".each-gallery").each(function(i){\n+ // Initially set opacity on thumbs and add\n+ // additional styling for hover effect on thumbs\n+ var onMouseOutOpacity = 0.67;\n+ $(\'#thumbs + i + ul.thumbs li\').opacityrollover({\n+ mouseOutOpacity: onMouseOutOpacity,\n+ mouseOverOpacity: 1.0,\n+ fadeSpeed: \'fast\',\n+ exemptionSelector: \'.selected\'\n+ });\n+ \n+ // Initialize Advanced Galleriffic Gallery\n+ var gallery = $(\'#thumbs\'+i).galleriffic({\n+ delay: 2500,\n+ numThumbs: 22,\n+ preloadAhead: 10,\n+ enableTopPager: true,\n+ enableBottomPager: true,\n+ maxPagesToShow: 7,\n+ imageContainerSel: \'#slideshow\'+ i,\n+ controlsContainerSel: \'#controls\' + i,\n+ captionContainerSel: \'#caption\' + i,\n+ loadingContainerSel: \'#loading\' + i,\n+ renderSSControls: true,\n+ renderNavControls: true,\n+ playLinkText: \'Play\',\n+ pauseLinkText: \'Pause\',\n+ prevLinkText: \'‹ Previous\',\n+ nextLinkText: \'Next ›\',\n+ nextPageLinkText: \'Next ›\',\n+ prevPageLinkText: \'‹ Prev\',\n+ enableHistory: false,\n+ autoStart: false,\n+ syncTransitions: true,\n+ defaultTransitionDuration: 900,\n+ onSlideChange: function(prevIndex, nextIndex) {\n+ // \'this\' refers to the gallery, which is an extension of $(\'#thumbs\')\n+ this.find(\'ul.thumbs\').children()\n+ .eq(prevIndex).fadeTo(\'fast\', onMouseOutOpacity).end()\n+ .eq(nextIndex).fadeTo(\'fast\', 1.0);\n+ },\n+ onPageTransitionOut: function(callback) {\n+ this.fadeTo(\'fast\', 0.0, callback);\n+ },\n+ onPageTransitionIn: function() {\n+ this.fadeTo(\'fast\', 1.0);\n+ }\n+ });\n+ });\n+ });\n+ </script>\n+ </body>\n+ </html>\n+ \n\\ No newline at end of file\n' |
| b |
| diff -r 9645d995fb3c -r 9185ca0a7b43 test-data/res_files/reads-sample-small.fastq/subgroups/PPPartners/MAX_I/antisens.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/res_files/reads-sample-small.fastq/subgroups/PPPartners/MAX_I/antisens.txt Wed Jan 16 08:18:13 2019 -0500 |
| b |
| @@ -0,0 +1,40 @@ +>35|16|MAX_I|1 +TCTTGATTTTTCCGCAAGGAGCGCT +>68|16|MAX_I|2 +CACGGACGGAATAAGATTTAAAGC +>85|16|MAX_I|1 +AAAAACGAAAATGGCGACCACGGAC +>92|16|MAX_I|1 +GTTGGAAAAACGAAAATGGCGAC +>94|16|MAX_I|1 +CCGTTGGAAAAACGAAAATGGCG +>105|16|MAX_I|1 +AAGAATAAACGCCGTTGGAAAAAC +>115|16|MAX_I|1 +GATGGACGGAAAGAATAAACGCCG +>116|16|MAX_I|1 +CGGATGGACGGAAAGAATAAACGCC +>126|16|MAX_I|7 +TCACTTGATACGGATGGACGGAAAG +>127|16|MAX_I|1 +CACTTGATACGGATGGACGGAAA +>127|16|MAX_I|10 +TCACTTGATACGGATGGACGGAAA +>128|16|MAX_I|1 +TCACTTGATACGGATGGACGGAA +>130|16|MAX_I|1 +TTTCACTTGATACGGATGGACGG +>131|16|MAX_I|1 +TTTTCACTTGATACGGATGGACG +>171|16|MAX_I|1 +TAATCACGGCGGCTGGGCGCATG +>236|16|MAX_I|1 +CACCGTGAGACGAATTAGGGGGC +>236|16|MAX_I|1 +TCACCGTGAGACGAATTAGGGGGC +>251|16|MAX_I|1 +GCTTGGATACCAGCGGATCACCGTGA +>263|16|MAX_I|1 +TATGTATATGCGCTTGGATACCAGC +>310|16|MAX_I|1 +TAGCAGCGGACGATAATAGTGAATT |
| b |
| diff -r 9645d995fb3c -r 9185ca0a7b43 test-data/res_files/reads-sample-small.fastq/subgroups/PPPartners/MAX_I/antisensPPP.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/res_files/reads-sample-small.fastq/subgroups/PPPartners/MAX_I/antisensPPP.txt Wed Jan 16 08:18:13 2019 -0500 |
| b |
| @@ -0,0 +1,14 @@ +>106|16|MAX_I|2 +AAAGAATAAACGCCGTTGGAAAAA +>106|16|MAX_I|14 +GAAAGAATAAACGCCGTTGGAAAAA +>107|16|MAX_I|3 +AAAGAATAAACGCCGTTGGAAAA +>107|16|MAX_I|10 +GAAAGAATAAACGCCGTTGGAAAA +>108|16|MAX_I|1 +GAAAGAATAAACGCCGTTGGAAA +>301|16|MAX_I|1 +GACGATAATAGTGAATTTTGGACAGT +>303|16|MAX_I|3 +GACGATAATAGTGAATTTTGGACA |
| b |
| diff -r 9645d995fb3c -r 9185ca0a7b43 test-data/res_files/reads-sample-small.fastq/subgroups/PPPartners/MAX_I/histogram.png |
| b |
| Binary file test-data/res_files/reads-sample-small.fastq/subgroups/PPPartners/MAX_I/histogram.png has changed |
| b |
| diff -r 9645d995fb3c -r 9185ca0a7b43 test-data/res_files/reads-sample-small.fastq/subgroups/PPPartners/MAX_I/overlap_size.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/res_files/reads-sample-small.fastq/subgroups/PPPartners/MAX_I/overlap_size.txt Wed Jan 16 08:18:13 2019 -0500 |
| b |
| @@ -0,0 +1,24 @@ +size number percentage of the total overlap number +1 2 3.70 +2 2 3.70 +3 3 5.56 +4 1 1.85 +5 1 1.85 +6 2 3.70 +7 0 0.00 +8 2 3.70 +9 3 5.56 +10 11 20.37 +11 5 9.26 +12 0 0.00 +13 1 1.85 +14 0 0.00 +15 0 0.00 +16 0 0.00 +17 1 1.85 +18 3 5.56 +19 1 1.85 +20 3 5.56 +21 4 7.41 +22 6 11.11 +23 3 5.56 |
| b |
| diff -r 9645d995fb3c -r 9185ca0a7b43 test-data/res_files/reads-sample-small.fastq/subgroups/PPPartners/MAX_I/sens.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/res_files/reads-sample-small.fastq/subgroups/PPPartners/MAX_I/sens.txt Wed Jan 16 08:18:13 2019 -0500 |
| b |
| @@ -0,0 +1,20 @@ +>54|0|MAX_I|1 +TCAAGATAAGTACGGCTTTAAATCT +>55|0|MAX_I|1 +CAAGATAAGTACGGCTTTAAATC +>60|0|MAX_I|2 +TAAGTACGGCTTTAAATCTTATTCC +>81|0|MAX_I|1 +TTCCGTCCGTGGTCGCCATTTTCG +>88|0|MAX_I|1 +CGTGGTCGCCATTTTCGTTTTTCC +>93|0|MAX_I|1 +TCGCCATTTTCGTTTTTCCAACGGC +>109|0|MAX_I|1 +TTCCAACGGCGTTTATTCTTTCC +>128|0|MAX_I|1 +TTCCGTCCATCCGTATCAAGTGAA +>231|0|MAX_I|1 +TACCGGCCCCCTAATTCGTCTCAC +>239|0|MAX_I|1 +CCCTAATTCGTCTCACGGTGATCCG |
| b |
| diff -r 9645d995fb3c -r 9185ca0a7b43 test-data/res_files/reads-sample-small.fastq/subgroups/PPPartners/MAX_I/sensPPP.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/res_files/reads-sample-small.fastq/subgroups/PPPartners/MAX_I/sensPPP.txt Wed Jan 16 08:18:13 2019 -0500 |
| b |
| @@ -0,0 +1,8 @@ +>120|0|MAX_I|1 +TTTATTCTTTCCGTCCATCCGTA +>121|0|MAX_I|1 +TTATTCTTTCCGTCCATCCGTATC +>317|0|MAX_I|2 +TATTATCGTCCGCTGCTAAACTAC +>317|0|MAX_I|2 +TATTATCGTCCGCTGCTAAACTACTG |
| b |
| diff -r 9645d995fb3c -r 9185ca0a7b43 test-data/res_files/reads-sample-small.fastq/subgroups/PPPartners/MAX_LTR.html --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/res_files/reads-sample-small.fastq/subgroups/PPPartners/MAX_LTR.html Wed Jan 16 08:18:13 2019 -0500 |
| b |
| b'@@ -0,0 +1,295 @@\n+\n+ <!DOCTYPE html>\n+ <html lang="en">\n+ <head>\n+ <meta charset="utf-8">\n+ <title>pipeline</title>\n+ <meta name="viewport" content="width=device-width, initial-scale=1.0">\n+ <meta name="description" content="">\n+ <meta name="author" content="">\n+ <!-- Le styles -->\n+ <link href="css/bootstrap.css" rel="stylesheet">\n+ <link href="css/bootstrap-table.css" rel="stylesheet">\n+ <style type="text/css">\n+ body {\n+ padding-top: 60px;\n+ padding-bottom: 40px;\n+ }\n+ div#page {\n+ width: 940px;\n+ background-color: #fff;\n+ margin: 0 auto;\n+ text-align: left;\n+ border-color: #fff;\n+ border-style: none solid solid;\n+ border-width: medium 1px 1px;\n+ }\n+\n+ div.content {\n+ \tdisplay: none;\n+\t float: right;\n+\t width: 550px;\n+ }\n+ div.content a, div.navigation a {\n+ text-decoration: none;\n+ \tcolor: #777;\n+ }\n+ div.content a:focus, div.content a:hover, div.content a:active {\n+ text-decoration: underline;\n+ }\n+ \n+ div.controls {\n+ margin-top: 5px;\n+\t height: 23px;\n+ }\n+ \n+ div.controls a {\n+\t padding: 5px;\n+ }\n+ div.ss-controls {\n+\t float: left;\n+ }\n+ div.nav-controls {\n+\t float: right;\n+ }\n+ div.slideshow-container {\n+\t position: relative;\n+\t clear: both;\n+\t height: 502px; /* This should be set to be at least the height of the largest image in the slideshow */\n+ }\n+ div.loader {\n+ \tposition: absolute;\n+ \ttop: 0;\n+ \tleft: 0;\n+ background-image: url(\'loader.gif\');\n+ background-repeat: no-repeat;\n+ background-position: center;\n+ \twidth: 550px;\n+ \theight: 502px; /* This should be set to be at least the height of the largest image in the slideshow */\n+ }\n+ div.slideshow {\n+ \n+ }\n+ \n+ div.slideshow span.image-wrapper {\n+\t display: block;\n+\t position: absolute;\n+\t top: 0;\n+\t left: 0;\n+ }\n+ div.slideshow a.advance-link {\n+\t display: block;\n+ \t width: 550px;\n+ height: 502px; /* This should be set to be at least the height of the largest image in the slideshow */\n+ line-height: 502px; /* This should be set to be at least the height of the largest image in the slideshow */\n+ text-align: center;\n+ }\n+ div.slideshow a.advance-link:hover, div.slideshow a.advance-link:active, div.slideshow a.advance-link:visited {\n+ text-decoration: none;\n+ }\n+ div.slideshow img {\n+ vertical-align: middle;\n+\tborder: 1px solid #ccc;\n+ }\n+\n+ div.image-title {\n+ font-weight: bold;\n+ font-size: 1.4em;\n+ }\n+\n+ div.image-desc {\n+ line-height: 1.3em;\n+ padding-top: 12px;\n+ }\n+ div.navigation {\n+\n+ }\n+ ul.thumbs {\n+\tclear: both;\n+\tmargin: 0;\n+\tpadding: 0;\n+ }\n+ ul.thumbs li {\n+\tfloat: none;\n+\tpadding: 0;\n+\tmargin: 0;\n+ list-style: none;\n+ }\n+ a.thumb {\n+\tpadding: 0;\n+\tdisplay: inline;\n+\tborder: none;\n+ }\n+ ul.thumbs li.selected a.thumb {\n+\tcolor: #000;\n+ font-weight: bold;\n+ }\n+ a.thumb:focus {\n+\toutline: none;\n+ }\n+ ul.thumbs img {\n+\tborder: none;\n+\tdisplay: block;\n+ }\n+ div.pagination {\n+\tclear: both;\n+ }\n+ div.navigation div.top {\n+ margin-bottom: 12px;\n+\theight: 11px;\n+ }\n+ div.navigation div.bottom {\n+ margin-top: 12px;\n+ }\n+ div.pagination a, div.pagination span.current, div.pagination span.ellipsis {\n+\tdisplay: block;\n+\tfloat: left;\n+ margin-right: 2px;\n+\tpadding: 4px 7px 2px 7px;\n+\tborder: 1px solid #ccc;\n+ }\n+ div.pagination a:hover {\n+ background-color: #eee;\n+ text-decoration: none;\n+ }\n+ div.pagination span.current {\n+ font-weight: bold;\n+ background-color: #000;\n+ border-color: #000;\n+\tcolor: #fff;\n+ }\n+ div.pagination span.ellipsis {\n+\tborder: none;\n+\tpadding: 5px 0 3px 2px;\n+ }\n+ \n+ div.download {\n+\tfloat: right;\n+ }\n+ \n+ div.caption-container {\n+\tposition: relative;\n+\tclear: left;\n+\theight: 75px;\n+ }\n+ span.image-caption {\n+\tdisplay: block;\n+\tposition: absolute;\n+\twidth: 550px;\n+\ttop: 0;\n+\tleft: 0;\n+ }\n+ div.caption {\n+\tpadding: 12px;\n+ }\n+\n+ /* Featurettes\n+ ------------------------- */\n+\n+ .featurette {\n+ padding-top: 20px; /* Vertica'..b'lly center images part 2: clear their floats. */\n+ text-align: center;\n+ }\n+\n+ .featurette-p\n+ {\n+ text-align: left;\n+ }\n+\n+ .featurette-image {\n+ margin-top: 10px; /* Vertically center images part 3: negative margin up the image the same amount of the padding to center it. */\n+ width: 450px;\n+ height: auto;\n+ }\n+\n+ </style>\n+ <link href="css/bootstrap-responsive.css" rel="stylesheet">\n+ </head>\n+ <body>\n+ \n+\t\t\t\t\t<div align="center">\n+\t\t\t\t\t<h2>MAX_LTR</h2>\n+\t\t\t\t\t<p> <img class="featurette-image" src="MAX_LTR/histogram.png"/></p>\n+\t\t\t\t\t<p><a href="MAX_LTR/overlap_size.txt">ping pong signature</a></p>\n+\t\t\t\t\t<p><a href="MAX_LTR/sensPPP.txt">sense reads with PPP</a></p>\n+\t\t\t\t\t<p><a href="MAX_LTR/antisensPPP.txt">reverse reads with PPP</a></p>\n+\t\t\t\t\t<p><a href="MAX_LTR/sens.txt">sense reads without PPP</a></p>\n+\t\t\t\t\t<p><a href="MAX_LTR/antisens.txt">reverse reads without PPP</a></p>\n+\t\t\t\t\t</div>\n+ <!-- FOOTER -->\n+ <div class="container">\n+ <footer>\n+ \n+ </footer>\n+ </div>\n+ <!-- Le javascript\n+ ================================================== -->\n+ <!-- Placed at the end of the document so the pages load faster -->\n+ <script type="text/javascript" src="js/filter.js"></script>\n+ <script type="text/javascript" src="js/jquery.js"></script>\n+ <script type="text/javascript" src="js/jquery-1.3.2.js"></script>\n+ <script type="text/javascript" src="js/jquery.galleriffic.js"></script>\n+ <script type="text/javascript" src="js/jquery.opacityrollover.js"></script>\n+ <script type="text/javascript" src="js/bootstrap-table.js"></script>\n+ <script type="text/javascript" src="js/bootstrap.min.js"></script>\n+ <script type="text/javascript">\n+ jQuery(document).ready(function($) {\n+ // We only want these styles applied when javascript is enabled\n+ $(\'div.navigation\').css({\'width\' : \'300px\', \'float\' : \'left\'});\n+ $(\'div.content\').css(\'display\', \'block\');\n+ \n+ $(".each-gallery").each(function(i){\n+ // Initially set opacity on thumbs and add\n+ // additional styling for hover effect on thumbs\n+ var onMouseOutOpacity = 0.67;\n+ $(\'#thumbs + i + ul.thumbs li\').opacityrollover({\n+ mouseOutOpacity: onMouseOutOpacity,\n+ mouseOverOpacity: 1.0,\n+ fadeSpeed: \'fast\',\n+ exemptionSelector: \'.selected\'\n+ });\n+ \n+ // Initialize Advanced Galleriffic Gallery\n+ var gallery = $(\'#thumbs\'+i).galleriffic({\n+ delay: 2500,\n+ numThumbs: 22,\n+ preloadAhead: 10,\n+ enableTopPager: true,\n+ enableBottomPager: true,\n+ maxPagesToShow: 7,\n+ imageContainerSel: \'#slideshow\'+ i,\n+ controlsContainerSel: \'#controls\' + i,\n+ captionContainerSel: \'#caption\' + i,\n+ loadingContainerSel: \'#loading\' + i,\n+ renderSSControls: true,\n+ renderNavControls: true,\n+ playLinkText: \'Play\',\n+ pauseLinkText: \'Pause\',\n+ prevLinkText: \'‹ Previous\',\n+ nextLinkText: \'Next ›\',\n+ nextPageLinkText: \'Next ›\',\n+ prevPageLinkText: \'‹ Prev\',\n+ enableHistory: false,\n+ autoStart: false,\n+ syncTransitions: true,\n+ defaultTransitionDuration: 900,\n+ onSlideChange: function(prevIndex, nextIndex) {\n+ // \'this\' refers to the gallery, which is an extension of $(\'#thumbs\')\n+ this.find(\'ul.thumbs\').children()\n+ .eq(prevIndex).fadeTo(\'fast\', onMouseOutOpacity).end()\n+ .eq(nextIndex).fadeTo(\'fast\', 1.0);\n+ },\n+ onPageTransitionOut: function(callback) {\n+ this.fadeTo(\'fast\', 0.0, callback);\n+ },\n+ onPageTransitionIn: function() {\n+ this.fadeTo(\'fast\', 1.0);\n+ }\n+ });\n+ });\n+ });\n+ </script>\n+ </body>\n+ </html>\n+ \n\\ No newline at end of file\n' |
| b |
| diff -r 9645d995fb3c -r 9185ca0a7b43 test-data/res_files/reads-sample-small.fastq/subgroups/PPPartners/MAX_LTR/antisens.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/res_files/reads-sample-small.fastq/subgroups/PPPartners/MAX_LTR/antisens.txt Wed Jan 16 08:18:13 2019 -0500 |
| b |
| @@ -0,0 +1,36 @@ +>5|16|MAX_LTR|9 +TCAACTGTTTGCGCCCTTCTGGCGTG +>14|16|MAX_LTR|1 +TGCCGCTCAACTGTTTGCGCCCT +>14|16|MAX_LTR|3 +CACTGCCGCTCAACTGTTTGCGCCCT +>15|16|MAX_LTR|6 +CACTGCCGCTCAACTGTTTGCGCCC +>16|16|MAX_LTR|6 +CACTGCCGCTCAACTGTTTGCGCC +>17|16|MAX_LTR|1 +TACACTGCCGCTCAACTGTTTGCGC +>53|16|MAX_LTR|1 +CCGTGGAGGAGCTTTGAGTACAAG +>85|16|MAX_LTR|1 +AGAGAAGGAGAGCGCGAGCAGCGGTG +>89|16|MAX_LTR|1 +GGAGAGAAGGAGAGCGCGAGCAGC +>95|16|MAX_LTR|1 +CGAGAGGAGAGAAGGAGAGCGCG +>134|16|MAX_LTR|1 +ACCGCGGAGTGGTGAATACCTTG +>134|16|MAX_LTR|2 +GGACCGCGGAGTGGTGAATACCTTG +>152|16|MAX_LTR|2 +CATTGGAAATACCGCGGGACCGC +>152|16|MAX_LTR|1 +AACATTGGAAATACCGCGGGACCGC +>153|16|MAX_LTR|1 +ACATTGGAAATACCGCGGGACCG +>153|16|MAX_LTR|1 +AACATTGGAAATACCGCGGGACCG +>154|16|MAX_LTR|3 +TAACATTGGAAATACCGCGGGACC +>155|16|MAX_LTR|1 +TAACATTGGAAATACCGCGGGAC |
| b |
| diff -r 9645d995fb3c -r 9185ca0a7b43 test-data/res_files/reads-sample-small.fastq/subgroups/PPPartners/MAX_LTR/histogram.png |
| b |
| Binary file test-data/res_files/reads-sample-small.fastq/subgroups/PPPartners/MAX_LTR/histogram.png has changed |
| b |
| diff -r 9645d995fb3c -r 9185ca0a7b43 test-data/res_files/reads-sample-small.fastq/subgroups/PPPartners/MAX_LTR/overlap_size.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/res_files/reads-sample-small.fastq/subgroups/PPPartners/MAX_LTR/overlap_size.txt Wed Jan 16 08:18:13 2019 -0500 |
| b |
| @@ -0,0 +1,24 @@ +size number percentage of the total overlap number +1 0 0.00 +2 0 0.00 +3 0 0.00 +4 0 0.00 +5 0 0.00 +6 0 0.00 +7 0 0.00 +8 0 0.00 +9 2 12.50 +10 0 0.00 +11 0 0.00 +12 0 0.00 +13 0 0.00 +14 0 0.00 +15 1 6.25 +16 0 0.00 +17 0 0.00 +18 8 50.00 +19 0 0.00 +20 3 18.75 +21 0 0.00 +22 2 12.50 +23 0 0.00 |
| b |
| diff -r 9645d995fb3c -r 9185ca0a7b43 test-data/res_files/reads-sample-small.fastq/subgroups/PPPartners/MAX_LTR/sens.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/res_files/reads-sample-small.fastq/subgroups/PPPartners/MAX_LTR/sens.txt Wed Jan 16 08:18:13 2019 -0500 |
| b |
| @@ -0,0 +1,22 @@ +>13|0|MAX_LTR|1 +AAGGGCGCAAACAGTTGAGCGGCA +>22|0|MAX_LTR|2 +AACAGTTGAGCGGCAGTGTAAGC +>49|0|MAX_LTR|1 +AATGCTTGTACTCAAAGCTCCTCC +>53|0|MAX_LTR|1 +CTTGTACTCAAAGCTCCTCCACG +>53|0|MAX_LTR|1 +CTTGTACTCAAAGCTCCTCCACGG +>53|0|MAX_LTR|2 +CTTGTACTCAAAGCTCCTCCACGGC +>53|0|MAX_LTR|1 +CTTGTACTCAAAGCTCCTCCACGGCT +>81|0|MAX_LTR|5 +CAAGCACCGCTGCTCGCGCTCTCCT +>89|0|MAX_LTR|1 +GCTGCTCGCGCTCTCCTTCTCTCCT +>135|0|MAX_LTR|2 +AAGGTATTCACCACTCCGCGGTCCC +>139|0|MAX_LTR|6 +TATTCACCACTCCGCGGTCCCGC |
| b |
| diff -r 9645d995fb3c -r 9185ca0a7b43 test-data/res_files/reads-sample-small.fastq/subgroups/PPPartners/PROTOP.html --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/res_files/reads-sample-small.fastq/subgroups/PPPartners/PROTOP.html Wed Jan 16 08:18:13 2019 -0500 |
| b |
| b'@@ -0,0 +1,295 @@\n+\n+ <!DOCTYPE html>\n+ <html lang="en">\n+ <head>\n+ <meta charset="utf-8">\n+ <title>pipeline</title>\n+ <meta name="viewport" content="width=device-width, initial-scale=1.0">\n+ <meta name="description" content="">\n+ <meta name="author" content="">\n+ <!-- Le styles -->\n+ <link href="css/bootstrap.css" rel="stylesheet">\n+ <link href="css/bootstrap-table.css" rel="stylesheet">\n+ <style type="text/css">\n+ body {\n+ padding-top: 60px;\n+ padding-bottom: 40px;\n+ }\n+ div#page {\n+ width: 940px;\n+ background-color: #fff;\n+ margin: 0 auto;\n+ text-align: left;\n+ border-color: #fff;\n+ border-style: none solid solid;\n+ border-width: medium 1px 1px;\n+ }\n+\n+ div.content {\n+ \tdisplay: none;\n+\t float: right;\n+\t width: 550px;\n+ }\n+ div.content a, div.navigation a {\n+ text-decoration: none;\n+ \tcolor: #777;\n+ }\n+ div.content a:focus, div.content a:hover, div.content a:active {\n+ text-decoration: underline;\n+ }\n+ \n+ div.controls {\n+ margin-top: 5px;\n+\t height: 23px;\n+ }\n+ \n+ div.controls a {\n+\t padding: 5px;\n+ }\n+ div.ss-controls {\n+\t float: left;\n+ }\n+ div.nav-controls {\n+\t float: right;\n+ }\n+ div.slideshow-container {\n+\t position: relative;\n+\t clear: both;\n+\t height: 502px; /* This should be set to be at least the height of the largest image in the slideshow */\n+ }\n+ div.loader {\n+ \tposition: absolute;\n+ \ttop: 0;\n+ \tleft: 0;\n+ background-image: url(\'loader.gif\');\n+ background-repeat: no-repeat;\n+ background-position: center;\n+ \twidth: 550px;\n+ \theight: 502px; /* This should be set to be at least the height of the largest image in the slideshow */\n+ }\n+ div.slideshow {\n+ \n+ }\n+ \n+ div.slideshow span.image-wrapper {\n+\t display: block;\n+\t position: absolute;\n+\t top: 0;\n+\t left: 0;\n+ }\n+ div.slideshow a.advance-link {\n+\t display: block;\n+ \t width: 550px;\n+ height: 502px; /* This should be set to be at least the height of the largest image in the slideshow */\n+ line-height: 502px; /* This should be set to be at least the height of the largest image in the slideshow */\n+ text-align: center;\n+ }\n+ div.slideshow a.advance-link:hover, div.slideshow a.advance-link:active, div.slideshow a.advance-link:visited {\n+ text-decoration: none;\n+ }\n+ div.slideshow img {\n+ vertical-align: middle;\n+\tborder: 1px solid #ccc;\n+ }\n+\n+ div.image-title {\n+ font-weight: bold;\n+ font-size: 1.4em;\n+ }\n+\n+ div.image-desc {\n+ line-height: 1.3em;\n+ padding-top: 12px;\n+ }\n+ div.navigation {\n+\n+ }\n+ ul.thumbs {\n+\tclear: both;\n+\tmargin: 0;\n+\tpadding: 0;\n+ }\n+ ul.thumbs li {\n+\tfloat: none;\n+\tpadding: 0;\n+\tmargin: 0;\n+ list-style: none;\n+ }\n+ a.thumb {\n+\tpadding: 0;\n+\tdisplay: inline;\n+\tborder: none;\n+ }\n+ ul.thumbs li.selected a.thumb {\n+\tcolor: #000;\n+ font-weight: bold;\n+ }\n+ a.thumb:focus {\n+\toutline: none;\n+ }\n+ ul.thumbs img {\n+\tborder: none;\n+\tdisplay: block;\n+ }\n+ div.pagination {\n+\tclear: both;\n+ }\n+ div.navigation div.top {\n+ margin-bottom: 12px;\n+\theight: 11px;\n+ }\n+ div.navigation div.bottom {\n+ margin-top: 12px;\n+ }\n+ div.pagination a, div.pagination span.current, div.pagination span.ellipsis {\n+\tdisplay: block;\n+\tfloat: left;\n+ margin-right: 2px;\n+\tpadding: 4px 7px 2px 7px;\n+\tborder: 1px solid #ccc;\n+ }\n+ div.pagination a:hover {\n+ background-color: #eee;\n+ text-decoration: none;\n+ }\n+ div.pagination span.current {\n+ font-weight: bold;\n+ background-color: #000;\n+ border-color: #000;\n+\tcolor: #fff;\n+ }\n+ div.pagination span.ellipsis {\n+\tborder: none;\n+\tpadding: 5px 0 3px 2px;\n+ }\n+ \n+ div.download {\n+\tfloat: right;\n+ }\n+ \n+ div.caption-container {\n+\tposition: relative;\n+\tclear: left;\n+\theight: 75px;\n+ }\n+ span.image-caption {\n+\tdisplay: block;\n+\tposition: absolute;\n+\twidth: 550px;\n+\ttop: 0;\n+\tleft: 0;\n+ }\n+ div.caption {\n+\tpadding: 12px;\n+ }\n+\n+ /* Featurettes\n+ ------------------------- */\n+\n+ .featurette {\n+ padding-top: 20px; /* Vertica'..b'Vertically center images part 2: clear their floats. */\n+ text-align: center;\n+ }\n+\n+ .featurette-p\n+ {\n+ text-align: left;\n+ }\n+\n+ .featurette-image {\n+ margin-top: 10px; /* Vertically center images part 3: negative margin up the image the same amount of the padding to center it. */\n+ width: 450px;\n+ height: auto;\n+ }\n+\n+ </style>\n+ <link href="css/bootstrap-responsive.css" rel="stylesheet">\n+ </head>\n+ <body>\n+ \n+\t\t\t\t\t<div align="center">\n+\t\t\t\t\t<h2>PROTOP</h2>\n+\t\t\t\t\t<p> <img class="featurette-image" src="PROTOP/histogram.png"/></p>\n+\t\t\t\t\t<p><a href="PROTOP/overlap_size.txt">ping pong signature</a></p>\n+\t\t\t\t\t<p><a href="PROTOP/sensPPP.txt">sense reads with PPP</a></p>\n+\t\t\t\t\t<p><a href="PROTOP/antisensPPP.txt">reverse reads with PPP</a></p>\n+\t\t\t\t\t<p><a href="PROTOP/sens.txt">sense reads without PPP</a></p>\n+\t\t\t\t\t<p><a href="PROTOP/antisens.txt">reverse reads without PPP</a></p>\n+\t\t\t\t\t</div>\n+ <!-- FOOTER -->\n+ <div class="container">\n+ <footer>\n+ \n+ </footer>\n+ </div>\n+ <!-- Le javascript\n+ ================================================== -->\n+ <!-- Placed at the end of the document so the pages load faster -->\n+ <script type="text/javascript" src="js/filter.js"></script>\n+ <script type="text/javascript" src="js/jquery.js"></script>\n+ <script type="text/javascript" src="js/jquery-1.3.2.js"></script>\n+ <script type="text/javascript" src="js/jquery.galleriffic.js"></script>\n+ <script type="text/javascript" src="js/jquery.opacityrollover.js"></script>\n+ <script type="text/javascript" src="js/bootstrap-table.js"></script>\n+ <script type="text/javascript" src="js/bootstrap.min.js"></script>\n+ <script type="text/javascript">\n+ jQuery(document).ready(function($) {\n+ // We only want these styles applied when javascript is enabled\n+ $(\'div.navigation\').css({\'width\' : \'300px\', \'float\' : \'left\'});\n+ $(\'div.content\').css(\'display\', \'block\');\n+ \n+ $(".each-gallery").each(function(i){\n+ // Initially set opacity on thumbs and add\n+ // additional styling for hover effect on thumbs\n+ var onMouseOutOpacity = 0.67;\n+ $(\'#thumbs + i + ul.thumbs li\').opacityrollover({\n+ mouseOutOpacity: onMouseOutOpacity,\n+ mouseOverOpacity: 1.0,\n+ fadeSpeed: \'fast\',\n+ exemptionSelector: \'.selected\'\n+ });\n+ \n+ // Initialize Advanced Galleriffic Gallery\n+ var gallery = $(\'#thumbs\'+i).galleriffic({\n+ delay: 2500,\n+ numThumbs: 22,\n+ preloadAhead: 10,\n+ enableTopPager: true,\n+ enableBottomPager: true,\n+ maxPagesToShow: 7,\n+ imageContainerSel: \'#slideshow\'+ i,\n+ controlsContainerSel: \'#controls\' + i,\n+ captionContainerSel: \'#caption\' + i,\n+ loadingContainerSel: \'#loading\' + i,\n+ renderSSControls: true,\n+ renderNavControls: true,\n+ playLinkText: \'Play\',\n+ pauseLinkText: \'Pause\',\n+ prevLinkText: \'‹ Previous\',\n+ nextLinkText: \'Next ›\',\n+ nextPageLinkText: \'Next ›\',\n+ prevPageLinkText: \'‹ Prev\',\n+ enableHistory: false,\n+ autoStart: false,\n+ syncTransitions: true,\n+ defaultTransitionDuration: 900,\n+ onSlideChange: function(prevIndex, nextIndex) {\n+ // \'this\' refers to the gallery, which is an extension of $(\'#thumbs\')\n+ this.find(\'ul.thumbs\').children()\n+ .eq(prevIndex).fadeTo(\'fast\', onMouseOutOpacity).end()\n+ .eq(nextIndex).fadeTo(\'fast\', 1.0);\n+ },\n+ onPageTransitionOut: function(callback) {\n+ this.fadeTo(\'fast\', 0.0, callback);\n+ },\n+ onPageTransitionIn: function() {\n+ this.fadeTo(\'fast\', 1.0);\n+ }\n+ });\n+ });\n+ });\n+ </script>\n+ </body>\n+ </html>\n+ \n\\ No newline at end of file\n' |
| b |
| diff -r 9645d995fb3c -r 9185ca0a7b43 test-data/res_files/reads-sample-small.fastq/subgroups/PPPartners/PROTOP/antisens.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/res_files/reads-sample-small.fastq/subgroups/PPPartners/PROTOP/antisens.txt Wed Jan 16 08:18:13 2019 -0500 |
| b |
| @@ -0,0 +1,110 @@ +>120|16|PROTOP|1 +GCTGTCTGCTGTAGCGCTCTCCG +>223|16|PROTOP|1 +TAAGAACTTCTGAGGTGAAGGGC +>223|16|PROTOP|1 +TCTAAGAACTTCTGAGGTGAAGGGC +>225|16|PROTOP|3 +TCTAAGAACTTCTGAGGTGAAGG +>226|16|PROTOP|2 +GTCTAAGAACTTCTGAGGTGAAG +>466|16|PROTOP|1 +GGCACGAAGTGCGGACACAAGCCCT +>504|16|PROTOP|1 +TGTTATTCTAGTGTCTTTGGTTT +>2349|16|PROTOP|1 +TAGTGAGGTACATTTTCTATTGTT +>2445|16|PROTOP|1 +TATTCCTATAGACTTGAAAAGATG +>2489|16|PROTOP|1 +TCAACTAGTCCGTCAGGGGTTGCT +>2492|16|PROTOP|1 +AAAGTCAACTAGTCCGTCAGGGGTT +>2493|16|PROTOP|2 +AAAGTCAACTAGTCCGTCAGGGGT +>2493|16|PROTOP|2 +CAAAGTCAACTAGTCCGTCAGGGGT +>2493|16|PROTOP|14 +TCAAAGTCAACTAGTCCGTCAGGGGT +>2494|16|PROTOP|1 +TCAAAGTCAACTAGTCCGTCAGGGG +>2508|16|PROTOP|1 +AACCTCTCGAATGAAATCAAAGTCAAC +>2535|16|PROTOP|2 +TTACTGATCCATGATGTAATTCGTA +>2553|16|PROTOP|1 +TAATTTAGTCATTCTCGTTACTGA +>2580|16|PROTOP|2 +TCTAGTTGGATTAACGTGACTCCT +>2592|16|PROTOP|6 +CATTAGCTCAAATCTAGTTGGATT +>2593|16|PROTOP|1 +CATTAGCTCAAATCTAGTTGGAT +>2686|16|PROTOP|1 +TCGGAACTATTTCGATGTAATTGCT +>2692|16|PROTOP|1 +TGCAACTTCGGAACTATTTCGATGTA +>2707|16|PROTOP|1 +AACCGTAGAAGCTGCAACTTCGG +>2707|16|PROTOP|2 +TGCAACCGTAGAAGCTGCAACTTCGG +>2711|16|PROTOP|2 +TAATGCAACCGTAGAAGCTGCAACT +>2718|16|PROTOP|2 +TTTGGACTAATGCAACCGTAGAAGC +>2720|16|PROTOP|2 +TTTTGGACTAATGCAACCGTAGAA +>2720|16|PROTOP|3 +TTTTTGGACTAATGCAACCGTAGAA +>2725|16|PROTOP|1 +TAACTTTTTGGACTAATGCAACCG +>2731|16|PROTOP|1 +TAATCATTAACTTTTTGGACTAATG +>2736|16|PROTOP|1 +CAAAGTAATCATTAACTTTTTGGAC +>2756|16|PROTOP|1 +TACTCTGCTATTCAGGCAATCAAAG +>2853|16|PROTOP|1 +TATTTAACGCTTTTTAAGTATTCCTG +>3060|16|PROTOP|1 +TTAAATTCGTTAACTGTAAGACT +>3060|16|PROTOP|2 +TATTAAATTCGTTAACTGTAAGACT +>3091|16|PROTOP|1 +TGTGTAGAGATATGAGCATGGCAA +>3161|16|PROTOP|1 +TCGAATCAAACTCTATTGACAAAATA +>3190|16|PROTOP|1 +TATTTTTTAATGCAAGGCTGATATA +>3222|16|PROTOP|1 +TATACGGAGTATTCTTGCTGCTG +>3272|16|PROTOP|3 +TTGCATATTTTGGTCAAAGTACCTC +>3371|16|PROTOP|1 +TTATCGATCTGCATTTATCGCATCTC +>3373|16|PROTOP|2 +TTATCGATCTGCATTTATCGCATC +>3382|16|PROTOP|1 +TCTTTTAAAATTATCGATCTGCATT +>3408|16|PROTOP|2 +TGATGGAGCTGTTAAATTCTCGGT +>3408|16|PROTOP|1 +TCTGATGGAGCTGTTAAATTCTCGGT +>3449|16|PROTOP|1 +TCAGAGTCTATTGAGTAGTTTTTC +>3479|16|PROTOP|1 +TAAATCAGATGGTGCCTTTAGTTTC +>3490|16|PROTOP|1 +TATTAAAAAAATAAATCAGATGGTG +>4354|16|PROTOP|1 +CCCGCTGAGAGCATAAGAAATCTAA +>4371|16|PROTOP|1 +CTCTTTCCGCTCGCTCCCGCTGA +>4372|16|PROTOP|2 +TCTCTTTCCGCTCGCTCCCGCTG +>4389|16|PROTOP|1 +TAGTGACGGCCAAAATTGCTCTCTT +>4393|16|PROTOP|1 +TTTTTAGTGACGGCCAAAATTGCTC +>4426|16|PROTOP|1 +TAACATACATTGGTTTGGCACTATG |
| b |
| diff -r 9645d995fb3c -r 9185ca0a7b43 test-data/res_files/reads-sample-small.fastq/subgroups/PPPartners/PROTOP/antisensPPP.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/res_files/reads-sample-small.fastq/subgroups/PPPartners/PROTOP/antisensPPP.txt Wed Jan 16 08:18:13 2019 -0500 |
| b |
| @@ -0,0 +1,18 @@ +>2334|16|PROTOP|1 +TTCTATTGTTACCTCCTTAATCGTA +>2428|16|PROTOP|7 +AAAAGATGCGGAATGTCATAAAACA +>2429|16|PROTOP|3 +AAAAGATGCGGAATGTCATAAAAC +>2684|16|PROTOP|1 +AACTATTTCGATGTAATTGCTTG +>2759|16|PROTOP|1 +TAATACTCTGCTATTCAGGCAATCA +>2760|16|PROTOP|1 +TAATACTCTGCTATTCAGGCAATC +>3384|16|PROTOP|3 +TTCTTTTAAAATTATCGATCTGCA +>4372|16|PROTOP|1 +TGCTCTCTTTCCGCTCGCTCCCGCTG +>4375|16|PROTOP|3 +TGCTCTCTTTCCGCTCGCTCCCG |
| b |
| diff -r 9645d995fb3c -r 9185ca0a7b43 test-data/res_files/reads-sample-small.fastq/subgroups/PPPartners/PROTOP/histogram.png |
| b |
| Binary file test-data/res_files/reads-sample-small.fastq/subgroups/PPPartners/PROTOP/histogram.png has changed |
| b |
| diff -r 9645d995fb3c -r 9185ca0a7b43 test-data/res_files/reads-sample-small.fastq/subgroups/PPPartners/PROTOP/overlap_size.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/res_files/reads-sample-small.fastq/subgroups/PPPartners/PROTOP/overlap_size.txt Wed Jan 16 08:18:13 2019 -0500 |
| b |
| @@ -0,0 +1,24 @@ +size number percentage of the total overlap number +1 3 6.12 +2 4 8.16 +3 0 0.00 +4 0 0.00 +5 1 2.04 +6 4 8.16 +7 3 6.12 +8 0 0.00 +9 3 6.12 +10 11 22.45 +11 0 0.00 +12 0 0.00 +13 2 4.08 +14 1 2.04 +15 2 4.08 +16 1 2.04 +17 1 2.04 +18 3 6.12 +19 3 6.12 +20 2 4.08 +21 3 6.12 +22 0 0.00 +23 2 4.08 |
| b |
| diff -r 9645d995fb3c -r 9185ca0a7b43 test-data/res_files/reads-sample-small.fastq/subgroups/PPPartners/PROTOP/sens.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/res_files/reads-sample-small.fastq/subgroups/PPPartners/PROTOP/sens.txt Wed Jan 16 08:18:13 2019 -0500 |
| b |
| @@ -0,0 +1,62 @@ +>15|0|PROTOP|1 +TAACAAGATACGTAACGCCATACC +>60|0|PROTOP|1 +TCGCCTTGGCTCTAGAGGTGGCTC +>65|0|PROTOP|2 +TTGGCTCTAGAGGTGGCTCCAGGC +>104|0|PROTOP|1 +TTAGAGAGCGAGAGAGCGGAGAGC +>104|0|PROTOP|2 +TTAGAGAGCGAGAGAGCGGAGAGCGC +>105|0|PROTOP|1 +TAGAGAGCGAGAGAGCGGAGAGCGC +>161|0|PROTOP|1 +TGATAGCAGACAATTTTATGTGTG +>210|0|PROTOP|7 +TTTGACAAAATATGCCCTTCACCTC +>210|0|PROTOP|3 +TTTGACAAAATATGCCCTTCACCTCA +>225|0|PROTOP|1 +CCTTCACCTCAGAAGTTCTTAGACTT +>446|0|PROTOP|1 +TAATAAGGCAATGATTGTTGAGG +>450|0|PROTOP|1 +AAGGCAATGATTGTTGAGGGCTT +>2375|0|PROTOP|1 +TGAAGTCACCCATGAGAAACCTTAC +>2541|0|PROTOP|1 +TTACATCATGGATCAGTAACGAGAA +>2616|0|PROTOP|2 +CGCGTATGTTTGGAAACTCAAACACT +>2648|0|PROTOP|1 +CACTGTTGCAGCGGCAATTAAGACT +>2649|0|PROTOP|1 +ACTGTTGCAGCGGCAATTAAGACT +>2654|0|PROTOP|2 +TGCAGCGGCAATTAAGACTTGTAAC +>2690|0|PROTOP|1 +ATTACATCGAAATAGTTCCGAAGTT +>2691|0|PROTOP|1 +TTACATCGAAATAGTTCCGAAGTTG +>2743|0|PROTOP|1 +AAGTTAATGATTACTTTGATTGCC +>2743|0|PROTOP|6 +AAGTTAATGATTACTTTGATTGCCT +>3328|0|PROTOP|1 +TAACTTCCAGTAGATATTTTGCT +>3453|0|PROTOP|1 +AACTACTCAATAGACTCTGACTTCGG +>4136|0|PROTOP|3 +TCTAAAAATATAATAGTCAGGGCGC +>4308|0|PROTOP|1 +GTTCTCGTCTCTTGTTTTCACTCACA +>4309|0|PROTOP|1 +TTCTCGTCTCTTGTTTTCACTCACA +>4361|0|PROTOP|1 +TCTTATGCTCTCAGCGGGAGCGAG +>4389|0|PROTOP|1 +AAGAGAGCAATTTTGGCCGTCACTA +>4399|0|PROTOP|1 +TTTTGGCCGTCACTAAAAAATTGG +>4399|0|PROTOP|1 +TTTTGGCCGTCACTAAAAAATTGGC |
| b |
| diff -r 9645d995fb3c -r 9185ca0a7b43 test-data/res_files/reads-sample-small.fastq/subgroups/PPPartners/PROTOP/sensPPP.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/res_files/reads-sample-small.fastq/subgroups/PPPartners/PROTOP/sensPPP.txt Wed Jan 16 08:18:13 2019 -0500 |
| b |
| @@ -0,0 +1,12 @@ +>2349|0|PROTOP|1 +AACAATAGAAAATGTACCTCACTACT +>2443|0|PROTOP|1 +CGCATCTTTTCAAGTCTATAGGA +>2697|0|PROTOP|1 +CGAAATAGTTCCGAAGTTGCAGC +>2774|0|PROTOP|1 +CAGAGTATTAACGACAAAAACCC +>3398|0|PROTOP|1 +TTTAAAAGAAACCGAGAATTTAACA +>4388|0|PROTOP|5 +AAAGAGAGCAATTTTGGCCGTCACT |
| b |
| diff -r 9645d995fb3c -r 9185ca0a7b43 test-data/res_files/reads-sample-small.fastq/subgroups/PPPartners/ppp.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/res_files/reads-sample-small.fastq/subgroups/PPPartners/ppp.txt Wed Jan 16 08:18:13 2019 -0500 |
| b |
| @@ -0,0 +1,17 @@ +BATUMI_I 92 22 4 6.26931797136554 2.87112570812537 0.00204506417965455 +BATUMI_LTR 13 1 0.565217391304348 0.824941998304795 0.52704627669473 0.299080726341764 +BS2 4418 610 192.086956521739 94.6508058457982 4.41531416181612 5.04316992888665e-06 +COPIA_DM_I 0 0 0 0 NA NA +COPIA_DM_LTR 0 0 0 0 NA NA +DMCR1A 109 30 4.73913043478261 6.40799359023961 3.94208720865353 4.03877968415678e-05 +DMRT1B 299 13 13 10.8266980794861 0 0.5 +FW 9995 1042 434.565217391304 141.421610207381 4.29520482561295 8.7266059448643e-06 +G6_DM 1084 129 47.1304347826087 28.7512636362392 2.84751189558847 0.0022031223713177 +Gypsy2-I_DM 0 0 0 0 NA NA +Gypsy2-LTR_DM 170 20 7.39130434782609 4.341299449171 2.90435981203315 0.00184002483108026 +I_DM 2 1 0.0869565217391304 0.281771334713385 3.24037034920393 0.000596872722436026 +MAX_I 54 11 2.34782608695652 2.44253424438055 3.5422938011818 0.00019833170283523 +MAX_LTR 16 0 0.695652173913043 1.75535906419012 -0.396301923694456 0.654058845865745 +PROTOP 49 11 2.1304347826087 2.30885531258291 3.84154224348902 6.11318444337927e-05 +ZAM_I 0 0 0 0 NA NA +ZAM_LTR 0 0 0 0 NA NA |
| b |
| diff -r 9645d995fb3c -r 9185ca0a7b43 test-data/res_files/reads-sample-small.fastq/subgroups/TEs.fai --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/res_files/reads-sample-small.fastq/subgroups/TEs.fai Wed Jan 16 08:18:13 2019 -0500 |
| b |
| @@ -0,0 +1,17 @@ +BATUMI_I 7963 +BATUMI_LTR 272 +BS2 4721 +COPIA_DM_I 4594 +COPIA_DM_LTR 276 +DMCR1A 4470 +DMRT1B 5183 +FW 4692 +G6_DM 2042 +Gypsy2-I_DM 6545 +Gypsy2-LTR_DM 338 +I_DM 5374 +MAX_I 7914 +MAX_LTR 321 +PROTOP 4480 +ZAM_I 7490 +ZAM_LTR 472 |
| b |
| diff -r 9645d995fb3c -r 9185ca0a7b43 test-data/res_files/reads-sample-small.fastq/subgroups/TEs.sam_aln.err --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/res_files/reads-sample-small.fastq/subgroups/TEs.sam_aln.err Wed Jan 16 08:18:13 2019 -0500 |
| [ |
| @@ -0,0 +1,6 @@ +[bwa_aln_core] calculate SA coordinate... 0.95 sec +[bwa_aln_core] write to the disk... 0.01 sec +[bwa_aln_core] 28283 sequences have been processed. +[main] Version: 0.7.12-r1039 +[main] CMD: bwa aln -t 8 -n 3 /data/galaxy/galaxy-server/database/jobs_directory/015/15696/dataset_35119_files/dataset_35111.dat_symlink.fa /data/galaxy/galaxy-server/database/jobs_directory/015/15696/dataset_35119_files/reads-sample-small.fastq/subgroups/rejected_transcripts.fastq +[main] Real time: 0.204 sec; CPU: 1.004 sec |
| b |
| diff -r 9645d995fb3c -r 9185ca0a7b43 test-data/res_files/reads-sample-small.fastq/subgroups/TEs.sam_samse.err --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/res_files/reads-sample-small.fastq/subgroups/TEs.sam_samse.err Wed Jan 16 08:18:13 2019 -0500 |
| [ |
| @@ -0,0 +1,7 @@ +[bwa_aln_core] convert to sequence coordinate... 0.07 sec +[bwa_aln_core] refine gapped alignments... 0.01 sec +[bwa_aln_core] print alignments... 0.05 sec +[bwa_aln_core] 28283 sequences have been processed. +[main] Version: 0.7.12-r1039 +[main] CMD: bwa samse /data/galaxy/galaxy-server/database/jobs_directory/015/15696/dataset_35119_files/dataset_35111.dat_symlink.fa /dev/stdin /data/galaxy/galaxy-server/database/jobs_directory/015/15696/dataset_35119_files/reads-sample-small.fastq/subgroups/rejected_transcripts.fastq +[main] Real time: 0.388 sec; CPU: 0.172 sec |
| b |
| diff -r 9645d995fb3c -r 9185ca0a7b43 test-data/res_files/reads-sample-small.fastq/subgroups/bonafide_reads/Gviz_TEs/BATUMI_I.png |
| b |
| Binary file test-data/res_files/reads-sample-small.fastq/subgroups/bonafide_reads/Gviz_TEs/BATUMI_I.png has changed |
| b |
| diff -r 9645d995fb3c -r 9185ca0a7b43 test-data/res_files/reads-sample-small.fastq/subgroups/bonafide_reads/Gviz_TEs/BATUMI_LTR.png |
| b |
| Binary file test-data/res_files/reads-sample-small.fastq/subgroups/bonafide_reads/Gviz_TEs/BATUMI_LTR.png has changed |
| b |
| diff -r 9645d995fb3c -r 9185ca0a7b43 test-data/res_files/reads-sample-small.fastq/subgroups/bonafide_reads/Gviz_TEs/BS2.png |
| b |
| Binary file test-data/res_files/reads-sample-small.fastq/subgroups/bonafide_reads/Gviz_TEs/BS2.png has changed |
| b |
| diff -r 9645d995fb3c -r 9185ca0a7b43 test-data/res_files/reads-sample-small.fastq/subgroups/bonafide_reads/Gviz_TEs/DMCR1A.png |
| b |
| Binary file test-data/res_files/reads-sample-small.fastq/subgroups/bonafide_reads/Gviz_TEs/DMCR1A.png has changed |
| b |
| diff -r 9645d995fb3c -r 9185ca0a7b43 test-data/res_files/reads-sample-small.fastq/subgroups/bonafide_reads/Gviz_TEs/DMRT1B.png |
| b |
| Binary file test-data/res_files/reads-sample-small.fastq/subgroups/bonafide_reads/Gviz_TEs/DMRT1B.png has changed |
| b |
| diff -r 9645d995fb3c -r 9185ca0a7b43 test-data/res_files/reads-sample-small.fastq/subgroups/bonafide_reads/Gviz_TEs/FW.png |
| b |
| Binary file test-data/res_files/reads-sample-small.fastq/subgroups/bonafide_reads/Gviz_TEs/FW.png has changed |
| b |
| diff -r 9645d995fb3c -r 9185ca0a7b43 test-data/res_files/reads-sample-small.fastq/subgroups/bonafide_reads/Gviz_TEs/G6_DM.png |
| b |
| Binary file test-data/res_files/reads-sample-small.fastq/subgroups/bonafide_reads/Gviz_TEs/G6_DM.png has changed |
| b |
| diff -r 9645d995fb3c -r 9185ca0a7b43 test-data/res_files/reads-sample-small.fastq/subgroups/bonafide_reads/Gviz_TEs/Gypsy2-LTR_DM.png |
| b |
| Binary file test-data/res_files/reads-sample-small.fastq/subgroups/bonafide_reads/Gviz_TEs/Gypsy2-LTR_DM.png has changed |
| b |
| diff -r 9645d995fb3c -r 9185ca0a7b43 test-data/res_files/reads-sample-small.fastq/subgroups/bonafide_reads/Gviz_TEs/I_DM.png |
| b |
| Binary file test-data/res_files/reads-sample-small.fastq/subgroups/bonafide_reads/Gviz_TEs/I_DM.png has changed |
| b |
| diff -r 9645d995fb3c -r 9185ca0a7b43 test-data/res_files/reads-sample-small.fastq/subgroups/bonafide_reads/Gviz_TEs/MAX_I.png |
| b |
| Binary file test-data/res_files/reads-sample-small.fastq/subgroups/bonafide_reads/Gviz_TEs/MAX_I.png has changed |
| b |
| diff -r 9645d995fb3c -r 9185ca0a7b43 test-data/res_files/reads-sample-small.fastq/subgroups/bonafide_reads/Gviz_TEs/MAX_LTR.png |
| b |
| Binary file test-data/res_files/reads-sample-small.fastq/subgroups/bonafide_reads/Gviz_TEs/MAX_LTR.png has changed |
| b |
| diff -r 9645d995fb3c -r 9185ca0a7b43 test-data/res_files/reads-sample-small.fastq/subgroups/bonafide_reads/Gviz_TEs/PROTOP.png |
| b |
| Binary file test-data/res_files/reads-sample-small.fastq/subgroups/bonafide_reads/Gviz_TEs/PROTOP.png has changed |
| b |
| diff -r 9645d995fb3c -r 9185ca0a7b43 test-data/res_files/reads-sample-small.fastq/subgroups/bonafide_reads/Gviz_genome/rand/chrom_1.png |
| b |
| Binary file test-data/res_files/reads-sample-small.fastq/subgroups/bonafide_reads/Gviz_genome/rand/chrom_1.png has changed |
| b |
| diff -r 9645d995fb3c -r 9185ca0a7b43 test-data/res_files/reads-sample-small.fastq/subgroups/bonafide_reads/Gviz_genome/rand/chrom_2.png |
| b |
| Binary file test-data/res_files/reads-sample-small.fastq/subgroups/bonafide_reads/Gviz_genome/rand/chrom_2.png has changed |
| b |
| diff -r 9645d995fb3c -r 9185ca0a7b43 test-data/res_files/reads-sample-small.fastq/subgroups/bonafide_reads/Gviz_genome/rand/chrom_4.png |
| b |
| Binary file test-data/res_files/reads-sample-small.fastq/subgroups/bonafide_reads/Gviz_genome/rand/chrom_4.png has changed |
| b |
| diff -r 9645d995fb3c -r 9185ca0a7b43 test-data/res_files/reads-sample-small.fastq/subgroups/bonafide_reads/Gviz_genome/rand/chrom_5.png |
| b |
| Binary file test-data/res_files/reads-sample-small.fastq/subgroups/bonafide_reads/Gviz_genome/rand/chrom_5.png has changed |
| b |
| diff -r 9645d995fb3c -r 9185ca0a7b43 test-data/res_files/reads-sample-small.fastq/subgroups/bonafide_reads/Gviz_genome/rand/chrom_6.png |
| b |
| Binary file test-data/res_files/reads-sample-small.fastq/subgroups/bonafide_reads/Gviz_genome/rand/chrom_6.png has changed |
| b |
| diff -r 9645d995fb3c -r 9185ca0a7b43 test-data/res_files/reads-sample-small.fastq/subgroups/bonafide_reads/Gviz_genome/unique/chrom_1.png |
| b |
| Binary file test-data/res_files/reads-sample-small.fastq/subgroups/bonafide_reads/Gviz_genome/unique/chrom_1.png has changed |
| b |
| diff -r 9645d995fb3c -r 9185ca0a7b43 test-data/res_files/reads-sample-small.fastq/subgroups/bonafide_reads/Gviz_genome/unique/chrom_2.png |
| b |
| Binary file test-data/res_files/reads-sample-small.fastq/subgroups/bonafide_reads/Gviz_genome/unique/chrom_2.png has changed |
| b |
| diff -r 9645d995fb3c -r 9185ca0a7b43 test-data/res_files/reads-sample-small.fastq/subgroups/bonafide_reads/Gviz_genome/unique/chrom_4.png |
| b |
| Binary file test-data/res_files/reads-sample-small.fastq/subgroups/bonafide_reads/Gviz_genome/unique/chrom_4.png has changed |
| b |
| diff -r 9645d995fb3c -r 9185ca0a7b43 test-data/res_files/reads-sample-small.fastq/subgroups/bonafide_reads/Gviz_genome/unique/chrom_5.png |
| b |
| Binary file test-data/res_files/reads-sample-small.fastq/subgroups/bonafide_reads/Gviz_genome/unique/chrom_5.png has changed |
| b |
| diff -r 9645d995fb3c -r 9185ca0a7b43 test-data/res_files/reads-sample-small.fastq/subgroups/bonafide_reads/Gviz_genome/unique/chrom_6.png |
| b |
| Binary file test-data/res_files/reads-sample-small.fastq/subgroups/bonafide_reads/Gviz_genome/unique/chrom_6.png has changed |
| b |
| diff -r 9645d995fb3c -r 9185ca0a7b43 test-data/res_files/reads-sample-small.fastq/subgroups/bonafide_reads/bonafide_reads-TEs_minus.bedgraph --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/res_files/reads-sample-small.fastq/subgroups/bonafide_reads/bonafide_reads-TEs_minus.bedgraph Wed Jan 16 08:18:13 2019 -0500 |
| b |
| b'@@ -0,0 +1,4935 @@\n+BATUMI_I\t0\t3\t25.6148\n+BATUMI_I\t3\t4\t230.533\n+BATUMI_I\t4\t5\t332.992\n+BATUMI_I\t5\t12\t358.607\n+BATUMI_I\t12\t14\t384.221\n+BATUMI_I\t14\t21\t409.836\n+BATUMI_I\t21\t25\t204.918\n+BATUMI_I\t25\t27\t230.533\n+BATUMI_I\t27\t29\t128.074\n+BATUMI_I\t29\t35\t102.459\n+BATUMI_I\t35\t38\t76.8443\n+BATUMI_I\t38\t47\t51.2295\n+BATUMI_I\t47\t48\t25.6148\n+BATUMI_I\t48\t53\t0\n+BATUMI_I\t53\t76\t25.6148\n+BATUMI_I\t76\t93\t0\n+BATUMI_I\t93\t95\t25.6148\n+BATUMI_I\t95\t96\t51.2295\n+BATUMI_I\t96\t97\t76.8443\n+BATUMI_I\t97\t99\t102.459\n+BATUMI_I\t99\t120\t128.074\n+BATUMI_I\t120\t121\t102.459\n+BATUMI_I\t121\t123\t25.6148\n+BATUMI_I\t123\t145\t51.2295\n+BATUMI_I\t145\t148\t25.6148\n+BATUMI_I\t148\t160\t0\n+BATUMI_I\t160\t164\t128.074\n+BATUMI_I\t164\t165\t179.303\n+BATUMI_I\t165\t167\t307.377\n+BATUMI_I\t167\t169\t332.992\n+BATUMI_I\t169\t183\t358.607\n+BATUMI_I\t183\t185\t281.762\n+BATUMI_I\t185\t186\t256.148\n+BATUMI_I\t186\t187\t230.533\n+BATUMI_I\t187\t188\t128.074\n+BATUMI_I\t188\t191\t51.2295\n+BATUMI_I\t191\t195\t25.6148\n+BATUMI_I\t195\t214\t0\n+BATUMI_I\t214\t219\t25.6148\n+BATUMI_I\t219\t238\t51.2295\n+BATUMI_I\t238\t239\t25.6148\n+BATUMI_I\t239\t247\t0\n+BATUMI_I\t247\t261\t25.6148\n+BATUMI_I\t261\t270\t51.2295\n+BATUMI_I\t270\t277\t25.6148\n+BATUMI_I\t277\t278\t0\n+BATUMI_I\t278\t279\t25.6148\n+BATUMI_I\t279\t286\t51.2295\n+BATUMI_I\t286\t295\t25.6148\n+BATUMI_I\t295\t297\t102.459\n+BATUMI_I\t297\t299\t128.074\n+BATUMI_I\t299\t320\t102.459\n+BATUMI_I\t320\t321\t76.8443\n+BATUMI_I\t321\t348\t0\n+BATUMI_I\t348\t349\t51.2295\n+BATUMI_I\t349\t350\t153.689\n+BATUMI_I\t350\t352\t435.451\n+BATUMI_I\t352\t353\t461.066\n+BATUMI_I\t353\t354\t537.91\n+BATUMI_I\t354\t355\t614.754\n+BATUMI_I\t355\t357\t640.369\n+BATUMI_I\t357\t358\t768.443\n+BATUMI_I\t358\t359\t896.516\n+BATUMI_I\t359\t360\t1306.35\n+BATUMI_I\t360\t369\t1434.43\n+BATUMI_I\t369\t370\t1511.27\n+BATUMI_I\t370\t374\t1536.89\n+BATUMI_I\t374\t375\t1075.82\n+BATUMI_I\t375\t376\t1050.2\n+BATUMI_I\t376\t377\t998.975\n+BATUMI_I\t377\t378\t922.131\n+BATUMI_I\t378\t379\t896.516\n+BATUMI_I\t379\t383\t922.131\n+BATUMI_I\t383\t384\t742.828\n+BATUMI_I\t384\t385\t589.139\n+BATUMI_I\t385\t391\t640.369\n+BATUMI_I\t391\t393\t614.754\n+BATUMI_I\t393\t394\t563.525\n+BATUMI_I\t394\t402\t537.91\n+BATUMI_I\t402\t403\t512.295\n+BATUMI_I\t403\t407\t435.451\n+BATUMI_I\t407\t409\t409.836\n+BATUMI_I\t409\t410\t179.303\n+BATUMI_I\t410\t411\t51.2295\n+BATUMI_I\t411\t413\t0\n+BATUMI_I\t413\t418\t25.6148\n+BATUMI_I\t418\t419\t128.074\n+BATUMI_I\t419\t420\t230.533\n+BATUMI_I\t420\t424\t256.148\n+BATUMI_I\t424\t439\t332.992\n+BATUMI_I\t439\t440\t102.459\n+BATUMI_I\t440\t443\t281.762\n+BATUMI_I\t443\t444\t204.918\n+BATUMI_I\t444\t481\t0\n+BATUMI_I\t481\t484\t25.6148\n+BATUMI_I\t484\t501\t51.2295\n+BATUMI_I\t501\t508\t25.6148\n+BATUMI_I\t508\t7004\t0\n+BATUMI_I\t7004\t7005\t76.8443\n+BATUMI_I\t7005\t7006\t128.074\n+BATUMI_I\t7006\t7028\t153.689\n+BATUMI_I\t7028\t7077\t0\n+BATUMI_I\t7077\t7078\t25.6148\n+BATUMI_I\t7078\t7079\t51.2295\n+BATUMI_I\t7079\t7100\t76.8443\n+BATUMI_I\t7100\t7101\t51.2295\n+BATUMI_I\t7101\t7963\t0\n+BATUMI_LTR\t0\t45\t0\n+BATUMI_LTR\t45\t66\t25.6148\n+BATUMI_LTR\t66\t67\t0\n+BATUMI_LTR\t67\t69\t25.6148\n+BATUMI_LTR\t69\t89\t51.2295\n+BATUMI_LTR\t89\t93\t25.6148\n+BATUMI_LTR\t93\t99\t0\n+BATUMI_LTR\t99\t102\t51.2295\n+BATUMI_LTR\t102\t105\t102.459\n+BATUMI_LTR\t105\t106\t973.361\n+BATUMI_LTR\t106\t107\t1767.42\n+BATUMI_LTR\t107\t108\t1793.03\n+BATUMI_LTR\t108\t109\t1818.65\n+BATUMI_LTR\t109\t110\t1869.88\n+BATUMI_LTR\t110\t111\t1895.49\n+BATUMI_LTR\t111\t121\t1972.34\n+BATUMI_LTR\t121\t124\t1946.72\n+BATUMI_LTR\t124\t127\t1921.11\n+BATUMI_LTR\t127\t128\t1895.49\n+BATUMI_LTR\t128\t129\t1844.26\n+BATUMI_LTR\t129\t130\t1818.65\n+BATUMI_LTR\t130\t137\t25.6148\n+BATUMI_LTR\t137\t171\t0\n+BATUMI_LTR\t171\t177\t25.6148\n+BATUMI_LTR\t177\t179\t76.8443\n+BATUMI_LTR\t179\t181\t102.459\n+BATUMI_LTR\t181\t186\t128.074\n+BATUMI_LTR\t186\t191\t102.459\n+BATUMI_LTR\t191\t192\t128.074\n+BATUMI_LTR\t192\t193\t204.918\n+BATUMI_LTR\t193\t202\t358.607\n+BATUMI_LTR\t202\t204\t256.148\n+BATUMI_LTR\t204\t207\t281.762\n+BATUMI_LTR\t207\t215\t307.377\n+BATUMI_LTR\t215\t216\t281.762\n+BATUMI_LTR\t216\t217\t256.148\n+BATUMI_LTR\t217\t218\t153.689\n+BATUMI_LTR\t218\t219\t102.459\n+BATUMI_LTR\t219\t228\t76.8443\n+BATUMI_LTR\t228\t230\t51.2295\n+BATUMI_LTR\t230\t242\t25.6148\n+BATUMI_LTR\t242\t272\t0\n+BS2\t0\t12\t0\n+BS2\t12\t13\t76.8443\n+BS2\t13\t28\t102.459\n+BS2\t28\t32\t128.074\n+BS2\t32\t35\t153.689\n+BS2\t35\t38\t102.459\n+BS2\t38\t47\t76.8443\n+BS2\t47\t52\t51.2295\n+BS2\t52\t53\t102.459\n+BS2\t53\t'..b'LTR\t52\t76\t25.6148\n+MAX_LTR\t76\t80\t0\n+MAX_LTR\t80\t84\t76.8443\n+MAX_LTR\t84\t87\t102.459\n+MAX_LTR\t87\t88\t128.074\n+MAX_LTR\t88\t91\t153.689\n+MAX_LTR\t91\t94\t179.303\n+MAX_LTR\t94\t95\t204.918\n+MAX_LTR\t95\t97\t256.148\n+MAX_LTR\t97\t98\t307.377\n+MAX_LTR\t98\t99\t332.992\n+MAX_LTR\t99\t101\t384.221\n+MAX_LTR\t101\t102\t307.377\n+MAX_LTR\t102\t104\t358.607\n+MAX_LTR\t104\t107\t384.221\n+MAX_LTR\t107\t110\t358.607\n+MAX_LTR\t110\t112\t332.992\n+MAX_LTR\t112\t114\t307.377\n+MAX_LTR\t114\t117\t256.148\n+MAX_LTR\t117\t118\t204.918\n+MAX_LTR\t118\t120\t153.689\n+MAX_LTR\t120\t121\t102.459\n+MAX_LTR\t121\t122\t76.8443\n+MAX_LTR\t122\t123\t51.2295\n+MAX_LTR\t123\t133\t25.6148\n+MAX_LTR\t133\t135\t102.459\n+MAX_LTR\t135\t151\t76.8443\n+MAX_LTR\t151\t152\t153.689\n+MAX_LTR\t152\t153\t204.918\n+MAX_LTR\t153\t154\t281.762\n+MAX_LTR\t154\t156\t409.836\n+MAX_LTR\t156\t158\t384.221\n+MAX_LTR\t158\t174\t332.992\n+MAX_LTR\t174\t175\t204.918\n+MAX_LTR\t175\t176\t153.689\n+MAX_LTR\t176\t177\t102.459\n+MAX_LTR\t177\t268\t0\n+MAX_LTR\t268\t274\t25.6148\n+MAX_LTR\t274\t286\t51.2295\n+MAX_LTR\t286\t293\t25.6148\n+MAX_LTR\t293\t321\t0\n+PROTOP\t0\t57\t0\n+PROTOP\t57\t79\t25.6148\n+PROTOP\t79\t119\t0\n+PROTOP\t119\t142\t25.6148\n+PROTOP\t142\t222\t0\n+PROTOP\t222\t224\t51.2295\n+PROTOP\t224\t225\t128.074\n+PROTOP\t225\t226\t179.303\n+PROTOP\t226\t227\t204.918\n+PROTOP\t227\t245\t256.148\n+PROTOP\t245\t247\t179.303\n+PROTOP\t247\t248\t51.2295\n+PROTOP\t248\t465\t0\n+PROTOP\t465\t490\t25.6148\n+PROTOP\t490\t503\t0\n+PROTOP\t503\t526\t25.6148\n+PROTOP\t526\t2333\t0\n+PROTOP\t2333\t2348\t25.6148\n+PROTOP\t2348\t2358\t51.2295\n+PROTOP\t2358\t2372\t25.6148\n+PROTOP\t2372\t2427\t0\n+PROTOP\t2427\t2428\t179.303\n+PROTOP\t2428\t2444\t256.148\n+PROTOP\t2444\t2452\t281.762\n+PROTOP\t2452\t2461\t25.6148\n+PROTOP\t2461\t2462\t0\n+PROTOP\t2462\t2469\t25.6148\n+PROTOP\t2469\t2488\t0\n+PROTOP\t2488\t2491\t25.6148\n+PROTOP\t2491\t2492\t51.2295\n+PROTOP\t2492\t2493\t563.525\n+PROTOP\t2493\t2494\t614.754\n+PROTOP\t2494\t2496\t640.369\n+PROTOP\t2496\t2507\t665.984\n+PROTOP\t2507\t2512\t691.598\n+PROTOP\t2512\t2513\t614.754\n+PROTOP\t2513\t2514\t589.139\n+PROTOP\t2514\t2516\t563.525\n+PROTOP\t2516\t2517\t486.68\n+PROTOP\t2517\t2518\t435.451\n+PROTOP\t2518\t2534\t25.6148\n+PROTOP\t2534\t2552\t51.2295\n+PROTOP\t2552\t2559\t76.8443\n+PROTOP\t2559\t2576\t25.6148\n+PROTOP\t2576\t2579\t0\n+PROTOP\t2579\t2591\t76.8443\n+PROTOP\t2591\t2592\t230.533\n+PROTOP\t2592\t2601\t256.148\n+PROTOP\t2601\t2603\t230.533\n+PROTOP\t2603\t2615\t179.303\n+PROTOP\t2615\t2683\t0\n+PROTOP\t2683\t2685\t25.6148\n+PROTOP\t2685\t2691\t51.2295\n+PROTOP\t2691\t2706\t76.8443\n+PROTOP\t2706\t2707\t128.074\n+PROTOP\t2707\t2710\t153.689\n+PROTOP\t2710\t2717\t179.303\n+PROTOP\t2717\t2719\t204.918\n+PROTOP\t2719\t2724\t332.992\n+PROTOP\t2724\t2729\t358.607\n+PROTOP\t2729\t2730\t307.377\n+PROTOP\t2730\t2732\t332.992\n+PROTOP\t2732\t2735\t281.762\n+PROTOP\t2735\t2742\t256.148\n+PROTOP\t2742\t2743\t204.918\n+PROTOP\t2743\t2744\t153.689\n+PROTOP\t2744\t2748\t76.8443\n+PROTOP\t2748\t2758\t51.2295\n+PROTOP\t2758\t2759\t76.8443\n+PROTOP\t2759\t2760\t102.459\n+PROTOP\t2760\t2763\t76.8443\n+PROTOP\t2763\t2780\t102.459\n+PROTOP\t2780\t2783\t76.8443\n+PROTOP\t2783\t2852\t0\n+PROTOP\t2852\t2878\t25.6148\n+PROTOP\t2878\t3059\t0\n+PROTOP\t3059\t3082\t76.8443\n+PROTOP\t3082\t3084\t51.2295\n+PROTOP\t3084\t3090\t0\n+PROTOP\t3090\t3114\t25.6148\n+PROTOP\t3114\t3160\t0\n+PROTOP\t3160\t3186\t25.6148\n+PROTOP\t3186\t3189\t0\n+PROTOP\t3189\t3214\t25.6148\n+PROTOP\t3214\t3221\t0\n+PROTOP\t3221\t3223\t25.6148\n+PROTOP\t3223\t3244\t51.2295\n+PROTOP\t3244\t3271\t0\n+PROTOP\t3271\t3296\t76.8443\n+PROTOP\t3296\t3370\t0\n+PROTOP\t3370\t3372\t25.6148\n+PROTOP\t3372\t3381\t76.8443\n+PROTOP\t3381\t3383\t102.459\n+PROTOP\t3383\t3396\t179.303\n+PROTOP\t3396\t3406\t102.459\n+PROTOP\t3406\t3431\t76.8443\n+PROTOP\t3431\t3433\t25.6148\n+PROTOP\t3433\t3448\t0\n+PROTOP\t3448\t3464\t25.6148\n+PROTOP\t3464\t3472\t51.2295\n+PROTOP\t3472\t3478\t25.6148\n+PROTOP\t3478\t3485\t76.8443\n+PROTOP\t3485\t3487\t51.2295\n+PROTOP\t3487\t3489\t76.8443\n+PROTOP\t3489\t3499\t102.459\n+PROTOP\t3499\t3503\t76.8443\n+PROTOP\t3503\t3508\t51.2295\n+PROTOP\t3508\t3513\t25.6148\n+PROTOP\t3513\t4353\t0\n+PROTOP\t4353\t4370\t25.6148\n+PROTOP\t4370\t4371\t51.2295\n+PROTOP\t4371\t4374\t128.074\n+PROTOP\t4374\t4378\t204.918\n+PROTOP\t4378\t4388\t179.303\n+PROTOP\t4388\t4392\t204.918\n+PROTOP\t4392\t4393\t230.533\n+PROTOP\t4393\t4394\t204.918\n+PROTOP\t4394\t4397\t153.689\n+PROTOP\t4397\t4413\t51.2295\n+PROTOP\t4413\t4417\t25.6148\n+PROTOP\t4417\t4425\t0\n+PROTOP\t4425\t4450\t25.6148\n+PROTOP\t4450\t4480\t0\n' |
| b |
| diff -r 9645d995fb3c -r 9185ca0a7b43 test-data/res_files/reads-sample-small.fastq/subgroups/bonafide_reads/bonafide_reads-TEs_plus.bedgraph --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/res_files/reads-sample-small.fastq/subgroups/bonafide_reads/bonafide_reads-TEs_plus.bedgraph Wed Jan 16 08:18:13 2019 -0500 |
| b |
| b'@@ -0,0 +1,2914 @@\n+BATUMI_I\t0\t1\t25.6148\n+BATUMI_I\t1\t6\t51.2295\n+BATUMI_I\t6\t22\t76.8443\n+BATUMI_I\t22\t26\t51.2295\n+BATUMI_I\t26\t32\t25.6148\n+BATUMI_I\t32\t119\t0\n+BATUMI_I\t119\t123\t51.2295\n+BATUMI_I\t123\t144\t76.8443\n+BATUMI_I\t144\t150\t0\n+BATUMI_I\t150\t159\t25.6148\n+BATUMI_I\t159\t160\t51.2295\n+BATUMI_I\t160\t176\t76.8443\n+BATUMI_I\t176\t179\t51.2295\n+BATUMI_I\t179\t185\t25.6148\n+BATUMI_I\t185\t385\t0\n+BATUMI_I\t385\t386\t25.6148\n+BATUMI_I\t386\t407\t51.2295\n+BATUMI_I\t407\t411\t25.6148\n+BATUMI_I\t411\t417\t0\n+BATUMI_I\t417\t418\t25.6148\n+BATUMI_I\t418\t419\t128.074\n+BATUMI_I\t419\t437\t179.303\n+BATUMI_I\t437\t441\t153.689\n+BATUMI_I\t441\t442\t102.459\n+BATUMI_I\t442\t443\t25.6148\n+BATUMI_I\t443\t7006\t0\n+BATUMI_I\t7006\t7007\t25.6148\n+BATUMI_I\t7007\t7008\t51.2295\n+BATUMI_I\t7008\t7009\t179.303\n+BATUMI_I\t7009\t7010\t486.68\n+BATUMI_I\t7010\t7015\t512.295\n+BATUMI_I\t7015\t7016\t537.91\n+BATUMI_I\t7016\t7017\t1101.43\n+BATUMI_I\t7017\t7018\t2459.02\n+BATUMI_I\t7018\t7030\t4123.98\n+BATUMI_I\t7030\t7031\t4021.52\n+BATUMI_I\t7031\t7033\t3765.37\n+BATUMI_I\t7033\t7034\t3739.75\n+BATUMI_I\t7034\t7035\t3611.68\n+BATUMI_I\t7035\t7036\t3560.45\n+BATUMI_I\t7036\t7037\t3073.77\n+BATUMI_I\t7037\t7038\t3022.54\n+BATUMI_I\t7038\t7039\t2715.16\n+BATUMI_I\t7039\t7040\t1716.19\n+BATUMI_I\t7040\t7041\t1511.27\n+BATUMI_I\t7041\t7042\t281.762\n+BATUMI_I\t7042\t7043\t25.6148\n+BATUMI_I\t7043\t7963\t0\n+BATUMI_LTR\t0\t32\t0\n+BATUMI_LTR\t32\t57\t25.6148\n+BATUMI_LTR\t57\t118\t0\n+BATUMI_LTR\t118\t142\t25.6148\n+BATUMI_LTR\t142\t192\t0\n+BATUMI_LTR\t192\t195\t25.6148\n+BATUMI_LTR\t195\t213\t51.2295\n+BATUMI_LTR\t213\t218\t25.6148\n+BATUMI_LTR\t218\t272\t0\n+BS2\t0\t21\t0\n+BS2\t21\t42\t51.2295\n+BS2\t42\t45\t76.8443\n+BS2\t45\t68\t25.6148\n+BS2\t68\t69\t384.221\n+BS2\t69\t72\t435.451\n+BS2\t72\t77\t486.68\n+BS2\t77\t79\t512.295\n+BS2\t79\t80\t537.91\n+BS2\t80\t81\t563.525\n+BS2\t81\t82\t717.213\n+BS2\t82\t91\t742.828\n+BS2\t91\t93\t717.213\n+BS2\t93\t94\t384.221\n+BS2\t94\t97\t307.377\n+BS2\t97\t98\t281.762\n+BS2\t98\t102\t256.148\n+BS2\t102\t106\t230.533\n+BS2\t106\t107\t102.459\n+BS2\t107\t108\t51.2295\n+BS2\t108\t186\t0\n+BS2\t186\t187\t25.6148\n+BS2\t187\t188\t76.8443\n+BS2\t188\t192\t128.074\n+BS2\t192\t193\t204.918\n+BS2\t193\t194\t230.533\n+BS2\t194\t195\t358.607\n+BS2\t195\t196\t384.221\n+BS2\t196\t208\t409.836\n+BS2\t208\t211\t384.221\n+BS2\t211\t213\t332.992\n+BS2\t213\t215\t307.377\n+BS2\t215\t219\t281.762\n+BS2\t219\t220\t230.533\n+BS2\t220\t221\t204.918\n+BS2\t221\t222\t179.303\n+BS2\t222\t223\t230.533\n+BS2\t223\t224\t256.148\n+BS2\t224\t225\t537.91\n+BS2\t225\t235\t563.525\n+BS2\t235\t237\t537.91\n+BS2\t237\t238\t486.68\n+BS2\t238\t241\t461.066\n+BS2\t241\t246\t435.451\n+BS2\t246\t248\t332.992\n+BS2\t248\t276\t0\n+BS2\t276\t277\t76.8443\n+BS2\t277\t284\t102.459\n+BS2\t284\t285\t128.074\n+BS2\t285\t297\t179.303\n+BS2\t297\t298\t128.074\n+BS2\t298\t303\t76.8443\n+BS2\t303\t304\t102.459\n+BS2\t304\t308\t128.074\n+BS2\t308\t329\t51.2295\n+BS2\t329\t335\t25.6148\n+BS2\t335\t338\t51.2295\n+BS2\t338\t339\t281.762\n+BS2\t339\t341\t409.836\n+BS2\t341\t344\t435.451\n+BS2\t344\t350\t537.91\n+BS2\t350\t353\t589.139\n+BS2\t353\t362\t563.525\n+BS2\t362\t363\t435.451\n+BS2\t363\t364\t256.148\n+BS2\t364\t365\t153.689\n+BS2\t365\t367\t179.303\n+BS2\t367\t368\t153.689\n+BS2\t368\t372\t128.074\n+BS2\t372\t374\t102.459\n+BS2\t374\t386\t76.8443\n+BS2\t386\t390\t25.6148\n+BS2\t390\t430\t0\n+BS2\t430\t440\t25.6148\n+BS2\t440\t454\t76.8443\n+BS2\t454\t455\t51.2295\n+BS2\t455\t456\t76.8443\n+BS2\t456\t457\t230.533\n+BS2\t457\t463\t256.148\n+BS2\t463\t465\t230.533\n+BS2\t465\t471\t204.918\n+BS2\t471\t474\t230.533\n+BS2\t474\t475\t256.148\n+BS2\t475\t480\t281.762\n+BS2\t480\t484\t102.459\n+BS2\t484\t490\t153.689\n+BS2\t490\t492\t179.303\n+BS2\t492\t493\t204.918\n+BS2\t493\t495\t281.762\n+BS2\t495\t496\t307.377\n+BS2\t496\t499\t281.762\n+BS2\t499\t501\t332.992\n+BS2\t501\t503\t307.377\n+BS2\t503\t504\t358.607\n+BS2\t504\t506\t307.377\n+BS2\t506\t509\t332.992\n+BS2\t509\t511\t358.607\n+BS2\t511\t512\t537.91\n+BS2\t512\t513\t512.295\n+BS2\t513\t516\t486.68\n+BS2\t516\t518\t461.066\n+BS2\t518\t519\t435.451\n+BS2\t519\t522\t409.836\n+BS2\t522\t528\t332.992\n+BS2\t528\t530\t281.762\n+BS2\t530\t533\t256.148\n+BS2\t533\t534\t230.533\n+BS2\t534\t535\t76.8443\n+BS2\t535\t537\t25.6148\n+BS2\t537\t562\t0\n+BS2\t562\t566\t102.459\n+BS2\t566\t576\t179.303\n+BS2\t576\t582\t204.918\n+BS2\t582\t586\t230.533\n+BS2\t586\t587\t204.918\n+BS2\t587\t588\t281.762\n+BS2\t588\t589\t230.533\n+BS2\t589\t591\t256.148\n+BS2\t591\t592\t230.533\n+BS2\t592\t593\t281.762\n+BS2\t593\t601\t307.377\n+BS2\t601\t607\t281.762\n+BS2\t607\t608\t256.148\n+BS2\t608'..b'DM\t2222\t2223\t0\n+I_DM\t2223\t2230\t25.6148\n+I_DM\t2230\t3190\t0\n+I_DM\t3190\t3215\t76.8443\n+I_DM\t3215\t3235\t25.6148\n+I_DM\t3235\t3237\t51.2295\n+I_DM\t3237\t3239\t76.8443\n+I_DM\t3239\t3261\t51.2295\n+I_DM\t3261\t3262\t25.6148\n+I_DM\t3262\t4260\t0\n+I_DM\t4260\t4282\t25.6148\n+I_DM\t4282\t4623\t0\n+I_DM\t4623\t4646\t25.6148\n+I_DM\t4646\t4825\t0\n+I_DM\t4825\t4849\t25.6148\n+I_DM\t4849\t4908\t0\n+I_DM\t4908\t4912\t25.6148\n+I_DM\t4912\t4929\t51.2295\n+I_DM\t4929\t4939\t25.6148\n+I_DM\t4939\t5104\t0\n+I_DM\t5104\t5128\t25.6148\n+I_DM\t5128\t5374\t0\n+MAX_I\t0\t40\t0\n+MAX_I\t40\t53\t25.6148\n+MAX_I\t53\t54\t51.2295\n+MAX_I\t54\t55\t76.8443\n+MAX_I\t55\t59\t102.459\n+MAX_I\t59\t77\t128.074\n+MAX_I\t77\t78\t76.8443\n+MAX_I\t78\t80\t51.2295\n+MAX_I\t80\t84\t76.8443\n+MAX_I\t84\t87\t25.6148\n+MAX_I\t87\t92\t51.2295\n+MAX_I\t92\t104\t76.8443\n+MAX_I\t104\t105\t25.6148\n+MAX_I\t105\t108\t51.2295\n+MAX_I\t108\t111\t76.8443\n+MAX_I\t111\t118\t51.2295\n+MAX_I\t118\t119\t25.6148\n+MAX_I\t119\t120\t76.8443\n+MAX_I\t120\t127\t256.148\n+MAX_I\t127\t131\t281.762\n+MAX_I\t131\t139\t256.148\n+MAX_I\t139\t140\t230.533\n+MAX_I\t140\t142\t128.074\n+MAX_I\t142\t144\t51.2295\n+MAX_I\t144\t151\t25.6148\n+MAX_I\t151\t230\t0\n+MAX_I\t230\t237\t25.6148\n+MAX_I\t237\t238\t51.2295\n+MAX_I\t238\t254\t76.8443\n+MAX_I\t254\t257\t51.2295\n+MAX_I\t257\t263\t25.6148\n+MAX_I\t263\t316\t0\n+MAX_I\t316\t338\t128.074\n+MAX_I\t338\t340\t102.459\n+MAX_I\t340\t342\t51.2295\n+MAX_I\t342\t4085\t0\n+MAX_I\t4085\t4103\t51.2295\n+MAX_I\t4103\t7914\t0\n+MAX_LTR\t0\t12\t25.6148\n+MAX_LTR\t12\t15\t51.2295\n+MAX_LTR\t15\t18\t76.8443\n+MAX_LTR\t18\t21\t51.2295\n+MAX_LTR\t21\t22\t102.459\n+MAX_LTR\t22\t23\t128.074\n+MAX_LTR\t23\t35\t153.689\n+MAX_LTR\t35\t36\t128.074\n+MAX_LTR\t36\t44\t102.459\n+MAX_LTR\t44\t45\t25.6148\n+MAX_LTR\t45\t48\t0\n+MAX_LTR\t48\t52\t51.2295\n+MAX_LTR\t52\t70\t230.533\n+MAX_LTR\t70\t72\t204.918\n+MAX_LTR\t72\t74\t153.689\n+MAX_LTR\t74\t75\t128.074\n+MAX_LTR\t75\t76\t102.459\n+MAX_LTR\t76\t77\t76.8443\n+MAX_LTR\t77\t78\t25.6148\n+MAX_LTR\t78\t80\t0\n+MAX_LTR\t80\t84\t153.689\n+MAX_LTR\t84\t88\t204.918\n+MAX_LTR\t88\t100\t230.533\n+MAX_LTR\t100\t105\t204.918\n+MAX_LTR\t105\t113\t25.6148\n+MAX_LTR\t113\t134\t0\n+MAX_LTR\t134\t138\t51.2295\n+MAX_LTR\t138\t159\t230.533\n+MAX_LTR\t159\t161\t153.689\n+MAX_LTR\t161\t321\t0\n+PROTOP\t0\t14\t0\n+PROTOP\t14\t38\t25.6148\n+PROTOP\t38\t59\t0\n+PROTOP\t59\t64\t25.6148\n+PROTOP\t64\t83\t102.459\n+PROTOP\t83\t86\t76.8443\n+PROTOP\t86\t88\t51.2295\n+PROTOP\t88\t103\t0\n+PROTOP\t103\t104\t76.8443\n+PROTOP\t104\t106\t102.459\n+PROTOP\t106\t108\t128.074\n+PROTOP\t108\t125\t153.689\n+PROTOP\t125\t126\t128.074\n+PROTOP\t126\t127\t102.459\n+PROTOP\t127\t129\t76.8443\n+PROTOP\t129\t160\t0\n+PROTOP\t160\t179\t51.2295\n+PROTOP\t179\t184\t25.6148\n+PROTOP\t184\t209\t0\n+PROTOP\t209\t224\t256.148\n+PROTOP\t224\t234\t281.762\n+PROTOP\t234\t235\t102.459\n+PROTOP\t235\t250\t25.6148\n+PROTOP\t250\t445\t0\n+PROTOP\t445\t449\t25.6148\n+PROTOP\t449\t468\t128.074\n+PROTOP\t468\t469\t102.459\n+PROTOP\t469\t470\t51.2295\n+PROTOP\t470\t472\t25.6148\n+PROTOP\t472\t2348\t0\n+PROTOP\t2348\t2399\t25.6148\n+PROTOP\t2399\t2442\t0\n+PROTOP\t2442\t2465\t25.6148\n+PROTOP\t2465\t2499\t0\n+PROTOP\t2499\t2520\t25.6148\n+PROTOP\t2520\t2540\t0\n+PROTOP\t2540\t2565\t25.6148\n+PROTOP\t2565\t2615\t0\n+PROTOP\t2615\t2641\t51.2295\n+PROTOP\t2641\t2647\t0\n+PROTOP\t2647\t2648\t25.6148\n+PROTOP\t2648\t2653\t51.2295\n+PROTOP\t2653\t2672\t102.459\n+PROTOP\t2672\t2678\t51.2295\n+PROTOP\t2678\t2689\t0\n+PROTOP\t2689\t2690\t25.6148\n+PROTOP\t2690\t2696\t51.2295\n+PROTOP\t2696\t2714\t128.074\n+PROTOP\t2714\t2715\t102.459\n+PROTOP\t2715\t2718\t76.8443\n+PROTOP\t2718\t2719\t25.6148\n+PROTOP\t2719\t2742\t0\n+PROTOP\t2742\t2745\t179.303\n+PROTOP\t2745\t2746\t256.148\n+PROTOP\t2746\t2749\t332.992\n+PROTOP\t2749\t2752\t358.607\n+PROTOP\t2752\t2766\t384.221\n+PROTOP\t2766\t2767\t307.377\n+PROTOP\t2767\t2785\t25.6148\n+PROTOP\t2785\t2786\t0\n+PROTOP\t2786\t2797\t25.6148\n+PROTOP\t2797\t3258\t0\n+PROTOP\t3258\t3279\t51.2295\n+PROTOP\t3279\t3327\t0\n+PROTOP\t3327\t3350\t25.6148\n+PROTOP\t3350\t3397\t0\n+PROTOP\t3397\t3422\t25.6148\n+PROTOP\t3422\t3452\t0\n+PROTOP\t3452\t3462\t25.6148\n+PROTOP\t3462\t3478\t51.2295\n+PROTOP\t3478\t3484\t25.6148\n+PROTOP\t3484\t4135\t0\n+PROTOP\t4135\t4160\t76.8443\n+PROTOP\t4160\t4307\t0\n+PROTOP\t4307\t4308\t25.6148\n+PROTOP\t4308\t4333\t51.2295\n+PROTOP\t4333\t4360\t0\n+PROTOP\t4360\t4384\t25.6148\n+PROTOP\t4384\t4387\t0\n+PROTOP\t4387\t4388\t128.074\n+PROTOP\t4388\t4398\t153.689\n+PROTOP\t4398\t4412\t204.918\n+PROTOP\t4412\t4413\t76.8443\n+PROTOP\t4413\t4422\t51.2295\n+PROTOP\t4422\t4423\t25.6148\n+PROTOP\t4423\t4480\t0\n' |
| b |
| diff -r 9645d995fb3c -r 9185ca0a7b43 test-data/res_files/reads-sample-small.fastq/subgroups/bonafide_reads/bonafide_reads-TEs_reads_counts.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/res_files/reads-sample-small.fastq/subgroups/bonafide_reads/bonafide_reads-TEs_reads_counts.txt Wed Jan 16 08:18:13 2019 -0500 |
| b |
| @@ -0,0 +1,18 @@ +ID reads counts RPKM per million of piRNAs per million of miRNAs per million of bonafide reads sense reads counts reverse reads counts % of sense 1U % of sense 10A % of reverse 1U % of reverse 10A +BATUMI_I 333 1071.17 14443.10 5285714.29 10907.30 179 154 94.413407821229 38.5474860335196 42.2077922077922 20.7792207792208 +BATUMI_LTR 102 9605.53 4424.01 1619047.62 3340.98 4 98 75 0 2.04081632653061 40.8163265306122 +BS2 7237 39265.83 313887.93 114873015.87 237045.53 1487 5750 44.7209145931406 40.2824478816409 15.7913043478261 31.5130434782609 +COPIA_DM_I 0 0.00 0.00 0.00 0.00 0 0 0 0 0 0 +COPIA_DM_LTR 0 0.00 0.00 0.00 0.00 0 0 0 0 0 0 +DMCR1A 393 2252.04 17045.45 6238095.24 12872.58 93 300 52.6881720430108 51.6129032258064 20.6666666666667 32.3333333333333 +DMRT1B 377 1863.16 16351.49 5984126.98 12348.51 199 178 40.2010050251256 37.1859296482412 4.49438202247191 18.5393258426966 +FW 15168 82805.75 657876.47 240761904.76 496822.80 2680 12488 40.1492537313433 57.3880597014925 14.9263292761051 26.0009609224856 +G6_DM 2055 25777.83 89130.81 32619047.62 67310.84 427 1628 54.8009367681499 49.1803278688525 2.08845208845209 29.8525798525799 +Gypsy2-I_DM 0 0.00 0.00 0.00 0.00 0 0 0 0 0 0 +Gypsy2-LTR_DM 195 14777.74 8457.67 3095238.10 6387.16 82 113 54.8780487804878 31.7073170731707 9.73451327433628 18.5840707964602 +I_DM 48 228.79 2081.89 761904.76 1572.22 18 30 50 33.3333333333333 23.3333333333333 43.3333333333333 +MAX_I 120 388.40 5204.72 1904761.90 3930.56 30 90 73.3333333333333 6.66666666666667 62.2222222222222 17.7777777777778 +MAX_LTR 102 8139.27 4424.01 1619047.62 3340.98 34 68 23.5294117647059 38.2352941176471 4.41176470588235 29.4117647058824 +PROTOP 210 1200.69 9108.26 3333333.33 6878.48 81 129 58.0246913580247 64.1975308641975 23.2558139534884 29.4573643410853 +ZAM_I 0 0.00 0.00 0.00 0.00 0 0 0 0 0 0 +ZAM_LTR 0 0.00 0.00 0.00 0.00 0 0 0 0 0 0 |
| b |
| diff -r 9645d995fb3c -r 9185ca0a7b43 test-data/res_files/reads-sample-small.fastq/subgroups/bonafide_reads/bonafide_reads-TEs_reads_counts_mismatches.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/res_files/reads-sample-small.fastq/subgroups/bonafide_reads/bonafide_reads-TEs_reads_counts_mismatches.txt Wed Jan 16 08:18:13 2019 -0500 |
| b |
| @@ -0,0 +1,18 @@ +ID reads counts RPKM per million of piRNAs per million of miRNAs per million of bonafide reads sense reads counts reverse reads counts % of sense 1U % of sense 10A % of reverse 1U % of reverse 10A +BATUMI_I 274 881.38 11884.11 4349206.35 8974.78 169 105 96.4497041420118 39.6449704142012 41.9047619047619 23.8095238095238 +BATUMI_LTR 96 9040.50 4163.78 1523809.52 3144.45 3 93 66.6666666666667 0 2.1505376344086 39.7849462365591 +BS2 227 1231.64 9845.59 3603174.60 7435.31 57 170 59.6491228070175 35.0877192982456 7.05882352941176 37.6470588235294 +COPIA_DM_I 0 0.00 0.00 0.00 0.00 0 0 0 0 0 0 +COPIA_DM_LTR 0 0.00 0.00 0.00 0.00 0 0 0 0 0 0 +DMCR1A 78 446.97 3383.07 1238095.24 2554.86 7 71 85.7142857142857 42.8571428571429 23.943661971831 26.7605633802817 +DMRT1B 216 1067.49 9368.49 3428571.43 7075.01 132 84 48.4848484848485 48.4848484848485 8.33333333333333 32.1428571428571 +FW 91 496.79 3946.91 1444444.44 2980.67 31 60 70.9677419354839 80.6451612903226 8.33333333333333 31.6666666666667 +G6_DM 0 0.00 0.00 0.00 0.00 0 0 0 0 0 0 +Gypsy2-I_DM 0 0.00 0.00 0.00 0.00 0 0 0 0 0 0 +Gypsy2-LTR_DM 4 303.13 173.49 63492.06 131.02 0 4 0 0 0 25 +I_DM 38 181.12 1648.16 603174.60 1244.68 12 26 50 33.3333333333333 19.2307692307692 50 +MAX_I 36 116.52 1561.42 571428.57 1179.17 15 21 60 6.66666666666667 23.8095238095238 23.8095238095238 +MAX_LTR 45 3590.85 1951.77 714285.71 1473.96 12 33 0 91.6666666666667 9.09090909090909 3.03030303030303 +PROTOP 127 726.13 5508.33 2015873.02 4159.84 55 72 65.4545454545455 63.6363636363636 27.7777777777778 23.6111111111111 +ZAM_I 0 0.00 0.00 0.00 0.00 0 0 0 0 0 0 +ZAM_LTR 0 0.00 0.00 0.00 0.00 0 0 0 0 0 0 |
| b |
| diff -r 9645d995fb3c -r 9185ca0a7b43 test-data/res_files/reads-sample-small.fastq/subgroups/bonafide_reads/bonafide_reads-TEs_reads_counts_nomismatches.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/res_files/reads-sample-small.fastq/subgroups/bonafide_reads/bonafide_reads-TEs_reads_counts_nomismatches.txt Wed Jan 16 08:18:13 2019 -0500 |
| b |
| @@ -0,0 +1,18 @@ +ID reads counts RPKM per million of piRNAs per million of miRNAs per million of bonafide reads sense reads counts reverse reads counts % of sense 1U % of sense 10A % of reverse 1U % of reverse 10A +BATUMI_I 59 189.79 2558.99 936507.94 1932.53 10 49 60 20 42.8571428571429 14.2857142857143 +BATUMI_LTR 6 565.03 260.24 95238.10 196.53 1 5 100 0 0 60 +BS2 7010 38034.19 304042.33 111269841.27 229610.22 1430 5580 44.1258741258741 40.4895104895105 16.0573476702509 31.326164874552 +COPIA_DM_I 0 0.00 0.00 0.00 0.00 0 0 0 0 0 0 +COPIA_DM_LTR 0 0.00 0.00 0.00 0.00 0 0 0 0 0 0 +DMCR1A 315 1805.07 13662.39 5000000.00 10317.72 86 229 50 52.3255813953488 19.6506550218341 34.061135371179 +DMRT1B 161 795.67 6983.00 2555555.56 5273.50 67 94 23.8805970149254 14.9253731343284 1.06382978723404 6.38297872340426 +FW 15077 82308.96 653929.56 239317460.32 493842.12 2649 12428 39.7885994714987 57.115892789732 14.9581589958159 25.9736079819762 +G6_DM 2055 25777.83 89130.81 32619047.62 67310.84 427 1628 54.8009367681499 49.1803278688525 2.08845208845209 29.8525798525799 +Gypsy2-I_DM 0 0.00 0.00 0.00 0.00 0 0 0 0 0 0 +Gypsy2-LTR_DM 191 14474.61 8284.18 3031746.03 6256.14 82 109 54.8780487804878 31.7073170731707 10.0917431192661 18.348623853211 +I_DM 10 47.66 433.73 158730.16 327.55 6 4 50 33.3333333333333 50 0 +MAX_I 84 271.88 3643.30 1333333.33 2751.39 15 69 86.6666666666667 6.66666666666667 73.9130434782609 15.9420289855072 +MAX_LTR 57 4548.41 2472.24 904761.90 1867.02 22 35 36.3636363636364 9.09090909090909 0 54.2857142857143 +PROTOP 83 474.56 3599.93 1317460.32 2718.64 26 57 42.3076923076923 65.3846153846154 17.5438596491228 36.8421052631579 +ZAM_I 0 0.00 0.00 0.00 0.00 0 0 0 0 0 0 +ZAM_LTR 0 0.00 0.00 0.00 0.00 0 0 0 0 0 0 |
| b |
| diff -r 9645d995fb3c -r 9185ca0a7b43 test-data/res_files/reads-sample-small.fastq/subgroups/bonafide_reads/bonafide_reads-TEs_sorted.bam |
| b |
| Binary file test-data/res_files/reads-sample-small.fastq/subgroups/bonafide_reads/bonafide_reads-TEs_sorted.bam has changed |
| b |
| diff -r 9645d995fb3c -r 9185ca0a7b43 test-data/res_files/reads-sample-small.fastq/subgroups/bonafide_reads/bonafide_reads-TEs_unique_sorted.bam |
| b |
| Binary file test-data/res_files/reads-sample-small.fastq/subgroups/bonafide_reads/bonafide_reads-TEs_unique_sorted.bam has changed |
| b |
| diff -r 9645d995fb3c -r 9185ca0a7b43 test-data/res_files/reads-sample-small.fastq/subgroups/bonafide_reads/bonafide_reads-genome_minus.bedgraph --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/res_files/reads-sample-small.fastq/subgroups/bonafide_reads/bonafide_reads-genome_minus.bedgraph Wed Jan 16 08:18:13 2019 -0500 |
| b |
| b'@@ -0,0 +1,4612 @@\n+chrom_1\t0\t3964\t0\n+chrom_1\t3964\t3988\t25.6148\n+chrom_1\t3988\t8675\t0\n+chrom_1\t8675\t8700\t25.6148\n+chrom_1\t8700\t9636\t0\n+chrom_1\t9636\t9661\t25.6148\n+chrom_1\t9661\t10201\t0\n+chrom_1\t10201\t10226\t25.6148\n+chrom_1\t10226\t11637\t0\n+chrom_1\t11637\t11661\t25.6148\n+chrom_1\t11661\t12140\t0\n+chrom_1\t12140\t12161\t25.6148\n+chrom_1\t12161\t12187\t0\n+chrom_1\t12187\t12211\t25.6148\n+chrom_1\t12211\t12214\t0\n+chrom_1\t12214\t12215\t25.6148\n+chrom_1\t12215\t12238\t51.2295\n+chrom_1\t12238\t13134\t0\n+chrom_1\t13134\t13159\t25.6148\n+chrom_1\t13159\t13465\t0\n+chrom_1\t13465\t13470\t25.6148\n+chrom_1\t13470\t13491\t51.2295\n+chrom_1\t13491\t13493\t25.6148\n+chrom_1\t13493\t14233\t0\n+chrom_1\t14233\t14258\t25.6148\n+chrom_1\t14258\t14318\t0\n+chrom_1\t14318\t14321\t25.6148\n+chrom_1\t14321\t14344\t51.2295\n+chrom_1\t14344\t14438\t0\n+chrom_1\t14438\t14463\t25.6148\n+chrom_1\t14463\t14500\t0\n+chrom_1\t14500\t14523\t25.6148\n+chrom_1\t14523\t14778\t0\n+chrom_1\t14778\t14790\t51.2295\n+chrom_1\t14790\t14803\t76.8443\n+chrom_1\t14803\t14804\t51.2295\n+chrom_1\t14804\t14814\t25.6148\n+chrom_1\t14814\t14840\t0\n+chrom_1\t14840\t14860\t51.2295\n+chrom_1\t14860\t14865\t25.6148\n+chrom_1\t14865\t14968\t0\n+chrom_1\t14968\t14973\t25.6148\n+chrom_1\t14973\t14977\t51.2295\n+chrom_1\t14977\t14985\t76.8443\n+chrom_1\t14985\t14992\t128.074\n+chrom_1\t14992\t14999\t102.459\n+chrom_1\t14999\t15002\t76.8443\n+chrom_1\t15002\t15005\t51.2295\n+chrom_1\t15005\t15009\t76.8443\n+chrom_1\t15009\t15025\t25.6148\n+chrom_1\t15025\t15089\t0\n+chrom_1\t15089\t15112\t25.6148\n+chrom_1\t15112\t15114\t51.2295\n+chrom_1\t15114\t15130\t25.6148\n+chrom_1\t15130\t15132\t76.8443\n+chrom_1\t15132\t15134\t128.074\n+chrom_1\t15134\t15137\t102.459\n+chrom_1\t15137\t15155\t128.074\n+chrom_1\t15155\t15157\t76.8443\n+chrom_1\t15157\t15160\t0\n+chrom_1\t15160\t15161\t51.2295\n+chrom_1\t15161\t15164\t102.459\n+chrom_1\t15164\t15184\t128.074\n+chrom_1\t15184\t15185\t76.8443\n+chrom_1\t15185\t15201\t0\n+chrom_1\t15201\t15225\t25.6148\n+chrom_1\t15225\t15250\t0\n+chrom_1\t15250\t15251\t25.6148\n+chrom_1\t15251\t15255\t76.8443\n+chrom_1\t15255\t15260\t102.459\n+chrom_1\t15260\t15274\t128.074\n+chrom_1\t15274\t15287\t25.6148\n+chrom_1\t15287\t15288\t51.2295\n+chrom_1\t15288\t15289\t76.8443\n+chrom_1\t15289\t15290\t204.918\n+chrom_1\t15290\t15291\t281.762\n+chrom_1\t15291\t15306\t307.377\n+chrom_1\t15306\t15313\t281.762\n+chrom_1\t15313\t15315\t128.074\n+chrom_1\t15315\t15348\t0\n+chrom_1\t15348\t15349\t25.6148\n+chrom_1\t15349\t15350\t51.2295\n+chrom_1\t15350\t15366\t76.8443\n+chrom_1\t15366\t15370\t102.459\n+chrom_1\t15370\t15372\t76.8443\n+chrom_1\t15372\t15390\t25.6148\n+chrom_1\t15390\t15444\t0\n+chrom_1\t15444\t15445\t51.2295\n+chrom_1\t15445\t15446\t76.8443\n+chrom_1\t15446\t15469\t128.074\n+chrom_1\t15469\t15470\t51.2295\n+chrom_1\t15470\t15471\t25.6148\n+chrom_1\t15471\t15476\t0\n+chrom_1\t15476\t15477\t25.6148\n+chrom_1\t15477\t15478\t51.2295\n+chrom_1\t15478\t15482\t102.459\n+chrom_1\t15482\t15499\t128.074\n+chrom_1\t15499\t15500\t153.689\n+chrom_1\t15500\t15504\t102.459\n+chrom_1\t15504\t15506\t51.2295\n+chrom_1\t15506\t15523\t25.6148\n+chrom_1\t15523\t15534\t0\n+chrom_1\t15534\t15535\t51.2295\n+chrom_1\t15535\t15536\t76.8443\n+chrom_1\t15536\t15558\t102.459\n+chrom_1\t15558\t15559\t51.2295\n+chrom_1\t15559\t15560\t128.074\n+chrom_1\t15560\t15580\t76.8443\n+chrom_1\t15580\t15584\t51.2295\n+chrom_1\t15584\t15586\t25.6148\n+chrom_1\t15586\t15587\t281.762\n+chrom_1\t15587\t15594\t307.377\n+chrom_1\t15594\t15598\t358.607\n+chrom_1\t15598\t15609\t461.066\n+chrom_1\t15609\t15620\t153.689\n+chrom_1\t15620\t15622\t102.459\n+chrom_1\t15622\t15623\t25.6148\n+chrom_1\t15623\t15688\t0\n+chrom_1\t15688\t15700\t25.6148\n+chrom_1\t15700\t15714\t76.8443\n+chrom_1\t15714\t15722\t51.2295\n+chrom_1\t15722\t15726\t76.8443\n+chrom_1\t15726\t15727\t51.2295\n+chrom_1\t15727\t15728\t102.459\n+chrom_1\t15728\t15730\t128.074\n+chrom_1\t15730\t15745\t204.918\n+chrom_1\t15745\t15750\t179.303\n+chrom_1\t15750\t15752\t76.8443\n+chrom_1\t15752\t15754\t51.2295\n+chrom_1\t15754\t15791\t0\n+chrom_1\t15791\t15793\t51.2295\n+chrom_1\t15793\t15794\t76.8443\n+chrom_1\t15794\t15796\t153.689\n+chrom_1\t15796\t15805\t179.303\n+chrom_1\t15805\t15806\t281.762\n+chrom_1\t15806\t15815\t307.377\n+chrom_1\t15815\t15816\t256.148\n+chrom_1\t15816\t15817\t230.533\n+chrom_1\t15817\t15819\t153.689\n+chrom_1\t15819\t15825\t128.074\n+chrom_1\t15825\t15828\t76.8443\n+chrom_1\t15828\t15925\t0\n+chrom_1\t15925\t15926\t128.074\n+chrom_1\t15926\t15'..b'rom_1\t69802\t70934\t0\n+chrom_1\t70934\t70955\t25.6148\n+chrom_1\t70955\t71363\t0\n+chrom_1\t71363\t71384\t25.6148\n+chrom_1\t71384\t71705\t0\n+chrom_1\t71705\t71726\t25.6148\n+chrom_1\t71726\t71760\t0\n+chrom_1\t71760\t71781\t25.6148\n+chrom_1\t71781\t72252\t0\n+chrom_1\t72252\t72273\t25.6148\n+chrom_1\t72273\t72315\t0\n+chrom_1\t72315\t72336\t25.6148\n+chrom_1\t72336\t72363\t0\n+chrom_1\t72363\t72387\t25.6148\n+chrom_1\t72387\t73124\t0\n+chrom_1\t73124\t73145\t25.6148\n+chrom_1\t73145\t73249\t0\n+chrom_1\t73249\t73270\t25.6148\n+chrom_1\t73270\t73315\t0\n+chrom_1\t73315\t73336\t25.6148\n+chrom_1\t73336\t73759\t0\n+chrom_1\t73759\t73780\t25.6148\n+chrom_1\t73780\t74181\t0\n+chrom_1\t74181\t74205\t25.6148\n+chrom_1\t74205\t74260\t0\n+chrom_1\t74260\t74281\t25.6148\n+chrom_1\t74281\t74954\t0\n+chrom_1\t74954\t74975\t25.6148\n+chrom_1\t74975\t75015\t0\n+chrom_1\t75015\t75035\t25.6148\n+chrom_1\t75035\t75554\t0\n+chrom_1\t75554\t75575\t25.6148\n+chrom_1\t75575\t76156\t0\n+chrom_1\t76156\t76181\t25.6148\n+chrom_1\t76181\t76310\t0\n+chrom_1\t76310\t76328\t25.6148\n+chrom_1\t76328\t77319\t0\n+chrom_1\t77319\t77320\t25.6148\n+chrom_1\t77320\t77340\t51.2295\n+chrom_1\t77340\t77341\t25.6148\n+chrom_1\t77341\t77411\t0\n+chrom_1\t77411\t77431\t51.2295\n+chrom_1\t77431\t77433\t25.6148\n+chrom_1\t77433\t77516\t0\n+chrom_1\t77516\t77537\t25.6148\n+chrom_1\t77537\t78553\t0\n+chrom_1\t78553\t78573\t25.6148\n+chrom_1\t78573\t79059\t0\n+chrom_1\t79059\t79080\t25.6148\n+chrom_1\t79080\t80057\t0\n+chrom_1\t80057\t80078\t25.6148\n+chrom_1\t80078\t80319\t0\n+chrom_1\t80319\t80340\t25.6148\n+chrom_1\t80340\t80395\t0\n+chrom_1\t80395\t80413\t25.6148\n+chrom_1\t80413\t80904\t0\n+chrom_1\t80904\t80923\t25.6148\n+chrom_1\t80923\t80929\t51.2295\n+chrom_1\t80929\t80949\t25.6148\n+chrom_1\t80949\t80959\t0\n+chrom_1\t80959\t80982\t25.6148\n+chrom_1\t80982\t81627\t0\n+chrom_1\t81627\t81650\t25.6148\n+chrom_1\t81650\t81784\t0\n+chrom_1\t81784\t81805\t25.6148\n+chrom_1\t81805\t82063\t0\n+chrom_1\t82063\t82083\t25.6148\n+chrom_1\t82083\t82123\t0\n+chrom_1\t82123\t82146\t25.6148\n+chrom_1\t82146\t82339\t0\n+chrom_1\t82339\t82360\t25.6148\n+chrom_1\t82360\t82455\t0\n+chrom_1\t82455\t82459\t25.6148\n+chrom_1\t82459\t82479\t51.2295\n+chrom_1\t82479\t82480\t25.6148\n+chrom_1\t82480\t83079\t0\n+chrom_1\t83079\t83100\t25.6148\n+chrom_1\t83100\t83396\t0\n+chrom_1\t83396\t83422\t25.6148\n+chrom_1\t83422\t83426\t0\n+chrom_1\t83426\t83450\t51.2295\n+chrom_1\t83450\t83540\t0\n+chrom_1\t83540\t83561\t25.6148\n+chrom_1\t83561\t83868\t0\n+chrom_1\t83868\t83891\t25.6148\n+chrom_1\t83891\t83901\t0\n+chrom_1\t83901\t83922\t25.6148\n+chrom_1\t83922\t83991\t0\n+chrom_1\t83991\t84014\t25.6148\n+chrom_1\t84014\t85181\t0\n+chrom_1\t85181\t85202\t51.2295\n+chrom_1\t85202\t85205\t25.6148\n+chrom_1\t85205\t85252\t0\n+chrom_1\t85252\t85273\t25.6148\n+chrom_1\t85273\t85366\t0\n+chrom_1\t85366\t85390\t25.6148\n+chrom_1\t85390\t85640\t0\n+chrom_1\t85640\t85662\t25.6148\n+chrom_1\t85662\t85759\t0\n+chrom_1\t85759\t85783\t25.6148\n+chrom_1\t85783\t86402\t0\n+chrom_1\t86402\t86424\t25.6148\n+chrom_1\t86424\t86453\t0\n+chrom_1\t86453\t86474\t25.6148\n+chrom_1\t86474\t86632\t0\n+chrom_1\t86632\t86658\t25.6148\n+chrom_1\t86658\t86941\t0\n+chrom_1\t86941\t86967\t25.6148\n+chrom_1\t86967\t87002\t0\n+chrom_1\t87002\t87022\t25.6148\n+chrom_1\t87022\t87066\t0\n+chrom_1\t87066\t87087\t25.6148\n+chrom_1\t87087\t87142\t0\n+chrom_1\t87142\t87163\t25.6148\n+chrom_1\t87163\t87223\t0\n+chrom_1\t87223\t87244\t25.6148\n+chrom_1\t87244\t87446\t0\n+chrom_1\t87446\t87467\t25.6148\n+chrom_1\t87467\t87524\t0\n+chrom_1\t87524\t87546\t25.6148\n+chrom_1\t87546\t87581\t0\n+chrom_1\t87581\t87582\t25.6148\n+chrom_1\t87582\t87602\t51.2295\n+chrom_1\t87602\t87665\t0\n+chrom_1\t87665\t87683\t25.6148\n+chrom_1\t87683\t87819\t0\n+chrom_1\t87819\t87839\t25.6148\n+chrom_1\t87839\t87853\t0\n+chrom_1\t87853\t87878\t25.6148\n+chrom_1\t87878\t88309\t0\n+chrom_1\t88309\t88330\t25.6148\n+chrom_1\t88330\t88443\t0\n+chrom_1\t88443\t88464\t25.6148\n+chrom_1\t88464\t88710\t0\n+chrom_1\t88710\t88731\t25.6148\n+chrom_1\t88731\t89102\t0\n+chrom_1\t89102\t89120\t25.6148\n+chrom_1\t89120\t89812\t0\n+chrom_1\t89812\t89833\t25.6148\n+chrom_1\t89833\t89999\t0\n+chrom_2\t0\t32272\t0\n+chrom_2\t32272\t32289\t25.6148\n+chrom_2\t32289\t32292\t51.2295\n+chrom_2\t32292\t32296\t76.8443\n+chrom_2\t32296\t32310\t51.2295\n+chrom_2\t32310\t39255\t0\n+chrom_2\t39255\t39276\t25.6148\n+chrom_2\t39276\t49999\t0\n+chrom_5\t0\t450\t0\n+chrom_5\t450\t468\t51.2295\n+chrom_5\t468\t1999\t0\n+chrom_6\t0\t3076\t0\n+chrom_6\t3076\t3096\t25.6148\n+chrom_6\t3096\t3999\t0\n' |
| b |
| diff -r 9645d995fb3c -r 9185ca0a7b43 test-data/res_files/reads-sample-small.fastq/subgroups/bonafide_reads/bonafide_reads-genome_plus.bedgraph --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/res_files/reads-sample-small.fastq/subgroups/bonafide_reads/bonafide_reads-genome_plus.bedgraph Wed Jan 16 08:18:13 2019 -0500 |
| b |
| b'@@ -0,0 +1,5801 @@\n+chrom_1\t0\t1967\t0\n+chrom_1\t1967\t1991\t25.6148\n+chrom_1\t1991\t2932\t0\n+chrom_1\t2932\t2954\t25.6148\n+chrom_1\t2954\t3456\t0\n+chrom_1\t3456\t3481\t25.6148\n+chrom_1\t3481\t7648\t0\n+chrom_1\t7648\t7671\t25.6148\n+chrom_1\t7671\t7953\t0\n+chrom_1\t7953\t7978\t25.6148\n+chrom_1\t7978\t8721\t0\n+chrom_1\t8721\t8742\t25.6148\n+chrom_1\t8742\t8747\t51.2295\n+chrom_1\t8747\t8758\t25.6148\n+chrom_1\t8758\t8767\t51.2295\n+chrom_1\t8767\t8783\t25.6148\n+chrom_1\t8783\t9642\t0\n+chrom_1\t9642\t9668\t25.6148\n+chrom_1\t9668\t10407\t0\n+chrom_1\t10407\t10428\t25.6148\n+chrom_1\t10428\t14236\t0\n+chrom_1\t14236\t14261\t25.6148\n+chrom_1\t14261\t14309\t0\n+chrom_1\t14309\t14336\t25.6148\n+chrom_1\t14336\t14439\t0\n+chrom_1\t14439\t14463\t25.6148\n+chrom_1\t14463\t14523\t0\n+chrom_1\t14523\t14544\t25.6148\n+chrom_1\t14544\t14551\t0\n+chrom_1\t14551\t14552\t25.6148\n+chrom_1\t14552\t14554\t76.8443\n+chrom_1\t14554\t14578\t179.303\n+chrom_1\t14578\t14580\t25.6148\n+chrom_1\t14580\t14592\t0\n+chrom_1\t14592\t14616\t25.6148\n+chrom_1\t14616\t14979\t0\n+chrom_1\t14979\t15004\t25.6148\n+chrom_1\t15004\t15062\t0\n+chrom_1\t15062\t15087\t25.6148\n+chrom_1\t15087\t15089\t0\n+chrom_1\t15089\t15092\t25.6148\n+chrom_1\t15092\t15115\t128.074\n+chrom_1\t15115\t15117\t102.459\n+chrom_1\t15117\t15139\t0\n+chrom_1\t15139\t15164\t25.6148\n+chrom_1\t15164\t15258\t0\n+chrom_1\t15258\t15260\t25.6148\n+chrom_1\t15260\t15264\t76.8443\n+chrom_1\t15264\t15269\t102.459\n+chrom_1\t15269\t15283\t128.074\n+chrom_1\t15283\t15284\t102.459\n+chrom_1\t15284\t15290\t51.2295\n+chrom_1\t15290\t15293\t25.6148\n+chrom_1\t15293\t15395\t0\n+chrom_1\t15395\t15399\t25.6148\n+chrom_1\t15399\t15400\t76.8443\n+chrom_1\t15400\t15407\t281.762\n+chrom_1\t15407\t15420\t307.377\n+chrom_1\t15420\t15421\t281.762\n+chrom_1\t15421\t15422\t204.918\n+chrom_1\t15422\t15423\t102.459\n+chrom_1\t15423\t15424\t51.2295\n+chrom_1\t15424\t15433\t25.6148\n+chrom_1\t15433\t15460\t0\n+chrom_1\t15460\t15484\t25.6148\n+chrom_1\t15484\t15528\t0\n+chrom_1\t15528\t15529\t25.6148\n+chrom_1\t15529\t15530\t51.2295\n+chrom_1\t15530\t15545\t76.8443\n+chrom_1\t15545\t15546\t102.459\n+chrom_1\t15546\t15548\t486.68\n+chrom_1\t15548\t15550\t461.066\n+chrom_1\t15550\t15555\t435.451\n+chrom_1\t15555\t15567\t409.836\n+chrom_1\t15567\t15569\t384.221\n+chrom_1\t15569\t15570\t204.918\n+chrom_1\t15570\t15572\t25.6148\n+chrom_1\t15572\t15716\t0\n+chrom_1\t15716\t15739\t25.6148\n+chrom_1\t15739\t15801\t0\n+chrom_1\t15801\t15824\t25.6148\n+chrom_1\t15824\t15970\t0\n+chrom_1\t15970\t15993\t76.8443\n+chrom_1\t15993\t16004\t0\n+chrom_1\t16004\t16027\t76.8443\n+chrom_1\t16027\t16028\t25.6148\n+chrom_1\t16028\t16229\t0\n+chrom_1\t16229\t16232\t25.6148\n+chrom_1\t16232\t16237\t51.2295\n+chrom_1\t16237\t16239\t76.8443\n+chrom_1\t16239\t16250\t128.074\n+chrom_1\t16250\t16256\t102.459\n+chrom_1\t16256\t16262\t76.8443\n+chrom_1\t16262\t16336\t0\n+chrom_1\t16336\t16338\t256.148\n+chrom_1\t16338\t16339\t281.762\n+chrom_1\t16339\t16342\t307.377\n+chrom_1\t16342\t16359\t332.992\n+chrom_1\t16359\t16360\t128.074\n+chrom_1\t16360\t16363\t76.8443\n+chrom_1\t16363\t16364\t51.2295\n+chrom_1\t16364\t16365\t25.6148\n+chrom_1\t16365\t16380\t0\n+chrom_1\t16380\t16402\t25.6148\n+chrom_1\t16402\t16496\t0\n+chrom_1\t16496\t16521\t25.6148\n+chrom_1\t16521\t16619\t0\n+chrom_1\t16619\t16628\t25.6148\n+chrom_1\t16628\t16630\t76.8443\n+chrom_1\t16630\t16643\t256.148\n+chrom_1\t16643\t16653\t230.533\n+chrom_1\t16653\t16654\t153.689\n+chrom_1\t16654\t16655\t76.8443\n+chrom_1\t16655\t16656\t25.6148\n+chrom_1\t16656\t16661\t0\n+chrom_1\t16661\t16685\t25.6148\n+chrom_1\t16685\t16772\t0\n+chrom_1\t16772\t16798\t25.6148\n+chrom_1\t16798\t16800\t51.2295\n+chrom_1\t16800\t16801\t179.303\n+chrom_1\t16801\t16808\t461.066\n+chrom_1\t16808\t16810\t486.68\n+chrom_1\t16810\t16811\t512.295\n+chrom_1\t16811\t16819\t537.91\n+chrom_1\t16819\t16823\t512.295\n+chrom_1\t16823\t16825\t461.066\n+chrom_1\t16825\t16829\t128.074\n+chrom_1\t16829\t16835\t102.459\n+chrom_1\t16835\t16849\t51.2295\n+chrom_1\t16849\t16850\t25.6148\n+chrom_1\t16850\t16864\t0\n+chrom_1\t16864\t16866\t25.6148\n+chrom_1\t16866\t16867\t76.8443\n+chrom_1\t16867\t16868\t179.303\n+chrom_1\t16868\t16869\t307.377\n+chrom_1\t16869\t16870\t332.992\n+chrom_1\t16870\t16875\t358.607\n+chrom_1\t16875\t16881\t384.221\n+chrom_1\t16881\t16883\t435.451\n+chrom_1\t16883\t16884\t461.066\n+chrom_1\t16884\t16885\t537.91\n+chrom_1\t16885\t16886\t589.139\n+chrom_1\t16886\t16887\t640.369\n+chrom_1\t16887\t16892\t614.754\n+chrom_1\t16892\t16893\t435.451\n+chrom_1\t16893\t16894\t33'..b'_1\t72261\t72282\t25.6148\n+chrom_1\t72282\t72356\t0\n+chrom_1\t72356\t72360\t25.6148\n+chrom_1\t72360\t72382\t51.2295\n+chrom_1\t72382\t72385\t25.6148\n+chrom_1\t72385\t72667\t0\n+chrom_1\t72667\t72688\t25.6148\n+chrom_1\t72688\t72713\t0\n+chrom_1\t72713\t72737\t25.6148\n+chrom_1\t72737\t72996\t0\n+chrom_1\t72996\t73017\t25.6148\n+chrom_1\t73017\t73230\t0\n+chrom_1\t73230\t73252\t25.6148\n+chrom_1\t73252\t73254\t0\n+chrom_1\t73254\t73275\t25.6148\n+chrom_1\t73275\t73572\t0\n+chrom_1\t73572\t73593\t25.6148\n+chrom_1\t73593\t73860\t0\n+chrom_1\t73860\t73885\t25.6148\n+chrom_1\t73885\t73976\t0\n+chrom_1\t73976\t73997\t25.6148\n+chrom_1\t73997\t74302\t0\n+chrom_1\t74302\t74323\t25.6148\n+chrom_1\t74323\t74376\t0\n+chrom_1\t74376\t74400\t25.6148\n+chrom_1\t74400\t74487\t0\n+chrom_1\t74487\t74508\t25.6148\n+chrom_1\t74508\t75553\t0\n+chrom_1\t75553\t75574\t25.6148\n+chrom_1\t75574\t77140\t0\n+chrom_1\t77140\t77161\t25.6148\n+chrom_1\t77161\t77234\t0\n+chrom_1\t77234\t77255\t25.6148\n+chrom_1\t77255\t77443\t0\n+chrom_1\t77443\t77464\t25.6148\n+chrom_1\t77464\t77597\t0\n+chrom_1\t77597\t77616\t25.6148\n+chrom_1\t77616\t78651\t0\n+chrom_1\t78651\t78673\t25.6148\n+chrom_1\t78673\t79352\t0\n+chrom_1\t79352\t79371\t25.6148\n+chrom_1\t79371\t79422\t0\n+chrom_1\t79422\t79447\t25.6148\n+chrom_1\t79447\t80012\t0\n+chrom_1\t80012\t80022\t25.6148\n+chrom_1\t80022\t80033\t51.2295\n+chrom_1\t80033\t80041\t25.6148\n+chrom_1\t80041\t80862\t0\n+chrom_1\t80862\t80887\t25.6148\n+chrom_1\t80887\t81326\t0\n+chrom_1\t81326\t81351\t25.6148\n+chrom_1\t81351\t81505\t0\n+chrom_1\t81505\t81528\t25.6148\n+chrom_1\t81528\t82019\t0\n+chrom_1\t82019\t82040\t25.6148\n+chrom_1\t82040\t82213\t0\n+chrom_1\t82213\t82237\t25.6148\n+chrom_1\t82237\t82623\t0\n+chrom_1\t82623\t82644\t25.6148\n+chrom_1\t82644\t82981\t0\n+chrom_1\t82981\t83002\t25.6148\n+chrom_1\t83002\t83100\t0\n+chrom_1\t83100\t83121\t25.6148\n+chrom_1\t83121\t83268\t0\n+chrom_1\t83268\t83289\t25.6148\n+chrom_1\t83289\t83437\t0\n+chrom_1\t83437\t83458\t25.6148\n+chrom_1\t83458\t83567\t0\n+chrom_1\t83567\t83592\t25.6148\n+chrom_1\t83592\t84065\t0\n+chrom_1\t84065\t84089\t25.6148\n+chrom_1\t84089\t84524\t0\n+chrom_1\t84524\t84545\t25.6148\n+chrom_1\t84545\t84948\t0\n+chrom_1\t84948\t84969\t25.6148\n+chrom_1\t84969\t85094\t0\n+chrom_1\t85094\t85115\t51.2295\n+chrom_1\t85115\t85355\t0\n+chrom_1\t85355\t85376\t25.6148\n+chrom_1\t85376\t85397\t0\n+chrom_1\t85397\t85407\t25.6148\n+chrom_1\t85407\t85422\t51.2295\n+chrom_1\t85422\t85428\t25.6148\n+chrom_1\t85428\t85513\t0\n+chrom_1\t85513\t85534\t25.6148\n+chrom_1\t85534\t85980\t0\n+chrom_1\t85980\t86005\t25.6148\n+chrom_1\t86005\t86344\t0\n+chrom_1\t86344\t86354\t51.2295\n+chrom_1\t86354\t86362\t76.8443\n+chrom_1\t86362\t86365\t102.459\n+chrom_1\t86365\t86376\t51.2295\n+chrom_1\t86376\t86383\t25.6148\n+chrom_1\t86383\t86432\t0\n+chrom_1\t86432\t86453\t25.6148\n+chrom_1\t86453\t86950\t0\n+chrom_1\t86950\t86971\t25.6148\n+chrom_1\t86971\t87113\t0\n+chrom_1\t87113\t87134\t25.6148\n+chrom_1\t87134\t87255\t0\n+chrom_1\t87255\t87278\t25.6148\n+chrom_1\t87278\t88301\t0\n+chrom_1\t88301\t88325\t25.6148\n+chrom_1\t88325\t88633\t0\n+chrom_1\t88633\t88654\t25.6148\n+chrom_1\t88654\t88989\t0\n+chrom_1\t88989\t89015\t25.6148\n+chrom_1\t89015\t89111\t0\n+chrom_1\t89111\t89137\t25.6148\n+chrom_1\t89137\t89597\t0\n+chrom_1\t89597\t89618\t25.6148\n+chrom_1\t89618\t89999\t0\n+chrom_2\t0\t41979\t0\n+chrom_2\t41979\t42001\t51.2295\n+chrom_2\t42001\t49999\t0\n+chrom_4\t0\t1047\t0\n+chrom_4\t1047\t1066\t76.8443\n+chrom_4\t1066\t1067\t51.2295\n+chrom_4\t1067\t1071\t25.6148\n+chrom_4\t1071\t1151\t0\n+chrom_4\t1151\t1172\t25.6148\n+chrom_4\t1172\t1208\t0\n+chrom_4\t1208\t1212\t76.8443\n+chrom_4\t1212\t1230\t102.459\n+chrom_4\t1230\t1543\t0\n+chrom_4\t1543\t1566\t25.6148\n+chrom_4\t1566\t1587\t0\n+chrom_4\t1587\t1605\t25.6148\n+chrom_4\t1605\t1733\t0\n+chrom_4\t1733\t1754\t25.6148\n+chrom_4\t1754\t2000\t0\n+chrom_5\t0\t1648\t0\n+chrom_5\t1648\t1669\t25.6148\n+chrom_5\t1669\t1782\t0\n+chrom_5\t1782\t1803\t25.6148\n+chrom_5\t1803\t1999\t0\n+chrom_6\t0\t440\t0\n+chrom_6\t440\t464\t25.6148\n+chrom_6\t464\t885\t0\n+chrom_6\t885\t905\t51.2295\n+chrom_6\t905\t906\t25.6148\n+chrom_6\t906\t1038\t0\n+chrom_6\t1038\t1060\t25.6148\n+chrom_6\t1060\t1109\t0\n+chrom_6\t1109\t1110\t25.6148\n+chrom_6\t1110\t1115\t51.2295\n+chrom_6\t1115\t1117\t102.459\n+chrom_6\t1117\t1125\t128.074\n+chrom_6\t1125\t1130\t153.689\n+chrom_6\t1130\t1133\t102.459\n+chrom_6\t1133\t1136\t76.8443\n+chrom_6\t1136\t1142\t51.2295\n+chrom_6\t1142\t1143\t25.6148\n+chrom_6\t1143\t3002\t0\n+chrom_6\t3002\t3027\t25.6148\n+chrom_6\t3027\t3999\t0\n' |
| b |
| diff -r 9645d995fb3c -r 9185ca0a7b43 test-data/res_files/reads-sample-small.fastq/subgroups/bonafide_reads/bonafide_reads-genome_sorted.bam |
| b |
| Binary file test-data/res_files/reads-sample-small.fastq/subgroups/bonafide_reads/bonafide_reads-genome_sorted.bam has changed |
| b |
| diff -r 9645d995fb3c -r 9185ca0a7b43 test-data/res_files/reads-sample-small.fastq/subgroups/bonafide_reads/bonafide_reads-genome_unique_minus.bedgraph --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/res_files/reads-sample-small.fastq/subgroups/bonafide_reads/bonafide_reads-genome_unique_minus.bedgraph Wed Jan 16 08:18:13 2019 -0500 |
| b |
| b'@@ -0,0 +1,4604 @@\n+chrom_1\t0\t3964\t0\n+chrom_1\t3964\t3988\t25.6148\n+chrom_1\t3988\t8675\t0\n+chrom_1\t8675\t8700\t25.6148\n+chrom_1\t8700\t9636\t0\n+chrom_1\t9636\t9661\t25.6148\n+chrom_1\t9661\t10201\t0\n+chrom_1\t10201\t10226\t25.6148\n+chrom_1\t10226\t11637\t0\n+chrom_1\t11637\t11661\t25.6148\n+chrom_1\t11661\t12140\t0\n+chrom_1\t12140\t12161\t25.6148\n+chrom_1\t12161\t12187\t0\n+chrom_1\t12187\t12211\t25.6148\n+chrom_1\t12211\t12214\t0\n+chrom_1\t12214\t12215\t25.6148\n+chrom_1\t12215\t12238\t51.2295\n+chrom_1\t12238\t13134\t0\n+chrom_1\t13134\t13159\t25.6148\n+chrom_1\t13159\t13465\t0\n+chrom_1\t13465\t13470\t25.6148\n+chrom_1\t13470\t13491\t51.2295\n+chrom_1\t13491\t13493\t25.6148\n+chrom_1\t13493\t14233\t0\n+chrom_1\t14233\t14258\t25.6148\n+chrom_1\t14258\t14318\t0\n+chrom_1\t14318\t14321\t25.6148\n+chrom_1\t14321\t14344\t51.2295\n+chrom_1\t14344\t14438\t0\n+chrom_1\t14438\t14463\t25.6148\n+chrom_1\t14463\t14500\t0\n+chrom_1\t14500\t14523\t25.6148\n+chrom_1\t14523\t14778\t0\n+chrom_1\t14778\t14790\t51.2295\n+chrom_1\t14790\t14803\t76.8443\n+chrom_1\t14803\t14804\t51.2295\n+chrom_1\t14804\t14814\t25.6148\n+chrom_1\t14814\t14840\t0\n+chrom_1\t14840\t14860\t51.2295\n+chrom_1\t14860\t14865\t25.6148\n+chrom_1\t14865\t14968\t0\n+chrom_1\t14968\t14973\t25.6148\n+chrom_1\t14973\t14977\t51.2295\n+chrom_1\t14977\t14985\t76.8443\n+chrom_1\t14985\t14992\t128.074\n+chrom_1\t14992\t14999\t102.459\n+chrom_1\t14999\t15002\t76.8443\n+chrom_1\t15002\t15005\t51.2295\n+chrom_1\t15005\t15009\t76.8443\n+chrom_1\t15009\t15025\t25.6148\n+chrom_1\t15025\t15089\t0\n+chrom_1\t15089\t15112\t25.6148\n+chrom_1\t15112\t15114\t51.2295\n+chrom_1\t15114\t15130\t25.6148\n+chrom_1\t15130\t15132\t76.8443\n+chrom_1\t15132\t15134\t128.074\n+chrom_1\t15134\t15137\t102.459\n+chrom_1\t15137\t15155\t128.074\n+chrom_1\t15155\t15157\t76.8443\n+chrom_1\t15157\t15160\t0\n+chrom_1\t15160\t15161\t51.2295\n+chrom_1\t15161\t15164\t102.459\n+chrom_1\t15164\t15184\t128.074\n+chrom_1\t15184\t15185\t76.8443\n+chrom_1\t15185\t15201\t0\n+chrom_1\t15201\t15225\t25.6148\n+chrom_1\t15225\t15250\t0\n+chrom_1\t15250\t15251\t25.6148\n+chrom_1\t15251\t15255\t76.8443\n+chrom_1\t15255\t15260\t102.459\n+chrom_1\t15260\t15274\t128.074\n+chrom_1\t15274\t15287\t25.6148\n+chrom_1\t15287\t15288\t51.2295\n+chrom_1\t15288\t15289\t76.8443\n+chrom_1\t15289\t15290\t204.918\n+chrom_1\t15290\t15291\t281.762\n+chrom_1\t15291\t15306\t307.377\n+chrom_1\t15306\t15313\t281.762\n+chrom_1\t15313\t15315\t128.074\n+chrom_1\t15315\t15348\t0\n+chrom_1\t15348\t15349\t25.6148\n+chrom_1\t15349\t15350\t51.2295\n+chrom_1\t15350\t15366\t76.8443\n+chrom_1\t15366\t15370\t102.459\n+chrom_1\t15370\t15372\t76.8443\n+chrom_1\t15372\t15390\t25.6148\n+chrom_1\t15390\t15444\t0\n+chrom_1\t15444\t15445\t51.2295\n+chrom_1\t15445\t15446\t76.8443\n+chrom_1\t15446\t15469\t128.074\n+chrom_1\t15469\t15470\t51.2295\n+chrom_1\t15470\t15471\t25.6148\n+chrom_1\t15471\t15476\t0\n+chrom_1\t15476\t15477\t25.6148\n+chrom_1\t15477\t15478\t51.2295\n+chrom_1\t15478\t15482\t102.459\n+chrom_1\t15482\t15499\t128.074\n+chrom_1\t15499\t15500\t153.689\n+chrom_1\t15500\t15504\t102.459\n+chrom_1\t15504\t15506\t51.2295\n+chrom_1\t15506\t15523\t25.6148\n+chrom_1\t15523\t15534\t0\n+chrom_1\t15534\t15535\t51.2295\n+chrom_1\t15535\t15536\t76.8443\n+chrom_1\t15536\t15558\t102.459\n+chrom_1\t15558\t15559\t51.2295\n+chrom_1\t15559\t15560\t128.074\n+chrom_1\t15560\t15580\t76.8443\n+chrom_1\t15580\t15584\t51.2295\n+chrom_1\t15584\t15586\t25.6148\n+chrom_1\t15586\t15587\t281.762\n+chrom_1\t15587\t15594\t307.377\n+chrom_1\t15594\t15598\t358.607\n+chrom_1\t15598\t15609\t461.066\n+chrom_1\t15609\t15620\t153.689\n+chrom_1\t15620\t15622\t102.459\n+chrom_1\t15622\t15623\t25.6148\n+chrom_1\t15623\t15688\t0\n+chrom_1\t15688\t15700\t25.6148\n+chrom_1\t15700\t15714\t76.8443\n+chrom_1\t15714\t15722\t51.2295\n+chrom_1\t15722\t15726\t76.8443\n+chrom_1\t15726\t15727\t51.2295\n+chrom_1\t15727\t15728\t102.459\n+chrom_1\t15728\t15730\t128.074\n+chrom_1\t15730\t15745\t204.918\n+chrom_1\t15745\t15750\t179.303\n+chrom_1\t15750\t15752\t76.8443\n+chrom_1\t15752\t15754\t51.2295\n+chrom_1\t15754\t15791\t0\n+chrom_1\t15791\t15793\t51.2295\n+chrom_1\t15793\t15794\t76.8443\n+chrom_1\t15794\t15796\t153.689\n+chrom_1\t15796\t15805\t179.303\n+chrom_1\t15805\t15806\t281.762\n+chrom_1\t15806\t15815\t307.377\n+chrom_1\t15815\t15816\t256.148\n+chrom_1\t15816\t15817\t230.533\n+chrom_1\t15817\t15819\t153.689\n+chrom_1\t15819\t15825\t128.074\n+chrom_1\t15825\t15828\t76.8443\n+chrom_1\t15828\t15925\t0\n+chrom_1\t15925\t15926\t128.074\n+chrom_1\t15926\t15'..b'84\t25.6148\n+chrom_1\t68884\t69781\t0\n+chrom_1\t69781\t69802\t25.6148\n+chrom_1\t69802\t70934\t0\n+chrom_1\t70934\t70955\t25.6148\n+chrom_1\t70955\t71363\t0\n+chrom_1\t71363\t71384\t25.6148\n+chrom_1\t71384\t71705\t0\n+chrom_1\t71705\t71726\t25.6148\n+chrom_1\t71726\t71760\t0\n+chrom_1\t71760\t71781\t25.6148\n+chrom_1\t71781\t72252\t0\n+chrom_1\t72252\t72273\t25.6148\n+chrom_1\t72273\t72315\t0\n+chrom_1\t72315\t72336\t25.6148\n+chrom_1\t72336\t72363\t0\n+chrom_1\t72363\t72387\t25.6148\n+chrom_1\t72387\t73124\t0\n+chrom_1\t73124\t73145\t25.6148\n+chrom_1\t73145\t73249\t0\n+chrom_1\t73249\t73270\t25.6148\n+chrom_1\t73270\t73315\t0\n+chrom_1\t73315\t73336\t25.6148\n+chrom_1\t73336\t73759\t0\n+chrom_1\t73759\t73780\t25.6148\n+chrom_1\t73780\t74181\t0\n+chrom_1\t74181\t74205\t25.6148\n+chrom_1\t74205\t74260\t0\n+chrom_1\t74260\t74281\t25.6148\n+chrom_1\t74281\t74954\t0\n+chrom_1\t74954\t74975\t25.6148\n+chrom_1\t74975\t75015\t0\n+chrom_1\t75015\t75035\t25.6148\n+chrom_1\t75035\t75554\t0\n+chrom_1\t75554\t75575\t25.6148\n+chrom_1\t75575\t76156\t0\n+chrom_1\t76156\t76181\t25.6148\n+chrom_1\t76181\t76310\t0\n+chrom_1\t76310\t76328\t25.6148\n+chrom_1\t76328\t77319\t0\n+chrom_1\t77319\t77320\t25.6148\n+chrom_1\t77320\t77340\t51.2295\n+chrom_1\t77340\t77341\t25.6148\n+chrom_1\t77341\t77411\t0\n+chrom_1\t77411\t77431\t51.2295\n+chrom_1\t77431\t77433\t25.6148\n+chrom_1\t77433\t77516\t0\n+chrom_1\t77516\t77537\t25.6148\n+chrom_1\t77537\t78553\t0\n+chrom_1\t78553\t78573\t25.6148\n+chrom_1\t78573\t79059\t0\n+chrom_1\t79059\t79080\t25.6148\n+chrom_1\t79080\t80057\t0\n+chrom_1\t80057\t80078\t25.6148\n+chrom_1\t80078\t80319\t0\n+chrom_1\t80319\t80340\t25.6148\n+chrom_1\t80340\t80395\t0\n+chrom_1\t80395\t80413\t25.6148\n+chrom_1\t80413\t80904\t0\n+chrom_1\t80904\t80923\t25.6148\n+chrom_1\t80923\t80929\t51.2295\n+chrom_1\t80929\t80949\t25.6148\n+chrom_1\t80949\t80959\t0\n+chrom_1\t80959\t80982\t25.6148\n+chrom_1\t80982\t81627\t0\n+chrom_1\t81627\t81650\t25.6148\n+chrom_1\t81650\t81784\t0\n+chrom_1\t81784\t81805\t25.6148\n+chrom_1\t81805\t82063\t0\n+chrom_1\t82063\t82083\t25.6148\n+chrom_1\t82083\t82123\t0\n+chrom_1\t82123\t82146\t25.6148\n+chrom_1\t82146\t82339\t0\n+chrom_1\t82339\t82360\t25.6148\n+chrom_1\t82360\t82455\t0\n+chrom_1\t82455\t82459\t25.6148\n+chrom_1\t82459\t82479\t51.2295\n+chrom_1\t82479\t82480\t25.6148\n+chrom_1\t82480\t83079\t0\n+chrom_1\t83079\t83100\t25.6148\n+chrom_1\t83100\t83396\t0\n+chrom_1\t83396\t83422\t25.6148\n+chrom_1\t83422\t83426\t0\n+chrom_1\t83426\t83450\t51.2295\n+chrom_1\t83450\t83540\t0\n+chrom_1\t83540\t83561\t25.6148\n+chrom_1\t83561\t83868\t0\n+chrom_1\t83868\t83891\t25.6148\n+chrom_1\t83891\t83901\t0\n+chrom_1\t83901\t83922\t25.6148\n+chrom_1\t83922\t83991\t0\n+chrom_1\t83991\t84014\t25.6148\n+chrom_1\t84014\t85181\t0\n+chrom_1\t85181\t85202\t51.2295\n+chrom_1\t85202\t85205\t25.6148\n+chrom_1\t85205\t85252\t0\n+chrom_1\t85252\t85273\t25.6148\n+chrom_1\t85273\t85366\t0\n+chrom_1\t85366\t85390\t25.6148\n+chrom_1\t85390\t85640\t0\n+chrom_1\t85640\t85662\t25.6148\n+chrom_1\t85662\t85759\t0\n+chrom_1\t85759\t85783\t25.6148\n+chrom_1\t85783\t86402\t0\n+chrom_1\t86402\t86424\t25.6148\n+chrom_1\t86424\t86453\t0\n+chrom_1\t86453\t86474\t25.6148\n+chrom_1\t86474\t86632\t0\n+chrom_1\t86632\t86658\t25.6148\n+chrom_1\t86658\t86941\t0\n+chrom_1\t86941\t86967\t25.6148\n+chrom_1\t86967\t87002\t0\n+chrom_1\t87002\t87022\t25.6148\n+chrom_1\t87022\t87066\t0\n+chrom_1\t87066\t87087\t25.6148\n+chrom_1\t87087\t87142\t0\n+chrom_1\t87142\t87163\t25.6148\n+chrom_1\t87163\t87223\t0\n+chrom_1\t87223\t87244\t25.6148\n+chrom_1\t87244\t87446\t0\n+chrom_1\t87446\t87467\t25.6148\n+chrom_1\t87467\t87524\t0\n+chrom_1\t87524\t87546\t25.6148\n+chrom_1\t87546\t87581\t0\n+chrom_1\t87581\t87582\t25.6148\n+chrom_1\t87582\t87602\t51.2295\n+chrom_1\t87602\t87665\t0\n+chrom_1\t87665\t87683\t25.6148\n+chrom_1\t87683\t87819\t0\n+chrom_1\t87819\t87839\t25.6148\n+chrom_1\t87839\t87853\t0\n+chrom_1\t87853\t87878\t25.6148\n+chrom_1\t87878\t88309\t0\n+chrom_1\t88309\t88330\t25.6148\n+chrom_1\t88330\t88443\t0\n+chrom_1\t88443\t88464\t25.6148\n+chrom_1\t88464\t88710\t0\n+chrom_1\t88710\t88731\t25.6148\n+chrom_1\t88731\t89102\t0\n+chrom_1\t89102\t89120\t25.6148\n+chrom_1\t89120\t89812\t0\n+chrom_1\t89812\t89833\t25.6148\n+chrom_1\t89833\t89999\t0\n+chrom_2\t0\t32272\t0\n+chrom_2\t32272\t32289\t25.6148\n+chrom_2\t32289\t32292\t51.2295\n+chrom_2\t32292\t32296\t76.8443\n+chrom_2\t32296\t32310\t51.2295\n+chrom_2\t32310\t39255\t0\n+chrom_2\t39255\t39276\t25.6148\n+chrom_2\t39276\t49999\t0\n+chrom_5\t0\t450\t0\n+chrom_5\t450\t468\t51.2295\n+chrom_5\t468\t1999\t0\n' |
| b |
| diff -r 9645d995fb3c -r 9185ca0a7b43 test-data/res_files/reads-sample-small.fastq/subgroups/bonafide_reads/bonafide_reads-genome_unique_plus.bedgraph --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/res_files/reads-sample-small.fastq/subgroups/bonafide_reads/bonafide_reads-genome_unique_plus.bedgraph Wed Jan 16 08:18:13 2019 -0500 |
| b |
| b'@@ -0,0 +1,5793 @@\n+chrom_1\t0\t1967\t0\n+chrom_1\t1967\t1991\t25.6148\n+chrom_1\t1991\t2932\t0\n+chrom_1\t2932\t2954\t25.6148\n+chrom_1\t2954\t3456\t0\n+chrom_1\t3456\t3481\t25.6148\n+chrom_1\t3481\t7648\t0\n+chrom_1\t7648\t7671\t25.6148\n+chrom_1\t7671\t7953\t0\n+chrom_1\t7953\t7978\t25.6148\n+chrom_1\t7978\t8721\t0\n+chrom_1\t8721\t8742\t25.6148\n+chrom_1\t8742\t8747\t51.2295\n+chrom_1\t8747\t8758\t25.6148\n+chrom_1\t8758\t8767\t51.2295\n+chrom_1\t8767\t8783\t25.6148\n+chrom_1\t8783\t9642\t0\n+chrom_1\t9642\t9668\t25.6148\n+chrom_1\t9668\t10407\t0\n+chrom_1\t10407\t10428\t25.6148\n+chrom_1\t10428\t14236\t0\n+chrom_1\t14236\t14261\t25.6148\n+chrom_1\t14261\t14309\t0\n+chrom_1\t14309\t14336\t25.6148\n+chrom_1\t14336\t14439\t0\n+chrom_1\t14439\t14463\t25.6148\n+chrom_1\t14463\t14523\t0\n+chrom_1\t14523\t14544\t25.6148\n+chrom_1\t14544\t14551\t0\n+chrom_1\t14551\t14552\t25.6148\n+chrom_1\t14552\t14554\t76.8443\n+chrom_1\t14554\t14578\t179.303\n+chrom_1\t14578\t14580\t25.6148\n+chrom_1\t14580\t14592\t0\n+chrom_1\t14592\t14616\t25.6148\n+chrom_1\t14616\t14979\t0\n+chrom_1\t14979\t15004\t25.6148\n+chrom_1\t15004\t15062\t0\n+chrom_1\t15062\t15087\t25.6148\n+chrom_1\t15087\t15089\t0\n+chrom_1\t15089\t15092\t25.6148\n+chrom_1\t15092\t15115\t128.074\n+chrom_1\t15115\t15117\t102.459\n+chrom_1\t15117\t15139\t0\n+chrom_1\t15139\t15164\t25.6148\n+chrom_1\t15164\t15258\t0\n+chrom_1\t15258\t15260\t25.6148\n+chrom_1\t15260\t15264\t76.8443\n+chrom_1\t15264\t15269\t102.459\n+chrom_1\t15269\t15283\t128.074\n+chrom_1\t15283\t15284\t102.459\n+chrom_1\t15284\t15290\t51.2295\n+chrom_1\t15290\t15293\t25.6148\n+chrom_1\t15293\t15395\t0\n+chrom_1\t15395\t15399\t25.6148\n+chrom_1\t15399\t15400\t76.8443\n+chrom_1\t15400\t15407\t281.762\n+chrom_1\t15407\t15420\t307.377\n+chrom_1\t15420\t15421\t281.762\n+chrom_1\t15421\t15422\t204.918\n+chrom_1\t15422\t15423\t102.459\n+chrom_1\t15423\t15424\t51.2295\n+chrom_1\t15424\t15433\t25.6148\n+chrom_1\t15433\t15460\t0\n+chrom_1\t15460\t15484\t25.6148\n+chrom_1\t15484\t15528\t0\n+chrom_1\t15528\t15529\t25.6148\n+chrom_1\t15529\t15530\t51.2295\n+chrom_1\t15530\t15545\t76.8443\n+chrom_1\t15545\t15546\t102.459\n+chrom_1\t15546\t15548\t486.68\n+chrom_1\t15548\t15550\t461.066\n+chrom_1\t15550\t15555\t435.451\n+chrom_1\t15555\t15567\t409.836\n+chrom_1\t15567\t15569\t384.221\n+chrom_1\t15569\t15570\t204.918\n+chrom_1\t15570\t15572\t25.6148\n+chrom_1\t15572\t15716\t0\n+chrom_1\t15716\t15739\t25.6148\n+chrom_1\t15739\t15801\t0\n+chrom_1\t15801\t15824\t25.6148\n+chrom_1\t15824\t15970\t0\n+chrom_1\t15970\t15993\t76.8443\n+chrom_1\t15993\t16004\t0\n+chrom_1\t16004\t16027\t76.8443\n+chrom_1\t16027\t16028\t25.6148\n+chrom_1\t16028\t16229\t0\n+chrom_1\t16229\t16232\t25.6148\n+chrom_1\t16232\t16237\t51.2295\n+chrom_1\t16237\t16239\t76.8443\n+chrom_1\t16239\t16250\t128.074\n+chrom_1\t16250\t16256\t102.459\n+chrom_1\t16256\t16262\t76.8443\n+chrom_1\t16262\t16336\t0\n+chrom_1\t16336\t16338\t256.148\n+chrom_1\t16338\t16339\t281.762\n+chrom_1\t16339\t16342\t307.377\n+chrom_1\t16342\t16359\t332.992\n+chrom_1\t16359\t16360\t128.074\n+chrom_1\t16360\t16363\t76.8443\n+chrom_1\t16363\t16364\t51.2295\n+chrom_1\t16364\t16365\t25.6148\n+chrom_1\t16365\t16380\t0\n+chrom_1\t16380\t16402\t25.6148\n+chrom_1\t16402\t16496\t0\n+chrom_1\t16496\t16521\t25.6148\n+chrom_1\t16521\t16619\t0\n+chrom_1\t16619\t16628\t25.6148\n+chrom_1\t16628\t16630\t76.8443\n+chrom_1\t16630\t16643\t256.148\n+chrom_1\t16643\t16653\t230.533\n+chrom_1\t16653\t16654\t153.689\n+chrom_1\t16654\t16655\t76.8443\n+chrom_1\t16655\t16656\t25.6148\n+chrom_1\t16656\t16661\t0\n+chrom_1\t16661\t16685\t25.6148\n+chrom_1\t16685\t16772\t0\n+chrom_1\t16772\t16798\t25.6148\n+chrom_1\t16798\t16800\t51.2295\n+chrom_1\t16800\t16801\t179.303\n+chrom_1\t16801\t16808\t461.066\n+chrom_1\t16808\t16810\t486.68\n+chrom_1\t16810\t16811\t512.295\n+chrom_1\t16811\t16819\t537.91\n+chrom_1\t16819\t16823\t512.295\n+chrom_1\t16823\t16825\t461.066\n+chrom_1\t16825\t16829\t128.074\n+chrom_1\t16829\t16835\t102.459\n+chrom_1\t16835\t16849\t51.2295\n+chrom_1\t16849\t16850\t25.6148\n+chrom_1\t16850\t16864\t0\n+chrom_1\t16864\t16866\t25.6148\n+chrom_1\t16866\t16867\t76.8443\n+chrom_1\t16867\t16868\t179.303\n+chrom_1\t16868\t16869\t307.377\n+chrom_1\t16869\t16870\t332.992\n+chrom_1\t16870\t16875\t358.607\n+chrom_1\t16875\t16881\t384.221\n+chrom_1\t16881\t16883\t435.451\n+chrom_1\t16883\t16884\t461.066\n+chrom_1\t16884\t16885\t537.91\n+chrom_1\t16885\t16886\t589.139\n+chrom_1\t16886\t16887\t640.369\n+chrom_1\t16887\t16892\t614.754\n+chrom_1\t16892\t16893\t435.451\n+chrom_1\t16893\t16894\t33'..b'5.6148\n+chrom_1\t71579\t71872\t0\n+chrom_1\t71872\t71892\t25.6148\n+chrom_1\t71892\t72078\t0\n+chrom_1\t72078\t72102\t25.6148\n+chrom_1\t72102\t72167\t0\n+chrom_1\t72167\t72192\t25.6148\n+chrom_1\t72192\t72261\t0\n+chrom_1\t72261\t72282\t25.6148\n+chrom_1\t72282\t72356\t0\n+chrom_1\t72356\t72360\t25.6148\n+chrom_1\t72360\t72382\t51.2295\n+chrom_1\t72382\t72385\t25.6148\n+chrom_1\t72385\t72667\t0\n+chrom_1\t72667\t72688\t25.6148\n+chrom_1\t72688\t72713\t0\n+chrom_1\t72713\t72737\t25.6148\n+chrom_1\t72737\t72996\t0\n+chrom_1\t72996\t73017\t25.6148\n+chrom_1\t73017\t73230\t0\n+chrom_1\t73230\t73252\t25.6148\n+chrom_1\t73252\t73254\t0\n+chrom_1\t73254\t73275\t25.6148\n+chrom_1\t73275\t73572\t0\n+chrom_1\t73572\t73593\t25.6148\n+chrom_1\t73593\t73860\t0\n+chrom_1\t73860\t73885\t25.6148\n+chrom_1\t73885\t73976\t0\n+chrom_1\t73976\t73997\t25.6148\n+chrom_1\t73997\t74302\t0\n+chrom_1\t74302\t74323\t25.6148\n+chrom_1\t74323\t74376\t0\n+chrom_1\t74376\t74400\t25.6148\n+chrom_1\t74400\t74487\t0\n+chrom_1\t74487\t74508\t25.6148\n+chrom_1\t74508\t75553\t0\n+chrom_1\t75553\t75574\t25.6148\n+chrom_1\t75574\t77140\t0\n+chrom_1\t77140\t77161\t25.6148\n+chrom_1\t77161\t77234\t0\n+chrom_1\t77234\t77255\t25.6148\n+chrom_1\t77255\t77443\t0\n+chrom_1\t77443\t77464\t25.6148\n+chrom_1\t77464\t77597\t0\n+chrom_1\t77597\t77616\t25.6148\n+chrom_1\t77616\t78651\t0\n+chrom_1\t78651\t78673\t25.6148\n+chrom_1\t78673\t79352\t0\n+chrom_1\t79352\t79371\t25.6148\n+chrom_1\t79371\t79422\t0\n+chrom_1\t79422\t79447\t25.6148\n+chrom_1\t79447\t80012\t0\n+chrom_1\t80012\t80022\t25.6148\n+chrom_1\t80022\t80033\t51.2295\n+chrom_1\t80033\t80041\t25.6148\n+chrom_1\t80041\t80862\t0\n+chrom_1\t80862\t80887\t25.6148\n+chrom_1\t80887\t81326\t0\n+chrom_1\t81326\t81351\t25.6148\n+chrom_1\t81351\t81505\t0\n+chrom_1\t81505\t81528\t25.6148\n+chrom_1\t81528\t82019\t0\n+chrom_1\t82019\t82040\t25.6148\n+chrom_1\t82040\t82213\t0\n+chrom_1\t82213\t82237\t25.6148\n+chrom_1\t82237\t82623\t0\n+chrom_1\t82623\t82644\t25.6148\n+chrom_1\t82644\t82981\t0\n+chrom_1\t82981\t83002\t25.6148\n+chrom_1\t83002\t83100\t0\n+chrom_1\t83100\t83121\t25.6148\n+chrom_1\t83121\t83268\t0\n+chrom_1\t83268\t83289\t25.6148\n+chrom_1\t83289\t83437\t0\n+chrom_1\t83437\t83458\t25.6148\n+chrom_1\t83458\t83567\t0\n+chrom_1\t83567\t83592\t25.6148\n+chrom_1\t83592\t84065\t0\n+chrom_1\t84065\t84089\t25.6148\n+chrom_1\t84089\t84524\t0\n+chrom_1\t84524\t84545\t25.6148\n+chrom_1\t84545\t84948\t0\n+chrom_1\t84948\t84969\t25.6148\n+chrom_1\t84969\t85094\t0\n+chrom_1\t85094\t85115\t51.2295\n+chrom_1\t85115\t85355\t0\n+chrom_1\t85355\t85376\t25.6148\n+chrom_1\t85376\t85397\t0\n+chrom_1\t85397\t85407\t25.6148\n+chrom_1\t85407\t85422\t51.2295\n+chrom_1\t85422\t85428\t25.6148\n+chrom_1\t85428\t85513\t0\n+chrom_1\t85513\t85534\t25.6148\n+chrom_1\t85534\t85980\t0\n+chrom_1\t85980\t86005\t25.6148\n+chrom_1\t86005\t86344\t0\n+chrom_1\t86344\t86354\t51.2295\n+chrom_1\t86354\t86362\t76.8443\n+chrom_1\t86362\t86365\t102.459\n+chrom_1\t86365\t86376\t51.2295\n+chrom_1\t86376\t86383\t25.6148\n+chrom_1\t86383\t86432\t0\n+chrom_1\t86432\t86453\t25.6148\n+chrom_1\t86453\t86950\t0\n+chrom_1\t86950\t86971\t25.6148\n+chrom_1\t86971\t87113\t0\n+chrom_1\t87113\t87134\t25.6148\n+chrom_1\t87134\t87255\t0\n+chrom_1\t87255\t87278\t25.6148\n+chrom_1\t87278\t88301\t0\n+chrom_1\t88301\t88325\t25.6148\n+chrom_1\t88325\t88633\t0\n+chrom_1\t88633\t88654\t25.6148\n+chrom_1\t88654\t88989\t0\n+chrom_1\t88989\t89015\t25.6148\n+chrom_1\t89015\t89111\t0\n+chrom_1\t89111\t89137\t25.6148\n+chrom_1\t89137\t89597\t0\n+chrom_1\t89597\t89618\t25.6148\n+chrom_1\t89618\t89999\t0\n+chrom_2\t0\t41979\t0\n+chrom_2\t41979\t42001\t51.2295\n+chrom_2\t42001\t49999\t0\n+chrom_4\t0\t1047\t0\n+chrom_4\t1047\t1066\t76.8443\n+chrom_4\t1066\t1067\t51.2295\n+chrom_4\t1067\t1071\t25.6148\n+chrom_4\t1071\t1151\t0\n+chrom_4\t1151\t1172\t25.6148\n+chrom_4\t1172\t1208\t0\n+chrom_4\t1208\t1212\t76.8443\n+chrom_4\t1212\t1230\t102.459\n+chrom_4\t1230\t2000\t0\n+chrom_5\t0\t1648\t0\n+chrom_5\t1648\t1669\t25.6148\n+chrom_5\t1669\t1782\t0\n+chrom_5\t1782\t1803\t25.6148\n+chrom_5\t1803\t1999\t0\n+chrom_6\t0\t440\t0\n+chrom_6\t440\t464\t25.6148\n+chrom_6\t464\t885\t0\n+chrom_6\t885\t905\t51.2295\n+chrom_6\t905\t906\t25.6148\n+chrom_6\t906\t1038\t0\n+chrom_6\t1038\t1060\t25.6148\n+chrom_6\t1060\t1109\t0\n+chrom_6\t1109\t1110\t25.6148\n+chrom_6\t1110\t1115\t51.2295\n+chrom_6\t1115\t1117\t102.459\n+chrom_6\t1117\t1125\t128.074\n+chrom_6\t1125\t1130\t153.689\n+chrom_6\t1130\t1133\t102.459\n+chrom_6\t1133\t1136\t76.8443\n+chrom_6\t1136\t1142\t51.2295\n+chrom_6\t1142\t1143\t25.6148\n+chrom_6\t1143\t3999\t0\n' |
| b |
| diff -r 9645d995fb3c -r 9185ca0a7b43 test-data/res_files/reads-sample-small.fastq/subgroups/bonafide_reads/bonafide_reads-genome_unique_sorted.bam |
| b |
| Binary file test-data/res_files/reads-sample-small.fastq/subgroups/bonafide_reads/bonafide_reads-genome_unique_sorted.bam has changed |
| b |
| diff -r 9645d995fb3c -r 9185ca0a7b43 test-data/res_files/reads-sample-small.fastq/subgroups/bonafide_reads/bonafide_reads-transcripts_reads_counts.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/res_files/reads-sample-small.fastq/subgroups/bonafide_reads/bonafide_reads-transcripts_reads_counts.txt Wed Jan 16 08:18:13 2019 -0500 |
| b |
| @@ -0,0 +1,14 @@ +ID reads counts RPKM per million of piRNAs per million of miRNAs per million of bonafide reads sense reads counts reverse reads counts % of sense 1U % of sense 10A % of reverse 1U % of reverse 10A +FBtr0073689 195 1316.17 8457.67 3095238.10 6387.16 84 111 90.4761904761905 78.5714285714286 7.20720720720721 15.3153153153153 +FBtr0078666 307 3241.44 13315.41 4873015.87 10055.68 143 164 94.4055944055944 75.5244755244755 14.6341463414634 9.14634146341463 +FBtr0086080 142 918.74 6158.92 2253968.25 4651.16 73 69 69.8630136986301 31.5068493150685 0 24.6376811594203 +FBtr0089125 146 517.18 6332.41 2317460.32 4782.18 6 140 83.3333333333333 50 57.8571428571429 11.4285714285714 +FBtr0089196 450 2634.06 19517.70 7142857.14 14739.60 316 134 98.1012658227848 60.4430379746835 11.1940298507463 33.5820895522388 +FBtr0113825 91 797.45 3946.91 1444444.44 2980.67 73 18 84.9315068493151 68.4931506849315 5.55555555555556 27.7777777777778 +FBtr0114365 29 116.12 1257.81 460317.46 949.89 16 13 37.5 18.75 0 7.69230769230769 +FBtr0310270 52 434.01 2255.38 825396.83 1703.24 1 51 0 100 5.88235294117647 15.6862745098039 +FBtr0332656 30 220.63 1301.18 476190.48 982.64 30 0 100 46.6666666666667 0 0 +FBtr0345361 59 1172.44 2558.99 936507.94 1932.53 59 0 98.3050847457627 67.7966101694915 0 0 +FBtr0345575 294 2545.03 12751.56 4666666.67 9629.87 66 228 81.8181818181818 60.6060606060606 61.8421052631579 7.45614035087719 +FBtr0345650 377 1167.40 16351.49 5984126.98 12348.51 261 116 55.9386973180077 6.13026819923372 4.31034482758621 6.89655172413793 +FBtr0346343 74 303.62 3209.58 1174603.17 2423.85 72 2 97.2222222222222 4.16666666666667 50 50 |
| b |
| diff -r 9645d995fb3c -r 9185ca0a7b43 test-data/res_files/reads-sample-small.fastq/subgroups/bonafide_reads/bonafide_reads-transcripts_sorted.bam |
| b |
| Binary file test-data/res_files/reads-sample-small.fastq/subgroups/bonafide_reads/bonafide_reads-transcripts_sorted.bam has changed |
| b |
| diff -r 9645d995fb3c -r 9185ca0a7b43 test-data/res_files/reads-sample-small.fastq/subgroups/bonafide_reads/bonafide_reads-transcripts_unique_sorted.bam |
| b |
| Binary file test-data/res_files/reads-sample-small.fastq/subgroups/bonafide_reads/bonafide_reads-transcripts_unique_sorted.bam has changed |
| b |
| diff -r 9645d995fb3c -r 9185ca0a7b43 test-data/res_files/reads-sample-small.fastq/subgroups/miRNAs.sam_aln.err --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/res_files/reads-sample-small.fastq/subgroups/miRNAs.sam_aln.err Wed Jan 16 08:18:13 2019 -0500 |
| [ |
| @@ -0,0 +1,6 @@ +[bwa_aln_core] calculate SA coordinate... 0.26 sec +[bwa_aln_core] write to the disk... 0.00 sec +[bwa_aln_core] 39040 sequences have been processed. +[main] Version: 0.7.12-r1039 +[main] CMD: bwa aln -t 8 -n 0 /data/galaxy/galaxy-server/database/jobs_directory/015/15696/dataset_35119_files/dataset_35116.dat_symlink.fa fastq_dir/reads-sample-small.fastq_all_mappers.fastq +[main] Real time: 0.135 sec; CPU: 0.316 sec |
| b |
| diff -r 9645d995fb3c -r 9185ca0a7b43 test-data/res_files/reads-sample-small.fastq/subgroups/miRNAs.sam_samse.err --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/res_files/reads-sample-small.fastq/subgroups/miRNAs.sam_samse.err Wed Jan 16 08:18:13 2019 -0500 |
| [ |
| @@ -0,0 +1,7 @@ +[bwa_aln_core] convert to sequence coordinate... 0.00 sec +[bwa_aln_core] refine gapped alignments... 0.00 sec +[bwa_aln_core] print alignments... 0.02 sec +[bwa_aln_core] 39040 sequences have been processed. +[main] Version: 0.7.12-r1039 +[main] CMD: bwa samse /data/galaxy/galaxy-server/database/jobs_directory/015/15696/dataset_35119_files/dataset_35116.dat_symlink.fa /dev/stdin fastq_dir/reads-sample-small.fastq_all_mappers.fastq +[main] Real time: 0.295 sec; CPU: 0.080 sec |
| b |
| diff -r 9645d995fb3c -r 9185ca0a7b43 test-data/res_files/reads-sample-small.fastq/subgroups/miRNAs/Gviz_genome/rand/chrom_3.png |
| b |
| Binary file test-data/res_files/reads-sample-small.fastq/subgroups/miRNAs/Gviz_genome/rand/chrom_3.png has changed |
| b |
| diff -r 9645d995fb3c -r 9185ca0a7b43 test-data/res_files/reads-sample-small.fastq/subgroups/miRNAs/Gviz_genome/unique/chrom_3.png |
| b |
| Binary file test-data/res_files/reads-sample-small.fastq/subgroups/miRNAs/Gviz_genome/unique/chrom_3.png has changed |
| b |
| diff -r 9645d995fb3c -r 9185ca0a7b43 test-data/res_files/reads-sample-small.fastq/subgroups/miRNAs/miRNAs-TEs_reads_counts.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/res_files/reads-sample-small.fastq/subgroups/miRNAs/miRNAs-TEs_reads_counts.txt Wed Jan 16 08:18:13 2019 -0500 |
| b |
| @@ -0,0 +1,18 @@ +ID reads counts RPKM per million of piRNAs per million of miRNAs per million of bonafide reads sense reads counts reverse reads counts % of sense 1U % of sense 10A % of reverse 1U % of reverse 10A +BATUMI_I 0 0.00 0.00 0.00 0.00 0 0 0 0 0 0 +BATUMI_LTR 0 0.00 0.00 0.00 0.00 0 0 0 0 0 0 +BS2 0 0.00 0.00 0.00 0.00 0 0 0 0 0 0 +COPIA_DM_I 0 0.00 0.00 0.00 0.00 0 0 0 0 0 0 +COPIA_DM_LTR 0 0.00 0.00 0.00 0.00 0 0 0 0 0 0 +DMCR1A 0 0.00 0.00 0.00 0.00 0 0 0 0 0 0 +DMRT1B 0 0.00 0.00 0.00 0.00 0 0 0 0 0 0 +FW 0 0.00 0.00 0.00 0.00 0 0 0 0 0 0 +G6_DM 0 0.00 0.00 0.00 0.00 0 0 0 0 0 0 +Gypsy2-I_DM 0 0.00 0.00 0.00 0.00 0 0 0 0 0 0 +Gypsy2-LTR_DM 0 0.00 0.00 0.00 0.00 0 0 0 0 0 0 +I_DM 0 0.00 0.00 0.00 0.00 0 0 0 0 0 0 +MAX_I 0 0.00 0.00 0.00 0.00 0 0 0 0 0 0 +MAX_LTR 0 0.00 0.00 0.00 0.00 0 0 0 0 0 0 +PROTOP 0 0.00 0.00 0.00 0.00 0 0 0 0 0 0 +ZAM_I 0 0.00 0.00 0.00 0.00 0 0 0 0 0 0 +ZAM_LTR 0 0.00 0.00 0.00 0.00 0 0 0 0 0 0 |
| b |
| diff -r 9645d995fb3c -r 9185ca0a7b43 test-data/res_files/reads-sample-small.fastq/subgroups/miRNAs/miRNAs-TEs_reads_counts_mismatches.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/res_files/reads-sample-small.fastq/subgroups/miRNAs/miRNAs-TEs_reads_counts_mismatches.txt Wed Jan 16 08:18:13 2019 -0500 |
| b |
| @@ -0,0 +1,18 @@ +ID reads counts RPKM per million of piRNAs per million of miRNAs per million of bonafide reads sense reads counts reverse reads counts % of sense 1U % of sense 10A % of reverse 1U % of reverse 10A +BATUMI_I 0 0.00 0.00 0.00 0.00 0 0 0 0 0 0 +BATUMI_LTR 0 0.00 0.00 0.00 0.00 0 0 0 0 0 0 +BS2 0 0.00 0.00 0.00 0.00 0 0 0 0 0 0 +COPIA_DM_I 0 0.00 0.00 0.00 0.00 0 0 0 0 0 0 +COPIA_DM_LTR 0 0.00 0.00 0.00 0.00 0 0 0 0 0 0 +DMCR1A 0 0.00 0.00 0.00 0.00 0 0 0 0 0 0 +DMRT1B 0 0.00 0.00 0.00 0.00 0 0 0 0 0 0 +FW 0 0.00 0.00 0.00 0.00 0 0 0 0 0 0 +G6_DM 0 0.00 0.00 0.00 0.00 0 0 0 0 0 0 +Gypsy2-I_DM 0 0.00 0.00 0.00 0.00 0 0 0 0 0 0 +Gypsy2-LTR_DM 0 0.00 0.00 0.00 0.00 0 0 0 0 0 0 +I_DM 0 0.00 0.00 0.00 0.00 0 0 0 0 0 0 +MAX_I 0 0.00 0.00 0.00 0.00 0 0 0 0 0 0 +MAX_LTR 0 0.00 0.00 0.00 0.00 0 0 0 0 0 0 +PROTOP 0 0.00 0.00 0.00 0.00 0 0 0 0 0 0 +ZAM_I 0 0.00 0.00 0.00 0.00 0 0 0 0 0 0 +ZAM_LTR 0 0.00 0.00 0.00 0.00 0 0 0 0 0 0 |
| b |
| diff -r 9645d995fb3c -r 9185ca0a7b43 test-data/res_files/reads-sample-small.fastq/subgroups/miRNAs/miRNAs-TEs_reads_counts_nomismatches.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/res_files/reads-sample-small.fastq/subgroups/miRNAs/miRNAs-TEs_reads_counts_nomismatches.txt Wed Jan 16 08:18:13 2019 -0500 |
| b |
| @@ -0,0 +1,18 @@ +ID reads counts RPKM per million of piRNAs per million of miRNAs per million of bonafide reads sense reads counts reverse reads counts % of sense 1U % of sense 10A % of reverse 1U % of reverse 10A +BATUMI_I 0 0.00 0.00 0.00 0.00 0 0 0 0 0 0 +BATUMI_LTR 0 0.00 0.00 0.00 0.00 0 0 0 0 0 0 +BS2 0 0.00 0.00 0.00 0.00 0 0 0 0 0 0 +COPIA_DM_I 0 0.00 0.00 0.00 0.00 0 0 0 0 0 0 +COPIA_DM_LTR 0 0.00 0.00 0.00 0.00 0 0 0 0 0 0 +DMCR1A 0 0.00 0.00 0.00 0.00 0 0 0 0 0 0 +DMRT1B 0 0.00 0.00 0.00 0.00 0 0 0 0 0 0 +FW 0 0.00 0.00 0.00 0.00 0 0 0 0 0 0 +G6_DM 0 0.00 0.00 0.00 0.00 0 0 0 0 0 0 +Gypsy2-I_DM 0 0.00 0.00 0.00 0.00 0 0 0 0 0 0 +Gypsy2-LTR_DM 0 0.00 0.00 0.00 0.00 0 0 0 0 0 0 +I_DM 0 0.00 0.00 0.00 0.00 0 0 0 0 0 0 +MAX_I 0 0.00 0.00 0.00 0.00 0 0 0 0 0 0 +MAX_LTR 0 0.00 0.00 0.00 0.00 0 0 0 0 0 0 +PROTOP 0 0.00 0.00 0.00 0.00 0 0 0 0 0 0 +ZAM_I 0 0.00 0.00 0.00 0.00 0 0 0 0 0 0 +ZAM_LTR 0 0.00 0.00 0.00 0.00 0 0 0 0 0 0 |
| b |
| diff -r 9645d995fb3c -r 9185ca0a7b43 test-data/res_files/reads-sample-small.fastq/subgroups/miRNAs/miRNAs-TEs_sorted.bam |
| b |
| Binary file test-data/res_files/reads-sample-small.fastq/subgroups/miRNAs/miRNAs-TEs_sorted.bam has changed |
| b |
| diff -r 9645d995fb3c -r 9185ca0a7b43 test-data/res_files/reads-sample-small.fastq/subgroups/miRNAs/miRNAs-TEs_unique_sorted.bam |
| b |
| Binary file test-data/res_files/reads-sample-small.fastq/subgroups/miRNAs/miRNAs-TEs_unique_sorted.bam has changed |
| b |
| diff -r 9645d995fb3c -r 9185ca0a7b43 test-data/res_files/reads-sample-small.fastq/subgroups/miRNAs/miRNAs-genome_plus.bedgraph --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/res_files/reads-sample-small.fastq/subgroups/miRNAs/miRNAs-genome_plus.bedgraph Wed Jan 16 08:18:13 2019 -0500 |
| b |
| @@ -0,0 +1,16 @@ +chrom_3 0 643 0 +chrom_3 643 663 461.066 +chrom_3 663 665 179.303 +chrom_3 665 682 0 +chrom_3 682 704 102.459 +chrom_3 704 1041 0 +chrom_3 1041 1042 896.516 +chrom_3 1042 1062 922.131 +chrom_3 1062 1063 870.902 +chrom_3 1063 1064 51.2295 +chrom_3 1064 1065 25.6148 +chrom_3 1065 1078 0 +chrom_3 1078 1079 25.6148 +chrom_3 1079 1080 51.2295 +chrom_3 1080 1101 128.074 +chrom_3 1101 1499 0 |
| b |
| diff -r 9645d995fb3c -r 9185ca0a7b43 test-data/res_files/reads-sample-small.fastq/subgroups/miRNAs/miRNAs-genome_sorted.bam |
| b |
| Binary file test-data/res_files/reads-sample-small.fastq/subgroups/miRNAs/miRNAs-genome_sorted.bam has changed |
| b |
| diff -r 9645d995fb3c -r 9185ca0a7b43 test-data/res_files/reads-sample-small.fastq/subgroups/miRNAs/miRNAs-genome_unique_plus.bedgraph --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/res_files/reads-sample-small.fastq/subgroups/miRNAs/miRNAs-genome_unique_plus.bedgraph Wed Jan 16 08:18:13 2019 -0500 |
| b |
| @@ -0,0 +1,16 @@ +chrom_3 0 643 0 +chrom_3 643 663 461.066 +chrom_3 663 665 179.303 +chrom_3 665 682 0 +chrom_3 682 704 102.459 +chrom_3 704 1041 0 +chrom_3 1041 1042 896.516 +chrom_3 1042 1062 922.131 +chrom_3 1062 1063 870.902 +chrom_3 1063 1064 51.2295 +chrom_3 1064 1065 25.6148 +chrom_3 1065 1078 0 +chrom_3 1078 1079 25.6148 +chrom_3 1079 1080 51.2295 +chrom_3 1080 1101 128.074 +chrom_3 1101 1499 0 |
| b |
| diff -r 9645d995fb3c -r 9185ca0a7b43 test-data/res_files/reads-sample-small.fastq/subgroups/miRNAs/miRNAs-genome_unique_sorted.bam |
| b |
| Binary file test-data/res_files/reads-sample-small.fastq/subgroups/miRNAs/miRNAs-genome_unique_sorted.bam has changed |
| b |
| diff -r 9645d995fb3c -r 9185ca0a7b43 test-data/res_files/reads-sample-small.fastq/subgroups/miRNAs/miRNAs-transcripts_reads_counts.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/res_files/reads-sample-small.fastq/subgroups/miRNAs/miRNAs-transcripts_reads_counts.txt Wed Jan 16 08:18:13 2019 -0500 |
| b |
| @@ -0,0 +1,14 @@ +ID reads counts RPKM per million of piRNAs per million of miRNAs per million of bonafide reads sense reads counts reverse reads counts % of sense 1U % of sense 10A % of reverse 1U % of reverse 10A +FBtr0073689 0 0.00 0.00 0.00 0.00 0 0 0 0 0 0 +FBtr0078666 0 0.00 0.00 0.00 0.00 0 0 0 0 0 0 +FBtr0086080 0 0.00 0.00 0.00 0.00 0 0 0 0 0 0 +FBtr0089125 0 0.00 0.00 0.00 0.00 0 0 0 0 0 0 +FBtr0089196 0 0.00 0.00 0.00 0.00 0 0 0 0 0 0 +FBtr0113825 0 0.00 0.00 0.00 0.00 0 0 0 0 0 0 +FBtr0114365 0 0.00 0.00 0.00 0.00 0 0 0 0 0 0 +FBtr0310270 0 0.00 0.00 0.00 0.00 0 0 0 0 0 0 +FBtr0332656 0 0.00 0.00 0.00 0.00 0 0 0 0 0 0 +FBtr0345361 0 0.00 0.00 0.00 0.00 0 0 0 0 0 0 +FBtr0345575 0 0.00 0.00 0.00 0.00 0 0 0 0 0 0 +FBtr0345650 0 0.00 0.00 0.00 0.00 0 0 0 0 0 0 +FBtr0346343 0 0.00 0.00 0.00 0.00 0 0 0 0 0 0 |
| b |
| diff -r 9645d995fb3c -r 9185ca0a7b43 test-data/res_files/reads-sample-small.fastq/subgroups/miRNAs/miRNAs-transcripts_sorted.bam |
| b |
| Binary file test-data/res_files/reads-sample-small.fastq/subgroups/miRNAs/miRNAs-transcripts_sorted.bam has changed |
| b |
| diff -r 9645d995fb3c -r 9185ca0a7b43 test-data/res_files/reads-sample-small.fastq/subgroups/miRNAs/miRNAs-transcripts_unique_sorted.bam |
| b |
| Binary file test-data/res_files/reads-sample-small.fastq/subgroups/miRNAs/miRNAs-transcripts_unique_sorted.bam has changed |
| b |
| diff -r 9645d995fb3c -r 9185ca0a7b43 test-data/res_files/reads-sample-small.fastq/subgroups/miRNAs/miRNAs_reads_counts.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/res_files/reads-sample-small.fastq/subgroups/miRNAs/miRNAs_reads_counts.txt Wed Jan 16 08:18:13 2019 -0500 |
| b |
| b'@@ -0,0 +1,257 @@\n+ID\treads counts\tRPKM\tper million of piRNAs\tper million of miRNAs\tper million of bonafide reads\n+dme-bantam_MI0000387\t0\t0.00\t0.00\t0.00\t0.00\n+dme-let-7_MI0000416\t0\t0.00\t0.00\t0.00\t0.00\n+dme-mir-1000_MI0005862\t0\t0.00\t0.00\t0.00\t0.00\n+dme-mir-1001_MI0005863\t0\t0.00\t0.00\t0.00\t0.00\n+dme-mir-1002_MI0005824\t0\t0.00\t0.00\t0.00\t0.00\n+dme-mir-1003_MI0005864\t0\t0.00\t0.00\t0.00\t0.00\n+dme-mir-1004_MI0005865\t0\t0.00\t0.00\t0.00\t0.00\n+dme-mir-1005_MI0005866\t0\t0.00\t0.00\t0.00\t0.00\n+dme-mir-1006_MI0005867\t0\t0.00\t0.00\t0.00\t0.00\n+dme-mir-1007_MI0005868\t0\t0.00\t0.00\t0.00\t0.00\n+dme-mir-1008_MI0005869\t0\t0.00\t0.00\t0.00\t0.00\n+dme-mir-1009_MI0005870\t0\t0.00\t0.00\t0.00\t0.00\n+dme-mir-100_MI0000378\t22\t5635.25\t954.20\t349206.35\t720.60\n+dme-mir-1010_MI0005871\t0\t0.00\t0.00\t0.00\t0.00\n+dme-mir-1011_MI0005872\t0\t0.00\t0.00\t0.00\t0.00\n+dme-mir-1012_MI0005873\t0\t0.00\t0.00\t0.00\t0.00\n+dme-mir-1013_MI0005874\t0\t0.00\t0.00\t0.00\t0.00\n+dme-mir-1014_MI0005875\t0\t0.00\t0.00\t0.00\t0.00\n+dme-mir-1015_MI0005876\t0\t0.00\t0.00\t0.00\t0.00\n+dme-mir-1016_MI0005877\t0\t0.00\t0.00\t0.00\t0.00\n+dme-mir-1017_MI0005878\t0\t0.00\t0.00\t0.00\t0.00\n+dme-mir-10_MI0000130\t0\t0.00\t0.00\t0.00\t0.00\n+dme-mir-11_MI0000131\t0\t0.00\t0.00\t0.00\t0.00\n+dme-mir-124_MI0000373\t0\t0.00\t0.00\t0.00\t0.00\n+dme-mir-125_MI0000417\t41\t9547.32\t1778.28\t650793.65\t1342.94\n+dme-mir-12_MI0000132\t0\t0.00\t0.00\t0.00\t0.00\n+dme-mir-133_MI0000362\t0\t0.00\t0.00\t0.00\t0.00\n+dme-mir-137_MI0005849\t0\t0.00\t0.00\t0.00\t0.00\n+dme-mir-13a_MI0000133\t0\t0.00\t0.00\t0.00\t0.00\n+dme-mir-13b-1_MI0000134\t0\t0.00\t0.00\t0.00\t0.00\n+dme-mir-13b-2_MI0000135\t0\t0.00\t0.00\t0.00\t0.00\n+dme-mir-14_MI0000136\t0\t0.00\t0.00\t0.00\t0.00\n+dme-mir-184_MI0000354\t0\t0.00\t0.00\t0.00\t0.00\n+dme-mir-190_MI0005808\t0\t0.00\t0.00\t0.00\t0.00\n+dme-mir-193_MI0005809\t0\t0.00\t0.00\t0.00\t0.00\n+dme-mir-1_MI0000116\t0\t0.00\t0.00\t0.00\t0.00\n+dme-mir-210_MI0000376\t0\t0.00\t0.00\t0.00\t0.00\n+dme-mir-219_MI0000358\t0\t0.00\t0.00\t0.00\t0.00\n+dme-mir-2279_MI0011289\t0\t0.00\t0.00\t0.00\t0.00\n+dme-mir-2280_MI0011290\t0\t0.00\t0.00\t0.00\t0.00\n+dme-mir-2281_MI0011291\t0\t0.00\t0.00\t0.00\t0.00\n+dme-mir-2282_MI0011292\t0\t0.00\t0.00\t0.00\t0.00\n+dme-mir-2283_MI0011293\t0\t0.00\t0.00\t0.00\t0.00\n+dme-mir-2489_MI0011578\t0\t0.00\t0.00\t0.00\t0.00\n+dme-mir-2490_MI0011579\t0\t0.00\t0.00\t0.00\t0.00\n+dme-mir-2491_MI0011580\t0\t0.00\t0.00\t0.00\t0.00\n+dme-mir-2492_MI0011581\t0\t0.00\t0.00\t0.00\t0.00\n+dme-mir-2493_MI0011582\t0\t0.00\t0.00\t0.00\t0.00\n+dme-mir-2494_MI0011583\t0\t0.00\t0.00\t0.00\t0.00\n+dme-mir-2495_MI0011584\t0\t0.00\t0.00\t0.00\t0.00\n+dme-mir-2496_MI0011585\t0\t0.00\t0.00\t0.00\t0.00\n+dme-mir-2497_MI0011586\t0\t0.00\t0.00\t0.00\t0.00\n+dme-mir-2498_MI0011587\t0\t0.00\t0.00\t0.00\t0.00\n+dme-mir-2499_MI0011588\t0\t0.00\t0.00\t0.00\t0.00\n+dme-mir-2500_MI0011589\t0\t0.00\t0.00\t0.00\t0.00\n+dme-mir-2501_MI0011590\t0\t0.00\t0.00\t0.00\t0.00\n+dme-mir-252_MI0005858\t0\t0.00\t0.00\t0.00\t0.00\n+dme-mir-2535b_MI0017699\t0\t0.00\t0.00\t0.00\t0.00\n+dme-mir-263a_MI0000343\t0\t0.00\t0.00\t0.00\t0.00\n+dme-mir-263b_MI0000383\t0\t0.00\t0.00\t0.00\t0.00\n+dme-mir-274_MI0000355\t0\t0.00\t0.00\t0.00\t0.00\n+dme-mir-275_MI0000356\t0\t0.00\t0.00\t0.00\t0.00\n+dme-mir-276a_MI0000359\t0\t0.00\t0.00\t0.00\t0.00\n+dme-mir-276b_MI0000375\t0\t0.00\t0.00\t0.00\t0.00\n+dme-mir-277_MI0000360\t0\t0.00\t0.00\t0.00\t0.00\n+dme-mir-278_MI0000361\t0\t0.00\t0.00\t0.00\t0.00\n+dme-mir-279_MI0000363\t0\t0.00\t0.00\t0.00\t0.00\n+dme-mir-280_MI0000365\t0\t0.00\t0.00\t0.00\t0.00\n+dme-mir-281-1_MI0000366\t0\t0.00\t0.00\t0.00\t0.00\n+dme-mir-281-2_MI0000370\t0\t0.00\t0.00\t0.00\t0.00\n+dme-mir-282_MI0000367\t0\t0.00\t0.00\t0.00\t0.00\n+dme-mir-283_MI0000368\t0\t0.00\t0.00\t0.00\t0.00\n+dme-mir-284_MI0000369\t0\t0.00\t0.00\t0.00\t0.00\n+dme-mir-285_MI0000377\t0\t0.00\t0.00\t0.00\t0.00\n+dme-mir-286_MI0000380\t0\t0.00\t0.00\t0.00\t0.00\n+dme-mir-287_MI0000381\t0\t0.00\t0.00\t0.00\t0.00\n+dme-mir-288_MI0000384\t0\t0.00\t0.00\t0.00\t0.00\n+dme-mir-289_MI0000385\t0\t0.00\t0.00\t0.00\t0.00\n+dme-mir-2a-1_MI0000117\t0\t0.00\t0.00\t0.00\t0.00\n+dme-mir-2a-2_MI0000118\t0\t0.00\t0.00\t0.00\t0.00\n+dme-mir-2b-1_MI0000119\t0\t0.00\t0.00\t0.00\t0.00\n+dme-mir-2b-2_MI0000120\t0\t0.00\t0.00\t0.00\t0.00\n+dme-mir-2c_MI0000431\t0\t0.00\t0.00\t0.00\t0.00\n+dme-mir-303_MI0000409\t0\t0.00\t0.00\t0.00\t0.00\n+dme-mir-304_MI0000411\t0\t0.00\t0.0'..b'0\t0.00\t0.00\t0.00\t0.00\n+dme-mir-4984_MI0017770\t0\t0.00\t0.00\t0.00\t0.00\n+dme-mir-4985_MI0017771\t0\t0.00\t0.00\t0.00\t0.00\n+dme-mir-4986_MI0017772\t0\t0.00\t0.00\t0.00\t0.00\n+dme-mir-4987_MI0017773\t0\t0.00\t0.00\t0.00\t0.00\n+dme-mir-4_MI0000122\t0\t0.00\t0.00\t0.00\t0.00\n+dme-mir-5_MI0000123\t0\t0.00\t0.00\t0.00\t0.00\n+dme-mir-6-1_MI0000124\t0\t0.00\t0.00\t0.00\t0.00\n+dme-mir-6-2_MI0000125\t0\t0.00\t0.00\t0.00\t0.00\n+dme-mir-6-3_MI0000126\t0\t0.00\t0.00\t0.00\t0.00\n+dme-mir-79_MI0000374\t0\t0.00\t0.00\t0.00\t0.00\n+dme-mir-7_MI0000127\t0\t0.00\t0.00\t0.00\t0.00\n+dme-mir-87_MI0000382\t0\t0.00\t0.00\t0.00\t0.00\n+dme-mir-8_MI0000128\t0\t0.00\t0.00\t0.00\t0.00\n+dme-mir-927_MI0005843\t0\t0.00\t0.00\t0.00\t0.00\n+dme-mir-929_MI0005853\t0\t0.00\t0.00\t0.00\t0.00\n+dme-mir-92a_MI0000357\t0\t0.00\t0.00\t0.00\t0.00\n+dme-mir-92b_MI0000379\t0\t0.00\t0.00\t0.00\t0.00\n+dme-mir-932_MI0005820\t0\t0.00\t0.00\t0.00\t0.00\n+dme-mir-9369_MI0028918\t0\t0.00\t0.00\t0.00\t0.00\n+dme-mir-9370_MI0028919\t0\t0.00\t0.00\t0.00\t0.00\n+dme-mir-9371_MI0028920\t0\t0.00\t0.00\t0.00\t0.00\n+dme-mir-9372_MI0028921\t0\t0.00\t0.00\t0.00\t0.00\n+dme-mir-9373_MI0028922\t0\t0.00\t0.00\t0.00\t0.00\n+dme-mir-9374_MI0028923\t0\t0.00\t0.00\t0.00\t0.00\n+dme-mir-9375_MI0028924\t0\t0.00\t0.00\t0.00\t0.00\n+dme-mir-9376_MI0028925\t0\t0.00\t0.00\t0.00\t0.00\n+dme-mir-9377_MI0028926\t0\t0.00\t0.00\t0.00\t0.00\n+dme-mir-9378_MI0028927\t0\t0.00\t0.00\t0.00\t0.00\n+dme-mir-9379_MI0028928\t0\t0.00\t0.00\t0.00\t0.00\n+dme-mir-9380_MI0028929\t0\t0.00\t0.00\t0.00\t0.00\n+dme-mir-9381_MI0028930\t0\t0.00\t0.00\t0.00\t0.00\n+dme-mir-9382_MI0028931\t0\t0.00\t0.00\t0.00\t0.00\n+dme-mir-9383_MI0028932\t0\t0.00\t0.00\t0.00\t0.00\n+dme-mir-9384_MI0028933\t0\t0.00\t0.00\t0.00\t0.00\n+dme-mir-9385_MI0028934\t0\t0.00\t0.00\t0.00\t0.00\n+dme-mir-9388_MI0028938\t0\t0.00\t0.00\t0.00\t0.00\n+dme-mir-954_MI0005806\t0\t0.00\t0.00\t0.00\t0.00\n+dme-mir-955_MI0005807\t0\t0.00\t0.00\t0.00\t0.00\n+dme-mir-956_MI0005810\t0\t0.00\t0.00\t0.00\t0.00\n+dme-mir-957_MI0005811\t0\t0.00\t0.00\t0.00\t0.00\n+dme-mir-958_MI0005812\t0\t0.00\t0.00\t0.00\t0.00\n+dme-mir-959_MI0005814\t0\t0.00\t0.00\t0.00\t0.00\n+dme-mir-960_MI0005815\t0\t0.00\t0.00\t0.00\t0.00\n+dme-mir-961_MI0005816\t0\t0.00\t0.00\t0.00\t0.00\n+dme-mir-962_MI0005817\t0\t0.00\t0.00\t0.00\t0.00\n+dme-mir-963_MI0005818\t0\t0.00\t0.00\t0.00\t0.00\n+dme-mir-964_MI0005819\t0\t0.00\t0.00\t0.00\t0.00\n+dme-mir-965_MI0005821\t0\t0.00\t0.00\t0.00\t0.00\n+dme-mir-966_MI0005822\t0\t0.00\t0.00\t0.00\t0.00\n+dme-mir-967_MI0005823\t0\t0.00\t0.00\t0.00\t0.00\n+dme-mir-968_MI0005825\t0\t0.00\t0.00\t0.00\t0.00\n+dme-mir-969_MI0005826\t0\t0.00\t0.00\t0.00\t0.00\n+dme-mir-970_MI0005827\t0\t0.00\t0.00\t0.00\t0.00\n+dme-mir-971_MI0005828\t0\t0.00\t0.00\t0.00\t0.00\n+dme-mir-972_MI0005829\t0\t0.00\t0.00\t0.00\t0.00\n+dme-mir-973_MI0005830\t0\t0.00\t0.00\t0.00\t0.00\n+dme-mir-974_MI0005831\t0\t0.00\t0.00\t0.00\t0.00\n+dme-mir-975_MI0005832\t0\t0.00\t0.00\t0.00\t0.00\n+dme-mir-976_MI0005833\t0\t0.00\t0.00\t0.00\t0.00\n+dme-mir-977_MI0005834\t0\t0.00\t0.00\t0.00\t0.00\n+dme-mir-978_MI0005835\t0\t0.00\t0.00\t0.00\t0.00\n+dme-mir-979_MI0005836\t0\t0.00\t0.00\t0.00\t0.00\n+dme-mir-980_MI0005837\t0\t0.00\t0.00\t0.00\t0.00\n+dme-mir-981_MI0005838\t0\t0.00\t0.00\t0.00\t0.00\n+dme-mir-982_MI0005839\t0\t0.00\t0.00\t0.00\t0.00\n+dme-mir-983-1_MI0005840\t0\t0.00\t0.00\t0.00\t0.00\n+dme-mir-983-2_MI0005841\t0\t0.00\t0.00\t0.00\t0.00\n+dme-mir-984_MI0005842\t0\t0.00\t0.00\t0.00\t0.00\n+dme-mir-985_MI0005844\t0\t0.00\t0.00\t0.00\t0.00\n+dme-mir-986_MI0005845\t0\t0.00\t0.00\t0.00\t0.00\n+dme-mir-987_MI0005846\t0\t0.00\t0.00\t0.00\t0.00\n+dme-mir-988_MI0005847\t0\t0.00\t0.00\t0.00\t0.00\n+dme-mir-989_MI0005848\t0\t0.00\t0.00\t0.00\t0.00\n+dme-mir-990_MI0005850\t0\t0.00\t0.00\t0.00\t0.00\n+dme-mir-991_MI0005851\t0\t0.00\t0.00\t0.00\t0.00\n+dme-mir-992_MI0005852\t0\t0.00\t0.00\t0.00\t0.00\n+dme-mir-993_MI0005854\t0\t0.00\t0.00\t0.00\t0.00\n+dme-mir-994_MI0005855\t0\t0.00\t0.00\t0.00\t0.00\n+dme-mir-995_MI0005856\t0\t0.00\t0.00\t0.00\t0.00\n+dme-mir-996_MI0005857\t0\t0.00\t0.00\t0.00\t0.00\n+dme-mir-997_MI0005859\t0\t0.00\t0.00\t0.00\t0.00\n+dme-mir-998_MI0005860\t0\t0.00\t0.00\t0.00\t0.00\n+dme-mir-999_MI0005861\t0\t0.00\t0.00\t0.00\t0.00\n+dme-mir-9a_MI0000129\t0\t0.00\t0.00\t0.00\t0.00\n+dme-mir-9b_MI0000415\t0\t0.00\t0.00\t0.00\t0.00\n+dme-mir-9c_MI0000413\t0\t0.00\t0.00\t0.00\t0.00\n+dme-mir-iab-4_MI0000432\t0\t0.00\t0.00\t0.00\t0.00\n+dme-mir-iab-8_MI0005805\t0\t0.00\t0.00\t0.00\t0.00\n' |
| b |
| diff -r 9645d995fb3c -r 9185ca0a7b43 test-data/res_files/reads-sample-small.fastq/subgroups/piRNAs/Gviz_TEs/BATUMI_I.png |
| b |
| Binary file test-data/res_files/reads-sample-small.fastq/subgroups/piRNAs/Gviz_TEs/BATUMI_I.png has changed |
| b |
| diff -r 9645d995fb3c -r 9185ca0a7b43 test-data/res_files/reads-sample-small.fastq/subgroups/piRNAs/Gviz_TEs/BATUMI_LTR.png |
| b |
| Binary file test-data/res_files/reads-sample-small.fastq/subgroups/piRNAs/Gviz_TEs/BATUMI_LTR.png has changed |
| b |
| diff -r 9645d995fb3c -r 9185ca0a7b43 test-data/res_files/reads-sample-small.fastq/subgroups/piRNAs/Gviz_TEs/BS2.png |
| b |
| Binary file test-data/res_files/reads-sample-small.fastq/subgroups/piRNAs/Gviz_TEs/BS2.png has changed |
| b |
| diff -r 9645d995fb3c -r 9185ca0a7b43 test-data/res_files/reads-sample-small.fastq/subgroups/piRNAs/Gviz_TEs/DMCR1A.png |
| b |
| Binary file test-data/res_files/reads-sample-small.fastq/subgroups/piRNAs/Gviz_TEs/DMCR1A.png has changed |
| b |
| diff -r 9645d995fb3c -r 9185ca0a7b43 test-data/res_files/reads-sample-small.fastq/subgroups/piRNAs/Gviz_TEs/DMRT1B.png |
| b |
| Binary file test-data/res_files/reads-sample-small.fastq/subgroups/piRNAs/Gviz_TEs/DMRT1B.png has changed |
| b |
| diff -r 9645d995fb3c -r 9185ca0a7b43 test-data/res_files/reads-sample-small.fastq/subgroups/piRNAs/Gviz_TEs/FW.png |
| b |
| Binary file test-data/res_files/reads-sample-small.fastq/subgroups/piRNAs/Gviz_TEs/FW.png has changed |
| b |
| diff -r 9645d995fb3c -r 9185ca0a7b43 test-data/res_files/reads-sample-small.fastq/subgroups/piRNAs/Gviz_TEs/G6_DM.png |
| b |
| Binary file test-data/res_files/reads-sample-small.fastq/subgroups/piRNAs/Gviz_TEs/G6_DM.png has changed |
| b |
| diff -r 9645d995fb3c -r 9185ca0a7b43 test-data/res_files/reads-sample-small.fastq/subgroups/piRNAs/Gviz_TEs/Gypsy2-LTR_DM.png |
| b |
| Binary file test-data/res_files/reads-sample-small.fastq/subgroups/piRNAs/Gviz_TEs/Gypsy2-LTR_DM.png has changed |
| b |
| diff -r 9645d995fb3c -r 9185ca0a7b43 test-data/res_files/reads-sample-small.fastq/subgroups/piRNAs/Gviz_TEs/I_DM.png |
| b |
| Binary file test-data/res_files/reads-sample-small.fastq/subgroups/piRNAs/Gviz_TEs/I_DM.png has changed |
| b |
| diff -r 9645d995fb3c -r 9185ca0a7b43 test-data/res_files/reads-sample-small.fastq/subgroups/piRNAs/Gviz_TEs/MAX_I.png |
| b |
| Binary file test-data/res_files/reads-sample-small.fastq/subgroups/piRNAs/Gviz_TEs/MAX_I.png has changed |
| b |
| diff -r 9645d995fb3c -r 9185ca0a7b43 test-data/res_files/reads-sample-small.fastq/subgroups/piRNAs/Gviz_TEs/MAX_LTR.png |
| b |
| Binary file test-data/res_files/reads-sample-small.fastq/subgroups/piRNAs/Gviz_TEs/MAX_LTR.png has changed |
| b |
| diff -r 9645d995fb3c -r 9185ca0a7b43 test-data/res_files/reads-sample-small.fastq/subgroups/piRNAs/Gviz_TEs/PROTOP.png |
| b |
| Binary file test-data/res_files/reads-sample-small.fastq/subgroups/piRNAs/Gviz_TEs/PROTOP.png has changed |
| b |
| diff -r 9645d995fb3c -r 9185ca0a7b43 test-data/res_files/reads-sample-small.fastq/subgroups/piRNAs/Gviz_genome/rand/chrom_1.png |
| b |
| Binary file test-data/res_files/reads-sample-small.fastq/subgroups/piRNAs/Gviz_genome/rand/chrom_1.png has changed |
| b |
| diff -r 9645d995fb3c -r 9185ca0a7b43 test-data/res_files/reads-sample-small.fastq/subgroups/piRNAs/Gviz_genome/rand/chrom_2.png |
| b |
| Binary file test-data/res_files/reads-sample-small.fastq/subgroups/piRNAs/Gviz_genome/rand/chrom_2.png has changed |
| b |
| diff -r 9645d995fb3c -r 9185ca0a7b43 test-data/res_files/reads-sample-small.fastq/subgroups/piRNAs/Gviz_genome/rand/chrom_4.png |
| b |
| Binary file test-data/res_files/reads-sample-small.fastq/subgroups/piRNAs/Gviz_genome/rand/chrom_4.png has changed |
| b |
| diff -r 9645d995fb3c -r 9185ca0a7b43 test-data/res_files/reads-sample-small.fastq/subgroups/piRNAs/Gviz_genome/rand/chrom_6.png |
| b |
| Binary file test-data/res_files/reads-sample-small.fastq/subgroups/piRNAs/Gviz_genome/rand/chrom_6.png has changed |
| b |
| diff -r 9645d995fb3c -r 9185ca0a7b43 test-data/res_files/reads-sample-small.fastq/subgroups/piRNAs/Gviz_genome/unique/chrom_1.png |
| b |
| Binary file test-data/res_files/reads-sample-small.fastq/subgroups/piRNAs/Gviz_genome/unique/chrom_1.png has changed |
| b |
| diff -r 9645d995fb3c -r 9185ca0a7b43 test-data/res_files/reads-sample-small.fastq/subgroups/piRNAs/Gviz_genome/unique/chrom_2.png |
| b |
| Binary file test-data/res_files/reads-sample-small.fastq/subgroups/piRNAs/Gviz_genome/unique/chrom_2.png has changed |
| b |
| diff -r 9645d995fb3c -r 9185ca0a7b43 test-data/res_files/reads-sample-small.fastq/subgroups/piRNAs/Gviz_genome/unique/chrom_4.png |
| b |
| Binary file test-data/res_files/reads-sample-small.fastq/subgroups/piRNAs/Gviz_genome/unique/chrom_4.png has changed |
| b |
| diff -r 9645d995fb3c -r 9185ca0a7b43 test-data/res_files/reads-sample-small.fastq/subgroups/piRNAs/Gviz_genome/unique/chrom_6.png |
| b |
| Binary file test-data/res_files/reads-sample-small.fastq/subgroups/piRNAs/Gviz_genome/unique/chrom_6.png has changed |
| b |
| diff -r 9645d995fb3c -r 9185ca0a7b43 test-data/res_files/reads-sample-small.fastq/subgroups/piRNAs/piRNAs-TEs_minus.bedgraph --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/res_files/reads-sample-small.fastq/subgroups/piRNAs/piRNAs-TEs_minus.bedgraph Wed Jan 16 08:18:13 2019 -0500 |
| b |
| b'@@ -0,0 +1,3960 @@\n+BATUMI_I\t0\t4\t0\n+BATUMI_I\t4\t12\t102.459\n+BATUMI_I\t12\t14\t128.074\n+BATUMI_I\t14\t22\t153.689\n+BATUMI_I\t22\t25\t179.303\n+BATUMI_I\t25\t27\t204.918\n+BATUMI_I\t27\t29\t128.074\n+BATUMI_I\t29\t35\t102.459\n+BATUMI_I\t35\t38\t76.8443\n+BATUMI_I\t38\t47\t51.2295\n+BATUMI_I\t47\t48\t25.6148\n+BATUMI_I\t48\t53\t0\n+BATUMI_I\t53\t76\t25.6148\n+BATUMI_I\t76\t93\t0\n+BATUMI_I\t93\t95\t25.6148\n+BATUMI_I\t95\t96\t51.2295\n+BATUMI_I\t96\t97\t76.8443\n+BATUMI_I\t97\t120\t102.459\n+BATUMI_I\t120\t121\t76.8443\n+BATUMI_I\t121\t123\t25.6148\n+BATUMI_I\t123\t145\t51.2295\n+BATUMI_I\t145\t148\t25.6148\n+BATUMI_I\t148\t160\t0\n+BATUMI_I\t160\t164\t128.074\n+BATUMI_I\t164\t165\t179.303\n+BATUMI_I\t165\t169\t256.148\n+BATUMI_I\t169\t183\t281.762\n+BATUMI_I\t183\t185\t204.918\n+BATUMI_I\t185\t186\t179.303\n+BATUMI_I\t186\t187\t153.689\n+BATUMI_I\t187\t188\t128.074\n+BATUMI_I\t188\t191\t51.2295\n+BATUMI_I\t191\t195\t25.6148\n+BATUMI_I\t195\t214\t0\n+BATUMI_I\t214\t238\t25.6148\n+BATUMI_I\t238\t247\t0\n+BATUMI_I\t247\t261\t25.6148\n+BATUMI_I\t261\t270\t51.2295\n+BATUMI_I\t270\t277\t25.6148\n+BATUMI_I\t277\t278\t0\n+BATUMI_I\t278\t286\t25.6148\n+BATUMI_I\t286\t295\t0\n+BATUMI_I\t295\t297\t76.8443\n+BATUMI_I\t297\t320\t102.459\n+BATUMI_I\t320\t321\t76.8443\n+BATUMI_I\t321\t348\t0\n+BATUMI_I\t348\t349\t51.2295\n+BATUMI_I\t349\t350\t153.689\n+BATUMI_I\t350\t352\t435.451\n+BATUMI_I\t352\t353\t461.066\n+BATUMI_I\t353\t354\t512.295\n+BATUMI_I\t354\t357\t563.525\n+BATUMI_I\t357\t358\t614.754\n+BATUMI_I\t358\t359\t742.828\n+BATUMI_I\t359\t360\t1152.66\n+BATUMI_I\t360\t369\t1280.74\n+BATUMI_I\t369\t370\t1331.97\n+BATUMI_I\t370\t374\t1357.58\n+BATUMI_I\t374\t376\t922.131\n+BATUMI_I\t376\t377\t896.516\n+BATUMI_I\t377\t378\t845.287\n+BATUMI_I\t378\t379\t870.902\n+BATUMI_I\t379\t383\t896.516\n+BATUMI_I\t383\t384\t717.213\n+BATUMI_I\t384\t385\t563.525\n+BATUMI_I\t385\t393\t614.754\n+BATUMI_I\t393\t394\t563.525\n+BATUMI_I\t394\t402\t537.91\n+BATUMI_I\t402\t403\t512.295\n+BATUMI_I\t403\t407\t435.451\n+BATUMI_I\t407\t409\t409.836\n+BATUMI_I\t409\t410\t179.303\n+BATUMI_I\t410\t411\t51.2295\n+BATUMI_I\t411\t413\t0\n+BATUMI_I\t413\t418\t25.6148\n+BATUMI_I\t418\t419\t102.459\n+BATUMI_I\t419\t420\t204.918\n+BATUMI_I\t420\t439\t230.533\n+BATUMI_I\t439\t440\t25.6148\n+BATUMI_I\t440\t443\t204.918\n+BATUMI_I\t443\t444\t179.303\n+BATUMI_I\t444\t484\t0\n+BATUMI_I\t484\t508\t25.6148\n+BATUMI_I\t508\t7004\t0\n+BATUMI_I\t7004\t7005\t76.8443\n+BATUMI_I\t7005\t7028\t128.074\n+BATUMI_I\t7028\t7077\t0\n+BATUMI_I\t7077\t7101\t25.6148\n+BATUMI_I\t7101\t7963\t0\n+BATUMI_LTR\t0\t69\t0\n+BATUMI_LTR\t69\t93\t25.6148\n+BATUMI_LTR\t93\t99\t0\n+BATUMI_LTR\t99\t102\t25.6148\n+BATUMI_LTR\t102\t105\t76.8443\n+BATUMI_LTR\t105\t106\t947.746\n+BATUMI_LTR\t106\t107\t1716.19\n+BATUMI_LTR\t107\t111\t1741.8\n+BATUMI_LTR\t111\t124\t1767.42\n+BATUMI_LTR\t124\t127\t1741.8\n+BATUMI_LTR\t127\t128\t1716.19\n+BATUMI_LTR\t128\t130\t1690.57\n+BATUMI_LTR\t130\t137\t25.6148\n+BATUMI_LTR\t137\t177\t0\n+BATUMI_LTR\t177\t179\t51.2295\n+BATUMI_LTR\t179\t191\t76.8443\n+BATUMI_LTR\t191\t192\t102.459\n+BATUMI_LTR\t192\t193\t179.303\n+BATUMI_LTR\t193\t202\t332.992\n+BATUMI_LTR\t202\t204\t256.148\n+BATUMI_LTR\t204\t207\t281.762\n+BATUMI_LTR\t207\t215\t307.377\n+BATUMI_LTR\t215\t216\t281.762\n+BATUMI_LTR\t216\t217\t256.148\n+BATUMI_LTR\t217\t218\t153.689\n+BATUMI_LTR\t218\t219\t102.459\n+BATUMI_LTR\t219\t228\t76.8443\n+BATUMI_LTR\t228\t230\t51.2295\n+BATUMI_LTR\t230\t242\t25.6148\n+BATUMI_LTR\t242\t272\t0\n+BS2\t0\t12\t0\n+BS2\t12\t13\t51.2295\n+BS2\t13\t35\t76.8443\n+BS2\t35\t38\t25.6148\n+BS2\t38\t52\t0\n+BS2\t52\t55\t51.2295\n+BS2\t55\t78\t76.8443\n+BS2\t78\t119\t0\n+BS2\t119\t121\t25.6148\n+BS2\t121\t134\t153.689\n+BS2\t134\t138\t204.918\n+BS2\t138\t139\t230.533\n+BS2\t139\t144\t307.377\n+BS2\t144\t146\t281.762\n+BS2\t146\t158\t153.689\n+BS2\t158\t162\t102.459\n+BS2\t162\t163\t76.8443\n+BS2\t163\t205\t0\n+BS2\t205\t214\t25.6148\n+BS2\t214\t215\t204.918\n+BS2\t215\t216\t281.762\n+BS2\t216\t217\t358.607\n+BS2\t217\t218\t819.672\n+BS2\t218\t219\t870.902\n+BS2\t219\t220\t896.516\n+BS2\t220\t221\t922.131\n+BS2\t221\t225\t947.746\n+BS2\t225\t230\t973.361\n+BS2\t230\t236\t947.746\n+BS2\t236\t238\t973.361\n+BS2\t238\t239\t922.131\n+BS2\t239\t240\t742.828\n+BS2\t240\t241\t230.533\n+BS2\t241\t242\t204.918\n+BS2\t242\t244\t102.459\n+BS2\t244\t247\t76.8443\n+BS2\t247\t248\t51.2295\n+BS2\t248\t251\t25.6148\n+BS2\t251\t260\t51.2295\n+BS2\t260\t261\t25.6148\n+BS2\t261\t263\t51.2295\n+BS2\t263\t267\t102.459\n+BS2\t267\t268\t153.689\n+BS2\t268\t269\t486.68\n+BS2\t269\t270\t563.525\n+BS2\t270\t276\t614.754\n+BS2\t276\t284\t589.139\n+BS2\t284\t286\t563.525\n+BS2\t'..b'91\t93\t51.2295\n+MAX_I\t93\t105\t76.8443\n+MAX_I\t105\t106\t512.295\n+MAX_I\t106\t107\t845.287\n+MAX_I\t107\t109\t870.902\n+MAX_I\t109\t115\t845.287\n+MAX_I\t115\t117\t870.902\n+MAX_I\t117\t125\t845.287\n+MAX_I\t125\t126\t1024.59\n+MAX_I\t126\t127\t1306.35\n+MAX_I\t127\t128\t1331.97\n+MAX_I\t128\t129\t1306.35\n+MAX_I\t129\t130\t1203.89\n+MAX_I\t130\t138\t589.139\n+MAX_I\t138\t140\t563.525\n+MAX_I\t140\t149\t537.91\n+MAX_I\t149\t150\t512.295\n+MAX_I\t150\t152\t51.2295\n+MAX_I\t152\t153\t25.6148\n+MAX_I\t153\t170\t0\n+MAX_I\t170\t193\t25.6148\n+MAX_I\t193\t235\t0\n+MAX_I\t235\t250\t51.2295\n+MAX_I\t250\t258\t76.8443\n+MAX_I\t258\t259\t51.2295\n+MAX_I\t259\t262\t25.6148\n+MAX_I\t262\t276\t51.2295\n+MAX_I\t276\t287\t25.6148\n+MAX_I\t287\t300\t0\n+MAX_I\t300\t302\t25.6148\n+MAX_I\t302\t309\t102.459\n+MAX_I\t309\t326\t128.074\n+MAX_I\t326\t334\t25.6148\n+MAX_I\t334\t7914\t0\n+MAX_LTR\t0\t4\t0\n+MAX_LTR\t4\t13\t230.533\n+MAX_LTR\t13\t14\t332.992\n+MAX_LTR\t14\t15\t486.68\n+MAX_LTR\t15\t16\t640.369\n+MAX_LTR\t16\t30\t665.984\n+MAX_LTR\t30\t36\t435.451\n+MAX_LTR\t36\t39\t409.836\n+MAX_LTR\t39\t41\t25.6148\n+MAX_LTR\t41\t52\t0\n+MAX_LTR\t52\t76\t25.6148\n+MAX_LTR\t76\t84\t0\n+MAX_LTR\t84\t88\t25.6148\n+MAX_LTR\t88\t94\t51.2295\n+MAX_LTR\t94\t110\t76.8443\n+MAX_LTR\t110\t112\t51.2295\n+MAX_LTR\t112\t117\t25.6148\n+MAX_LTR\t117\t133\t0\n+MAX_LTR\t133\t151\t76.8443\n+MAX_LTR\t151\t152\t153.689\n+MAX_LTR\t152\t153\t204.918\n+MAX_LTR\t153\t154\t281.762\n+MAX_LTR\t154\t156\t307.377\n+MAX_LTR\t156\t158\t281.762\n+MAX_LTR\t158\t174\t230.533\n+MAX_LTR\t174\t175\t179.303\n+MAX_LTR\t175\t176\t153.689\n+MAX_LTR\t176\t177\t102.459\n+MAX_LTR\t177\t321\t0\n+PROTOP\t0\t119\t0\n+PROTOP\t119\t142\t25.6148\n+PROTOP\t142\t222\t0\n+PROTOP\t222\t224\t51.2295\n+PROTOP\t224\t225\t128.074\n+PROTOP\t225\t245\t179.303\n+PROTOP\t245\t247\t153.689\n+PROTOP\t247\t248\t51.2295\n+PROTOP\t248\t465\t0\n+PROTOP\t465\t490\t25.6148\n+PROTOP\t490\t503\t0\n+PROTOP\t503\t526\t25.6148\n+PROTOP\t526\t2333\t0\n+PROTOP\t2333\t2348\t25.6148\n+PROTOP\t2348\t2358\t51.2295\n+PROTOP\t2358\t2372\t25.6148\n+PROTOP\t2372\t2427\t0\n+PROTOP\t2427\t2428\t179.303\n+PROTOP\t2428\t2444\t256.148\n+PROTOP\t2444\t2452\t281.762\n+PROTOP\t2452\t2461\t25.6148\n+PROTOP\t2461\t2462\t0\n+PROTOP\t2462\t2469\t25.6148\n+PROTOP\t2469\t2488\t0\n+PROTOP\t2488\t2491\t25.6148\n+PROTOP\t2491\t2492\t51.2295\n+PROTOP\t2492\t2493\t512.295\n+PROTOP\t2493\t2507\t537.91\n+PROTOP\t2507\t2512\t563.525\n+PROTOP\t2512\t2516\t537.91\n+PROTOP\t2516\t2517\t461.066\n+PROTOP\t2517\t2518\t409.836\n+PROTOP\t2518\t2534\t25.6148\n+PROTOP\t2534\t2552\t51.2295\n+PROTOP\t2552\t2559\t76.8443\n+PROTOP\t2559\t2576\t25.6148\n+PROTOP\t2576\t2579\t0\n+PROTOP\t2579\t2591\t51.2295\n+PROTOP\t2591\t2592\t204.918\n+PROTOP\t2592\t2603\t230.533\n+PROTOP\t2603\t2615\t179.303\n+PROTOP\t2615\t2683\t0\n+PROTOP\t2683\t2685\t25.6148\n+PROTOP\t2685\t2691\t51.2295\n+PROTOP\t2691\t2706\t76.8443\n+PROTOP\t2706\t2710\t128.074\n+PROTOP\t2710\t2717\t153.689\n+PROTOP\t2717\t2719\t179.303\n+PROTOP\t2719\t2724\t307.377\n+PROTOP\t2724\t2729\t332.992\n+PROTOP\t2729\t2730\t307.377\n+PROTOP\t2730\t2732\t332.992\n+PROTOP\t2732\t2735\t281.762\n+PROTOP\t2735\t2742\t256.148\n+PROTOP\t2742\t2743\t204.918\n+PROTOP\t2743\t2744\t153.689\n+PROTOP\t2744\t2748\t76.8443\n+PROTOP\t2748\t2758\t51.2295\n+PROTOP\t2758\t2759\t76.8443\n+PROTOP\t2759\t2760\t102.459\n+PROTOP\t2760\t2780\t76.8443\n+PROTOP\t2780\t2783\t51.2295\n+PROTOP\t2783\t2852\t0\n+PROTOP\t2852\t2878\t25.6148\n+PROTOP\t2878\t3059\t0\n+PROTOP\t3059\t3082\t76.8443\n+PROTOP\t3082\t3084\t51.2295\n+PROTOP\t3084\t3090\t0\n+PROTOP\t3090\t3114\t25.6148\n+PROTOP\t3114\t3160\t0\n+PROTOP\t3160\t3186\t25.6148\n+PROTOP\t3186\t3189\t0\n+PROTOP\t3189\t3214\t25.6148\n+PROTOP\t3214\t3221\t0\n+PROTOP\t3221\t3244\t25.6148\n+PROTOP\t3244\t3271\t0\n+PROTOP\t3271\t3296\t76.8443\n+PROTOP\t3296\t3370\t0\n+PROTOP\t3370\t3372\t25.6148\n+PROTOP\t3372\t3381\t76.8443\n+PROTOP\t3381\t3383\t102.459\n+PROTOP\t3383\t3396\t179.303\n+PROTOP\t3396\t3406\t102.459\n+PROTOP\t3406\t3431\t76.8443\n+PROTOP\t3431\t3433\t25.6148\n+PROTOP\t3433\t3448\t0\n+PROTOP\t3448\t3472\t25.6148\n+PROTOP\t3472\t3478\t0\n+PROTOP\t3478\t3489\t25.6148\n+PROTOP\t3489\t3503\t51.2295\n+PROTOP\t3503\t3513\t25.6148\n+PROTOP\t3513\t4353\t0\n+PROTOP\t4353\t4370\t25.6148\n+PROTOP\t4370\t4371\t51.2295\n+PROTOP\t4371\t4374\t128.074\n+PROTOP\t4374\t4378\t204.918\n+PROTOP\t4378\t4388\t179.303\n+PROTOP\t4388\t4392\t204.918\n+PROTOP\t4392\t4393\t230.533\n+PROTOP\t4393\t4394\t204.918\n+PROTOP\t4394\t4397\t153.689\n+PROTOP\t4397\t4413\t51.2295\n+PROTOP\t4413\t4417\t25.6148\n+PROTOP\t4417\t4425\t0\n+PROTOP\t4425\t4450\t25.6148\n+PROTOP\t4450\t4480\t0\n' |
| b |
| diff -r 9645d995fb3c -r 9185ca0a7b43 test-data/res_files/reads-sample-small.fastq/subgroups/piRNAs/piRNAs-TEs_plus.bedgraph --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/res_files/reads-sample-small.fastq/subgroups/piRNAs/piRNAs-TEs_plus.bedgraph Wed Jan 16 08:18:13 2019 -0500 |
| b |
| b'@@ -0,0 +1,2185 @@\n+BATUMI_I\t0\t1\t25.6148\n+BATUMI_I\t1\t6\t51.2295\n+BATUMI_I\t6\t22\t76.8443\n+BATUMI_I\t22\t26\t51.2295\n+BATUMI_I\t26\t32\t25.6148\n+BATUMI_I\t32\t119\t0\n+BATUMI_I\t119\t144\t51.2295\n+BATUMI_I\t144\t150\t0\n+BATUMI_I\t150\t160\t25.6148\n+BATUMI_I\t160\t176\t51.2295\n+BATUMI_I\t176\t185\t25.6148\n+BATUMI_I\t185\t386\t0\n+BATUMI_I\t386\t411\t25.6148\n+BATUMI_I\t411\t417\t0\n+BATUMI_I\t417\t418\t25.6148\n+BATUMI_I\t418\t419\t128.074\n+BATUMI_I\t419\t441\t153.689\n+BATUMI_I\t441\t442\t102.459\n+BATUMI_I\t442\t443\t25.6148\n+BATUMI_I\t443\t7006\t0\n+BATUMI_I\t7006\t7007\t25.6148\n+BATUMI_I\t7007\t7008\t51.2295\n+BATUMI_I\t7008\t7009\t128.074\n+BATUMI_I\t7009\t7016\t281.762\n+BATUMI_I\t7016\t7017\t640.369\n+BATUMI_I\t7017\t7018\t1664.96\n+BATUMI_I\t7018\t7031\t3201.84\n+BATUMI_I\t7031\t7033\t3073.77\n+BATUMI_I\t7033\t7034\t3048.16\n+BATUMI_I\t7034\t7038\t2920.08\n+BATUMI_I\t7038\t7039\t2715.16\n+BATUMI_I\t7039\t7040\t1716.19\n+BATUMI_I\t7040\t7041\t1511.27\n+BATUMI_I\t7041\t7042\t281.762\n+BATUMI_I\t7042\t7043\t25.6148\n+BATUMI_I\t7043\t7963\t0\n+BATUMI_LTR\t0\t32\t0\n+BATUMI_LTR\t32\t57\t25.6148\n+BATUMI_LTR\t57\t118\t0\n+BATUMI_LTR\t118\t142\t25.6148\n+BATUMI_LTR\t142\t195\t0\n+BATUMI_LTR\t195\t218\t25.6148\n+BATUMI_LTR\t218\t272\t0\n+BS2\t0\t21\t0\n+BS2\t21\t42\t51.2295\n+BS2\t42\t45\t76.8443\n+BS2\t45\t68\t25.6148\n+BS2\t68\t69\t384.221\n+BS2\t69\t72\t435.451\n+BS2\t72\t77\t486.68\n+BS2\t77\t79\t512.295\n+BS2\t79\t80\t537.91\n+BS2\t80\t81\t563.525\n+BS2\t81\t82\t717.213\n+BS2\t82\t91\t742.828\n+BS2\t91\t93\t717.213\n+BS2\t93\t94\t384.221\n+BS2\t94\t97\t307.377\n+BS2\t97\t98\t281.762\n+BS2\t98\t102\t256.148\n+BS2\t102\t106\t230.533\n+BS2\t106\t107\t102.459\n+BS2\t107\t108\t51.2295\n+BS2\t108\t186\t0\n+BS2\t186\t187\t25.6148\n+BS2\t187\t188\t51.2295\n+BS2\t188\t192\t102.459\n+BS2\t192\t193\t128.074\n+BS2\t193\t194\t153.689\n+BS2\t194\t196\t256.148\n+BS2\t196\t211\t281.762\n+BS2\t211\t213\t256.148\n+BS2\t213\t214\t230.533\n+BS2\t214\t215\t307.377\n+BS2\t215\t219\t281.762\n+BS2\t219\t220\t230.533\n+BS2\t220\t221\t204.918\n+BS2\t221\t222\t179.303\n+BS2\t222\t223\t230.533\n+BS2\t223\t224\t256.148\n+BS2\t224\t235\t537.91\n+BS2\t235\t237\t512.295\n+BS2\t237\t238\t461.066\n+BS2\t238\t241\t435.451\n+BS2\t241\t246\t409.836\n+BS2\t246\t248\t332.992\n+BS2\t248\t284\t0\n+BS2\t284\t285\t25.6148\n+BS2\t285\t303\t76.8443\n+BS2\t303\t304\t102.459\n+BS2\t304\t308\t128.074\n+BS2\t308\t329\t51.2295\n+BS2\t329\t335\t25.6148\n+BS2\t335\t338\t51.2295\n+BS2\t338\t339\t281.762\n+BS2\t339\t341\t409.836\n+BS2\t341\t344\t435.451\n+BS2\t344\t350\t512.295\n+BS2\t350\t353\t537.91\n+BS2\t353\t362\t512.295\n+BS2\t362\t363\t384.221\n+BS2\t363\t364\t204.918\n+BS2\t364\t365\t128.074\n+BS2\t365\t367\t153.689\n+BS2\t367\t368\t128.074\n+BS2\t368\t374\t76.8443\n+BS2\t374\t386\t51.2295\n+BS2\t386\t390\t25.6148\n+BS2\t390\t430\t0\n+BS2\t430\t440\t25.6148\n+BS2\t440\t454\t76.8443\n+BS2\t454\t455\t51.2295\n+BS2\t455\t456\t76.8443\n+BS2\t456\t457\t230.533\n+BS2\t457\t463\t256.148\n+BS2\t463\t465\t230.533\n+BS2\t465\t471\t204.918\n+BS2\t471\t475\t230.533\n+BS2\t475\t480\t256.148\n+BS2\t480\t483\t76.8443\n+BS2\t483\t484\t51.2295\n+BS2\t484\t492\t76.8443\n+BS2\t492\t493\t102.459\n+BS2\t493\t495\t128.074\n+BS2\t495\t499\t153.689\n+BS2\t499\t501\t204.918\n+BS2\t501\t503\t179.303\n+BS2\t503\t506\t230.533\n+BS2\t506\t509\t256.148\n+BS2\t509\t511\t281.762\n+BS2\t511\t516\t461.066\n+BS2\t516\t518\t435.451\n+BS2\t518\t519\t409.836\n+BS2\t519\t522\t384.221\n+BS2\t522\t528\t307.377\n+BS2\t528\t530\t256.148\n+BS2\t530\t534\t230.533\n+BS2\t534\t535\t76.8443\n+BS2\t535\t537\t25.6148\n+BS2\t537\t562\t0\n+BS2\t562\t566\t102.459\n+BS2\t566\t576\t153.689\n+BS2\t576\t582\t179.303\n+BS2\t582\t586\t204.918\n+BS2\t586\t588\t179.303\n+BS2\t588\t591\t153.689\n+BS2\t591\t592\t128.074\n+BS2\t592\t593\t179.303\n+BS2\t593\t601\t204.918\n+BS2\t601\t608\t179.303\n+BS2\t608\t612\t153.689\n+BS2\t612\t615\t102.459\n+BS2\t615\t617\t51.2295\n+BS2\t617\t618\t25.6148\n+BS2\t618\t626\t0\n+BS2\t626\t638\t25.6148\n+BS2\t638\t650\t51.2295\n+BS2\t650\t652\t76.8443\n+BS2\t652\t663\t51.2295\n+BS2\t663\t677\t25.6148\n+BS2\t677\t746\t0\n+BS2\t746\t763\t25.6148\n+BS2\t763\t771\t51.2295\n+BS2\t771\t772\t179.303\n+BS2\t772\t788\t204.918\n+BS2\t788\t794\t179.303\n+BS2\t794\t795\t25.6148\n+BS2\t795\t796\t102.459\n+BS2\t796\t797\t128.074\n+BS2\t797\t818\t102.459\n+BS2\t818\t819\t76.8443\n+BS2\t819\t820\t25.6148\n+BS2\t820\t859\t0\n+BS2\t859\t862\t25.6148\n+BS2\t862\t871\t51.2295\n+BS2\t871\t884\t102.459\n+BS2\t884\t885\t76.8443\n+BS2\t885\t895\t51.2295\n+BS2\t895\t898\t0\n+BS2\t898\t899\t1050.2\n+BS2\t899\t901\t2228.48\n+BS2\t901\t902\t2305.33\n+BS2\t902\t921\t2330.94\n+BS2\t921\t922\t2305.33\n+BS2\t922\t923\t2151.64\n+BS2\t923'..b'169\t307.377\n+Gypsy2-LTR_DM\t169\t170\t256.148\n+Gypsy2-LTR_DM\t170\t172\t204.918\n+Gypsy2-LTR_DM\t172\t180\t179.303\n+Gypsy2-LTR_DM\t180\t182\t128.074\n+Gypsy2-LTR_DM\t182\t191\t25.6148\n+Gypsy2-LTR_DM\t191\t205\t0\n+Gypsy2-LTR_DM\t205\t206\t25.6148\n+Gypsy2-LTR_DM\t206\t207\t76.8443\n+Gypsy2-LTR_DM\t207\t222\t102.459\n+Gypsy2-LTR_DM\t222\t229\t128.074\n+Gypsy2-LTR_DM\t229\t230\t76.8443\n+Gypsy2-LTR_DM\t230\t231\t51.2295\n+Gypsy2-LTR_DM\t231\t248\t25.6148\n+Gypsy2-LTR_DM\t248\t258\t0\n+Gypsy2-LTR_DM\t258\t259\t51.2295\n+Gypsy2-LTR_DM\t259\t262\t76.8443\n+Gypsy2-LTR_DM\t262\t263\t102.459\n+Gypsy2-LTR_DM\t263\t265\t153.689\n+Gypsy2-LTR_DM\t265\t266\t281.762\n+Gypsy2-LTR_DM\t266\t283\t461.066\n+Gypsy2-LTR_DM\t283\t286\t384.221\n+Gypsy2-LTR_DM\t286\t288\t358.607\n+Gypsy2-LTR_DM\t288\t289\t307.377\n+Gypsy2-LTR_DM\t289\t290\t281.762\n+Gypsy2-LTR_DM\t290\t297\t51.2295\n+Gypsy2-LTR_DM\t297\t314\t76.8443\n+Gypsy2-LTR_DM\t314\t315\t51.2295\n+Gypsy2-LTR_DM\t315\t321\t25.6148\n+Gypsy2-LTR_DM\t321\t338\t0\n+I_DM\t0\t902\t0\n+I_DM\t902\t929\t25.6148\n+I_DM\t929\t1427\t0\n+I_DM\t1427\t1452\t25.6148\n+I_DM\t1452\t1720\t0\n+I_DM\t1720\t1743\t25.6148\n+I_DM\t1743\t3190\t0\n+I_DM\t3190\t3215\t76.8443\n+I_DM\t3215\t3235\t25.6148\n+I_DM\t3235\t3237\t51.2295\n+I_DM\t3237\t3239\t76.8443\n+I_DM\t3239\t3261\t51.2295\n+I_DM\t3261\t3262\t25.6148\n+I_DM\t3262\t4623\t0\n+I_DM\t4623\t4646\t25.6148\n+I_DM\t4646\t4825\t0\n+I_DM\t4825\t4849\t25.6148\n+I_DM\t4849\t4912\t0\n+I_DM\t4912\t4939\t25.6148\n+I_DM\t4939\t5104\t0\n+I_DM\t5104\t5128\t25.6148\n+I_DM\t5128\t5374\t0\n+MAX_I\t0\t53\t0\n+MAX_I\t53\t54\t25.6148\n+MAX_I\t54\t59\t51.2295\n+MAX_I\t59\t77\t102.459\n+MAX_I\t77\t78\t76.8443\n+MAX_I\t78\t80\t51.2295\n+MAX_I\t80\t84\t76.8443\n+MAX_I\t84\t87\t25.6148\n+MAX_I\t87\t92\t51.2295\n+MAX_I\t92\t104\t76.8443\n+MAX_I\t104\t105\t25.6148\n+MAX_I\t105\t108\t51.2295\n+MAX_I\t108\t111\t76.8443\n+MAX_I\t111\t118\t51.2295\n+MAX_I\t118\t119\t25.6148\n+MAX_I\t119\t120\t51.2295\n+MAX_I\t120\t127\t76.8443\n+MAX_I\t127\t131\t102.459\n+MAX_I\t131\t142\t76.8443\n+MAX_I\t142\t144\t51.2295\n+MAX_I\t144\t151\t25.6148\n+MAX_I\t151\t230\t0\n+MAX_I\t230\t238\t25.6148\n+MAX_I\t238\t254\t51.2295\n+MAX_I\t254\t263\t25.6148\n+MAX_I\t263\t316\t0\n+MAX_I\t316\t340\t102.459\n+MAX_I\t340\t342\t51.2295\n+MAX_I\t342\t7914\t0\n+MAX_LTR\t0\t12\t0\n+MAX_LTR\t12\t21\t25.6148\n+MAX_LTR\t21\t36\t76.8443\n+MAX_LTR\t36\t44\t51.2295\n+MAX_LTR\t44\t48\t0\n+MAX_LTR\t48\t52\t25.6148\n+MAX_LTR\t52\t72\t153.689\n+MAX_LTR\t72\t75\t128.074\n+MAX_LTR\t75\t76\t102.459\n+MAX_LTR\t76\t77\t76.8443\n+MAX_LTR\t77\t78\t25.6148\n+MAX_LTR\t78\t80\t0\n+MAX_LTR\t80\t88\t128.074\n+MAX_LTR\t88\t105\t153.689\n+MAX_LTR\t105\t113\t25.6148\n+MAX_LTR\t113\t134\t0\n+MAX_LTR\t134\t138\t51.2295\n+MAX_LTR\t138\t159\t204.918\n+MAX_LTR\t159\t161\t153.689\n+MAX_LTR\t161\t321\t0\n+PROTOP\t0\t14\t0\n+PROTOP\t14\t38\t25.6148\n+PROTOP\t38\t59\t0\n+PROTOP\t59\t64\t25.6148\n+PROTOP\t64\t83\t76.8443\n+PROTOP\t83\t88\t51.2295\n+PROTOP\t88\t103\t0\n+PROTOP\t103\t104\t76.8443\n+PROTOP\t104\t127\t102.459\n+PROTOP\t127\t129\t76.8443\n+PROTOP\t129\t160\t0\n+PROTOP\t160\t184\t25.6148\n+PROTOP\t184\t209\t0\n+PROTOP\t209\t224\t256.148\n+PROTOP\t224\t234\t281.762\n+PROTOP\t234\t235\t102.459\n+PROTOP\t235\t250\t25.6148\n+PROTOP\t250\t445\t0\n+PROTOP\t445\t449\t25.6148\n+PROTOP\t449\t468\t51.2295\n+PROTOP\t468\t472\t25.6148\n+PROTOP\t472\t2348\t0\n+PROTOP\t2348\t2399\t25.6148\n+PROTOP\t2399\t2442\t0\n+PROTOP\t2442\t2465\t25.6148\n+PROTOP\t2465\t2540\t0\n+PROTOP\t2540\t2565\t25.6148\n+PROTOP\t2565\t2615\t0\n+PROTOP\t2615\t2641\t51.2295\n+PROTOP\t2641\t2647\t0\n+PROTOP\t2647\t2648\t25.6148\n+PROTOP\t2648\t2653\t51.2295\n+PROTOP\t2653\t2672\t102.459\n+PROTOP\t2672\t2678\t51.2295\n+PROTOP\t2678\t2689\t0\n+PROTOP\t2689\t2690\t25.6148\n+PROTOP\t2690\t2696\t51.2295\n+PROTOP\t2696\t2714\t76.8443\n+PROTOP\t2714\t2715\t51.2295\n+PROTOP\t2715\t2719\t25.6148\n+PROTOP\t2719\t2742\t0\n+PROTOP\t2742\t2766\t179.303\n+PROTOP\t2766\t2767\t153.689\n+PROTOP\t2767\t2773\t0\n+PROTOP\t2773\t2785\t25.6148\n+PROTOP\t2785\t2786\t0\n+PROTOP\t2786\t2797\t25.6148\n+PROTOP\t2797\t3327\t0\n+PROTOP\t3327\t3350\t25.6148\n+PROTOP\t3350\t3397\t0\n+PROTOP\t3397\t3422\t25.6148\n+PROTOP\t3422\t3452\t0\n+PROTOP\t3452\t3478\t25.6148\n+PROTOP\t3478\t4135\t0\n+PROTOP\t4135\t4160\t76.8443\n+PROTOP\t4160\t4307\t0\n+PROTOP\t4307\t4308\t25.6148\n+PROTOP\t4308\t4333\t51.2295\n+PROTOP\t4333\t4360\t0\n+PROTOP\t4360\t4384\t25.6148\n+PROTOP\t4384\t4387\t0\n+PROTOP\t4387\t4388\t128.074\n+PROTOP\t4388\t4398\t153.689\n+PROTOP\t4398\t4412\t204.918\n+PROTOP\t4412\t4413\t76.8443\n+PROTOP\t4413\t4422\t51.2295\n+PROTOP\t4422\t4423\t25.6148\n+PROTOP\t4423\t4480\t0\n' |
| b |
| diff -r 9645d995fb3c -r 9185ca0a7b43 test-data/res_files/reads-sample-small.fastq/subgroups/piRNAs/piRNAs-TEs_reads_counts.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/res_files/reads-sample-small.fastq/subgroups/piRNAs/piRNAs-TEs_reads_counts.txt Wed Jan 16 08:18:13 2019 -0500 |
| b |
| @@ -0,0 +1,18 @@ +ID reads counts RPKM per million of piRNAs per million of miRNAs per million of bonafide reads sense reads counts reverse reads counts % of sense 1U % of sense 10A % of reverse 1U % of reverse 10A +BATUMI_I 262 842.78 11363.64 4158730.16 8581.72 139 123 95.6834532374101 44.6043165467626 37.3983739837398 21.1382113821138 +BATUMI_LTR 89 8381.30 3860.17 1412698.41 2915.17 3 86 100 0 2.32558139534884 39.5348837209302 +BS2 5896 31989.96 255725.19 93587301.59 193121.52 1224 4672 47.3856209150327 39.5424836601307 17.8724315068493 32.7696917808219 +COPIA_DM_I 0 0.00 0.00 0.00 0.00 0 0 0 0 0 0 +COPIA_DM_LTR 0 0.00 0.00 0.00 0.00 0 0 0 0 0 0 +DMCR1A 347 1988.44 15050.31 5507936.51 11365.87 81 266 49.3827160493827 58.0246913580247 21.4285714285714 34.5864661654135 +DMRT1B 291 1438.14 12621.44 4619047.62 9531.61 163 128 41.7177914110429 38.0368098159509 2.34375 13.28125 +FW 11088 60532.05 480916.03 176000000.00 363183.75 1669 9419 43.4991012582385 63.0317555422409 16.2437626074955 27.9329015819089 +G6_DM 1586 19894.71 68789.04 25174603.17 51948.90 340 1246 61.7647058823529 45.5882352941176 2.1669341894061 31.7014446227929 +Gypsy2-I_DM 0 0.00 0.00 0.00 0.00 0 0 0 0 0 0 +Gypsy2-LTR_DM 147 11140.14 6375.78 2333333.33 4814.94 59 88 62.7118644067797 38.9830508474576 11.3636363636364 17.0454545454545 +I_DM 33 157.29 1431.30 523809.52 1080.90 13 20 61.5384615384615 30.7692307692308 25 50 +MAX_I 87 281.59 3773.42 1380952.38 2849.66 17 70 82.3529411764706 0 65.7142857142857 20 +MAX_LTR 65 5186.79 2819.22 1031746.03 2129.05 23 42 26.0869565217391 39.1304347826087 0 47.6190476190476 +PROTOP 173 989.14 7503.47 2746031.75 5666.56 60 113 56.6666666666667 66.6666666666667 23.0088495575221 29.2035398230088 +ZAM_I 0 0.00 0.00 0.00 0.00 0 0 0 0 0 0 +ZAM_LTR 0 0.00 0.00 0.00 0.00 0 0 0 0 0 0 |
| b |
| diff -r 9645d995fb3c -r 9185ca0a7b43 test-data/res_files/reads-sample-small.fastq/subgroups/piRNAs/piRNAs-TEs_reads_counts_mismatches.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/res_files/reads-sample-small.fastq/subgroups/piRNAs/piRNAs-TEs_reads_counts_mismatches.txt Wed Jan 16 08:18:13 2019 -0500 |
| b |
| @@ -0,0 +1,18 @@ +ID reads counts RPKM per million of piRNAs per million of miRNAs per million of bonafide reads sense reads counts reverse reads counts % of sense 1U % of sense 10A % of reverse 1U % of reverse 10A +BATUMI_I 224 720.55 9715.48 3555555.56 7337.05 135 89 97.037037037037 45.1851851851852 38.2022471910112 23.5955056179775 +BATUMI_LTR 88 8287.13 3816.79 1396825.40 2882.41 2 86 100 0 2.32558139534884 39.5348837209302 +BS2 192 1041.74 8327.55 3047619.05 6288.90 48 144 68.75 29.1666666666667 8.33333333333333 40.2777777777778 +COPIA_DM_I 0 0.00 0.00 0.00 0.00 0 0 0 0 0 0 +COPIA_DM_LTR 0 0.00 0.00 0.00 0.00 0 0 0 0 0 0 +DMCR1A 65 372.47 2819.22 1031746.03 2129.05 6 59 100 50 25.4237288135593 28.8135593220339 +DMRT1B 159 785.79 6896.25 2523809.52 5207.99 111 48 50.4504504504504 50.4504504504504 6.25 25 +FW 69 376.69 2992.71 1095238.10 2260.07 24 45 70.8333333333333 83.3333333333333 11.1111111111111 37.7777777777778 +G6_DM 0 0.00 0.00 0.00 0.00 0 0 0 0 0 0 +Gypsy2-I_DM 0 0.00 0.00 0.00 0.00 0 0 0 0 0 0 +Gypsy2-LTR_DM 3 227.35 130.12 47619.05 98.26 0 3 0 0 0 0 +I_DM 25 119.16 1084.32 396825.40 818.87 8 17 62.5 25 17.6470588235294 58.8235294117647 +MAX_I 25 80.92 1084.32 396825.40 818.87 10 15 80 0 26.6666666666667 20 +MAX_LTR 24 1915.12 1040.94 380952.38 786.11 9 15 0 88.8888888888889 0 6.66666666666667 +PROTOP 108 617.50 4684.25 1714285.71 3537.50 44 64 70.4545454545455 59.0909090909091 25 20.3125 +ZAM_I 0 0.00 0.00 0.00 0.00 0 0 0 0 0 0 +ZAM_LTR 0 0.00 0.00 0.00 0.00 0 0 0 0 0 0 |
| b |
| diff -r 9645d995fb3c -r 9185ca0a7b43 test-data/res_files/reads-sample-small.fastq/subgroups/piRNAs/piRNAs-TEs_reads_counts_nomismatches.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/res_files/reads-sample-small.fastq/subgroups/piRNAs/piRNAs-TEs_reads_counts_nomismatches.txt Wed Jan 16 08:18:13 2019 -0500 |
| b |
| @@ -0,0 +1,18 @@ +ID reads counts RPKM per million of piRNAs per million of miRNAs per million of bonafide reads sense reads counts reverse reads counts % of sense 1U % of sense 10A % of reverse 1U % of reverse 10A +BATUMI_I 38 122.24 1648.16 603174.60 1244.68 4 34 50 25 35.2941176470588 14.7058823529412 +BATUMI_LTR 1 94.17 43.37 15873.02 32.75 1 0 100 0 0 0 +BS2 5704 30948.22 247397.64 90539682.54 186832.62 1176 4528 46.5136054421769 39.9659863945578 18.1757950530035 32.5309187279152 +COPIA_DM_I 0 0.00 0.00 0.00 0.00 0 0 0 0 0 0 +COPIA_DM_LTR 0 0.00 0.00 0.00 0.00 0 0 0 0 0 0 +DMCR1A 282 1615.96 12231.09 4476190.48 9236.82 75 207 45.3333333333333 58.6666666666667 20.2898550724638 36.231884057971 +DMRT1B 132 652.35 5725.19 2095238.10 4323.62 52 80 23.0769230769231 11.5384615384615 0 6.25 +FW 11019 60155.37 477923.32 174904761.90 360923.68 1645 9374 43.1003039513678 62.7355623100304 16.268401962876 27.8856411350544 +G6_DM 1586 19894.71 68789.04 25174603.17 51948.90 340 1246 61.7647058823529 45.5882352941176 2.1669341894061 31.7014446227929 +Gypsy2-I_DM 0 0.00 0.00 0.00 0.00 0 0 0 0 0 0 +Gypsy2-LTR_DM 144 10912.79 6245.66 2285714.29 4716.67 59 85 62.7118644067797 38.9830508474576 11.7647058823529 17.6470588235294 +I_DM 8 38.13 346.98 126984.13 262.04 5 3 60 40 66.6666666666667 0 +MAX_I 62 200.67 2689.10 984126.98 2030.79 7 55 85.7142857142857 0 76.3636363636364 20 +MAX_LTR 41 3271.67 1778.28 650793.65 1342.94 14 27 42.8571428571429 7.14285714285714 0 70.3703703703704 +PROTOP 65 371.64 2819.22 1031746.03 2129.05 16 49 18.75 87.5 20.4081632653061 40.8163265306122 +ZAM_I 0 0.00 0.00 0.00 0.00 0 0 0 0 0 0 +ZAM_LTR 0 0.00 0.00 0.00 0.00 0 0 0 0 0 0 |
| b |
| diff -r 9645d995fb3c -r 9185ca0a7b43 test-data/res_files/reads-sample-small.fastq/subgroups/piRNAs/piRNAs-TEs_sorted.bam |
| b |
| Binary file test-data/res_files/reads-sample-small.fastq/subgroups/piRNAs/piRNAs-TEs_sorted.bam has changed |
| b |
| diff -r 9645d995fb3c -r 9185ca0a7b43 test-data/res_files/reads-sample-small.fastq/subgroups/piRNAs/piRNAs-TEs_unique_sorted.bam |
| b |
| Binary file test-data/res_files/reads-sample-small.fastq/subgroups/piRNAs/piRNAs-TEs_unique_sorted.bam has changed |
| b |
| diff -r 9645d995fb3c -r 9185ca0a7b43 test-data/res_files/reads-sample-small.fastq/subgroups/piRNAs/piRNAs-genome_minus.bedgraph --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/res_files/reads-sample-small.fastq/subgroups/piRNAs/piRNAs-genome_minus.bedgraph Wed Jan 16 08:18:13 2019 -0500 |
| b |
| b'@@ -0,0 +1,3268 @@\n+chrom_1\t0\t3964\t0\n+chrom_1\t3964\t3988\t25.6148\n+chrom_1\t3988\t8675\t0\n+chrom_1\t8675\t8700\t25.6148\n+chrom_1\t8700\t9636\t0\n+chrom_1\t9636\t9661\t25.6148\n+chrom_1\t9661\t10201\t0\n+chrom_1\t10201\t10226\t25.6148\n+chrom_1\t10226\t11637\t0\n+chrom_1\t11637\t11661\t25.6148\n+chrom_1\t11661\t12187\t0\n+chrom_1\t12187\t12211\t25.6148\n+chrom_1\t12211\t12214\t0\n+chrom_1\t12214\t12215\t25.6148\n+chrom_1\t12215\t12238\t51.2295\n+chrom_1\t12238\t13134\t0\n+chrom_1\t13134\t13159\t25.6148\n+chrom_1\t13159\t13465\t0\n+chrom_1\t13465\t13470\t25.6148\n+chrom_1\t13470\t13491\t51.2295\n+chrom_1\t13491\t13493\t25.6148\n+chrom_1\t13493\t14233\t0\n+chrom_1\t14233\t14258\t25.6148\n+chrom_1\t14258\t14318\t0\n+chrom_1\t14318\t14321\t25.6148\n+chrom_1\t14321\t14344\t51.2295\n+chrom_1\t14344\t14438\t0\n+chrom_1\t14438\t14463\t25.6148\n+chrom_1\t14463\t14500\t0\n+chrom_1\t14500\t14523\t25.6148\n+chrom_1\t14523\t14778\t0\n+chrom_1\t14778\t14790\t51.2295\n+chrom_1\t14790\t14803\t76.8443\n+chrom_1\t14803\t14804\t51.2295\n+chrom_1\t14804\t14814\t25.6148\n+chrom_1\t14814\t14840\t0\n+chrom_1\t14840\t14865\t25.6148\n+chrom_1\t14865\t14968\t0\n+chrom_1\t14968\t14973\t25.6148\n+chrom_1\t14973\t14977\t51.2295\n+chrom_1\t14977\t14985\t76.8443\n+chrom_1\t14985\t14992\t128.074\n+chrom_1\t14992\t14999\t102.459\n+chrom_1\t14999\t15002\t76.8443\n+chrom_1\t15002\t15009\t51.2295\n+chrom_1\t15009\t15089\t0\n+chrom_1\t15089\t15114\t25.6148\n+chrom_1\t15114\t15130\t0\n+chrom_1\t15130\t15132\t51.2295\n+chrom_1\t15132\t15155\t102.459\n+chrom_1\t15155\t15157\t51.2295\n+chrom_1\t15157\t15160\t0\n+chrom_1\t15160\t15161\t51.2295\n+chrom_1\t15161\t15184\t102.459\n+chrom_1\t15184\t15185\t51.2295\n+chrom_1\t15185\t15201\t0\n+chrom_1\t15201\t15225\t25.6148\n+chrom_1\t15225\t15250\t0\n+chrom_1\t15250\t15251\t25.6148\n+chrom_1\t15251\t15274\t76.8443\n+chrom_1\t15274\t15281\t0\n+chrom_1\t15281\t15287\t25.6148\n+chrom_1\t15287\t15288\t51.2295\n+chrom_1\t15288\t15289\t76.8443\n+chrom_1\t15289\t15290\t204.918\n+chrom_1\t15290\t15306\t281.762\n+chrom_1\t15306\t15313\t256.148\n+chrom_1\t15313\t15315\t128.074\n+chrom_1\t15315\t15348\t0\n+chrom_1\t15348\t15366\t25.6148\n+chrom_1\t15366\t15372\t51.2295\n+chrom_1\t15372\t15390\t25.6148\n+chrom_1\t15390\t15444\t0\n+chrom_1\t15444\t15445\t51.2295\n+chrom_1\t15445\t15446\t76.8443\n+chrom_1\t15446\t15469\t128.074\n+chrom_1\t15469\t15470\t51.2295\n+chrom_1\t15470\t15471\t25.6148\n+chrom_1\t15471\t15476\t0\n+chrom_1\t15476\t15477\t25.6148\n+chrom_1\t15477\t15478\t51.2295\n+chrom_1\t15478\t15499\t102.459\n+chrom_1\t15499\t15500\t128.074\n+chrom_1\t15500\t15504\t102.459\n+chrom_1\t15504\t15506\t51.2295\n+chrom_1\t15506\t15523\t25.6148\n+chrom_1\t15523\t15534\t0\n+chrom_1\t15534\t15535\t51.2295\n+chrom_1\t15535\t15536\t76.8443\n+chrom_1\t15536\t15558\t102.459\n+chrom_1\t15558\t15559\t51.2295\n+chrom_1\t15559\t15560\t102.459\n+chrom_1\t15560\t15584\t51.2295\n+chrom_1\t15584\t15586\t25.6148\n+chrom_1\t15586\t15594\t281.762\n+chrom_1\t15594\t15598\t332.992\n+chrom_1\t15598\t15609\t435.451\n+chrom_1\t15609\t15620\t153.689\n+chrom_1\t15620\t15622\t102.459\n+chrom_1\t15622\t15623\t25.6148\n+chrom_1\t15623\t15688\t0\n+chrom_1\t15688\t15700\t25.6148\n+chrom_1\t15700\t15714\t76.8443\n+chrom_1\t15714\t15722\t51.2295\n+chrom_1\t15722\t15726\t76.8443\n+chrom_1\t15726\t15727\t51.2295\n+chrom_1\t15727\t15730\t102.459\n+chrom_1\t15730\t15745\t153.689\n+chrom_1\t15745\t15750\t128.074\n+chrom_1\t15750\t15752\t76.8443\n+chrom_1\t15752\t15754\t51.2295\n+chrom_1\t15754\t15791\t0\n+chrom_1\t15791\t15793\t51.2295\n+chrom_1\t15793\t15794\t76.8443\n+chrom_1\t15794\t15796\t153.689\n+chrom_1\t15796\t15805\t179.303\n+chrom_1\t15805\t15815\t230.533\n+chrom_1\t15815\t15816\t179.303\n+chrom_1\t15816\t15817\t153.689\n+chrom_1\t15817\t15819\t76.8443\n+chrom_1\t15819\t15828\t51.2295\n+chrom_1\t15828\t15925\t0\n+chrom_1\t15925\t15926\t128.074\n+chrom_1\t15926\t15942\t153.689\n+chrom_1\t15942\t15950\t179.303\n+chrom_1\t15950\t15963\t25.6148\n+chrom_1\t15963\t15965\t102.459\n+chrom_1\t15965\t15979\t256.148\n+chrom_1\t15979\t15989\t281.762\n+chrom_1\t15989\t15990\t230.533\n+chrom_1\t15990\t15991\t461.066\n+chrom_1\t15991\t16003\t486.68\n+chrom_1\t16003\t16014\t461.066\n+chrom_1\t16014\t16059\t0\n+chrom_1\t16059\t16086\t25.6148\n+chrom_1\t16086\t16122\t0\n+chrom_1\t16122\t16124\t25.6148\n+chrom_1\t16124\t16125\t51.2295\n+chrom_1\t16125\t16126\t102.459\n+chrom_1\t16126\t16139\t179.303\n+chrom_1\t16139\t16142\t204.918\n+chrom_1\t16142\t16149\t230.533\n+chrom_1\t16149\t16151\t179.303\n+chrom_1\t16151\t16152\t51.2295\n+chrom_'..b'38963\t38964\t76.8443\n+chrom_1\t38964\t38965\t102.459\n+chrom_1\t38965\t38970\t179.303\n+chrom_1\t38970\t38971\t230.533\n+chrom_1\t38971\t38972\t256.148\n+chrom_1\t38972\t38973\t486.68\n+chrom_1\t38973\t38974\t512.295\n+chrom_1\t38974\t38982\t537.91\n+chrom_1\t38982\t38984\t512.295\n+chrom_1\t38984\t38987\t486.68\n+chrom_1\t38987\t38988\t461.066\n+chrom_1\t38988\t38990\t384.221\n+chrom_1\t38990\t38995\t358.607\n+chrom_1\t38995\t38996\t332.992\n+chrom_1\t38996\t38997\t102.459\n+chrom_1\t38997\t39001\t0\n+chrom_1\t39001\t39024\t25.6148\n+chrom_1\t39024\t39034\t0\n+chrom_1\t39034\t39035\t25.6148\n+chrom_1\t39035\t39036\t51.2295\n+chrom_1\t39036\t39037\t76.8443\n+chrom_1\t39037\t39038\t256.148\n+chrom_1\t39038\t39058\t358.607\n+chrom_1\t39058\t39061\t332.992\n+chrom_1\t39061\t39062\t281.762\n+chrom_1\t39062\t39063\t25.6148\n+chrom_1\t39063\t39069\t0\n+chrom_1\t39069\t39074\t25.6148\n+chrom_1\t39074\t39076\t51.2295\n+chrom_1\t39076\t39094\t76.8443\n+chrom_1\t39094\t39099\t51.2295\n+chrom_1\t39099\t39102\t25.6148\n+chrom_1\t39102\t39125\t0\n+chrom_1\t39125\t39140\t25.6148\n+chrom_1\t39140\t39150\t51.2295\n+chrom_1\t39150\t39153\t25.6148\n+chrom_1\t39153\t39164\t153.689\n+chrom_1\t39164\t39178\t128.074\n+chrom_1\t39178\t39179\t102.459\n+chrom_1\t39179\t39216\t0\n+chrom_1\t39216\t39218\t25.6148\n+chrom_1\t39218\t39224\t51.2295\n+chrom_1\t39224\t39226\t76.8443\n+chrom_1\t39226\t39233\t102.459\n+chrom_1\t39233\t39241\t128.074\n+chrom_1\t39241\t39242\t102.459\n+chrom_1\t39242\t39243\t76.8443\n+chrom_1\t39243\t39247\t102.459\n+chrom_1\t39247\t39252\t76.8443\n+chrom_1\t39252\t39253\t1946.72\n+chrom_1\t39253\t39254\t1997.95\n+chrom_1\t39254\t39259\t2023.57\n+chrom_1\t39259\t39267\t1997.95\n+chrom_1\t39267\t39277\t1972.34\n+chrom_1\t39277\t39278\t25.6148\n+chrom_1\t39278\t40964\t0\n+chrom_1\t40964\t40987\t25.6148\n+chrom_1\t40987\t42081\t0\n+chrom_1\t42081\t42106\t25.6148\n+chrom_1\t42106\t43035\t0\n+chrom_1\t43035\t43060\t25.6148\n+chrom_1\t43060\t43642\t0\n+chrom_1\t43642\t43666\t25.6148\n+chrom_1\t43666\t43938\t0\n+chrom_1\t43938\t43963\t25.6148\n+chrom_1\t43963\t45231\t0\n+chrom_1\t45231\t45256\t25.6148\n+chrom_1\t45256\t45966\t0\n+chrom_1\t45966\t45990\t25.6148\n+chrom_1\t45990\t47678\t0\n+chrom_1\t47678\t47701\t25.6148\n+chrom_1\t47701\t51206\t0\n+chrom_1\t51206\t51231\t25.6148\n+chrom_1\t51231\t51463\t0\n+chrom_1\t51463\t51486\t25.6148\n+chrom_1\t51486\t51577\t0\n+chrom_1\t51577\t51602\t25.6148\n+chrom_1\t51602\t52380\t0\n+chrom_1\t52380\t52405\t25.6148\n+chrom_1\t52405\t52942\t0\n+chrom_1\t52942\t52967\t51.2295\n+chrom_1\t52967\t54412\t0\n+chrom_1\t54412\t54440\t25.6148\n+chrom_1\t54440\t55754\t0\n+chrom_1\t55754\t55779\t25.6148\n+chrom_1\t55779\t55828\t0\n+chrom_1\t55828\t55852\t25.6148\n+chrom_1\t55852\t58435\t0\n+chrom_1\t58435\t58460\t25.6148\n+chrom_1\t58460\t59554\t0\n+chrom_1\t59554\t59579\t25.6148\n+chrom_1\t59579\t61962\t0\n+chrom_1\t61962\t61987\t25.6148\n+chrom_1\t61987\t62088\t0\n+chrom_1\t62088\t62113\t25.6148\n+chrom_1\t62113\t62288\t0\n+chrom_1\t62288\t62312\t25.6148\n+chrom_1\t62312\t64308\t0\n+chrom_1\t64308\t64333\t25.6148\n+chrom_1\t64333\t65694\t0\n+chrom_1\t65694\t65718\t25.6148\n+chrom_1\t65718\t65974\t0\n+chrom_1\t65974\t65983\t25.6148\n+chrom_1\t65983\t65999\t51.2295\n+chrom_1\t65999\t66008\t25.6148\n+chrom_1\t66008\t67277\t0\n+chrom_1\t67277\t67300\t25.6148\n+chrom_1\t67300\t72363\t0\n+chrom_1\t72363\t72387\t25.6148\n+chrom_1\t72387\t74181\t0\n+chrom_1\t74181\t74205\t25.6148\n+chrom_1\t74205\t76156\t0\n+chrom_1\t76156\t76181\t25.6148\n+chrom_1\t76181\t80904\t0\n+chrom_1\t80904\t80923\t25.6148\n+chrom_1\t80923\t80929\t51.2295\n+chrom_1\t80929\t80949\t25.6148\n+chrom_1\t80949\t80959\t0\n+chrom_1\t80959\t80982\t25.6148\n+chrom_1\t80982\t81627\t0\n+chrom_1\t81627\t81650\t25.6148\n+chrom_1\t81650\t82123\t0\n+chrom_1\t82123\t82146\t25.6148\n+chrom_1\t82146\t82455\t0\n+chrom_1\t82455\t82480\t25.6148\n+chrom_1\t82480\t83396\t0\n+chrom_1\t83396\t83422\t25.6148\n+chrom_1\t83422\t83426\t0\n+chrom_1\t83426\t83450\t51.2295\n+chrom_1\t83450\t83868\t0\n+chrom_1\t83868\t83891\t25.6148\n+chrom_1\t83891\t83991\t0\n+chrom_1\t83991\t84014\t25.6148\n+chrom_1\t84014\t85181\t0\n+chrom_1\t85181\t85205\t25.6148\n+chrom_1\t85205\t85366\t0\n+chrom_1\t85366\t85390\t25.6148\n+chrom_1\t85390\t85759\t0\n+chrom_1\t85759\t85783\t25.6148\n+chrom_1\t85783\t86632\t0\n+chrom_1\t86632\t86658\t25.6148\n+chrom_1\t86658\t86941\t0\n+chrom_1\t86941\t86967\t25.6148\n+chrom_1\t86967\t87853\t0\n+chrom_1\t87853\t87878\t25.6148\n+chrom_1\t87878\t89999\t0\n+chrom_2\t0\t32272\t0\n+chrom_2\t32272\t32296\t25.6148\n+chrom_2\t32296\t49999\t0\n' |
| b |
| diff -r 9645d995fb3c -r 9185ca0a7b43 test-data/res_files/reads-sample-small.fastq/subgroups/piRNAs/piRNAs-genome_plus.bedgraph --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/res_files/reads-sample-small.fastq/subgroups/piRNAs/piRNAs-genome_plus.bedgraph Wed Jan 16 08:18:13 2019 -0500 |
| b |
| b'@@ -0,0 +1,4415 @@\n+chrom_1\t0\t1967\t0\n+chrom_1\t1967\t1991\t25.6148\n+chrom_1\t1991\t3456\t0\n+chrom_1\t3456\t3481\t25.6148\n+chrom_1\t3481\t7648\t0\n+chrom_1\t7648\t7671\t25.6148\n+chrom_1\t7671\t7953\t0\n+chrom_1\t7953\t7978\t25.6148\n+chrom_1\t7978\t8721\t0\n+chrom_1\t8721\t8742\t25.6148\n+chrom_1\t8742\t8747\t51.2295\n+chrom_1\t8747\t8758\t25.6148\n+chrom_1\t8758\t8767\t51.2295\n+chrom_1\t8767\t8783\t25.6148\n+chrom_1\t8783\t9642\t0\n+chrom_1\t9642\t9668\t25.6148\n+chrom_1\t9668\t14236\t0\n+chrom_1\t14236\t14261\t25.6148\n+chrom_1\t14261\t14309\t0\n+chrom_1\t14309\t14336\t25.6148\n+chrom_1\t14336\t14439\t0\n+chrom_1\t14439\t14463\t25.6148\n+chrom_1\t14463\t14551\t0\n+chrom_1\t14551\t14552\t25.6148\n+chrom_1\t14552\t14554\t76.8443\n+chrom_1\t14554\t14578\t179.303\n+chrom_1\t14578\t14580\t25.6148\n+chrom_1\t14580\t14592\t0\n+chrom_1\t14592\t14616\t25.6148\n+chrom_1\t14616\t14979\t0\n+chrom_1\t14979\t15004\t25.6148\n+chrom_1\t15004\t15062\t0\n+chrom_1\t15062\t15087\t25.6148\n+chrom_1\t15087\t15089\t0\n+chrom_1\t15089\t15092\t25.6148\n+chrom_1\t15092\t15115\t128.074\n+chrom_1\t15115\t15117\t102.459\n+chrom_1\t15117\t15139\t0\n+chrom_1\t15139\t15164\t25.6148\n+chrom_1\t15164\t15258\t0\n+chrom_1\t15258\t15260\t25.6148\n+chrom_1\t15260\t15264\t76.8443\n+chrom_1\t15264\t15269\t102.459\n+chrom_1\t15269\t15283\t128.074\n+chrom_1\t15283\t15284\t102.459\n+chrom_1\t15284\t15290\t51.2295\n+chrom_1\t15290\t15293\t25.6148\n+chrom_1\t15293\t15395\t0\n+chrom_1\t15395\t15399\t25.6148\n+chrom_1\t15399\t15400\t76.8443\n+chrom_1\t15400\t15407\t102.459\n+chrom_1\t15407\t15420\t128.074\n+chrom_1\t15420\t15423\t102.459\n+chrom_1\t15423\t15424\t51.2295\n+chrom_1\t15424\t15433\t25.6148\n+chrom_1\t15433\t15460\t0\n+chrom_1\t15460\t15484\t25.6148\n+chrom_1\t15484\t15529\t0\n+chrom_1\t15529\t15545\t25.6148\n+chrom_1\t15545\t15546\t51.2295\n+chrom_1\t15546\t15555\t409.836\n+chrom_1\t15555\t15569\t384.221\n+chrom_1\t15569\t15570\t204.918\n+chrom_1\t15570\t15572\t25.6148\n+chrom_1\t15572\t15716\t0\n+chrom_1\t15716\t15739\t25.6148\n+chrom_1\t15739\t15801\t0\n+chrom_1\t15801\t15824\t25.6148\n+chrom_1\t15824\t15970\t0\n+chrom_1\t15970\t15993\t76.8443\n+chrom_1\t15993\t16004\t0\n+chrom_1\t16004\t16027\t76.8443\n+chrom_1\t16027\t16028\t25.6148\n+chrom_1\t16028\t16232\t0\n+chrom_1\t16232\t16237\t25.6148\n+chrom_1\t16237\t16239\t51.2295\n+chrom_1\t16239\t16256\t102.459\n+chrom_1\t16256\t16262\t76.8443\n+chrom_1\t16262\t16336\t0\n+chrom_1\t16336\t16338\t256.148\n+chrom_1\t16338\t16339\t281.762\n+chrom_1\t16339\t16342\t307.377\n+chrom_1\t16342\t16359\t332.992\n+chrom_1\t16359\t16360\t128.074\n+chrom_1\t16360\t16363\t76.8443\n+chrom_1\t16363\t16364\t51.2295\n+chrom_1\t16364\t16365\t25.6148\n+chrom_1\t16365\t16496\t0\n+chrom_1\t16496\t16521\t25.6148\n+chrom_1\t16521\t16619\t0\n+chrom_1\t16619\t16628\t25.6148\n+chrom_1\t16628\t16630\t76.8443\n+chrom_1\t16630\t16643\t256.148\n+chrom_1\t16643\t16653\t230.533\n+chrom_1\t16653\t16654\t153.689\n+chrom_1\t16654\t16655\t76.8443\n+chrom_1\t16655\t16656\t25.6148\n+chrom_1\t16656\t16661\t0\n+chrom_1\t16661\t16685\t25.6148\n+chrom_1\t16685\t16772\t0\n+chrom_1\t16772\t16798\t25.6148\n+chrom_1\t16798\t16800\t51.2295\n+chrom_1\t16800\t16801\t179.303\n+chrom_1\t16801\t16810\t461.066\n+chrom_1\t16810\t16811\t486.68\n+chrom_1\t16811\t16819\t512.295\n+chrom_1\t16819\t16823\t486.68\n+chrom_1\t16823\t16825\t435.451\n+chrom_1\t16825\t16835\t102.459\n+chrom_1\t16835\t16849\t51.2295\n+chrom_1\t16849\t16850\t25.6148\n+chrom_1\t16850\t16864\t0\n+chrom_1\t16864\t16866\t25.6148\n+chrom_1\t16866\t16867\t76.8443\n+chrom_1\t16867\t16868\t179.303\n+chrom_1\t16868\t16869\t307.377\n+chrom_1\t16869\t16870\t332.992\n+chrom_1\t16870\t16881\t358.607\n+chrom_1\t16881\t16883\t409.836\n+chrom_1\t16883\t16884\t435.451\n+chrom_1\t16884\t16887\t461.066\n+chrom_1\t16887\t16892\t435.451\n+chrom_1\t16892\t16893\t256.148\n+chrom_1\t16893\t16894\t153.689\n+chrom_1\t16894\t16906\t102.459\n+chrom_1\t16906\t16907\t76.8443\n+chrom_1\t16907\t16943\t0\n+chrom_1\t16943\t16962\t25.6148\n+chrom_1\t16962\t16967\t51.2295\n+chrom_1\t16967\t16988\t25.6148\n+chrom_1\t16988\t16999\t0\n+chrom_1\t16999\t17023\t25.6148\n+chrom_1\t17023\t17024\t0\n+chrom_1\t17024\t17044\t25.6148\n+chrom_1\t17044\t17047\t51.2295\n+chrom_1\t17047\t17049\t25.6148\n+chrom_1\t17049\t17050\t76.8443\n+chrom_1\t17050\t17053\t128.074\n+chrom_1\t17053\t17054\t153.689\n+chrom_1\t17054\t17068\t409.836\n+chrom_1\t17068\t17073\t384.221\n+chrom_1\t17073\t17076\t281.762\n+chrom_1\t17076\t17077\t256.148\n+chrom_1\t17077\t17078\t25.6148\n+chrom_1\t17078\t17081\t0\n+chrom_1\t17081\t17'..b'1\t40966\t40976\t25.6148\n+chrom_1\t40976\t40977\t51.2295\n+chrom_1\t40977\t40992\t76.8443\n+chrom_1\t40992\t41001\t51.2295\n+chrom_1\t41001\t41285\t0\n+chrom_1\t41285\t41309\t51.2295\n+chrom_1\t41309\t41449\t0\n+chrom_1\t41449\t41451\t25.6148\n+chrom_1\t41451\t41474\t51.2295\n+chrom_1\t41474\t41476\t25.6148\n+chrom_1\t41476\t41788\t0\n+chrom_1\t41788\t41811\t25.6148\n+chrom_1\t41811\t42508\t0\n+chrom_1\t42508\t42533\t25.6148\n+chrom_1\t42533\t42909\t0\n+chrom_1\t42909\t42934\t25.6148\n+chrom_1\t42934\t43034\t0\n+chrom_1\t43034\t43059\t25.6148\n+chrom_1\t43059\t43075\t0\n+chrom_1\t43075\t43100\t25.6148\n+chrom_1\t43100\t44091\t0\n+chrom_1\t44091\t44116\t25.6148\n+chrom_1\t44116\t44344\t0\n+chrom_1\t44344\t44371\t25.6148\n+chrom_1\t44371\t44956\t0\n+chrom_1\t44956\t44980\t25.6148\n+chrom_1\t44980\t47326\t0\n+chrom_1\t47326\t47349\t25.6148\n+chrom_1\t47349\t47451\t0\n+chrom_1\t47451\t47475\t25.6148\n+chrom_1\t47475\t48345\t0\n+chrom_1\t48345\t48369\t25.6148\n+chrom_1\t48369\t51118\t0\n+chrom_1\t51118\t51143\t25.6148\n+chrom_1\t51143\t51577\t0\n+chrom_1\t51577\t51578\t25.6148\n+chrom_1\t51578\t51602\t51.2295\n+chrom_1\t51602\t51976\t0\n+chrom_1\t51976\t52001\t25.6148\n+chrom_1\t52001\t52284\t0\n+chrom_1\t52284\t52288\t25.6148\n+chrom_1\t52288\t52309\t51.2295\n+chrom_1\t52309\t52313\t25.6148\n+chrom_1\t52313\t54564\t0\n+chrom_1\t54564\t54573\t25.6148\n+chrom_1\t54573\t54588\t51.2295\n+chrom_1\t54588\t54599\t25.6148\n+chrom_1\t54599\t55385\t0\n+chrom_1\t55385\t55433\t25.6148\n+chrom_1\t55433\t55528\t0\n+chrom_1\t55528\t55552\t25.6148\n+chrom_1\t55552\t57239\t0\n+chrom_1\t57239\t57264\t25.6148\n+chrom_1\t57264\t59083\t0\n+chrom_1\t59083\t59107\t25.6148\n+chrom_1\t59107\t61842\t0\n+chrom_1\t61842\t61865\t25.6148\n+chrom_1\t61865\t63378\t0\n+chrom_1\t63378\t63401\t25.6148\n+chrom_1\t63401\t63530\t0\n+chrom_1\t63530\t63555\t25.6148\n+chrom_1\t63555\t65375\t0\n+chrom_1\t65375\t65400\t25.6148\n+chrom_1\t65400\t65546\t0\n+chrom_1\t65546\t65571\t25.6148\n+chrom_1\t65571\t65986\t0\n+chrom_1\t65986\t66009\t25.6148\n+chrom_1\t66009\t66305\t0\n+chrom_1\t66305\t66330\t25.6148\n+chrom_1\t66330\t66468\t0\n+chrom_1\t66468\t66494\t25.6148\n+chrom_1\t66494\t66717\t0\n+chrom_1\t66717\t66742\t25.6148\n+chrom_1\t66742\t67040\t0\n+chrom_1\t67040\t67065\t25.6148\n+chrom_1\t67065\t67545\t0\n+chrom_1\t67545\t67569\t25.6148\n+chrom_1\t67569\t67964\t0\n+chrom_1\t67964\t67989\t25.6148\n+chrom_1\t67989\t68011\t0\n+chrom_1\t68011\t68036\t25.6148\n+chrom_1\t68036\t68067\t0\n+chrom_1\t68067\t68093\t25.6148\n+chrom_1\t68093\t68111\t0\n+chrom_1\t68111\t68136\t25.6148\n+chrom_1\t68136\t68181\t0\n+chrom_1\t68181\t68205\t25.6148\n+chrom_1\t68205\t68206\t0\n+chrom_1\t68206\t68218\t25.6148\n+chrom_1\t68218\t68230\t51.2295\n+chrom_1\t68230\t68243\t25.6148\n+chrom_1\t68243\t68269\t0\n+chrom_1\t68269\t68317\t25.6148\n+chrom_1\t68317\t68544\t0\n+chrom_1\t68544\t68569\t25.6148\n+chrom_1\t68569\t69749\t0\n+chrom_1\t69749\t69774\t25.6148\n+chrom_1\t69774\t70096\t0\n+chrom_1\t70096\t70122\t25.6148\n+chrom_1\t70122\t71037\t0\n+chrom_1\t71037\t71062\t25.6148\n+chrom_1\t71062\t72078\t0\n+chrom_1\t72078\t72102\t25.6148\n+chrom_1\t72102\t72167\t0\n+chrom_1\t72167\t72192\t25.6148\n+chrom_1\t72192\t72356\t0\n+chrom_1\t72356\t72360\t25.6148\n+chrom_1\t72360\t72382\t51.2295\n+chrom_1\t72382\t72385\t25.6148\n+chrom_1\t72385\t72713\t0\n+chrom_1\t72713\t72737\t25.6148\n+chrom_1\t72737\t73860\t0\n+chrom_1\t73860\t73885\t25.6148\n+chrom_1\t73885\t74376\t0\n+chrom_1\t74376\t74400\t25.6148\n+chrom_1\t74400\t79422\t0\n+chrom_1\t79422\t79447\t25.6148\n+chrom_1\t79447\t80862\t0\n+chrom_1\t80862\t80887\t25.6148\n+chrom_1\t80887\t81326\t0\n+chrom_1\t81326\t81351\t25.6148\n+chrom_1\t81351\t81505\t0\n+chrom_1\t81505\t81528\t25.6148\n+chrom_1\t81528\t82213\t0\n+chrom_1\t82213\t82237\t25.6148\n+chrom_1\t82237\t83567\t0\n+chrom_1\t83567\t83592\t25.6148\n+chrom_1\t83592\t84065\t0\n+chrom_1\t84065\t84089\t25.6148\n+chrom_1\t84089\t85397\t0\n+chrom_1\t85397\t85422\t25.6148\n+chrom_1\t85422\t85980\t0\n+chrom_1\t85980\t86005\t25.6148\n+chrom_1\t86005\t87255\t0\n+chrom_1\t87255\t87278\t25.6148\n+chrom_1\t87278\t88301\t0\n+chrom_1\t88301\t88325\t25.6148\n+chrom_1\t88325\t88989\t0\n+chrom_1\t88989\t89015\t25.6148\n+chrom_1\t89015\t89111\t0\n+chrom_1\t89111\t89137\t25.6148\n+chrom_1\t89137\t89999\t0\n+chrom_4\t0\t1047\t0\n+chrom_4\t1047\t1071\t25.6148\n+chrom_4\t1071\t1543\t0\n+chrom_4\t1543\t1566\t25.6148\n+chrom_4\t1566\t2000\t0\n+chrom_6\t0\t440\t0\n+chrom_6\t440\t464\t25.6148\n+chrom_6\t464\t1117\t0\n+chrom_6\t1117\t1142\t25.6148\n+chrom_6\t1142\t3002\t0\n+chrom_6\t3002\t3027\t25.6148\n+chrom_6\t3027\t3999\t0\n' |
| b |
| diff -r 9645d995fb3c -r 9185ca0a7b43 test-data/res_files/reads-sample-small.fastq/subgroups/piRNAs/piRNAs-genome_sorted.bam |
| b |
| Binary file test-data/res_files/reads-sample-small.fastq/subgroups/piRNAs/piRNAs-genome_sorted.bam has changed |
| b |
| diff -r 9645d995fb3c -r 9185ca0a7b43 test-data/res_files/reads-sample-small.fastq/subgroups/piRNAs/piRNAs-genome_unique_minus.bedgraph --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/res_files/reads-sample-small.fastq/subgroups/piRNAs/piRNAs-genome_unique_minus.bedgraph Wed Jan 16 08:18:13 2019 -0500 |
| b |
| b'@@ -0,0 +1,3267 @@\n+chrom_1\t0\t3964\t0\n+chrom_1\t3964\t3988\t25.6148\n+chrom_1\t3988\t8675\t0\n+chrom_1\t8675\t8700\t25.6148\n+chrom_1\t8700\t9636\t0\n+chrom_1\t9636\t9661\t25.6148\n+chrom_1\t9661\t10201\t0\n+chrom_1\t10201\t10226\t25.6148\n+chrom_1\t10226\t11637\t0\n+chrom_1\t11637\t11661\t25.6148\n+chrom_1\t11661\t12187\t0\n+chrom_1\t12187\t12211\t25.6148\n+chrom_1\t12211\t12214\t0\n+chrom_1\t12214\t12215\t25.6148\n+chrom_1\t12215\t12238\t51.2295\n+chrom_1\t12238\t13134\t0\n+chrom_1\t13134\t13159\t25.6148\n+chrom_1\t13159\t13465\t0\n+chrom_1\t13465\t13470\t25.6148\n+chrom_1\t13470\t13491\t51.2295\n+chrom_1\t13491\t13493\t25.6148\n+chrom_1\t13493\t14233\t0\n+chrom_1\t14233\t14258\t25.6148\n+chrom_1\t14258\t14318\t0\n+chrom_1\t14318\t14321\t25.6148\n+chrom_1\t14321\t14344\t51.2295\n+chrom_1\t14344\t14438\t0\n+chrom_1\t14438\t14463\t25.6148\n+chrom_1\t14463\t14500\t0\n+chrom_1\t14500\t14523\t25.6148\n+chrom_1\t14523\t14778\t0\n+chrom_1\t14778\t14790\t51.2295\n+chrom_1\t14790\t14803\t76.8443\n+chrom_1\t14803\t14804\t51.2295\n+chrom_1\t14804\t14814\t25.6148\n+chrom_1\t14814\t14840\t0\n+chrom_1\t14840\t14865\t25.6148\n+chrom_1\t14865\t14968\t0\n+chrom_1\t14968\t14973\t25.6148\n+chrom_1\t14973\t14977\t51.2295\n+chrom_1\t14977\t14985\t76.8443\n+chrom_1\t14985\t14992\t128.074\n+chrom_1\t14992\t14999\t102.459\n+chrom_1\t14999\t15002\t76.8443\n+chrom_1\t15002\t15009\t51.2295\n+chrom_1\t15009\t15089\t0\n+chrom_1\t15089\t15114\t25.6148\n+chrom_1\t15114\t15130\t0\n+chrom_1\t15130\t15132\t51.2295\n+chrom_1\t15132\t15155\t102.459\n+chrom_1\t15155\t15157\t51.2295\n+chrom_1\t15157\t15160\t0\n+chrom_1\t15160\t15161\t51.2295\n+chrom_1\t15161\t15184\t102.459\n+chrom_1\t15184\t15185\t51.2295\n+chrom_1\t15185\t15201\t0\n+chrom_1\t15201\t15225\t25.6148\n+chrom_1\t15225\t15250\t0\n+chrom_1\t15250\t15251\t25.6148\n+chrom_1\t15251\t15274\t76.8443\n+chrom_1\t15274\t15281\t0\n+chrom_1\t15281\t15287\t25.6148\n+chrom_1\t15287\t15288\t51.2295\n+chrom_1\t15288\t15289\t76.8443\n+chrom_1\t15289\t15290\t204.918\n+chrom_1\t15290\t15306\t281.762\n+chrom_1\t15306\t15313\t256.148\n+chrom_1\t15313\t15315\t128.074\n+chrom_1\t15315\t15348\t0\n+chrom_1\t15348\t15366\t25.6148\n+chrom_1\t15366\t15372\t51.2295\n+chrom_1\t15372\t15390\t25.6148\n+chrom_1\t15390\t15444\t0\n+chrom_1\t15444\t15445\t51.2295\n+chrom_1\t15445\t15446\t76.8443\n+chrom_1\t15446\t15469\t128.074\n+chrom_1\t15469\t15470\t51.2295\n+chrom_1\t15470\t15471\t25.6148\n+chrom_1\t15471\t15476\t0\n+chrom_1\t15476\t15477\t25.6148\n+chrom_1\t15477\t15478\t51.2295\n+chrom_1\t15478\t15499\t102.459\n+chrom_1\t15499\t15500\t128.074\n+chrom_1\t15500\t15504\t102.459\n+chrom_1\t15504\t15506\t51.2295\n+chrom_1\t15506\t15523\t25.6148\n+chrom_1\t15523\t15534\t0\n+chrom_1\t15534\t15535\t51.2295\n+chrom_1\t15535\t15536\t76.8443\n+chrom_1\t15536\t15558\t102.459\n+chrom_1\t15558\t15559\t51.2295\n+chrom_1\t15559\t15560\t102.459\n+chrom_1\t15560\t15584\t51.2295\n+chrom_1\t15584\t15586\t25.6148\n+chrom_1\t15586\t15594\t281.762\n+chrom_1\t15594\t15598\t332.992\n+chrom_1\t15598\t15609\t435.451\n+chrom_1\t15609\t15620\t153.689\n+chrom_1\t15620\t15622\t102.459\n+chrom_1\t15622\t15623\t25.6148\n+chrom_1\t15623\t15688\t0\n+chrom_1\t15688\t15700\t25.6148\n+chrom_1\t15700\t15714\t76.8443\n+chrom_1\t15714\t15722\t51.2295\n+chrom_1\t15722\t15726\t76.8443\n+chrom_1\t15726\t15727\t51.2295\n+chrom_1\t15727\t15730\t102.459\n+chrom_1\t15730\t15745\t153.689\n+chrom_1\t15745\t15750\t128.074\n+chrom_1\t15750\t15752\t76.8443\n+chrom_1\t15752\t15754\t51.2295\n+chrom_1\t15754\t15791\t0\n+chrom_1\t15791\t15793\t51.2295\n+chrom_1\t15793\t15794\t76.8443\n+chrom_1\t15794\t15796\t153.689\n+chrom_1\t15796\t15805\t179.303\n+chrom_1\t15805\t15815\t230.533\n+chrom_1\t15815\t15816\t179.303\n+chrom_1\t15816\t15817\t153.689\n+chrom_1\t15817\t15819\t76.8443\n+chrom_1\t15819\t15828\t51.2295\n+chrom_1\t15828\t15925\t0\n+chrom_1\t15925\t15926\t128.074\n+chrom_1\t15926\t15942\t153.689\n+chrom_1\t15942\t15950\t179.303\n+chrom_1\t15950\t15963\t25.6148\n+chrom_1\t15963\t15965\t102.459\n+chrom_1\t15965\t15979\t256.148\n+chrom_1\t15979\t15989\t281.762\n+chrom_1\t15989\t15990\t230.533\n+chrom_1\t15990\t15991\t461.066\n+chrom_1\t15991\t16003\t486.68\n+chrom_1\t16003\t16014\t461.066\n+chrom_1\t16014\t16059\t0\n+chrom_1\t16059\t16086\t25.6148\n+chrom_1\t16086\t16122\t0\n+chrom_1\t16122\t16124\t25.6148\n+chrom_1\t16124\t16125\t51.2295\n+chrom_1\t16125\t16126\t102.459\n+chrom_1\t16126\t16139\t179.303\n+chrom_1\t16139\t16142\t204.918\n+chrom_1\t16142\t16149\t230.533\n+chrom_1\t16149\t16151\t179.303\n+chrom_1\t16151\t16152\t51.2295\n+chrom_'..b'38963\t38964\t76.8443\n+chrom_1\t38964\t38965\t102.459\n+chrom_1\t38965\t38970\t179.303\n+chrom_1\t38970\t38971\t230.533\n+chrom_1\t38971\t38972\t256.148\n+chrom_1\t38972\t38973\t486.68\n+chrom_1\t38973\t38974\t512.295\n+chrom_1\t38974\t38982\t537.91\n+chrom_1\t38982\t38984\t512.295\n+chrom_1\t38984\t38987\t486.68\n+chrom_1\t38987\t38988\t461.066\n+chrom_1\t38988\t38990\t384.221\n+chrom_1\t38990\t38995\t358.607\n+chrom_1\t38995\t38996\t332.992\n+chrom_1\t38996\t38997\t102.459\n+chrom_1\t38997\t39001\t0\n+chrom_1\t39001\t39024\t25.6148\n+chrom_1\t39024\t39034\t0\n+chrom_1\t39034\t39035\t25.6148\n+chrom_1\t39035\t39036\t51.2295\n+chrom_1\t39036\t39037\t76.8443\n+chrom_1\t39037\t39038\t256.148\n+chrom_1\t39038\t39058\t358.607\n+chrom_1\t39058\t39061\t332.992\n+chrom_1\t39061\t39062\t281.762\n+chrom_1\t39062\t39063\t25.6148\n+chrom_1\t39063\t39069\t0\n+chrom_1\t39069\t39074\t25.6148\n+chrom_1\t39074\t39076\t51.2295\n+chrom_1\t39076\t39094\t76.8443\n+chrom_1\t39094\t39099\t51.2295\n+chrom_1\t39099\t39102\t25.6148\n+chrom_1\t39102\t39125\t0\n+chrom_1\t39125\t39140\t25.6148\n+chrom_1\t39140\t39150\t51.2295\n+chrom_1\t39150\t39153\t25.6148\n+chrom_1\t39153\t39164\t153.689\n+chrom_1\t39164\t39178\t128.074\n+chrom_1\t39178\t39179\t102.459\n+chrom_1\t39179\t39216\t0\n+chrom_1\t39216\t39218\t25.6148\n+chrom_1\t39218\t39224\t51.2295\n+chrom_1\t39224\t39226\t76.8443\n+chrom_1\t39226\t39233\t102.459\n+chrom_1\t39233\t39241\t128.074\n+chrom_1\t39241\t39242\t102.459\n+chrom_1\t39242\t39243\t76.8443\n+chrom_1\t39243\t39247\t102.459\n+chrom_1\t39247\t39252\t76.8443\n+chrom_1\t39252\t39253\t1946.72\n+chrom_1\t39253\t39254\t1997.95\n+chrom_1\t39254\t39259\t2023.57\n+chrom_1\t39259\t39267\t1997.95\n+chrom_1\t39267\t39277\t1972.34\n+chrom_1\t39277\t39278\t25.6148\n+chrom_1\t39278\t40964\t0\n+chrom_1\t40964\t40987\t25.6148\n+chrom_1\t40987\t42081\t0\n+chrom_1\t42081\t42106\t25.6148\n+chrom_1\t42106\t43035\t0\n+chrom_1\t43035\t43060\t25.6148\n+chrom_1\t43060\t43642\t0\n+chrom_1\t43642\t43666\t25.6148\n+chrom_1\t43666\t43938\t0\n+chrom_1\t43938\t43963\t25.6148\n+chrom_1\t43963\t45231\t0\n+chrom_1\t45231\t45256\t25.6148\n+chrom_1\t45256\t45966\t0\n+chrom_1\t45966\t45990\t25.6148\n+chrom_1\t45990\t47678\t0\n+chrom_1\t47678\t47701\t25.6148\n+chrom_1\t47701\t51206\t0\n+chrom_1\t51206\t51231\t25.6148\n+chrom_1\t51231\t51463\t0\n+chrom_1\t51463\t51486\t25.6148\n+chrom_1\t51486\t51577\t0\n+chrom_1\t51577\t51602\t25.6148\n+chrom_1\t51602\t52380\t0\n+chrom_1\t52380\t52405\t25.6148\n+chrom_1\t52405\t52942\t0\n+chrom_1\t52942\t52967\t51.2295\n+chrom_1\t52967\t54412\t0\n+chrom_1\t54412\t54440\t25.6148\n+chrom_1\t54440\t55754\t0\n+chrom_1\t55754\t55779\t25.6148\n+chrom_1\t55779\t55828\t0\n+chrom_1\t55828\t55852\t25.6148\n+chrom_1\t55852\t58435\t0\n+chrom_1\t58435\t58460\t25.6148\n+chrom_1\t58460\t59554\t0\n+chrom_1\t59554\t59579\t25.6148\n+chrom_1\t59579\t61962\t0\n+chrom_1\t61962\t61987\t25.6148\n+chrom_1\t61987\t62088\t0\n+chrom_1\t62088\t62113\t25.6148\n+chrom_1\t62113\t62288\t0\n+chrom_1\t62288\t62312\t25.6148\n+chrom_1\t62312\t64308\t0\n+chrom_1\t64308\t64333\t25.6148\n+chrom_1\t64333\t65694\t0\n+chrom_1\t65694\t65718\t25.6148\n+chrom_1\t65718\t65974\t0\n+chrom_1\t65974\t65983\t25.6148\n+chrom_1\t65983\t65999\t51.2295\n+chrom_1\t65999\t66008\t25.6148\n+chrom_1\t66008\t67277\t0\n+chrom_1\t67277\t67300\t25.6148\n+chrom_1\t67300\t72363\t0\n+chrom_1\t72363\t72387\t25.6148\n+chrom_1\t72387\t74181\t0\n+chrom_1\t74181\t74205\t25.6148\n+chrom_1\t74205\t76156\t0\n+chrom_1\t76156\t76181\t25.6148\n+chrom_1\t76181\t80904\t0\n+chrom_1\t80904\t80923\t25.6148\n+chrom_1\t80923\t80929\t51.2295\n+chrom_1\t80929\t80949\t25.6148\n+chrom_1\t80949\t80959\t0\n+chrom_1\t80959\t80982\t25.6148\n+chrom_1\t80982\t81627\t0\n+chrom_1\t81627\t81650\t25.6148\n+chrom_1\t81650\t82123\t0\n+chrom_1\t82123\t82146\t25.6148\n+chrom_1\t82146\t82455\t0\n+chrom_1\t82455\t82480\t25.6148\n+chrom_1\t82480\t83396\t0\n+chrom_1\t83396\t83422\t25.6148\n+chrom_1\t83422\t83426\t0\n+chrom_1\t83426\t83450\t51.2295\n+chrom_1\t83450\t83868\t0\n+chrom_1\t83868\t83891\t25.6148\n+chrom_1\t83891\t83991\t0\n+chrom_1\t83991\t84014\t25.6148\n+chrom_1\t84014\t85181\t0\n+chrom_1\t85181\t85205\t25.6148\n+chrom_1\t85205\t85366\t0\n+chrom_1\t85366\t85390\t25.6148\n+chrom_1\t85390\t85759\t0\n+chrom_1\t85759\t85783\t25.6148\n+chrom_1\t85783\t86632\t0\n+chrom_1\t86632\t86658\t25.6148\n+chrom_1\t86658\t86941\t0\n+chrom_1\t86941\t86967\t25.6148\n+chrom_1\t86967\t87853\t0\n+chrom_1\t87853\t87878\t25.6148\n+chrom_1\t87878\t89999\t0\n+chrom_2\t0\t32272\t0\n+chrom_2\t32272\t32296\t25.6148\n+chrom_2\t32296\t49999\t0\n' |
| b |
| diff -r 9645d995fb3c -r 9185ca0a7b43 test-data/res_files/reads-sample-small.fastq/subgroups/piRNAs/piRNAs-genome_unique_plus.bedgraph --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/res_files/reads-sample-small.fastq/subgroups/piRNAs/piRNAs-genome_unique_plus.bedgraph Wed Jan 16 08:18:13 2019 -0500 |
| b |
| b'@@ -0,0 +1,4411 @@\n+chrom_1\t0\t1967\t0\n+chrom_1\t1967\t1991\t25.6148\n+chrom_1\t1991\t3456\t0\n+chrom_1\t3456\t3481\t25.6148\n+chrom_1\t3481\t7648\t0\n+chrom_1\t7648\t7671\t25.6148\n+chrom_1\t7671\t7953\t0\n+chrom_1\t7953\t7978\t25.6148\n+chrom_1\t7978\t8721\t0\n+chrom_1\t8721\t8742\t25.6148\n+chrom_1\t8742\t8747\t51.2295\n+chrom_1\t8747\t8758\t25.6148\n+chrom_1\t8758\t8767\t51.2295\n+chrom_1\t8767\t8783\t25.6148\n+chrom_1\t8783\t9642\t0\n+chrom_1\t9642\t9668\t25.6148\n+chrom_1\t9668\t14236\t0\n+chrom_1\t14236\t14261\t25.6148\n+chrom_1\t14261\t14309\t0\n+chrom_1\t14309\t14336\t25.6148\n+chrom_1\t14336\t14439\t0\n+chrom_1\t14439\t14463\t25.6148\n+chrom_1\t14463\t14551\t0\n+chrom_1\t14551\t14552\t25.6148\n+chrom_1\t14552\t14554\t76.8443\n+chrom_1\t14554\t14578\t179.303\n+chrom_1\t14578\t14580\t25.6148\n+chrom_1\t14580\t14592\t0\n+chrom_1\t14592\t14616\t25.6148\n+chrom_1\t14616\t14979\t0\n+chrom_1\t14979\t15004\t25.6148\n+chrom_1\t15004\t15062\t0\n+chrom_1\t15062\t15087\t25.6148\n+chrom_1\t15087\t15089\t0\n+chrom_1\t15089\t15092\t25.6148\n+chrom_1\t15092\t15115\t128.074\n+chrom_1\t15115\t15117\t102.459\n+chrom_1\t15117\t15139\t0\n+chrom_1\t15139\t15164\t25.6148\n+chrom_1\t15164\t15258\t0\n+chrom_1\t15258\t15260\t25.6148\n+chrom_1\t15260\t15264\t76.8443\n+chrom_1\t15264\t15269\t102.459\n+chrom_1\t15269\t15283\t128.074\n+chrom_1\t15283\t15284\t102.459\n+chrom_1\t15284\t15290\t51.2295\n+chrom_1\t15290\t15293\t25.6148\n+chrom_1\t15293\t15395\t0\n+chrom_1\t15395\t15399\t25.6148\n+chrom_1\t15399\t15400\t76.8443\n+chrom_1\t15400\t15407\t102.459\n+chrom_1\t15407\t15420\t128.074\n+chrom_1\t15420\t15423\t102.459\n+chrom_1\t15423\t15424\t51.2295\n+chrom_1\t15424\t15433\t25.6148\n+chrom_1\t15433\t15460\t0\n+chrom_1\t15460\t15484\t25.6148\n+chrom_1\t15484\t15529\t0\n+chrom_1\t15529\t15545\t25.6148\n+chrom_1\t15545\t15546\t51.2295\n+chrom_1\t15546\t15555\t409.836\n+chrom_1\t15555\t15569\t384.221\n+chrom_1\t15569\t15570\t204.918\n+chrom_1\t15570\t15572\t25.6148\n+chrom_1\t15572\t15716\t0\n+chrom_1\t15716\t15739\t25.6148\n+chrom_1\t15739\t15801\t0\n+chrom_1\t15801\t15824\t25.6148\n+chrom_1\t15824\t15970\t0\n+chrom_1\t15970\t15993\t76.8443\n+chrom_1\t15993\t16004\t0\n+chrom_1\t16004\t16027\t76.8443\n+chrom_1\t16027\t16028\t25.6148\n+chrom_1\t16028\t16232\t0\n+chrom_1\t16232\t16237\t25.6148\n+chrom_1\t16237\t16239\t51.2295\n+chrom_1\t16239\t16256\t102.459\n+chrom_1\t16256\t16262\t76.8443\n+chrom_1\t16262\t16336\t0\n+chrom_1\t16336\t16338\t256.148\n+chrom_1\t16338\t16339\t281.762\n+chrom_1\t16339\t16342\t307.377\n+chrom_1\t16342\t16359\t332.992\n+chrom_1\t16359\t16360\t128.074\n+chrom_1\t16360\t16363\t76.8443\n+chrom_1\t16363\t16364\t51.2295\n+chrom_1\t16364\t16365\t25.6148\n+chrom_1\t16365\t16496\t0\n+chrom_1\t16496\t16521\t25.6148\n+chrom_1\t16521\t16619\t0\n+chrom_1\t16619\t16628\t25.6148\n+chrom_1\t16628\t16630\t76.8443\n+chrom_1\t16630\t16643\t256.148\n+chrom_1\t16643\t16653\t230.533\n+chrom_1\t16653\t16654\t153.689\n+chrom_1\t16654\t16655\t76.8443\n+chrom_1\t16655\t16656\t25.6148\n+chrom_1\t16656\t16661\t0\n+chrom_1\t16661\t16685\t25.6148\n+chrom_1\t16685\t16772\t0\n+chrom_1\t16772\t16798\t25.6148\n+chrom_1\t16798\t16800\t51.2295\n+chrom_1\t16800\t16801\t179.303\n+chrom_1\t16801\t16810\t461.066\n+chrom_1\t16810\t16811\t486.68\n+chrom_1\t16811\t16819\t512.295\n+chrom_1\t16819\t16823\t486.68\n+chrom_1\t16823\t16825\t435.451\n+chrom_1\t16825\t16835\t102.459\n+chrom_1\t16835\t16849\t51.2295\n+chrom_1\t16849\t16850\t25.6148\n+chrom_1\t16850\t16864\t0\n+chrom_1\t16864\t16866\t25.6148\n+chrom_1\t16866\t16867\t76.8443\n+chrom_1\t16867\t16868\t179.303\n+chrom_1\t16868\t16869\t307.377\n+chrom_1\t16869\t16870\t332.992\n+chrom_1\t16870\t16881\t358.607\n+chrom_1\t16881\t16883\t409.836\n+chrom_1\t16883\t16884\t435.451\n+chrom_1\t16884\t16887\t461.066\n+chrom_1\t16887\t16892\t435.451\n+chrom_1\t16892\t16893\t256.148\n+chrom_1\t16893\t16894\t153.689\n+chrom_1\t16894\t16906\t102.459\n+chrom_1\t16906\t16907\t76.8443\n+chrom_1\t16907\t16943\t0\n+chrom_1\t16943\t16962\t25.6148\n+chrom_1\t16962\t16967\t51.2295\n+chrom_1\t16967\t16988\t25.6148\n+chrom_1\t16988\t16999\t0\n+chrom_1\t16999\t17023\t25.6148\n+chrom_1\t17023\t17024\t0\n+chrom_1\t17024\t17044\t25.6148\n+chrom_1\t17044\t17047\t51.2295\n+chrom_1\t17047\t17049\t25.6148\n+chrom_1\t17049\t17050\t76.8443\n+chrom_1\t17050\t17053\t128.074\n+chrom_1\t17053\t17054\t153.689\n+chrom_1\t17054\t17068\t409.836\n+chrom_1\t17068\t17073\t384.221\n+chrom_1\t17073\t17076\t281.762\n+chrom_1\t17076\t17077\t256.148\n+chrom_1\t17077\t17078\t25.6148\n+chrom_1\t17078\t17081\t0\n+chrom_1\t17081\t17'..b'40735\t25.6148\n+chrom_1\t40735\t40854\t0\n+chrom_1\t40854\t40879\t25.6148\n+chrom_1\t40879\t40966\t0\n+chrom_1\t40966\t40976\t25.6148\n+chrom_1\t40976\t40977\t51.2295\n+chrom_1\t40977\t40992\t76.8443\n+chrom_1\t40992\t41001\t51.2295\n+chrom_1\t41001\t41285\t0\n+chrom_1\t41285\t41309\t51.2295\n+chrom_1\t41309\t41449\t0\n+chrom_1\t41449\t41451\t25.6148\n+chrom_1\t41451\t41474\t51.2295\n+chrom_1\t41474\t41476\t25.6148\n+chrom_1\t41476\t41788\t0\n+chrom_1\t41788\t41811\t25.6148\n+chrom_1\t41811\t42508\t0\n+chrom_1\t42508\t42533\t25.6148\n+chrom_1\t42533\t42909\t0\n+chrom_1\t42909\t42934\t25.6148\n+chrom_1\t42934\t43034\t0\n+chrom_1\t43034\t43059\t25.6148\n+chrom_1\t43059\t43075\t0\n+chrom_1\t43075\t43100\t25.6148\n+chrom_1\t43100\t44091\t0\n+chrom_1\t44091\t44116\t25.6148\n+chrom_1\t44116\t44344\t0\n+chrom_1\t44344\t44371\t25.6148\n+chrom_1\t44371\t44956\t0\n+chrom_1\t44956\t44980\t25.6148\n+chrom_1\t44980\t47326\t0\n+chrom_1\t47326\t47349\t25.6148\n+chrom_1\t47349\t47451\t0\n+chrom_1\t47451\t47475\t25.6148\n+chrom_1\t47475\t48345\t0\n+chrom_1\t48345\t48369\t25.6148\n+chrom_1\t48369\t51118\t0\n+chrom_1\t51118\t51143\t25.6148\n+chrom_1\t51143\t51577\t0\n+chrom_1\t51577\t51578\t25.6148\n+chrom_1\t51578\t51602\t51.2295\n+chrom_1\t51602\t51976\t0\n+chrom_1\t51976\t52001\t25.6148\n+chrom_1\t52001\t52284\t0\n+chrom_1\t52284\t52288\t25.6148\n+chrom_1\t52288\t52309\t51.2295\n+chrom_1\t52309\t52313\t25.6148\n+chrom_1\t52313\t54564\t0\n+chrom_1\t54564\t54573\t25.6148\n+chrom_1\t54573\t54588\t51.2295\n+chrom_1\t54588\t54599\t25.6148\n+chrom_1\t54599\t55385\t0\n+chrom_1\t55385\t55433\t25.6148\n+chrom_1\t55433\t55528\t0\n+chrom_1\t55528\t55552\t25.6148\n+chrom_1\t55552\t57239\t0\n+chrom_1\t57239\t57264\t25.6148\n+chrom_1\t57264\t59083\t0\n+chrom_1\t59083\t59107\t25.6148\n+chrom_1\t59107\t61842\t0\n+chrom_1\t61842\t61865\t25.6148\n+chrom_1\t61865\t63378\t0\n+chrom_1\t63378\t63401\t25.6148\n+chrom_1\t63401\t63530\t0\n+chrom_1\t63530\t63555\t25.6148\n+chrom_1\t63555\t65375\t0\n+chrom_1\t65375\t65400\t25.6148\n+chrom_1\t65400\t65546\t0\n+chrom_1\t65546\t65571\t25.6148\n+chrom_1\t65571\t65986\t0\n+chrom_1\t65986\t66009\t25.6148\n+chrom_1\t66009\t66305\t0\n+chrom_1\t66305\t66330\t25.6148\n+chrom_1\t66330\t66468\t0\n+chrom_1\t66468\t66494\t25.6148\n+chrom_1\t66494\t66717\t0\n+chrom_1\t66717\t66742\t25.6148\n+chrom_1\t66742\t67040\t0\n+chrom_1\t67040\t67065\t25.6148\n+chrom_1\t67065\t67545\t0\n+chrom_1\t67545\t67569\t25.6148\n+chrom_1\t67569\t67964\t0\n+chrom_1\t67964\t67989\t25.6148\n+chrom_1\t67989\t68011\t0\n+chrom_1\t68011\t68036\t25.6148\n+chrom_1\t68036\t68067\t0\n+chrom_1\t68067\t68093\t25.6148\n+chrom_1\t68093\t68111\t0\n+chrom_1\t68111\t68136\t25.6148\n+chrom_1\t68136\t68181\t0\n+chrom_1\t68181\t68205\t25.6148\n+chrom_1\t68205\t68206\t0\n+chrom_1\t68206\t68218\t25.6148\n+chrom_1\t68218\t68230\t51.2295\n+chrom_1\t68230\t68243\t25.6148\n+chrom_1\t68243\t68269\t0\n+chrom_1\t68269\t68317\t25.6148\n+chrom_1\t68317\t68544\t0\n+chrom_1\t68544\t68569\t25.6148\n+chrom_1\t68569\t69749\t0\n+chrom_1\t69749\t69774\t25.6148\n+chrom_1\t69774\t70096\t0\n+chrom_1\t70096\t70122\t25.6148\n+chrom_1\t70122\t71037\t0\n+chrom_1\t71037\t71062\t25.6148\n+chrom_1\t71062\t72078\t0\n+chrom_1\t72078\t72102\t25.6148\n+chrom_1\t72102\t72167\t0\n+chrom_1\t72167\t72192\t25.6148\n+chrom_1\t72192\t72356\t0\n+chrom_1\t72356\t72360\t25.6148\n+chrom_1\t72360\t72382\t51.2295\n+chrom_1\t72382\t72385\t25.6148\n+chrom_1\t72385\t72713\t0\n+chrom_1\t72713\t72737\t25.6148\n+chrom_1\t72737\t73860\t0\n+chrom_1\t73860\t73885\t25.6148\n+chrom_1\t73885\t74376\t0\n+chrom_1\t74376\t74400\t25.6148\n+chrom_1\t74400\t79422\t0\n+chrom_1\t79422\t79447\t25.6148\n+chrom_1\t79447\t80862\t0\n+chrom_1\t80862\t80887\t25.6148\n+chrom_1\t80887\t81326\t0\n+chrom_1\t81326\t81351\t25.6148\n+chrom_1\t81351\t81505\t0\n+chrom_1\t81505\t81528\t25.6148\n+chrom_1\t81528\t82213\t0\n+chrom_1\t82213\t82237\t25.6148\n+chrom_1\t82237\t83567\t0\n+chrom_1\t83567\t83592\t25.6148\n+chrom_1\t83592\t84065\t0\n+chrom_1\t84065\t84089\t25.6148\n+chrom_1\t84089\t85397\t0\n+chrom_1\t85397\t85422\t25.6148\n+chrom_1\t85422\t85980\t0\n+chrom_1\t85980\t86005\t25.6148\n+chrom_1\t86005\t87255\t0\n+chrom_1\t87255\t87278\t25.6148\n+chrom_1\t87278\t88301\t0\n+chrom_1\t88301\t88325\t25.6148\n+chrom_1\t88325\t88989\t0\n+chrom_1\t88989\t89015\t25.6148\n+chrom_1\t89015\t89111\t0\n+chrom_1\t89111\t89137\t25.6148\n+chrom_1\t89137\t89999\t0\n+chrom_4\t0\t1047\t0\n+chrom_4\t1047\t1071\t25.6148\n+chrom_4\t1071\t2000\t0\n+chrom_6\t0\t440\t0\n+chrom_6\t440\t464\t25.6148\n+chrom_6\t464\t1117\t0\n+chrom_6\t1117\t1142\t25.6148\n+chrom_6\t1142\t3999\t0\n' |
| b |
| diff -r 9645d995fb3c -r 9185ca0a7b43 test-data/res_files/reads-sample-small.fastq/subgroups/piRNAs/piRNAs-genome_unique_sorted.bam |
| b |
| Binary file test-data/res_files/reads-sample-small.fastq/subgroups/piRNAs/piRNAs-genome_unique_sorted.bam has changed |
| b |
| diff -r 9645d995fb3c -r 9185ca0a7b43 test-data/res_files/reads-sample-small.fastq/subgroups/piRNAs/piRNAs-transcripts_reads_counts.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/res_files/reads-sample-small.fastq/subgroups/piRNAs/piRNAs-transcripts_reads_counts.txt Wed Jan 16 08:18:13 2019 -0500 |
| b |
| @@ -0,0 +1,14 @@ +ID reads counts RPKM per million of piRNAs per million of miRNAs per million of bonafide reads sense reads counts reverse reads counts % of sense 1U % of sense 10A % of reverse 1U % of reverse 10A +FBtr0073689 162 1093.44 7026.37 2571428.57 5306.26 79 83 92.4050632911392 78.4810126582278 9.63855421686747 15.6626506024096 +FBtr0078666 230 2428.44 9975.71 3650793.65 7533.57 121 109 95.8677685950413 84.297520661157 20.1834862385321 9.1743119266055 +FBtr0086080 98 634.06 4250.52 1555555.56 3209.96 54 44 68.5185185185185 25.9259259259259 0 20.4545454545455 +FBtr0089125 126 446.34 5464.95 2000000.00 4127.09 5 121 80 60 65.2892561983471 0.826446280991736 +FBtr0089196 395 2312.12 17132.20 6269841.27 12938.09 285 110 98.5964912280702 61.7543859649123 10.9090909090909 35.4545454545455 +FBtr0113825 61 534.55 2645.73 968253.97 1998.03 50 11 84 78 9.09090909090909 36.3636363636364 +FBtr0114365 7 28.03 303.61 111111.11 229.28 4 3 25 25 0 0 +FBtr0310270 3 25.04 130.12 47619.05 98.26 0 3 0 0 66.6666666666667 33.3333333333333 +FBtr0332656 20 147.08 867.45 317460.32 655.09 20 0 100 70 0 0 +FBtr0345361 45 894.23 1951.77 714285.71 1473.96 45 0 100 88.8888888888889 0 0 +FBtr0345575 248 2146.83 10756.42 3936507.94 8123.16 49 199 85.7142857142857 73.469387755102 67.8391959798995 4.02010050251256 +FBtr0345650 322 997.09 13966.00 5111111.11 10547.00 217 105 52.9953917050691 6.91244239631336 1.9047619047619 5.71428571428571 +FBtr0346343 67 274.90 2905.97 1063492.06 2194.56 65 2 98.4615384615385 1.53846153846154 50 50 |
| b |
| diff -r 9645d995fb3c -r 9185ca0a7b43 test-data/res_files/reads-sample-small.fastq/subgroups/piRNAs/piRNAs-transcripts_sorted.bam |
| b |
| Binary file test-data/res_files/reads-sample-small.fastq/subgroups/piRNAs/piRNAs-transcripts_sorted.bam has changed |
| b |
| diff -r 9645d995fb3c -r 9185ca0a7b43 test-data/res_files/reads-sample-small.fastq/subgroups/piRNAs/piRNAs-transcripts_unique_sorted.bam |
| b |
| Binary file test-data/res_files/reads-sample-small.fastq/subgroups/piRNAs/piRNAs-transcripts_unique_sorted.bam has changed |
| b |
| diff -r 9645d995fb3c -r 9185ca0a7b43 test-data/res_files/reads-sample-small.fastq/subgroups/pie_chart.png |
| b |
| Binary file test-data/res_files/reads-sample-small.fastq/subgroups/pie_chart.png has changed |
| b |
| diff -r 9645d995fb3c -r 9185ca0a7b43 test-data/res_files/reads-sample-small.fastq/subgroups/repartition.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/res_files/reads-sample-small.fastq/subgroups/repartition.txt Wed Jan 16 08:18:13 2019 -0500 |
| b |
| @@ -0,0 +1,8 @@ +type number percentage +TEs 26344 67.48 +miRNAs 63 0.16 +others 1939 4.97 +rRNAs 8170 20.93 +snRNAs 81 0.21 +tRNAs 196 0.50 +transcripts 2247 5.76 |
| b |
| diff -r 9645d995fb3c -r 9185ca0a7b43 test-data/res_files/reads-sample-small.fastq/subgroups/siRNAs/Gviz_TEs/BATUMI_I.png |
| b |
| Binary file test-data/res_files/reads-sample-small.fastq/subgroups/siRNAs/Gviz_TEs/BATUMI_I.png has changed |
| b |
| diff -r 9645d995fb3c -r 9185ca0a7b43 test-data/res_files/reads-sample-small.fastq/subgroups/siRNAs/Gviz_TEs/BATUMI_LTR.png |
| b |
| Binary file test-data/res_files/reads-sample-small.fastq/subgroups/siRNAs/Gviz_TEs/BATUMI_LTR.png has changed |
| b |
| diff -r 9645d995fb3c -r 9185ca0a7b43 test-data/res_files/reads-sample-small.fastq/subgroups/siRNAs/Gviz_TEs/BS2.png |
| b |
| Binary file test-data/res_files/reads-sample-small.fastq/subgroups/siRNAs/Gviz_TEs/BS2.png has changed |
| b |
| diff -r 9645d995fb3c -r 9185ca0a7b43 test-data/res_files/reads-sample-small.fastq/subgroups/siRNAs/Gviz_TEs/DMCR1A.png |
| b |
| Binary file test-data/res_files/reads-sample-small.fastq/subgroups/siRNAs/Gviz_TEs/DMCR1A.png has changed |
| b |
| diff -r 9645d995fb3c -r 9185ca0a7b43 test-data/res_files/reads-sample-small.fastq/subgroups/siRNAs/Gviz_TEs/DMRT1B.png |
| b |
| Binary file test-data/res_files/reads-sample-small.fastq/subgroups/siRNAs/Gviz_TEs/DMRT1B.png has changed |
| b |
| diff -r 9645d995fb3c -r 9185ca0a7b43 test-data/res_files/reads-sample-small.fastq/subgroups/siRNAs/Gviz_TEs/FW.png |
| b |
| Binary file test-data/res_files/reads-sample-small.fastq/subgroups/siRNAs/Gviz_TEs/FW.png has changed |
| b |
| diff -r 9645d995fb3c -r 9185ca0a7b43 test-data/res_files/reads-sample-small.fastq/subgroups/siRNAs/Gviz_TEs/G6_DM.png |
| b |
| Binary file test-data/res_files/reads-sample-small.fastq/subgroups/siRNAs/Gviz_TEs/G6_DM.png has changed |
| b |
| diff -r 9645d995fb3c -r 9185ca0a7b43 test-data/res_files/reads-sample-small.fastq/subgroups/siRNAs/Gviz_TEs/Gypsy2-LTR_DM.png |
| b |
| Binary file test-data/res_files/reads-sample-small.fastq/subgroups/siRNAs/Gviz_TEs/Gypsy2-LTR_DM.png has changed |
| b |
| diff -r 9645d995fb3c -r 9185ca0a7b43 test-data/res_files/reads-sample-small.fastq/subgroups/siRNAs/Gviz_TEs/I_DM.png |
| b |
| Binary file test-data/res_files/reads-sample-small.fastq/subgroups/siRNAs/Gviz_TEs/I_DM.png has changed |
| b |
| diff -r 9645d995fb3c -r 9185ca0a7b43 test-data/res_files/reads-sample-small.fastq/subgroups/siRNAs/Gviz_TEs/MAX_I.png |
| b |
| Binary file test-data/res_files/reads-sample-small.fastq/subgroups/siRNAs/Gviz_TEs/MAX_I.png has changed |
| b |
| diff -r 9645d995fb3c -r 9185ca0a7b43 test-data/res_files/reads-sample-small.fastq/subgroups/siRNAs/Gviz_TEs/MAX_LTR.png |
| b |
| Binary file test-data/res_files/reads-sample-small.fastq/subgroups/siRNAs/Gviz_TEs/MAX_LTR.png has changed |
| b |
| diff -r 9645d995fb3c -r 9185ca0a7b43 test-data/res_files/reads-sample-small.fastq/subgroups/siRNAs/Gviz_TEs/PROTOP.png |
| b |
| Binary file test-data/res_files/reads-sample-small.fastq/subgroups/siRNAs/Gviz_TEs/PROTOP.png has changed |
| b |
| diff -r 9645d995fb3c -r 9185ca0a7b43 test-data/res_files/reads-sample-small.fastq/subgroups/siRNAs/Gviz_genome/rand/chrom_1.png |
| b |
| Binary file test-data/res_files/reads-sample-small.fastq/subgroups/siRNAs/Gviz_genome/rand/chrom_1.png has changed |
| b |
| diff -r 9645d995fb3c -r 9185ca0a7b43 test-data/res_files/reads-sample-small.fastq/subgroups/siRNAs/Gviz_genome/rand/chrom_2.png |
| b |
| Binary file test-data/res_files/reads-sample-small.fastq/subgroups/siRNAs/Gviz_genome/rand/chrom_2.png has changed |
| b |
| diff -r 9645d995fb3c -r 9185ca0a7b43 test-data/res_files/reads-sample-small.fastq/subgroups/siRNAs/Gviz_genome/rand/chrom_4.png |
| b |
| Binary file test-data/res_files/reads-sample-small.fastq/subgroups/siRNAs/Gviz_genome/rand/chrom_4.png has changed |
| b |
| diff -r 9645d995fb3c -r 9185ca0a7b43 test-data/res_files/reads-sample-small.fastq/subgroups/siRNAs/Gviz_genome/rand/chrom_5.png |
| b |
| Binary file test-data/res_files/reads-sample-small.fastq/subgroups/siRNAs/Gviz_genome/rand/chrom_5.png has changed |
| b |
| diff -r 9645d995fb3c -r 9185ca0a7b43 test-data/res_files/reads-sample-small.fastq/subgroups/siRNAs/Gviz_genome/rand/chrom_6.png |
| b |
| Binary file test-data/res_files/reads-sample-small.fastq/subgroups/siRNAs/Gviz_genome/rand/chrom_6.png has changed |
| b |
| diff -r 9645d995fb3c -r 9185ca0a7b43 test-data/res_files/reads-sample-small.fastq/subgroups/siRNAs/Gviz_genome/unique/chrom_1.png |
| b |
| Binary file test-data/res_files/reads-sample-small.fastq/subgroups/siRNAs/Gviz_genome/unique/chrom_1.png has changed |
| b |
| diff -r 9645d995fb3c -r 9185ca0a7b43 test-data/res_files/reads-sample-small.fastq/subgroups/siRNAs/Gviz_genome/unique/chrom_2.png |
| b |
| Binary file test-data/res_files/reads-sample-small.fastq/subgroups/siRNAs/Gviz_genome/unique/chrom_2.png has changed |
| b |
| diff -r 9645d995fb3c -r 9185ca0a7b43 test-data/res_files/reads-sample-small.fastq/subgroups/siRNAs/Gviz_genome/unique/chrom_4.png |
| b |
| Binary file test-data/res_files/reads-sample-small.fastq/subgroups/siRNAs/Gviz_genome/unique/chrom_4.png has changed |
| b |
| diff -r 9645d995fb3c -r 9185ca0a7b43 test-data/res_files/reads-sample-small.fastq/subgroups/siRNAs/Gviz_genome/unique/chrom_5.png |
| b |
| Binary file test-data/res_files/reads-sample-small.fastq/subgroups/siRNAs/Gviz_genome/unique/chrom_5.png has changed |
| b |
| diff -r 9645d995fb3c -r 9185ca0a7b43 test-data/res_files/reads-sample-small.fastq/subgroups/siRNAs/Gviz_genome/unique/chrom_6.png |
| b |
| Binary file test-data/res_files/reads-sample-small.fastq/subgroups/siRNAs/Gviz_genome/unique/chrom_6.png has changed |
| b |
| diff -r 9645d995fb3c -r 9185ca0a7b43 test-data/res_files/reads-sample-small.fastq/subgroups/siRNAs/siRNAs-TEs_minus.bedgraph --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/res_files/reads-sample-small.fastq/subgroups/siRNAs/siRNAs-TEs_minus.bedgraph Wed Jan 16 08:18:13 2019 -0500 |
| b |
| b'@@ -0,0 +1,1185 @@\n+BATUMI_I\t0\t219\t0\n+BATUMI_I\t219\t239\t25.6148\n+BATUMI_I\t239\t353\t0\n+BATUMI_I\t353\t354\t25.6148\n+BATUMI_I\t354\t355\t51.2295\n+BATUMI_I\t355\t357\t76.8443\n+BATUMI_I\t357\t374\t128.074\n+BATUMI_I\t374\t375\t102.459\n+BATUMI_I\t375\t376\t76.8443\n+BATUMI_I\t376\t378\t51.2295\n+BATUMI_I\t378\t7963\t0\n+BATUMI_LTR\t0\t45\t0\n+BATUMI_LTR\t45\t66\t25.6148\n+BATUMI_LTR\t66\t109\t0\n+BATUMI_LTR\t109\t130\t51.2295\n+BATUMI_LTR\t130\t181\t0\n+BATUMI_LTR\t181\t202\t25.6148\n+BATUMI_LTR\t202\t272\t0\n+BS2\t0\t12\t0\n+BS2\t12\t32\t25.6148\n+BS2\t32\t33\t51.2295\n+BS2\t33\t53\t25.6148\n+BS2\t53\t125\t0\n+BS2\t125\t146\t25.6148\n+BS2\t146\t212\t0\n+BS2\t212\t217\t25.6148\n+BS2\t217\t218\t76.8443\n+BS2\t218\t219\t128.074\n+BS2\t219\t233\t179.303\n+BS2\t233\t238\t153.689\n+BS2\t238\t239\t102.459\n+BS2\t239\t240\t51.2295\n+BS2\t240\t272\t0\n+BS2\t272\t273\t51.2295\n+BS2\t273\t293\t76.8443\n+BS2\t293\t294\t25.6148\n+BS2\t294\t500\t0\n+BS2\t500\t521\t461.066\n+BS2\t521\t522\t0\n+BS2\t522\t543\t25.6148\n+BS2\t543\t551\t0\n+BS2\t551\t572\t51.2295\n+BS2\t572\t604\t0\n+BS2\t604\t605\t25.6148\n+BS2\t605\t625\t51.2295\n+BS2\t625\t626\t25.6148\n+BS2\t626\t663\t0\n+BS2\t663\t678\t25.6148\n+BS2\t678\t684\t51.2295\n+BS2\t684\t685\t25.6148\n+BS2\t685\t689\t51.2295\n+BS2\t689\t699\t76.8443\n+BS2\t699\t706\t51.2295\n+BS2\t706\t710\t25.6148\n+BS2\t710\t858\t0\n+BS2\t858\t860\t25.6148\n+BS2\t860\t879\t128.074\n+BS2\t879\t881\t102.459\n+BS2\t881\t910\t0\n+BS2\t910\t930\t25.6148\n+BS2\t930\t931\t51.2295\n+BS2\t931\t933\t25.6148\n+BS2\t933\t936\t76.8443\n+BS2\t936\t937\t102.459\n+BS2\t937\t951\t128.074\n+BS2\t951\t954\t102.459\n+BS2\t954\t957\t51.2295\n+BS2\t957\t958\t25.6148\n+BS2\t958\t994\t0\n+BS2\t994\t1015\t25.6148\n+BS2\t1015\t1016\t0\n+BS2\t1016\t1037\t25.6148\n+BS2\t1037\t1042\t0\n+BS2\t1042\t1063\t51.2295\n+BS2\t1063\t1101\t0\n+BS2\t1101\t1122\t25.6148\n+BS2\t1122\t1173\t0\n+BS2\t1173\t1194\t51.2295\n+BS2\t1194\t1200\t0\n+BS2\t1200\t1221\t25.6148\n+BS2\t1221\t1248\t0\n+BS2\t1248\t1269\t25.6148\n+BS2\t1269\t1271\t0\n+BS2\t1271\t1292\t25.6148\n+BS2\t1292\t1313\t0\n+BS2\t1313\t1314\t25.6148\n+BS2\t1314\t1317\t51.2295\n+BS2\t1317\t1334\t76.8443\n+BS2\t1334\t1335\t51.2295\n+BS2\t1335\t1338\t25.6148\n+BS2\t1338\t1365\t0\n+BS2\t1365\t1386\t25.6148\n+BS2\t1386\t1502\t0\n+BS2\t1502\t1523\t51.2295\n+BS2\t1523\t1528\t0\n+BS2\t1528\t1555\t25.6148\n+BS2\t1555\t1569\t51.2295\n+BS2\t1569\t1570\t76.8443\n+BS2\t1570\t1576\t51.2295\n+BS2\t1576\t1579\t25.6148\n+BS2\t1579\t1585\t51.2295\n+BS2\t1585\t1590\t102.459\n+BS2\t1590\t1600\t76.8443\n+BS2\t1600\t1606\t51.2295\n+BS2\t1606\t1613\t0\n+BS2\t1613\t1630\t25.6148\n+BS2\t1630\t1633\t51.2295\n+BS2\t1633\t1634\t128.074\n+BS2\t1634\t1651\t102.459\n+BS2\t1651\t1652\t76.8443\n+BS2\t1652\t1654\t102.459\n+BS2\t1654\t1673\t25.6148\n+BS2\t1673\t1753\t0\n+BS2\t1753\t1770\t25.6148\n+BS2\t1770\t1774\t51.2295\n+BS2\t1774\t1791\t25.6148\n+BS2\t1791\t1864\t0\n+BS2\t1864\t1885\t25.6148\n+BS2\t1885\t1949\t0\n+BS2\t1949\t1970\t51.2295\n+BS2\t1970\t1983\t0\n+BS2\t1983\t1989\t25.6148\n+BS2\t1989\t2004\t51.2295\n+BS2\t2004\t2010\t25.6148\n+BS2\t2010\t2091\t0\n+BS2\t2091\t2112\t25.6148\n+BS2\t2112\t2144\t0\n+BS2\t2144\t2145\t896.516\n+BS2\t2145\t2146\t922.131\n+BS2\t2146\t2157\t973.361\n+BS2\t2157\t2165\t1024.59\n+BS2\t2165\t2166\t128.074\n+BS2\t2166\t2167\t102.459\n+BS2\t2167\t2178\t51.2295\n+BS2\t2178\t2207\t0\n+BS2\t2207\t2228\t25.6148\n+BS2\t2228\t2371\t0\n+BS2\t2371\t2392\t128.074\n+BS2\t2392\t2396\t0\n+BS2\t2396\t2417\t25.6148\n+BS2\t2417\t2440\t0\n+BS2\t2440\t2461\t25.6148\n+BS2\t2461\t2628\t0\n+BS2\t2628\t2649\t25.6148\n+BS2\t2649\t2670\t51.2295\n+BS2\t2670\t2675\t0\n+BS2\t2675\t2683\t25.6148\n+BS2\t2683\t2685\t51.2295\n+BS2\t2685\t2696\t281.762\n+BS2\t2696\t2704\t256.148\n+BS2\t2704\t2706\t230.533\n+BS2\t2706\t2717\t0\n+BS2\t2717\t2718\t537.91\n+BS2\t2718\t2738\t563.525\n+BS2\t2738\t2739\t25.6148\n+BS2\t2739\t2784\t0\n+BS2\t2784\t2805\t25.6148\n+BS2\t2805\t2850\t0\n+BS2\t2850\t2859\t25.6148\n+BS2\t2859\t2871\t51.2295\n+BS2\t2871\t2872\t25.6148\n+BS2\t2872\t2880\t51.2295\n+BS2\t2880\t2884\t25.6148\n+BS2\t2884\t2893\t51.2295\n+BS2\t2893\t2905\t25.6148\n+BS2\t2905\t2916\t0\n+BS2\t2916\t2937\t25.6148\n+BS2\t2937\t2958\t0\n+BS2\t2958\t2963\t25.6148\n+BS2\t2963\t2979\t102.459\n+BS2\t2979\t2984\t76.8443\n+BS2\t2984\t3027\t0\n+BS2\t3027\t3048\t25.6148\n+BS2\t3048\t3058\t0\n+BS2\t3058\t3079\t25.6148\n+BS2\t3079\t3116\t0\n+BS2\t3116\t3137\t25.6148\n+BS2\t3137\t3164\t0\n+BS2\t3164\t3185\t51.2295\n+BS2\t3185\t3219\t0\n+BS2\t3219\t3224\t51.2295\n+BS2\t3224\t3226\t435.451\n+BS2\t3226\t3228\t486.68\n+BS2\t3228\t3230\t845.287\n+BS2\t3230\t3234\t922.131\n+BS2\t3234\t3240\t947.746\n+BS2\t3240\t3245\t896.516\n+BS2\t3245\t3247\t512.295\n+BS2\t3247\t3249\t461.066\n+BS2\t'..b'310\t51.2295\n+FW\t4310\t4311\t25.6148\n+FW\t4311\t4314\t51.2295\n+FW\t4314\t4327\t76.8443\n+FW\t4327\t4332\t51.2295\n+FW\t4332\t4335\t25.6148\n+FW\t4335\t4344\t0\n+FW\t4344\t4365\t25.6148\n+FW\t4365\t4391\t0\n+FW\t4391\t4392\t230.533\n+FW\t4392\t4397\t691.598\n+FW\t4397\t4399\t717.213\n+FW\t4399\t4401\t742.828\n+FW\t4401\t4408\t794.057\n+FW\t4408\t4412\t870.902\n+FW\t4412\t4413\t640.369\n+FW\t4413\t4418\t179.303\n+FW\t4418\t4420\t153.689\n+FW\t4420\t4422\t128.074\n+FW\t4422\t4429\t76.8443\n+FW\t4429\t4454\t0\n+FW\t4454\t4468\t25.6148\n+FW\t4468\t4474\t102.459\n+FW\t4474\t4475\t153.689\n+FW\t4475\t4485\t128.074\n+FW\t4485\t4489\t230.533\n+FW\t4489\t4495\t153.689\n+FW\t4495\t4503\t230.533\n+FW\t4503\t4504\t281.762\n+FW\t4504\t4506\t307.377\n+FW\t4506\t4516\t230.533\n+FW\t4516\t4517\t102.459\n+FW\t4517\t4524\t128.074\n+FW\t4524\t4527\t76.8443\n+FW\t4527\t4538\t51.2295\n+FW\t4538\t4546\t25.6148\n+FW\t4546\t4692\t0\n+G6_DM\t0\t1166\t0\n+G6_DM\t1166\t1172\t25.6148\n+G6_DM\t1172\t1175\t51.2295\n+G6_DM\t1175\t1187\t76.8443\n+G6_DM\t1187\t1193\t51.2295\n+G6_DM\t1193\t1196\t25.6148\n+G6_DM\t1196\t1261\t0\n+G6_DM\t1261\t1265\t25.6148\n+G6_DM\t1265\t1273\t51.2295\n+G6_DM\t1273\t1282\t76.8443\n+G6_DM\t1282\t1286\t51.2295\n+G6_DM\t1286\t1315\t25.6148\n+G6_DM\t1315\t1321\t0\n+G6_DM\t1321\t1323\t25.6148\n+G6_DM\t1323\t1342\t51.2295\n+G6_DM\t1342\t1344\t25.6148\n+G6_DM\t1344\t1397\t0\n+G6_DM\t1397\t1410\t25.6148\n+G6_DM\t1410\t1411\t102.459\n+G6_DM\t1411\t1418\t128.074\n+G6_DM\t1418\t1431\t102.459\n+G6_DM\t1431\t1432\t25.6148\n+G6_DM\t1432\t1437\t0\n+G6_DM\t1437\t1438\t794.057\n+G6_DM\t1438\t1458\t922.131\n+G6_DM\t1458\t1459\t179.303\n+G6_DM\t1459\t1460\t51.2295\n+G6_DM\t1460\t1462\t76.8443\n+G6_DM\t1462\t1464\t512.295\n+G6_DM\t1464\t1479\t537.91\n+G6_DM\t1479\t1481\t486.68\n+G6_DM\t1481\t1483\t461.066\n+G6_DM\t1483\t1485\t25.6148\n+G6_DM\t1485\t1490\t0\n+G6_DM\t1490\t1511\t25.6148\n+G6_DM\t1511\t1577\t0\n+G6_DM\t1577\t1598\t25.6148\n+G6_DM\t1598\t1613\t0\n+G6_DM\t1613\t1614\t25.6148\n+G6_DM\t1614\t1634\t51.2295\n+G6_DM\t1634\t1635\t25.6148\n+G6_DM\t1635\t1654\t0\n+G6_DM\t1654\t1659\t25.6148\n+G6_DM\t1659\t1675\t51.2295\n+G6_DM\t1675\t1680\t25.6148\n+G6_DM\t1680\t1684\t0\n+G6_DM\t1684\t1690\t25.6148\n+G6_DM\t1690\t1691\t51.2295\n+G6_DM\t1691\t1692\t256.148\n+G6_DM\t1692\t1705\t307.377\n+G6_DM\t1705\t1711\t281.762\n+G6_DM\t1711\t1712\t256.148\n+G6_DM\t1712\t1713\t51.2295\n+G6_DM\t1713\t1887\t0\n+G6_DM\t1887\t1892\t25.6148\n+G6_DM\t1892\t1908\t51.2295\n+G6_DM\t1908\t1913\t25.6148\n+G6_DM\t1913\t2042\t0\n+Gypsy2-LTR_DM\t0\t19\t0\n+Gypsy2-LTR_DM\t19\t40\t25.6148\n+Gypsy2-LTR_DM\t40\t58\t0\n+Gypsy2-LTR_DM\t58\t61\t25.6148\n+Gypsy2-LTR_DM\t61\t79\t51.2295\n+Gypsy2-LTR_DM\t79\t82\t25.6148\n+Gypsy2-LTR_DM\t82\t107\t0\n+Gypsy2-LTR_DM\t107\t108\t51.2295\n+Gypsy2-LTR_DM\t108\t109\t128.074\n+Gypsy2-LTR_DM\t109\t128\t153.689\n+Gypsy2-LTR_DM\t128\t129\t102.459\n+Gypsy2-LTR_DM\t129\t130\t25.6148\n+Gypsy2-LTR_DM\t130\t146\t0\n+Gypsy2-LTR_DM\t146\t147\t25.6148\n+Gypsy2-LTR_DM\t147\t150\t51.2295\n+Gypsy2-LTR_DM\t150\t153\t76.8443\n+Gypsy2-LTR_DM\t153\t154\t102.459\n+Gypsy2-LTR_DM\t154\t156\t128.074\n+Gypsy2-LTR_DM\t156\t167\t153.689\n+Gypsy2-LTR_DM\t167\t168\t128.074\n+Gypsy2-LTR_DM\t168\t171\t102.459\n+Gypsy2-LTR_DM\t171\t174\t76.8443\n+Gypsy2-LTR_DM\t174\t175\t51.2295\n+Gypsy2-LTR_DM\t175\t177\t25.6148\n+Gypsy2-LTR_DM\t177\t280\t0\n+Gypsy2-LTR_DM\t280\t301\t25.6148\n+Gypsy2-LTR_DM\t301\t338\t0\n+I_DM\t0\t2989\t0\n+I_DM\t2989\t3010\t25.6148\n+I_DM\t3010\t3248\t0\n+I_DM\t3248\t3269\t25.6148\n+I_DM\t3269\t4914\t0\n+I_DM\t4914\t4919\t25.6148\n+I_DM\t4919\t4935\t51.2295\n+I_DM\t4935\t4940\t25.6148\n+I_DM\t4940\t5374\t0\n+MAX_I\t0\t29\t0\n+MAX_I\t29\t50\t25.6148\n+MAX_I\t50\t102\t0\n+MAX_I\t102\t122\t25.6148\n+MAX_I\t122\t123\t51.2295\n+MAX_I\t123\t128\t25.6148\n+MAX_I\t128\t131\t51.2295\n+MAX_I\t131\t143\t76.8443\n+MAX_I\t143\t149\t51.2295\n+MAX_I\t149\t152\t25.6148\n+MAX_I\t152\t237\t0\n+MAX_I\t237\t258\t51.2295\n+MAX_I\t258\t7914\t0\n+MAX_LTR\t0\t18\t0\n+MAX_LTR\t18\t39\t25.6148\n+MAX_LTR\t39\t80\t0\n+MAX_LTR\t80\t97\t76.8443\n+MAX_LTR\t97\t99\t102.459\n+MAX_LTR\t99\t101\t153.689\n+MAX_LTR\t101\t102\t76.8443\n+MAX_LTR\t102\t118\t102.459\n+MAX_LTR\t118\t120\t76.8443\n+MAX_LTR\t120\t123\t25.6148\n+MAX_LTR\t123\t154\t0\n+MAX_LTR\t154\t175\t25.6148\n+MAX_LTR\t175\t321\t0\n+PROTOP\t0\t2492\t0\n+PROTOP\t2492\t2493\t25.6148\n+PROTOP\t2493\t2513\t51.2295\n+PROTOP\t2513\t2514\t25.6148\n+PROTOP\t2514\t3223\t0\n+PROTOP\t3223\t3244\t25.6148\n+PROTOP\t3244\t3464\t0\n+PROTOP\t3464\t3478\t25.6148\n+PROTOP\t3478\t3485\t51.2295\n+PROTOP\t3485\t3487\t25.6148\n+PROTOP\t3487\t3499\t51.2295\n+PROTOP\t3499\t3508\t25.6148\n+PROTOP\t3508\t4480\t0\n' |
| b |
| diff -r 9645d995fb3c -r 9185ca0a7b43 test-data/res_files/reads-sample-small.fastq/subgroups/siRNAs/siRNAs-TEs_plus.bedgraph --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/res_files/reads-sample-small.fastq/subgroups/siRNAs/siRNAs-TEs_plus.bedgraph Wed Jan 16 08:18:13 2019 -0500 |
| b |
| b'@@ -0,0 +1,688 @@\n+BATUMI_I\t0\t123\t0\n+BATUMI_I\t123\t144\t25.6148\n+BATUMI_I\t144\t7009\t0\n+BATUMI_I\t7009\t7010\t51.2295\n+BATUMI_I\t7010\t7017\t76.8443\n+BATUMI_I\t7017\t7030\t358.607\n+BATUMI_I\t7030\t7031\t307.377\n+BATUMI_I\t7031\t7036\t281.762\n+BATUMI_I\t7036\t7963\t0\n+BATUMI_LTR\t0\t192\t0\n+BATUMI_LTR\t192\t213\t25.6148\n+BATUMI_LTR\t213\t272\t0\n+BS2\t0\t187\t0\n+BS2\t187\t208\t25.6148\n+BS2\t208\t225\t0\n+BS2\t225\t246\t25.6148\n+BS2\t246\t276\t0\n+BS2\t276\t277\t51.2295\n+BS2\t277\t297\t76.8443\n+BS2\t297\t298\t25.6148\n+BS2\t298\t483\t0\n+BS2\t483\t504\t25.6148\n+BS2\t504\t587\t0\n+BS2\t587\t608\t51.2295\n+BS2\t608\t704\t0\n+BS2\t704\t725\t25.6148\n+BS2\t725\t726\t0\n+BS2\t726\t747\t25.6148\n+BS2\t747\t771\t0\n+BS2\t771\t792\t25.6148\n+BS2\t792\t797\t0\n+BS2\t797\t818\t25.6148\n+BS2\t818\t893\t0\n+BS2\t893\t914\t25.6148\n+BS2\t914\t1173\t0\n+BS2\t1173\t1183\t25.6148\n+BS2\t1183\t1194\t51.2295\n+BS2\t1194\t1204\t25.6148\n+BS2\t1204\t1325\t0\n+BS2\t1325\t1346\t25.6148\n+BS2\t1346\t1478\t0\n+BS2\t1478\t1499\t51.2295\n+BS2\t1499\t1578\t0\n+BS2\t1578\t1599\t51.2295\n+BS2\t1599\t1886\t0\n+BS2\t1886\t1907\t25.6148\n+BS2\t1907\t1943\t0\n+BS2\t1943\t1964\t25.6148\n+BS2\t1964\t2158\t0\n+BS2\t2158\t2159\t25.6148\n+BS2\t2159\t2179\t51.2295\n+BS2\t2179\t2180\t25.6148\n+BS2\t2180\t2248\t0\n+BS2\t2248\t2269\t25.6148\n+BS2\t2269\t2303\t0\n+BS2\t2303\t2309\t25.6148\n+BS2\t2309\t2324\t51.2295\n+BS2\t2324\t2329\t25.6148\n+BS2\t2329\t2330\t51.2295\n+BS2\t2330\t2346\t25.6148\n+BS2\t2346\t2350\t51.2295\n+BS2\t2350\t2354\t25.6148\n+BS2\t2354\t2362\t204.918\n+BS2\t2362\t2367\t230.533\n+BS2\t2367\t2375\t204.918\n+BS2\t2375\t2382\t25.6148\n+BS2\t2382\t2383\t76.8443\n+BS2\t2383\t2403\t51.2295\n+BS2\t2403\t2471\t0\n+BS2\t2471\t2492\t128.074\n+BS2\t2492\t2558\t0\n+BS2\t2558\t2579\t25.6148\n+BS2\t2579\t2673\t0\n+BS2\t2673\t2694\t25.6148\n+BS2\t2694\t2801\t0\n+BS2\t2801\t2802\t25.6148\n+BS2\t2802\t2815\t51.2295\n+BS2\t2815\t2819\t76.8443\n+BS2\t2819\t2822\t102.459\n+BS2\t2822\t2823\t76.8443\n+BS2\t2823\t2836\t51.2295\n+BS2\t2836\t2840\t25.6148\n+BS2\t2840\t2858\t0\n+BS2\t2858\t2879\t25.6148\n+BS2\t2879\t2974\t0\n+BS2\t2974\t2979\t25.6148\n+BS2\t2979\t2995\t51.2295\n+BS2\t2995\t3000\t25.6148\n+BS2\t3000\t3078\t0\n+BS2\t3078\t3099\t76.8443\n+BS2\t3099\t3123\t0\n+BS2\t3123\t3131\t25.6148\n+BS2\t3131\t3132\t51.2295\n+BS2\t3132\t3144\t76.8443\n+BS2\t3144\t3152\t51.2295\n+BS2\t3152\t3153\t25.6148\n+BS2\t3153\t3362\t0\n+BS2\t3362\t3383\t51.2295\n+BS2\t3383\t3893\t0\n+BS2\t3893\t3894\t25.6148\n+BS2\t3894\t3908\t51.2295\n+BS2\t3908\t3914\t102.459\n+BS2\t3914\t3915\t76.8443\n+BS2\t3915\t3929\t51.2295\n+BS2\t3929\t3968\t0\n+BS2\t3968\t3989\t25.6148\n+BS2\t3989\t4138\t0\n+BS2\t4138\t4159\t25.6148\n+BS2\t4159\t4187\t0\n+BS2\t4187\t4206\t25.6148\n+BS2\t4206\t4208\t51.2295\n+BS2\t4208\t4227\t25.6148\n+BS2\t4227\t4244\t0\n+BS2\t4244\t4265\t25.6148\n+BS2\t4265\t4313\t0\n+BS2\t4313\t4334\t25.6148\n+BS2\t4334\t4415\t0\n+BS2\t4415\t4433\t102.459\n+BS2\t4433\t4436\t128.074\n+BS2\t4436\t4454\t25.6148\n+BS2\t4454\t4463\t0\n+BS2\t4463\t4464\t76.8443\n+BS2\t4464\t4484\t102.459\n+BS2\t4484\t4485\t25.6148\n+BS2\t4485\t4533\t0\n+BS2\t4533\t4554\t51.2295\n+BS2\t4554\t4668\t0\n+BS2\t4668\t4689\t25.6148\n+BS2\t4689\t4721\t0\n+DMCR1A\t0\t87\t0\n+DMCR1A\t87\t108\t25.6148\n+DMCR1A\t108\t979\t0\n+DMCR1A\t979\t1000\t76.8443\n+DMCR1A\t1000\t1161\t0\n+DMCR1A\t1161\t1182\t25.6148\n+DMCR1A\t1182\t1859\t0\n+DMCR1A\t1859\t1880\t25.6148\n+DMCR1A\t1880\t4470\t0\n+DMRT1B\t0\t424\t0\n+DMRT1B\t424\t445\t25.6148\n+DMRT1B\t445\t564\t0\n+DMRT1B\t564\t585\t25.6148\n+DMRT1B\t585\t798\t0\n+DMRT1B\t798\t819\t25.6148\n+DMRT1B\t819\t1226\t0\n+DMRT1B\t1226\t1247\t25.6148\n+DMRT1B\t1247\t1280\t0\n+DMRT1B\t1280\t1301\t25.6148\n+DMRT1B\t1301\t1316\t0\n+DMRT1B\t1316\t1337\t25.6148\n+DMRT1B\t1337\t1346\t0\n+DMRT1B\t1346\t1361\t25.6148\n+DMRT1B\t1361\t1363\t51.2295\n+DMRT1B\t1363\t1367\t76.8443\n+DMRT1B\t1367\t1370\t51.2295\n+DMRT1B\t1370\t1373\t76.8443\n+DMRT1B\t1373\t1382\t102.459\n+DMRT1B\t1382\t1384\t76.8443\n+DMRT1B\t1384\t1391\t51.2295\n+DMRT1B\t1391\t1394\t25.6148\n+DMRT1B\t1394\t5183\t0\n+FW\t0\t337\t0\n+FW\t337\t358\t25.6148\n+FW\t358\t400\t0\n+FW\t400\t411\t25.6148\n+FW\t411\t421\t51.2295\n+FW\t421\t432\t25.6148\n+FW\t432\t438\t0\n+FW\t438\t450\t25.6148\n+FW\t450\t451\t76.8443\n+FW\t451\t452\t102.459\n+FW\t452\t459\t128.074\n+FW\t459\t471\t102.459\n+FW\t471\t472\t51.2295\n+FW\t472\t473\t25.6148\n+FW\t473\t500\t0\n+FW\t500\t505\t614.754\n+FW\t505\t521\t640.369\n+FW\t521\t526\t25.6148\n+FW\t526\t566\t0\n+FW\t566\t571\t25.6148\n+FW\t571\t573\t51.2295\n+FW\t573\t587\t256.148\n+FW\t587\t592\t230.533\n+FW\t592\t594\t204.918\n+FW\t594\t629\t0\n+FW\t629\t650\t25.6148\n+FW\t650\t655\t0\n+FW\t655\t656\t25.6148\n+FW\t656\t671\t51.2295\n+FW\t671\t67'..b'\t3476\t102.459\n+FW\t3476\t3490\t25.6148\n+FW\t3490\t3504\t0\n+FW\t3504\t3525\t25.6148\n+FW\t3525\t3547\t0\n+FW\t3547\t3568\t25.6148\n+FW\t3568\t3579\t0\n+FW\t3579\t3580\t25.6148\n+FW\t3580\t3600\t51.2295\n+FW\t3600\t3601\t25.6148\n+FW\t3601\t3617\t0\n+FW\t3617\t3618\t25.6148\n+FW\t3618\t3622\t51.2295\n+FW\t3622\t3625\t76.8443\n+FW\t3625\t3627\t102.459\n+FW\t3627\t3628\t128.074\n+FW\t3628\t3638\t281.762\n+FW\t3638\t3639\t256.148\n+FW\t3639\t3643\t230.533\n+FW\t3643\t3646\t204.918\n+FW\t3646\t3648\t179.303\n+FW\t3648\t3649\t153.689\n+FW\t3649\t3659\t0\n+FW\t3659\t3680\t25.6148\n+FW\t3680\t3716\t0\n+FW\t3716\t3737\t51.2295\n+FW\t3737\t3745\t0\n+FW\t3745\t3750\t25.6148\n+FW\t3750\t3756\t51.2295\n+FW\t3756\t3759\t76.8443\n+FW\t3759\t3766\t102.459\n+FW\t3766\t3771\t76.8443\n+FW\t3771\t3777\t51.2295\n+FW\t3777\t3780\t25.6148\n+FW\t3780\t3916\t0\n+FW\t3916\t3937\t25.6148\n+FW\t3937\t3950\t0\n+FW\t3950\t3971\t25.6148\n+FW\t3971\t3994\t0\n+FW\t3994\t4008\t25.6148\n+FW\t4008\t4010\t51.2295\n+FW\t4010\t4013\t307.377\n+FW\t4013\t4014\t332.992\n+FW\t4014\t4015\t358.607\n+FW\t4015\t4029\t332.992\n+FW\t4029\t4030\t307.377\n+FW\t4030\t4031\t384.221\n+FW\t4031\t4034\t128.074\n+FW\t4034\t4035\t102.459\n+FW\t4035\t4044\t76.8443\n+FW\t4044\t4051\t102.459\n+FW\t4051\t4065\t25.6148\n+FW\t4065\t4089\t0\n+FW\t4089\t4098\t25.6148\n+FW\t4098\t4100\t51.2295\n+FW\t4100\t4110\t76.8443\n+FW\t4110\t4119\t51.2295\n+FW\t4119\t4121\t25.6148\n+FW\t4121\t4169\t0\n+FW\t4169\t4171\t25.6148\n+FW\t4171\t4174\t51.2295\n+FW\t4174\t4179\t76.8443\n+FW\t4179\t4186\t102.459\n+FW\t4186\t4190\t128.074\n+FW\t4190\t4192\t102.459\n+FW\t4192\t4195\t76.8443\n+FW\t4195\t4200\t51.2295\n+FW\t4200\t4207\t25.6148\n+FW\t4207\t4235\t0\n+FW\t4235\t4236\t51.2295\n+FW\t4236\t4238\t76.8443\n+FW\t4238\t4242\t102.459\n+FW\t4242\t4248\t128.074\n+FW\t4248\t4256\t153.689\n+FW\t4256\t4257\t128.074\n+FW\t4257\t4259\t102.459\n+FW\t4259\t4263\t76.8443\n+FW\t4263\t4269\t51.2295\n+FW\t4269\t4277\t25.6148\n+FW\t4277\t4322\t0\n+FW\t4322\t4343\t204.918\n+FW\t4343\t4346\t0\n+FW\t4346\t4347\t51.2295\n+FW\t4347\t4349\t76.8443\n+FW\t4349\t4355\t153.689\n+FW\t4355\t4366\t179.303\n+FW\t4366\t4367\t204.918\n+FW\t4367\t4368\t153.689\n+FW\t4368\t4370\t128.074\n+FW\t4370\t4376\t51.2295\n+FW\t4376\t4387\t25.6148\n+FW\t4387\t4499\t0\n+FW\t4499\t4520\t25.6148\n+FW\t4520\t4529\t0\n+FW\t4529\t4530\t153.689\n+FW\t4530\t4531\t179.303\n+FW\t4531\t4550\t204.918\n+FW\t4550\t4551\t51.2295\n+FW\t4551\t4552\t25.6148\n+FW\t4552\t4692\t0\n+G6_DM\t0\t1190\t0\n+G6_DM\t1190\t1211\t25.6148\n+G6_DM\t1211\t1225\t0\n+G6_DM\t1225\t1232\t25.6148\n+G6_DM\t1232\t1246\t51.2295\n+G6_DM\t1246\t1253\t25.6148\n+G6_DM\t1253\t1258\t0\n+G6_DM\t1258\t1279\t25.6148\n+G6_DM\t1279\t1310\t0\n+G6_DM\t1310\t1331\t25.6148\n+G6_DM\t1331\t1334\t0\n+G6_DM\t1334\t1350\t102.459\n+G6_DM\t1350\t1355\t128.074\n+G6_DM\t1355\t1371\t25.6148\n+G6_DM\t1371\t1413\t0\n+G6_DM\t1413\t1434\t25.6148\n+G6_DM\t1434\t1489\t0\n+G6_DM\t1489\t1510\t25.6148\n+G6_DM\t1510\t1533\t0\n+G6_DM\t1533\t1554\t204.918\n+G6_DM\t1554\t1620\t0\n+G6_DM\t1620\t1629\t25.6148\n+G6_DM\t1629\t1641\t51.2295\n+G6_DM\t1641\t1650\t25.6148\n+G6_DM\t1650\t1665\t0\n+G6_DM\t1665\t1667\t25.6148\n+G6_DM\t1667\t1673\t51.2295\n+G6_DM\t1673\t1686\t76.8443\n+G6_DM\t1686\t1688\t51.2295\n+G6_DM\t1688\t1694\t25.6148\n+G6_DM\t1694\t1702\t0\n+G6_DM\t1702\t1723\t51.2295\n+G6_DM\t1723\t2042\t0\n+Gypsy2-LTR_DM\t0\t90\t0\n+Gypsy2-LTR_DM\t90\t111\t25.6148\n+Gypsy2-LTR_DM\t111\t122\t0\n+Gypsy2-LTR_DM\t122\t134\t25.6148\n+Gypsy2-LTR_DM\t134\t136\t51.2295\n+Gypsy2-LTR_DM\t136\t143\t76.8443\n+Gypsy2-LTR_DM\t143\t146\t51.2295\n+Gypsy2-LTR_DM\t146\t155\t76.8443\n+Gypsy2-LTR_DM\t155\t157\t51.2295\n+Gypsy2-LTR_DM\t157\t164\t102.459\n+Gypsy2-LTR_DM\t164\t167\t128.074\n+Gypsy2-LTR_DM\t167\t178\t102.459\n+Gypsy2-LTR_DM\t178\t185\t25.6148\n+Gypsy2-LTR_DM\t185\t201\t0\n+Gypsy2-LTR_DM\t201\t207\t25.6148\n+Gypsy2-LTR_DM\t207\t222\t76.8443\n+Gypsy2-LTR_DM\t222\t228\t51.2295\n+Gypsy2-LTR_DM\t228\t258\t0\n+Gypsy2-LTR_DM\t258\t268\t25.6148\n+Gypsy2-LTR_DM\t268\t279\t51.2295\n+Gypsy2-LTR_DM\t279\t289\t25.6148\n+Gypsy2-LTR_DM\t289\t338\t0\n+I_DM\t0\t4908\t0\n+I_DM\t4908\t4929\t25.6148\n+I_DM\t4929\t5374\t0\n+MAX_I\t0\t119\t0\n+MAX_I\t119\t140\t25.6148\n+MAX_I\t140\t7914\t0\n+MAX_LTR\t0\t84\t0\n+MAX_LTR\t84\t105\t51.2295\n+MAX_LTR\t105\t138\t0\n+MAX_LTR\t138\t159\t25.6148\n+MAX_LTR\t159\t321\t0\n+PROTOP\t0\t449\t0\n+PROTOP\t449\t470\t25.6148\n+PROTOP\t470\t2499\t0\n+PROTOP\t2499\t2520\t25.6148\n+PROTOP\t2520\t2745\t0\n+PROTOP\t2745\t2746\t51.2295\n+PROTOP\t2746\t2752\t128.074\n+PROTOP\t2752\t2766\t153.689\n+PROTOP\t2766\t2767\t102.459\n+PROTOP\t2767\t2773\t25.6148\n+PROTOP\t2773\t3258\t0\n+PROTOP\t3258\t3279\t51.2295\n+PROTOP\t3279\t4480\t0\n' |
| b |
| diff -r 9645d995fb3c -r 9185ca0a7b43 test-data/res_files/reads-sample-small.fastq/subgroups/siRNAs/siRNAs-TEs_reads_counts.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/res_files/reads-sample-small.fastq/subgroups/siRNAs/siRNAs-TEs_reads_counts.txt Wed Jan 16 08:18:13 2019 -0500 |
| b |
| @@ -0,0 +1,18 @@ +ID reads counts RPKM per million of piRNAs per million of miRNAs per million of bonafide reads sense reads counts reverse reads counts % of sense 1U % of sense 10A % of reverse 1U % of reverse 10A +BATUMI_I 21 67.55 910.83 333333.33 687.85 15 6 86.6666666666667 0 50 50 +BATUMI_LTR 5 470.86 216.86 79365.08 163.77 1 4 0 0 0 25 +BS2 423 2295.07 18346.63 6714285.71 13855.22 83 340 38.5542168674699 40.9638554216867 3.82352941176471 22.6470588235294 +COPIA_DM_I 0 0.00 0.00 0.00 0.00 0 0 0 0 0 0 +COPIA_DM_LTR 0 0.00 0.00 0.00 0.00 0 0 0 0 0 0 +DMCR1A 14 80.23 607.22 222222.22 458.57 6 8 50 16.6666666666667 0 0 +DMRT1B 27 133.44 1171.06 428571.43 884.38 11 16 36.3636363636364 18.1818181818182 18.75 18.75 +FW 1588 8669.27 68875.78 25206349.21 52014.41 407 1181 28.992628992629 40.2948402948403 12.0237087214225 20.9991532599492 +G6_DM 118 1480.19 5117.97 1873015.87 3865.05 27 91 22.2222222222222 66.6666666666667 5.49450549450549 17.5824175824176 +Gypsy2-I_DM 0 0.00 0.00 0.00 0.00 0 0 0 0 0 0 +Gypsy2-LTR_DM 30 2273.50 1301.18 476190.48 982.64 14 16 35.7142857142857 14.2857142857143 0 25 +I_DM 5 23.83 216.86 79365.08 163.77 1 4 0 0 0 25 +MAX_I 8 25.89 346.98 126984.13 262.04 1 7 100 0 28.5714285714286 0 +MAX_LTR 12 957.56 520.47 190476.19 393.06 3 9 33.3333333333333 0 22.2222222222222 0 +PROTOP 16 91.48 693.96 253968.25 524.07 10 6 80 50 0 16.6666666666667 +ZAM_I 0 0.00 0.00 0.00 0.00 0 0 0 0 0 0 +ZAM_LTR 0 0.00 0.00 0.00 0.00 0 0 0 0 0 0 |
| b |
| diff -r 9645d995fb3c -r 9185ca0a7b43 test-data/res_files/reads-sample-small.fastq/subgroups/siRNAs/siRNAs-TEs_reads_counts_mismatches.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/res_files/reads-sample-small.fastq/subgroups/siRNAs/siRNAs-TEs_reads_counts_mismatches.txt Wed Jan 16 08:18:13 2019 -0500 |
| b |
| @@ -0,0 +1,18 @@ +ID reads counts RPKM per million of piRNAs per million of miRNAs per million of bonafide reads sense reads counts reverse reads counts % of sense 1U % of sense 10A % of reverse 1U % of reverse 10A +BATUMI_I 15 48.25 650.59 238095.24 491.32 12 3 91.6666666666667 0 66.6666666666667 33.3333333333333 +BATUMI_LTR 4 376.69 173.49 63492.06 131.02 1 3 0 0 0 33.3333333333333 +BS2 8 43.41 346.98 126984.13 262.04 4 4 25 25 0 50 +COPIA_DM_I 0 0.00 0.00 0.00 0.00 0 0 0 0 0 0 +COPIA_DM_LTR 0 0.00 0.00 0.00 0.00 0 0 0 0 0 0 +DMCR1A 4 22.92 173.49 63492.06 131.02 1 3 0 0 0 0 +DMRT1B 16 79.07 693.96 253968.25 524.07 6 10 33.3333333333333 16.6666666666667 30 20 +FW 12 65.51 520.47 190476.19 393.06 3 9 33.3333333333333 33.3333333333333 0 22.2222222222222 +G6_DM 0 0.00 0.00 0.00 0.00 0 0 0 0 0 0 +Gypsy2-I_DM 0 0.00 0.00 0.00 0.00 0 0 0 0 0 0 +Gypsy2-LTR_DM 0 0.00 0.00 0.00 0.00 0 0 0 0 0 0 +I_DM 3 14.30 130.12 47619.05 98.26 0 3 0 0 0 33.3333333333333 +MAX_I 3 9.71 130.12 47619.05 98.26 0 3 0 0 33.3333333333333 0 +MAX_LTR 5 398.98 216.86 79365.08 163.77 0 5 0 0 40 0 +PROTOP 7 40.02 303.61 111111.11 229.28 4 3 50 75 0 33.3333333333333 +ZAM_I 0 0.00 0.00 0.00 0.00 0 0 0 0 0 0 +ZAM_LTR 0 0.00 0.00 0.00 0.00 0 0 0 0 0 0 |
| b |
| diff -r 9645d995fb3c -r 9185ca0a7b43 test-data/res_files/reads-sample-small.fastq/subgroups/siRNAs/siRNAs-TEs_reads_counts_nomismatches.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/res_files/reads-sample-small.fastq/subgroups/siRNAs/siRNAs-TEs_reads_counts_nomismatches.txt Wed Jan 16 08:18:13 2019 -0500 |
| b |
| @@ -0,0 +1,18 @@ +ID reads counts RPKM per million of piRNAs per million of miRNAs per million of bonafide reads sense reads counts reverse reads counts % of sense 1U % of sense 10A % of reverse 1U % of reverse 10A +BATUMI_I 6 19.30 260.24 95238.10 196.53 3 3 66.6666666666667 0 33.3333333333333 66.6666666666667 +BATUMI_LTR 1 94.17 43.37 15873.02 32.75 0 1 0 0 0 0 +BS2 415 2251.67 17999.65 6587301.59 13593.19 79 336 39.2405063291139 41.7721518987342 3.86904761904762 22.3214285714286 +COPIA_DM_I 0 0.00 0.00 0.00 0.00 0 0 0 0 0 0 +COPIA_DM_LTR 0 0.00 0.00 0.00 0.00 0 0 0 0 0 0 +DMCR1A 10 57.30 433.73 158730.16 327.55 5 5 60 20 0 0 +DMRT1B 11 54.36 477.10 174603.17 360.30 5 6 40 20 0 16.6666666666667 +FW 1576 8603.76 68355.31 25015873.02 51621.36 404 1172 28.960396039604 40.3465346534653 12.1160409556314 20.9897610921502 +G6_DM 118 1480.19 5117.97 1873015.87 3865.05 27 91 22.2222222222222 66.6666666666667 5.49450549450549 17.5824175824176 +Gypsy2-I_DM 0 0.00 0.00 0.00 0.00 0 0 0 0 0 0 +Gypsy2-LTR_DM 30 2273.50 1301.18 476190.48 982.64 14 16 35.7142857142857 14.2857142857143 0 25 +I_DM 2 9.53 86.75 31746.03 65.51 1 1 0 0 0 0 +MAX_I 5 16.18 216.86 79365.08 163.77 1 4 100 0 25 0 +MAX_LTR 7 558.58 303.61 111111.11 229.28 3 4 33.3333333333333 0 0 0 +PROTOP 9 51.46 390.35 142857.14 294.79 6 3 100 33.3333333333333 0 0 +ZAM_I 0 0.00 0.00 0.00 0.00 0 0 0 0 0 0 +ZAM_LTR 0 0.00 0.00 0.00 0.00 0 0 0 0 0 0 |
| b |
| diff -r 9645d995fb3c -r 9185ca0a7b43 test-data/res_files/reads-sample-small.fastq/subgroups/siRNAs/siRNAs-TEs_sorted.bam |
| b |
| Binary file test-data/res_files/reads-sample-small.fastq/subgroups/siRNAs/siRNAs-TEs_sorted.bam has changed |
| b |
| diff -r 9645d995fb3c -r 9185ca0a7b43 test-data/res_files/reads-sample-small.fastq/subgroups/siRNAs/siRNAs-TEs_unique_sorted.bam |
| b |
| Binary file test-data/res_files/reads-sample-small.fastq/subgroups/siRNAs/siRNAs-TEs_unique_sorted.bam has changed |
| b |
| diff -r 9645d995fb3c -r 9185ca0a7b43 test-data/res_files/reads-sample-small.fastq/subgroups/siRNAs/siRNAs-genome_minus.bedgraph --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/res_files/reads-sample-small.fastq/subgroups/siRNAs/siRNAs-genome_minus.bedgraph Wed Jan 16 08:18:13 2019 -0500 |
| b |
| b'@@ -0,0 +1,1123 @@\n+chrom_1\t0\t12140\t0\n+chrom_1\t12140\t12161\t25.6148\n+chrom_1\t12161\t15164\t0\n+chrom_1\t15164\t15185\t25.6148\n+chrom_1\t15185\t15260\t0\n+chrom_1\t15260\t15281\t25.6148\n+chrom_1\t15281\t15349\t0\n+chrom_1\t15349\t15370\t25.6148\n+chrom_1\t15370\t15559\t0\n+chrom_1\t15559\t15580\t25.6148\n+chrom_1\t15580\t15981\t0\n+chrom_1\t15981\t15993\t25.6148\n+chrom_1\t15993\t16002\t51.2295\n+chrom_1\t16002\t16014\t25.6148\n+chrom_1\t16014\t16171\t0\n+chrom_1\t16171\t16192\t25.6148\n+chrom_1\t16192\t16427\t0\n+chrom_1\t16427\t16448\t25.6148\n+chrom_1\t16448\t16900\t0\n+chrom_1\t16900\t16921\t25.6148\n+chrom_1\t16921\t17063\t0\n+chrom_1\t17063\t17084\t25.6148\n+chrom_1\t17084\t17176\t0\n+chrom_1\t17176\t17197\t25.6148\n+chrom_1\t17197\t17449\t0\n+chrom_1\t17449\t17470\t25.6148\n+chrom_1\t17470\t17675\t0\n+chrom_1\t17675\t17678\t128.074\n+chrom_1\t17678\t17680\t153.689\n+chrom_1\t17680\t17696\t179.303\n+chrom_1\t17696\t17699\t51.2295\n+chrom_1\t17699\t17701\t25.6148\n+chrom_1\t17701\t17730\t0\n+chrom_1\t17730\t17751\t25.6148\n+chrom_1\t17751\t17829\t0\n+chrom_1\t17829\t17838\t25.6148\n+chrom_1\t17838\t17842\t51.2295\n+chrom_1\t17842\t17843\t76.8443\n+chrom_1\t17843\t17844\t102.459\n+chrom_1\t17844\t17845\t153.689\n+chrom_1\t17845\t17850\t332.992\n+chrom_1\t17850\t17859\t307.377\n+chrom_1\t17859\t17863\t281.762\n+chrom_1\t17863\t17864\t256.148\n+chrom_1\t17864\t17865\t230.533\n+chrom_1\t17865\t17866\t179.303\n+chrom_1\t17866\t18046\t0\n+chrom_1\t18046\t18067\t51.2295\n+chrom_1\t18067\t18157\t0\n+chrom_1\t18157\t18160\t25.6148\n+chrom_1\t18160\t18167\t51.2295\n+chrom_1\t18167\t18169\t76.8443\n+chrom_1\t18169\t18178\t102.459\n+chrom_1\t18178\t18181\t76.8443\n+chrom_1\t18181\t18184\t51.2295\n+chrom_1\t18184\t18188\t76.8443\n+chrom_1\t18188\t18190\t51.2295\n+chrom_1\t18190\t18205\t25.6148\n+chrom_1\t18205\t18214\t0\n+chrom_1\t18214\t18235\t25.6148\n+chrom_1\t18235\t18250\t0\n+chrom_1\t18250\t18271\t25.6148\n+chrom_1\t18271\t18304\t0\n+chrom_1\t18304\t18325\t25.6148\n+chrom_1\t18325\t18488\t0\n+chrom_1\t18488\t18509\t25.6148\n+chrom_1\t18509\t18722\t0\n+chrom_1\t18722\t18743\t25.6148\n+chrom_1\t18743\t18862\t0\n+chrom_1\t18862\t18883\t25.6148\n+chrom_1\t18883\t18973\t0\n+chrom_1\t18973\t18994\t25.6148\n+chrom_1\t18994\t19163\t0\n+chrom_1\t19163\t19184\t25.6148\n+chrom_1\t19184\t19238\t0\n+chrom_1\t19238\t19259\t25.6148\n+chrom_1\t19259\t19420\t0\n+chrom_1\t19420\t19441\t25.6148\n+chrom_1\t19441\t20045\t0\n+chrom_1\t20045\t20066\t25.6148\n+chrom_1\t20066\t20180\t0\n+chrom_1\t20180\t20201\t51.2295\n+chrom_1\t20201\t20249\t0\n+chrom_1\t20249\t20250\t25.6148\n+chrom_1\t20250\t20270\t102.459\n+chrom_1\t20270\t20271\t76.8443\n+chrom_1\t20271\t20280\t0\n+chrom_1\t20280\t20298\t25.6148\n+chrom_1\t20298\t20301\t128.074\n+chrom_1\t20301\t20319\t102.459\n+chrom_1\t20319\t20400\t0\n+chrom_1\t20400\t20421\t25.6148\n+chrom_1\t20421\t20469\t0\n+chrom_1\t20469\t20490\t25.6148\n+chrom_1\t20490\t20507\t0\n+chrom_1\t20507\t20526\t25.6148\n+chrom_1\t20526\t20528\t51.2295\n+chrom_1\t20528\t20547\t25.6148\n+chrom_1\t20547\t20575\t0\n+chrom_1\t20575\t20596\t25.6148\n+chrom_1\t20596\t20745\t0\n+chrom_1\t20745\t20766\t25.6148\n+chrom_1\t20766\t20805\t0\n+chrom_1\t20805\t20819\t51.2295\n+chrom_1\t20819\t20820\t76.8443\n+chrom_1\t20820\t20826\t102.459\n+chrom_1\t20826\t20840\t51.2295\n+chrom_1\t20840\t20841\t25.6148\n+chrom_1\t20841\t20960\t0\n+chrom_1\t20960\t20964\t25.6148\n+chrom_1\t20964\t20967\t51.2295\n+chrom_1\t20967\t20981\t102.459\n+chrom_1\t20981\t20985\t76.8443\n+chrom_1\t20985\t20988\t51.2295\n+chrom_1\t20988\t21008\t0\n+chrom_1\t21008\t21029\t102.459\n+chrom_1\t21029\t21071\t0\n+chrom_1\t21071\t21092\t51.2295\n+chrom_1\t21092\t21301\t0\n+chrom_1\t21301\t21302\t25.6148\n+chrom_1\t21302\t21310\t51.2295\n+chrom_1\t21310\t21322\t76.8443\n+chrom_1\t21322\t21323\t51.2295\n+chrom_1\t21323\t21331\t25.6148\n+chrom_1\t21331\t21355\t0\n+chrom_1\t21355\t21376\t76.8443\n+chrom_1\t21376\t21454\t0\n+chrom_1\t21454\t21459\t25.6148\n+chrom_1\t21459\t21475\t51.2295\n+chrom_1\t21475\t21480\t25.6148\n+chrom_1\t21480\t21575\t0\n+chrom_1\t21575\t21596\t25.6148\n+chrom_1\t21596\t21614\t0\n+chrom_1\t21614\t21618\t25.6148\n+chrom_1\t21618\t21631\t51.2295\n+chrom_1\t21631\t21632\t76.8443\n+chrom_1\t21632\t21635\t102.459\n+chrom_1\t21635\t21639\t76.8443\n+chrom_1\t21639\t21652\t51.2295\n+chrom_1\t21652\t21653\t25.6148\n+chrom_1\t21653\t21760\t0\n+chrom_1\t21760\t21781\t25.6148\n+chrom_1\t21781\t21875\t0\n+chrom_1\t21875\t21896\t25.6148\n+chrom_1\t21896\t21962\t0\n+chrom_1\t21962\t21983\t128.074\n+chrom_1\t21983\t22051\t0\n+chrom_1\t22051\t'..b'\t49875\t25.6148\n+chrom_1\t49875\t50715\t0\n+chrom_1\t50715\t50736\t25.6148\n+chrom_1\t50736\t50749\t0\n+chrom_1\t50749\t50770\t25.6148\n+chrom_1\t50770\t51663\t0\n+chrom_1\t51663\t51665\t25.6148\n+chrom_1\t51665\t51671\t51.2295\n+chrom_1\t51671\t51684\t76.8443\n+chrom_1\t51684\t51686\t51.2295\n+chrom_1\t51686\t51692\t25.6148\n+chrom_1\t51692\t51974\t0\n+chrom_1\t51974\t51995\t25.6148\n+chrom_1\t51995\t52373\t0\n+chrom_1\t52373\t52394\t51.2295\n+chrom_1\t52394\t53410\t0\n+chrom_1\t53410\t53431\t25.6148\n+chrom_1\t53431\t53763\t0\n+chrom_1\t53763\t53784\t25.6148\n+chrom_1\t53784\t54064\t0\n+chrom_1\t54064\t54085\t51.2295\n+chrom_1\t54085\t55267\t0\n+chrom_1\t55267\t55288\t25.6148\n+chrom_1\t55288\t55825\t0\n+chrom_1\t55825\t55837\t25.6148\n+chrom_1\t55837\t55846\t51.2295\n+chrom_1\t55846\t55858\t25.6148\n+chrom_1\t55858\t57223\t0\n+chrom_1\t57223\t57244\t25.6148\n+chrom_1\t57244\t58149\t0\n+chrom_1\t58149\t58170\t25.6148\n+chrom_1\t58170\t58175\t0\n+chrom_1\t58175\t58176\t25.6148\n+chrom_1\t58176\t58196\t51.2295\n+chrom_1\t58196\t58197\t25.6148\n+chrom_1\t58197\t58585\t0\n+chrom_1\t58585\t58606\t25.6148\n+chrom_1\t58606\t58798\t0\n+chrom_1\t58798\t58819\t25.6148\n+chrom_1\t58819\t58987\t0\n+chrom_1\t58987\t59008\t25.6148\n+chrom_1\t59008\t60022\t0\n+chrom_1\t60022\t60043\t25.6148\n+chrom_1\t60043\t60293\t0\n+chrom_1\t60293\t60314\t25.6148\n+chrom_1\t60314\t60537\t0\n+chrom_1\t60537\t60558\t25.6148\n+chrom_1\t60558\t61721\t0\n+chrom_1\t61721\t61742\t25.6148\n+chrom_1\t61742\t62018\t0\n+chrom_1\t62018\t62039\t25.6148\n+chrom_1\t62039\t62885\t0\n+chrom_1\t62885\t62906\t25.6148\n+chrom_1\t62906\t63072\t0\n+chrom_1\t63072\t63093\t25.6148\n+chrom_1\t63093\t63704\t0\n+chrom_1\t63704\t63725\t25.6148\n+chrom_1\t63725\t63787\t0\n+chrom_1\t63787\t63792\t25.6148\n+chrom_1\t63792\t63808\t51.2295\n+chrom_1\t63808\t63813\t25.6148\n+chrom_1\t63813\t64722\t0\n+chrom_1\t64722\t64743\t25.6148\n+chrom_1\t64743\t67433\t0\n+chrom_1\t67433\t67434\t25.6148\n+chrom_1\t67434\t67454\t51.2295\n+chrom_1\t67454\t67455\t25.6148\n+chrom_1\t67455\t67965\t0\n+chrom_1\t67965\t67986\t25.6148\n+chrom_1\t67986\t68548\t0\n+chrom_1\t68548\t68569\t25.6148\n+chrom_1\t68569\t68863\t0\n+chrom_1\t68863\t68884\t25.6148\n+chrom_1\t68884\t69781\t0\n+chrom_1\t69781\t69802\t25.6148\n+chrom_1\t69802\t70934\t0\n+chrom_1\t70934\t70955\t25.6148\n+chrom_1\t70955\t71363\t0\n+chrom_1\t71363\t71384\t25.6148\n+chrom_1\t71384\t71705\t0\n+chrom_1\t71705\t71726\t25.6148\n+chrom_1\t71726\t71760\t0\n+chrom_1\t71760\t71781\t25.6148\n+chrom_1\t71781\t72252\t0\n+chrom_1\t72252\t72273\t25.6148\n+chrom_1\t72273\t72315\t0\n+chrom_1\t72315\t72336\t25.6148\n+chrom_1\t72336\t73124\t0\n+chrom_1\t73124\t73145\t25.6148\n+chrom_1\t73145\t73249\t0\n+chrom_1\t73249\t73270\t25.6148\n+chrom_1\t73270\t73315\t0\n+chrom_1\t73315\t73336\t25.6148\n+chrom_1\t73336\t73759\t0\n+chrom_1\t73759\t73780\t25.6148\n+chrom_1\t73780\t74260\t0\n+chrom_1\t74260\t74281\t25.6148\n+chrom_1\t74281\t74954\t0\n+chrom_1\t74954\t74975\t25.6148\n+chrom_1\t74975\t75554\t0\n+chrom_1\t75554\t75575\t25.6148\n+chrom_1\t75575\t77319\t0\n+chrom_1\t77319\t77320\t25.6148\n+chrom_1\t77320\t77340\t51.2295\n+chrom_1\t77340\t77341\t25.6148\n+chrom_1\t77341\t77516\t0\n+chrom_1\t77516\t77537\t25.6148\n+chrom_1\t77537\t79059\t0\n+chrom_1\t79059\t79080\t25.6148\n+chrom_1\t79080\t80057\t0\n+chrom_1\t80057\t80078\t25.6148\n+chrom_1\t80078\t80319\t0\n+chrom_1\t80319\t80340\t25.6148\n+chrom_1\t80340\t81784\t0\n+chrom_1\t81784\t81805\t25.6148\n+chrom_1\t81805\t82339\t0\n+chrom_1\t82339\t82360\t25.6148\n+chrom_1\t82360\t83079\t0\n+chrom_1\t83079\t83100\t25.6148\n+chrom_1\t83100\t83540\t0\n+chrom_1\t83540\t83561\t25.6148\n+chrom_1\t83561\t83901\t0\n+chrom_1\t83901\t83922\t25.6148\n+chrom_1\t83922\t85181\t0\n+chrom_1\t85181\t85202\t25.6148\n+chrom_1\t85202\t85252\t0\n+chrom_1\t85252\t85273\t25.6148\n+chrom_1\t85273\t86453\t0\n+chrom_1\t86453\t86474\t25.6148\n+chrom_1\t86474\t87066\t0\n+chrom_1\t87066\t87087\t25.6148\n+chrom_1\t87087\t87142\t0\n+chrom_1\t87142\t87163\t25.6148\n+chrom_1\t87163\t87223\t0\n+chrom_1\t87223\t87244\t25.6148\n+chrom_1\t87244\t87446\t0\n+chrom_1\t87446\t87467\t25.6148\n+chrom_1\t87467\t87581\t0\n+chrom_1\t87581\t87602\t25.6148\n+chrom_1\t87602\t88309\t0\n+chrom_1\t88309\t88330\t25.6148\n+chrom_1\t88330\t88443\t0\n+chrom_1\t88443\t88464\t25.6148\n+chrom_1\t88464\t88710\t0\n+chrom_1\t88710\t88731\t25.6148\n+chrom_1\t88731\t89812\t0\n+chrom_1\t89812\t89833\t25.6148\n+chrom_1\t89833\t89999\t0\n+chrom_2\t0\t32289\t0\n+chrom_2\t32289\t32310\t25.6148\n+chrom_2\t32310\t39255\t0\n+chrom_2\t39255\t39276\t25.6148\n+chrom_2\t39276\t49999\t0\n' |
| b |
| diff -r 9645d995fb3c -r 9185ca0a7b43 test-data/res_files/reads-sample-small.fastq/subgroups/siRNAs/siRNAs-genome_plus.bedgraph --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/res_files/reads-sample-small.fastq/subgroups/siRNAs/siRNAs-genome_plus.bedgraph Wed Jan 16 08:18:13 2019 -0500 |
| b |
| b'@@ -0,0 +1,1514 @@\n+chrom_1\t0\t10407\t0\n+chrom_1\t10407\t10428\t25.6148\n+chrom_1\t10428\t14523\t0\n+chrom_1\t14523\t14544\t25.6148\n+chrom_1\t14544\t15400\t0\n+chrom_1\t15400\t15421\t76.8443\n+chrom_1\t15421\t15546\t0\n+chrom_1\t15546\t15567\t25.6148\n+chrom_1\t15567\t16229\t0\n+chrom_1\t16229\t16250\t25.6148\n+chrom_1\t16250\t16808\t0\n+chrom_1\t16808\t16829\t25.6148\n+chrom_1\t16829\t16875\t0\n+chrom_1\t16875\t16885\t25.6148\n+chrom_1\t16885\t16886\t76.8443\n+chrom_1\t16886\t16896\t102.459\n+chrom_1\t16896\t16906\t76.8443\n+chrom_1\t16906\t16907\t25.6148\n+chrom_1\t16907\t17054\t0\n+chrom_1\t17054\t17055\t768.443\n+chrom_1\t17055\t17056\t794.057\n+chrom_1\t17056\t17075\t819.672\n+chrom_1\t17075\t17076\t51.2295\n+chrom_1\t17076\t17077\t25.6148\n+chrom_1\t17077\t17236\t0\n+chrom_1\t17236\t17241\t25.6148\n+chrom_1\t17241\t17242\t76.8443\n+chrom_1\t17242\t17245\t153.689\n+chrom_1\t17245\t17257\t230.533\n+chrom_1\t17257\t17262\t204.918\n+chrom_1\t17262\t17263\t153.689\n+chrom_1\t17263\t17266\t76.8443\n+chrom_1\t17266\t17390\t0\n+chrom_1\t17390\t17411\t25.6148\n+chrom_1\t17411\t17421\t0\n+chrom_1\t17421\t17425\t25.6148\n+chrom_1\t17425\t17442\t51.2295\n+chrom_1\t17442\t17446\t25.6148\n+chrom_1\t17446\t17472\t0\n+chrom_1\t17472\t17493\t25.6148\n+chrom_1\t17493\t17622\t0\n+chrom_1\t17622\t17627\t25.6148\n+chrom_1\t17627\t17643\t51.2295\n+chrom_1\t17643\t17648\t25.6148\n+chrom_1\t17648\t17681\t0\n+chrom_1\t17681\t17702\t25.6148\n+chrom_1\t17702\t17825\t0\n+chrom_1\t17825\t17828\t25.6148\n+chrom_1\t17828\t17843\t51.2295\n+chrom_1\t17843\t17848\t76.8443\n+chrom_1\t17848\t17849\t102.459\n+chrom_1\t17849\t17864\t76.8443\n+chrom_1\t17864\t17867\t51.2295\n+chrom_1\t17867\t17869\t25.6148\n+chrom_1\t17869\t18057\t0\n+chrom_1\t18057\t18078\t51.2295\n+chrom_1\t18078\t18164\t0\n+chrom_1\t18164\t18171\t25.6148\n+chrom_1\t18171\t18174\t51.2295\n+chrom_1\t18174\t18175\t76.8443\n+chrom_1\t18175\t18185\t102.459\n+chrom_1\t18185\t18190\t76.8443\n+chrom_1\t18190\t18192\t102.459\n+chrom_1\t18192\t18196\t76.8443\n+chrom_1\t18196\t18211\t51.2295\n+chrom_1\t18211\t18216\t25.6148\n+chrom_1\t18216\t18269\t0\n+chrom_1\t18269\t18275\t25.6148\n+chrom_1\t18275\t18276\t51.2295\n+chrom_1\t18276\t18290\t76.8443\n+chrom_1\t18290\t18296\t51.2295\n+chrom_1\t18296\t18297\t25.6148\n+chrom_1\t18297\t18307\t0\n+chrom_1\t18307\t18328\t25.6148\n+chrom_1\t18328\t18407\t0\n+chrom_1\t18407\t18428\t51.2295\n+chrom_1\t18428\t18554\t0\n+chrom_1\t18554\t18575\t25.6148\n+chrom_1\t18575\t18666\t0\n+chrom_1\t18666\t18687\t51.2295\n+chrom_1\t18687\t18857\t0\n+chrom_1\t18857\t18878\t25.6148\n+chrom_1\t18878\t18983\t0\n+chrom_1\t18983\t19004\t25.6148\n+chrom_1\t19004\t19173\t0\n+chrom_1\t19173\t19194\t25.6148\n+chrom_1\t19194\t20163\t0\n+chrom_1\t20163\t20175\t25.6148\n+chrom_1\t20175\t20184\t51.2295\n+chrom_1\t20184\t20196\t25.6148\n+chrom_1\t20196\t20198\t0\n+chrom_1\t20198\t20216\t25.6148\n+chrom_1\t20216\t20219\t845.287\n+chrom_1\t20219\t20237\t819.672\n+chrom_1\t20237\t20258\t25.6148\n+chrom_1\t20258\t20260\t0\n+chrom_1\t20260\t20263\t25.6148\n+chrom_1\t20263\t20264\t51.2295\n+chrom_1\t20264\t20281\t76.8443\n+chrom_1\t20281\t20284\t51.2295\n+chrom_1\t20284\t20285\t25.6148\n+chrom_1\t20285\t20288\t0\n+chrom_1\t20288\t20290\t51.2295\n+chrom_1\t20290\t20309\t76.8443\n+chrom_1\t20309\t20311\t25.6148\n+chrom_1\t20311\t20346\t0\n+chrom_1\t20346\t20360\t25.6148\n+chrom_1\t20360\t20361\t51.2295\n+chrom_1\t20361\t20362\t230.533\n+chrom_1\t20362\t20363\t307.377\n+chrom_1\t20363\t20367\t384.221\n+chrom_1\t20367\t20381\t358.607\n+chrom_1\t20381\t20382\t332.992\n+chrom_1\t20382\t20383\t153.689\n+chrom_1\t20383\t20384\t76.8443\n+chrom_1\t20384\t20399\t0\n+chrom_1\t20399\t20420\t25.6148\n+chrom_1\t20420\t20430\t0\n+chrom_1\t20430\t20446\t25.6148\n+chrom_1\t20446\t20451\t51.2295\n+chrom_1\t20451\t20467\t25.6148\n+chrom_1\t20467\t20516\t0\n+chrom_1\t20516\t20537\t384.221\n+chrom_1\t20537\t20566\t0\n+chrom_1\t20566\t20587\t25.6148\n+chrom_1\t20587\t20596\t0\n+chrom_1\t20596\t20609\t25.6148\n+chrom_1\t20609\t20617\t256.148\n+chrom_1\t20617\t20630\t230.533\n+chrom_1\t20630\t20666\t0\n+chrom_1\t20666\t20676\t25.6148\n+chrom_1\t20676\t20687\t128.074\n+chrom_1\t20687\t20697\t102.459\n+chrom_1\t20697\t20817\t0\n+chrom_1\t20817\t20828\t51.2295\n+chrom_1\t20828\t20831\t76.8443\n+chrom_1\t20831\t20838\t102.459\n+chrom_1\t20838\t20852\t51.2295\n+chrom_1\t20852\t20870\t25.6148\n+chrom_1\t20870\t20908\t0\n+chrom_1\t20908\t20913\t25.6148\n+chrom_1\t20913\t20919\t51.2295\n+chrom_1\t20919\t20929\t76.8443\n+chrom_1\t20929\t20940\t51.2295\n+chrom_1\t20940\t20945\t25.6148\n+chrom_'..b'm_1\t51651\t51672\t25.6148\n+chrom_1\t51672\t52138\t0\n+chrom_1\t52138\t52159\t25.6148\n+chrom_1\t52159\t52948\t0\n+chrom_1\t52948\t52952\t25.6148\n+chrom_1\t52952\t52969\t51.2295\n+chrom_1\t52969\t52973\t25.6148\n+chrom_1\t52973\t53743\t0\n+chrom_1\t53743\t53764\t25.6148\n+chrom_1\t53764\t54553\t0\n+chrom_1\t54553\t54554\t25.6148\n+chrom_1\t54554\t54574\t51.2295\n+chrom_1\t54574\t54575\t25.6148\n+chrom_1\t54575\t54644\t0\n+chrom_1\t54644\t54665\t25.6148\n+chrom_1\t54665\t54784\t0\n+chrom_1\t54784\t54805\t25.6148\n+chrom_1\t54805\t54909\t0\n+chrom_1\t54909\t54930\t25.6148\n+chrom_1\t54930\t54937\t0\n+chrom_1\t54937\t54958\t25.6148\n+chrom_1\t54958\t55032\t0\n+chrom_1\t55032\t55053\t25.6148\n+chrom_1\t55053\t55242\t0\n+chrom_1\t55242\t55263\t25.6148\n+chrom_1\t55263\t55838\t0\n+chrom_1\t55838\t55859\t25.6148\n+chrom_1\t55859\t55869\t0\n+chrom_1\t55869\t55890\t25.6148\n+chrom_1\t55890\t56138\t0\n+chrom_1\t56138\t56159\t25.6148\n+chrom_1\t56159\t57711\t0\n+chrom_1\t57711\t57715\t25.6148\n+chrom_1\t57715\t57732\t51.2295\n+chrom_1\t57732\t57736\t25.6148\n+chrom_1\t57736\t61018\t0\n+chrom_1\t61018\t61039\t25.6148\n+chrom_1\t61039\t61628\t0\n+chrom_1\t61628\t61649\t25.6148\n+chrom_1\t61649\t61658\t0\n+chrom_1\t61658\t61679\t25.6148\n+chrom_1\t61679\t62663\t0\n+chrom_1\t62663\t62684\t25.6148\n+chrom_1\t62684\t63781\t0\n+chrom_1\t63781\t63802\t25.6148\n+chrom_1\t63802\t67427\t0\n+chrom_1\t67427\t67448\t25.6148\n+chrom_1\t67448\t67489\t0\n+chrom_1\t67489\t67510\t25.6148\n+chrom_1\t67510\t67687\t0\n+chrom_1\t67687\t67708\t25.6148\n+chrom_1\t67708\t68012\t0\n+chrom_1\t68012\t68033\t25.6148\n+chrom_1\t68033\t68570\t0\n+chrom_1\t68570\t68591\t25.6148\n+chrom_1\t68591\t69033\t0\n+chrom_1\t69033\t69054\t25.6148\n+chrom_1\t69054\t69081\t0\n+chrom_1\t69081\t69102\t25.6148\n+chrom_1\t69102\t69347\t0\n+chrom_1\t69347\t69368\t25.6148\n+chrom_1\t69368\t69803\t0\n+chrom_1\t69803\t69824\t51.2295\n+chrom_1\t69824\t70110\t0\n+chrom_1\t70110\t70131\t25.6148\n+chrom_1\t70131\t70209\t0\n+chrom_1\t70209\t70230\t25.6148\n+chrom_1\t70230\t70362\t0\n+chrom_1\t70362\t70383\t25.6148\n+chrom_1\t70383\t71173\t0\n+chrom_1\t71173\t71194\t25.6148\n+chrom_1\t71194\t71558\t0\n+chrom_1\t71558\t71579\t25.6148\n+chrom_1\t71579\t72261\t0\n+chrom_1\t72261\t72282\t25.6148\n+chrom_1\t72282\t72667\t0\n+chrom_1\t72667\t72688\t25.6148\n+chrom_1\t72688\t72996\t0\n+chrom_1\t72996\t73017\t25.6148\n+chrom_1\t73017\t73254\t0\n+chrom_1\t73254\t73275\t25.6148\n+chrom_1\t73275\t73572\t0\n+chrom_1\t73572\t73593\t25.6148\n+chrom_1\t73593\t73976\t0\n+chrom_1\t73976\t73997\t25.6148\n+chrom_1\t73997\t74302\t0\n+chrom_1\t74302\t74323\t25.6148\n+chrom_1\t74323\t74487\t0\n+chrom_1\t74487\t74508\t25.6148\n+chrom_1\t74508\t75553\t0\n+chrom_1\t75553\t75574\t25.6148\n+chrom_1\t75574\t77140\t0\n+chrom_1\t77140\t77161\t25.6148\n+chrom_1\t77161\t77234\t0\n+chrom_1\t77234\t77255\t25.6148\n+chrom_1\t77255\t77443\t0\n+chrom_1\t77443\t77464\t25.6148\n+chrom_1\t77464\t80012\t0\n+chrom_1\t80012\t80033\t25.6148\n+chrom_1\t80033\t82019\t0\n+chrom_1\t82019\t82040\t25.6148\n+chrom_1\t82040\t82623\t0\n+chrom_1\t82623\t82644\t25.6148\n+chrom_1\t82644\t82981\t0\n+chrom_1\t82981\t83002\t25.6148\n+chrom_1\t83002\t83100\t0\n+chrom_1\t83100\t83121\t25.6148\n+chrom_1\t83121\t83268\t0\n+chrom_1\t83268\t83289\t25.6148\n+chrom_1\t83289\t83437\t0\n+chrom_1\t83437\t83458\t25.6148\n+chrom_1\t83458\t84524\t0\n+chrom_1\t84524\t84545\t25.6148\n+chrom_1\t84545\t84948\t0\n+chrom_1\t84948\t84969\t25.6148\n+chrom_1\t84969\t85094\t0\n+chrom_1\t85094\t85115\t51.2295\n+chrom_1\t85115\t85355\t0\n+chrom_1\t85355\t85376\t25.6148\n+chrom_1\t85376\t85407\t0\n+chrom_1\t85407\t85428\t25.6148\n+chrom_1\t85428\t85513\t0\n+chrom_1\t85513\t85534\t25.6148\n+chrom_1\t85534\t86344\t0\n+chrom_1\t86344\t86362\t51.2295\n+chrom_1\t86362\t86365\t76.8443\n+chrom_1\t86365\t86383\t25.6148\n+chrom_1\t86383\t86432\t0\n+chrom_1\t86432\t86453\t25.6148\n+chrom_1\t86453\t86950\t0\n+chrom_1\t86950\t86971\t25.6148\n+chrom_1\t86971\t87113\t0\n+chrom_1\t87113\t87134\t25.6148\n+chrom_1\t87134\t88633\t0\n+chrom_1\t88633\t88654\t25.6148\n+chrom_1\t88654\t89597\t0\n+chrom_1\t89597\t89618\t25.6148\n+chrom_1\t89618\t89999\t0\n+chrom_4\t0\t1151\t0\n+chrom_4\t1151\t1172\t25.6148\n+chrom_4\t1172\t1733\t0\n+chrom_4\t1733\t1754\t25.6148\n+chrom_4\t1754\t2000\t0\n+chrom_5\t0\t1648\t0\n+chrom_5\t1648\t1669\t25.6148\n+chrom_5\t1669\t1782\t0\n+chrom_5\t1782\t1803\t25.6148\n+chrom_5\t1803\t1999\t0\n+chrom_6\t0\t885\t0\n+chrom_6\t885\t906\t25.6148\n+chrom_6\t906\t1109\t0\n+chrom_6\t1109\t1115\t25.6148\n+chrom_6\t1115\t1130\t51.2295\n+chrom_6\t1130\t1136\t25.6148\n+chrom_6\t1136\t3999\t0\n' |
| b |
| diff -r 9645d995fb3c -r 9185ca0a7b43 test-data/res_files/reads-sample-small.fastq/subgroups/siRNAs/siRNAs-genome_sorted.bam |
| b |
| Binary file test-data/res_files/reads-sample-small.fastq/subgroups/siRNAs/siRNAs-genome_sorted.bam has changed |
| b |
| diff -r 9645d995fb3c -r 9185ca0a7b43 test-data/res_files/reads-sample-small.fastq/subgroups/siRNAs/siRNAs-genome_unique_minus.bedgraph --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/res_files/reads-sample-small.fastq/subgroups/siRNAs/siRNAs-genome_unique_minus.bedgraph Wed Jan 16 08:18:13 2019 -0500 |
| b |
| b'@@ -0,0 +1,1123 @@\n+chrom_1\t0\t12140\t0\n+chrom_1\t12140\t12161\t25.6148\n+chrom_1\t12161\t15164\t0\n+chrom_1\t15164\t15185\t25.6148\n+chrom_1\t15185\t15260\t0\n+chrom_1\t15260\t15281\t25.6148\n+chrom_1\t15281\t15349\t0\n+chrom_1\t15349\t15370\t25.6148\n+chrom_1\t15370\t15559\t0\n+chrom_1\t15559\t15580\t25.6148\n+chrom_1\t15580\t15981\t0\n+chrom_1\t15981\t15993\t25.6148\n+chrom_1\t15993\t16002\t51.2295\n+chrom_1\t16002\t16014\t25.6148\n+chrom_1\t16014\t16171\t0\n+chrom_1\t16171\t16192\t25.6148\n+chrom_1\t16192\t16427\t0\n+chrom_1\t16427\t16448\t25.6148\n+chrom_1\t16448\t16900\t0\n+chrom_1\t16900\t16921\t25.6148\n+chrom_1\t16921\t17063\t0\n+chrom_1\t17063\t17084\t25.6148\n+chrom_1\t17084\t17176\t0\n+chrom_1\t17176\t17197\t25.6148\n+chrom_1\t17197\t17449\t0\n+chrom_1\t17449\t17470\t25.6148\n+chrom_1\t17470\t17675\t0\n+chrom_1\t17675\t17678\t128.074\n+chrom_1\t17678\t17680\t153.689\n+chrom_1\t17680\t17696\t179.303\n+chrom_1\t17696\t17699\t51.2295\n+chrom_1\t17699\t17701\t25.6148\n+chrom_1\t17701\t17730\t0\n+chrom_1\t17730\t17751\t25.6148\n+chrom_1\t17751\t17829\t0\n+chrom_1\t17829\t17838\t25.6148\n+chrom_1\t17838\t17842\t51.2295\n+chrom_1\t17842\t17843\t76.8443\n+chrom_1\t17843\t17844\t102.459\n+chrom_1\t17844\t17845\t153.689\n+chrom_1\t17845\t17850\t332.992\n+chrom_1\t17850\t17859\t307.377\n+chrom_1\t17859\t17863\t281.762\n+chrom_1\t17863\t17864\t256.148\n+chrom_1\t17864\t17865\t230.533\n+chrom_1\t17865\t17866\t179.303\n+chrom_1\t17866\t18046\t0\n+chrom_1\t18046\t18067\t51.2295\n+chrom_1\t18067\t18157\t0\n+chrom_1\t18157\t18160\t25.6148\n+chrom_1\t18160\t18167\t51.2295\n+chrom_1\t18167\t18169\t76.8443\n+chrom_1\t18169\t18178\t102.459\n+chrom_1\t18178\t18181\t76.8443\n+chrom_1\t18181\t18184\t51.2295\n+chrom_1\t18184\t18188\t76.8443\n+chrom_1\t18188\t18190\t51.2295\n+chrom_1\t18190\t18205\t25.6148\n+chrom_1\t18205\t18214\t0\n+chrom_1\t18214\t18235\t25.6148\n+chrom_1\t18235\t18250\t0\n+chrom_1\t18250\t18271\t25.6148\n+chrom_1\t18271\t18304\t0\n+chrom_1\t18304\t18325\t25.6148\n+chrom_1\t18325\t18488\t0\n+chrom_1\t18488\t18509\t25.6148\n+chrom_1\t18509\t18722\t0\n+chrom_1\t18722\t18743\t25.6148\n+chrom_1\t18743\t18862\t0\n+chrom_1\t18862\t18883\t25.6148\n+chrom_1\t18883\t18973\t0\n+chrom_1\t18973\t18994\t25.6148\n+chrom_1\t18994\t19163\t0\n+chrom_1\t19163\t19184\t25.6148\n+chrom_1\t19184\t19238\t0\n+chrom_1\t19238\t19259\t25.6148\n+chrom_1\t19259\t19420\t0\n+chrom_1\t19420\t19441\t25.6148\n+chrom_1\t19441\t20045\t0\n+chrom_1\t20045\t20066\t25.6148\n+chrom_1\t20066\t20180\t0\n+chrom_1\t20180\t20201\t51.2295\n+chrom_1\t20201\t20249\t0\n+chrom_1\t20249\t20250\t25.6148\n+chrom_1\t20250\t20270\t102.459\n+chrom_1\t20270\t20271\t76.8443\n+chrom_1\t20271\t20280\t0\n+chrom_1\t20280\t20298\t25.6148\n+chrom_1\t20298\t20301\t128.074\n+chrom_1\t20301\t20319\t102.459\n+chrom_1\t20319\t20400\t0\n+chrom_1\t20400\t20421\t25.6148\n+chrom_1\t20421\t20469\t0\n+chrom_1\t20469\t20490\t25.6148\n+chrom_1\t20490\t20507\t0\n+chrom_1\t20507\t20526\t25.6148\n+chrom_1\t20526\t20528\t51.2295\n+chrom_1\t20528\t20547\t25.6148\n+chrom_1\t20547\t20575\t0\n+chrom_1\t20575\t20596\t25.6148\n+chrom_1\t20596\t20745\t0\n+chrom_1\t20745\t20766\t25.6148\n+chrom_1\t20766\t20805\t0\n+chrom_1\t20805\t20819\t51.2295\n+chrom_1\t20819\t20820\t76.8443\n+chrom_1\t20820\t20826\t102.459\n+chrom_1\t20826\t20840\t51.2295\n+chrom_1\t20840\t20841\t25.6148\n+chrom_1\t20841\t20960\t0\n+chrom_1\t20960\t20964\t25.6148\n+chrom_1\t20964\t20967\t51.2295\n+chrom_1\t20967\t20981\t102.459\n+chrom_1\t20981\t20985\t76.8443\n+chrom_1\t20985\t20988\t51.2295\n+chrom_1\t20988\t21008\t0\n+chrom_1\t21008\t21029\t102.459\n+chrom_1\t21029\t21071\t0\n+chrom_1\t21071\t21092\t51.2295\n+chrom_1\t21092\t21301\t0\n+chrom_1\t21301\t21302\t25.6148\n+chrom_1\t21302\t21310\t51.2295\n+chrom_1\t21310\t21322\t76.8443\n+chrom_1\t21322\t21323\t51.2295\n+chrom_1\t21323\t21331\t25.6148\n+chrom_1\t21331\t21355\t0\n+chrom_1\t21355\t21376\t76.8443\n+chrom_1\t21376\t21454\t0\n+chrom_1\t21454\t21459\t25.6148\n+chrom_1\t21459\t21475\t51.2295\n+chrom_1\t21475\t21480\t25.6148\n+chrom_1\t21480\t21575\t0\n+chrom_1\t21575\t21596\t25.6148\n+chrom_1\t21596\t21614\t0\n+chrom_1\t21614\t21618\t25.6148\n+chrom_1\t21618\t21631\t51.2295\n+chrom_1\t21631\t21632\t76.8443\n+chrom_1\t21632\t21635\t102.459\n+chrom_1\t21635\t21639\t76.8443\n+chrom_1\t21639\t21652\t51.2295\n+chrom_1\t21652\t21653\t25.6148\n+chrom_1\t21653\t21760\t0\n+chrom_1\t21760\t21781\t25.6148\n+chrom_1\t21781\t21875\t0\n+chrom_1\t21875\t21896\t25.6148\n+chrom_1\t21896\t21962\t0\n+chrom_1\t21962\t21983\t128.074\n+chrom_1\t21983\t22051\t0\n+chrom_1\t22051\t'..b'\t49875\t25.6148\n+chrom_1\t49875\t50715\t0\n+chrom_1\t50715\t50736\t25.6148\n+chrom_1\t50736\t50749\t0\n+chrom_1\t50749\t50770\t25.6148\n+chrom_1\t50770\t51663\t0\n+chrom_1\t51663\t51665\t25.6148\n+chrom_1\t51665\t51671\t51.2295\n+chrom_1\t51671\t51684\t76.8443\n+chrom_1\t51684\t51686\t51.2295\n+chrom_1\t51686\t51692\t25.6148\n+chrom_1\t51692\t51974\t0\n+chrom_1\t51974\t51995\t25.6148\n+chrom_1\t51995\t52373\t0\n+chrom_1\t52373\t52394\t51.2295\n+chrom_1\t52394\t53410\t0\n+chrom_1\t53410\t53431\t25.6148\n+chrom_1\t53431\t53763\t0\n+chrom_1\t53763\t53784\t25.6148\n+chrom_1\t53784\t54064\t0\n+chrom_1\t54064\t54085\t51.2295\n+chrom_1\t54085\t55267\t0\n+chrom_1\t55267\t55288\t25.6148\n+chrom_1\t55288\t55825\t0\n+chrom_1\t55825\t55837\t25.6148\n+chrom_1\t55837\t55846\t51.2295\n+chrom_1\t55846\t55858\t25.6148\n+chrom_1\t55858\t57223\t0\n+chrom_1\t57223\t57244\t25.6148\n+chrom_1\t57244\t58149\t0\n+chrom_1\t58149\t58170\t25.6148\n+chrom_1\t58170\t58175\t0\n+chrom_1\t58175\t58176\t25.6148\n+chrom_1\t58176\t58196\t51.2295\n+chrom_1\t58196\t58197\t25.6148\n+chrom_1\t58197\t58585\t0\n+chrom_1\t58585\t58606\t25.6148\n+chrom_1\t58606\t58798\t0\n+chrom_1\t58798\t58819\t25.6148\n+chrom_1\t58819\t58987\t0\n+chrom_1\t58987\t59008\t25.6148\n+chrom_1\t59008\t60022\t0\n+chrom_1\t60022\t60043\t25.6148\n+chrom_1\t60043\t60293\t0\n+chrom_1\t60293\t60314\t25.6148\n+chrom_1\t60314\t60537\t0\n+chrom_1\t60537\t60558\t25.6148\n+chrom_1\t60558\t61721\t0\n+chrom_1\t61721\t61742\t25.6148\n+chrom_1\t61742\t62018\t0\n+chrom_1\t62018\t62039\t25.6148\n+chrom_1\t62039\t62885\t0\n+chrom_1\t62885\t62906\t25.6148\n+chrom_1\t62906\t63072\t0\n+chrom_1\t63072\t63093\t25.6148\n+chrom_1\t63093\t63704\t0\n+chrom_1\t63704\t63725\t25.6148\n+chrom_1\t63725\t63787\t0\n+chrom_1\t63787\t63792\t25.6148\n+chrom_1\t63792\t63808\t51.2295\n+chrom_1\t63808\t63813\t25.6148\n+chrom_1\t63813\t64722\t0\n+chrom_1\t64722\t64743\t25.6148\n+chrom_1\t64743\t67433\t0\n+chrom_1\t67433\t67434\t25.6148\n+chrom_1\t67434\t67454\t51.2295\n+chrom_1\t67454\t67455\t25.6148\n+chrom_1\t67455\t67965\t0\n+chrom_1\t67965\t67986\t25.6148\n+chrom_1\t67986\t68548\t0\n+chrom_1\t68548\t68569\t25.6148\n+chrom_1\t68569\t68863\t0\n+chrom_1\t68863\t68884\t25.6148\n+chrom_1\t68884\t69781\t0\n+chrom_1\t69781\t69802\t25.6148\n+chrom_1\t69802\t70934\t0\n+chrom_1\t70934\t70955\t25.6148\n+chrom_1\t70955\t71363\t0\n+chrom_1\t71363\t71384\t25.6148\n+chrom_1\t71384\t71705\t0\n+chrom_1\t71705\t71726\t25.6148\n+chrom_1\t71726\t71760\t0\n+chrom_1\t71760\t71781\t25.6148\n+chrom_1\t71781\t72252\t0\n+chrom_1\t72252\t72273\t25.6148\n+chrom_1\t72273\t72315\t0\n+chrom_1\t72315\t72336\t25.6148\n+chrom_1\t72336\t73124\t0\n+chrom_1\t73124\t73145\t25.6148\n+chrom_1\t73145\t73249\t0\n+chrom_1\t73249\t73270\t25.6148\n+chrom_1\t73270\t73315\t0\n+chrom_1\t73315\t73336\t25.6148\n+chrom_1\t73336\t73759\t0\n+chrom_1\t73759\t73780\t25.6148\n+chrom_1\t73780\t74260\t0\n+chrom_1\t74260\t74281\t25.6148\n+chrom_1\t74281\t74954\t0\n+chrom_1\t74954\t74975\t25.6148\n+chrom_1\t74975\t75554\t0\n+chrom_1\t75554\t75575\t25.6148\n+chrom_1\t75575\t77319\t0\n+chrom_1\t77319\t77320\t25.6148\n+chrom_1\t77320\t77340\t51.2295\n+chrom_1\t77340\t77341\t25.6148\n+chrom_1\t77341\t77516\t0\n+chrom_1\t77516\t77537\t25.6148\n+chrom_1\t77537\t79059\t0\n+chrom_1\t79059\t79080\t25.6148\n+chrom_1\t79080\t80057\t0\n+chrom_1\t80057\t80078\t25.6148\n+chrom_1\t80078\t80319\t0\n+chrom_1\t80319\t80340\t25.6148\n+chrom_1\t80340\t81784\t0\n+chrom_1\t81784\t81805\t25.6148\n+chrom_1\t81805\t82339\t0\n+chrom_1\t82339\t82360\t25.6148\n+chrom_1\t82360\t83079\t0\n+chrom_1\t83079\t83100\t25.6148\n+chrom_1\t83100\t83540\t0\n+chrom_1\t83540\t83561\t25.6148\n+chrom_1\t83561\t83901\t0\n+chrom_1\t83901\t83922\t25.6148\n+chrom_1\t83922\t85181\t0\n+chrom_1\t85181\t85202\t25.6148\n+chrom_1\t85202\t85252\t0\n+chrom_1\t85252\t85273\t25.6148\n+chrom_1\t85273\t86453\t0\n+chrom_1\t86453\t86474\t25.6148\n+chrom_1\t86474\t87066\t0\n+chrom_1\t87066\t87087\t25.6148\n+chrom_1\t87087\t87142\t0\n+chrom_1\t87142\t87163\t25.6148\n+chrom_1\t87163\t87223\t0\n+chrom_1\t87223\t87244\t25.6148\n+chrom_1\t87244\t87446\t0\n+chrom_1\t87446\t87467\t25.6148\n+chrom_1\t87467\t87581\t0\n+chrom_1\t87581\t87602\t25.6148\n+chrom_1\t87602\t88309\t0\n+chrom_1\t88309\t88330\t25.6148\n+chrom_1\t88330\t88443\t0\n+chrom_1\t88443\t88464\t25.6148\n+chrom_1\t88464\t88710\t0\n+chrom_1\t88710\t88731\t25.6148\n+chrom_1\t88731\t89812\t0\n+chrom_1\t89812\t89833\t25.6148\n+chrom_1\t89833\t89999\t0\n+chrom_2\t0\t32289\t0\n+chrom_2\t32289\t32310\t25.6148\n+chrom_2\t32310\t39255\t0\n+chrom_2\t39255\t39276\t25.6148\n+chrom_2\t39276\t49999\t0\n' |
| b |
| diff -r 9645d995fb3c -r 9185ca0a7b43 test-data/res_files/reads-sample-small.fastq/subgroups/siRNAs/siRNAs-genome_unique_plus.bedgraph --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/res_files/reads-sample-small.fastq/subgroups/siRNAs/siRNAs-genome_unique_plus.bedgraph Wed Jan 16 08:18:13 2019 -0500 |
| b |
| b'@@ -0,0 +1,1512 @@\n+chrom_1\t0\t10407\t0\n+chrom_1\t10407\t10428\t25.6148\n+chrom_1\t10428\t14523\t0\n+chrom_1\t14523\t14544\t25.6148\n+chrom_1\t14544\t15400\t0\n+chrom_1\t15400\t15421\t76.8443\n+chrom_1\t15421\t15546\t0\n+chrom_1\t15546\t15567\t25.6148\n+chrom_1\t15567\t16229\t0\n+chrom_1\t16229\t16250\t25.6148\n+chrom_1\t16250\t16808\t0\n+chrom_1\t16808\t16829\t25.6148\n+chrom_1\t16829\t16875\t0\n+chrom_1\t16875\t16885\t25.6148\n+chrom_1\t16885\t16886\t76.8443\n+chrom_1\t16886\t16896\t102.459\n+chrom_1\t16896\t16906\t76.8443\n+chrom_1\t16906\t16907\t25.6148\n+chrom_1\t16907\t17054\t0\n+chrom_1\t17054\t17055\t768.443\n+chrom_1\t17055\t17056\t794.057\n+chrom_1\t17056\t17075\t819.672\n+chrom_1\t17075\t17076\t51.2295\n+chrom_1\t17076\t17077\t25.6148\n+chrom_1\t17077\t17236\t0\n+chrom_1\t17236\t17241\t25.6148\n+chrom_1\t17241\t17242\t76.8443\n+chrom_1\t17242\t17245\t153.689\n+chrom_1\t17245\t17257\t230.533\n+chrom_1\t17257\t17262\t204.918\n+chrom_1\t17262\t17263\t153.689\n+chrom_1\t17263\t17266\t76.8443\n+chrom_1\t17266\t17390\t0\n+chrom_1\t17390\t17411\t25.6148\n+chrom_1\t17411\t17421\t0\n+chrom_1\t17421\t17425\t25.6148\n+chrom_1\t17425\t17442\t51.2295\n+chrom_1\t17442\t17446\t25.6148\n+chrom_1\t17446\t17472\t0\n+chrom_1\t17472\t17493\t25.6148\n+chrom_1\t17493\t17622\t0\n+chrom_1\t17622\t17627\t25.6148\n+chrom_1\t17627\t17643\t51.2295\n+chrom_1\t17643\t17648\t25.6148\n+chrom_1\t17648\t17681\t0\n+chrom_1\t17681\t17702\t25.6148\n+chrom_1\t17702\t17825\t0\n+chrom_1\t17825\t17828\t25.6148\n+chrom_1\t17828\t17843\t51.2295\n+chrom_1\t17843\t17848\t76.8443\n+chrom_1\t17848\t17849\t102.459\n+chrom_1\t17849\t17864\t76.8443\n+chrom_1\t17864\t17867\t51.2295\n+chrom_1\t17867\t17869\t25.6148\n+chrom_1\t17869\t18057\t0\n+chrom_1\t18057\t18078\t51.2295\n+chrom_1\t18078\t18164\t0\n+chrom_1\t18164\t18171\t25.6148\n+chrom_1\t18171\t18174\t51.2295\n+chrom_1\t18174\t18175\t76.8443\n+chrom_1\t18175\t18185\t102.459\n+chrom_1\t18185\t18190\t76.8443\n+chrom_1\t18190\t18192\t102.459\n+chrom_1\t18192\t18196\t76.8443\n+chrom_1\t18196\t18211\t51.2295\n+chrom_1\t18211\t18216\t25.6148\n+chrom_1\t18216\t18269\t0\n+chrom_1\t18269\t18275\t25.6148\n+chrom_1\t18275\t18276\t51.2295\n+chrom_1\t18276\t18290\t76.8443\n+chrom_1\t18290\t18296\t51.2295\n+chrom_1\t18296\t18297\t25.6148\n+chrom_1\t18297\t18307\t0\n+chrom_1\t18307\t18328\t25.6148\n+chrom_1\t18328\t18407\t0\n+chrom_1\t18407\t18428\t51.2295\n+chrom_1\t18428\t18554\t0\n+chrom_1\t18554\t18575\t25.6148\n+chrom_1\t18575\t18666\t0\n+chrom_1\t18666\t18687\t51.2295\n+chrom_1\t18687\t18857\t0\n+chrom_1\t18857\t18878\t25.6148\n+chrom_1\t18878\t18983\t0\n+chrom_1\t18983\t19004\t25.6148\n+chrom_1\t19004\t19173\t0\n+chrom_1\t19173\t19194\t25.6148\n+chrom_1\t19194\t20163\t0\n+chrom_1\t20163\t20175\t25.6148\n+chrom_1\t20175\t20184\t51.2295\n+chrom_1\t20184\t20196\t25.6148\n+chrom_1\t20196\t20198\t0\n+chrom_1\t20198\t20216\t25.6148\n+chrom_1\t20216\t20219\t845.287\n+chrom_1\t20219\t20237\t819.672\n+chrom_1\t20237\t20258\t25.6148\n+chrom_1\t20258\t20260\t0\n+chrom_1\t20260\t20263\t25.6148\n+chrom_1\t20263\t20264\t51.2295\n+chrom_1\t20264\t20281\t76.8443\n+chrom_1\t20281\t20284\t51.2295\n+chrom_1\t20284\t20285\t25.6148\n+chrom_1\t20285\t20288\t0\n+chrom_1\t20288\t20290\t51.2295\n+chrom_1\t20290\t20309\t76.8443\n+chrom_1\t20309\t20311\t25.6148\n+chrom_1\t20311\t20346\t0\n+chrom_1\t20346\t20360\t25.6148\n+chrom_1\t20360\t20361\t51.2295\n+chrom_1\t20361\t20362\t230.533\n+chrom_1\t20362\t20363\t307.377\n+chrom_1\t20363\t20367\t384.221\n+chrom_1\t20367\t20381\t358.607\n+chrom_1\t20381\t20382\t332.992\n+chrom_1\t20382\t20383\t153.689\n+chrom_1\t20383\t20384\t76.8443\n+chrom_1\t20384\t20399\t0\n+chrom_1\t20399\t20420\t25.6148\n+chrom_1\t20420\t20430\t0\n+chrom_1\t20430\t20446\t25.6148\n+chrom_1\t20446\t20451\t51.2295\n+chrom_1\t20451\t20467\t25.6148\n+chrom_1\t20467\t20516\t0\n+chrom_1\t20516\t20537\t384.221\n+chrom_1\t20537\t20566\t0\n+chrom_1\t20566\t20587\t25.6148\n+chrom_1\t20587\t20596\t0\n+chrom_1\t20596\t20609\t25.6148\n+chrom_1\t20609\t20617\t256.148\n+chrom_1\t20617\t20630\t230.533\n+chrom_1\t20630\t20666\t0\n+chrom_1\t20666\t20676\t25.6148\n+chrom_1\t20676\t20687\t128.074\n+chrom_1\t20687\t20697\t102.459\n+chrom_1\t20697\t20817\t0\n+chrom_1\t20817\t20828\t51.2295\n+chrom_1\t20828\t20831\t76.8443\n+chrom_1\t20831\t20838\t102.459\n+chrom_1\t20838\t20852\t51.2295\n+chrom_1\t20852\t20870\t25.6148\n+chrom_1\t20870\t20908\t0\n+chrom_1\t20908\t20913\t25.6148\n+chrom_1\t20913\t20919\t51.2295\n+chrom_1\t20919\t20929\t76.8443\n+chrom_1\t20929\t20940\t51.2295\n+chrom_1\t20940\t20945\t25.6148\n+chrom_'..b'51629\t51650\t25.6148\n+chrom_1\t51650\t51651\t0\n+chrom_1\t51651\t51672\t25.6148\n+chrom_1\t51672\t52138\t0\n+chrom_1\t52138\t52159\t25.6148\n+chrom_1\t52159\t52948\t0\n+chrom_1\t52948\t52952\t25.6148\n+chrom_1\t52952\t52969\t51.2295\n+chrom_1\t52969\t52973\t25.6148\n+chrom_1\t52973\t53743\t0\n+chrom_1\t53743\t53764\t25.6148\n+chrom_1\t53764\t54553\t0\n+chrom_1\t54553\t54554\t25.6148\n+chrom_1\t54554\t54574\t51.2295\n+chrom_1\t54574\t54575\t25.6148\n+chrom_1\t54575\t54644\t0\n+chrom_1\t54644\t54665\t25.6148\n+chrom_1\t54665\t54784\t0\n+chrom_1\t54784\t54805\t25.6148\n+chrom_1\t54805\t54909\t0\n+chrom_1\t54909\t54930\t25.6148\n+chrom_1\t54930\t54937\t0\n+chrom_1\t54937\t54958\t25.6148\n+chrom_1\t54958\t55032\t0\n+chrom_1\t55032\t55053\t25.6148\n+chrom_1\t55053\t55242\t0\n+chrom_1\t55242\t55263\t25.6148\n+chrom_1\t55263\t55838\t0\n+chrom_1\t55838\t55859\t25.6148\n+chrom_1\t55859\t55869\t0\n+chrom_1\t55869\t55890\t25.6148\n+chrom_1\t55890\t56138\t0\n+chrom_1\t56138\t56159\t25.6148\n+chrom_1\t56159\t57711\t0\n+chrom_1\t57711\t57715\t25.6148\n+chrom_1\t57715\t57732\t51.2295\n+chrom_1\t57732\t57736\t25.6148\n+chrom_1\t57736\t61018\t0\n+chrom_1\t61018\t61039\t25.6148\n+chrom_1\t61039\t61628\t0\n+chrom_1\t61628\t61649\t25.6148\n+chrom_1\t61649\t61658\t0\n+chrom_1\t61658\t61679\t25.6148\n+chrom_1\t61679\t62663\t0\n+chrom_1\t62663\t62684\t25.6148\n+chrom_1\t62684\t63781\t0\n+chrom_1\t63781\t63802\t25.6148\n+chrom_1\t63802\t67427\t0\n+chrom_1\t67427\t67448\t25.6148\n+chrom_1\t67448\t67489\t0\n+chrom_1\t67489\t67510\t25.6148\n+chrom_1\t67510\t67687\t0\n+chrom_1\t67687\t67708\t25.6148\n+chrom_1\t67708\t68012\t0\n+chrom_1\t68012\t68033\t25.6148\n+chrom_1\t68033\t68570\t0\n+chrom_1\t68570\t68591\t25.6148\n+chrom_1\t68591\t69033\t0\n+chrom_1\t69033\t69054\t25.6148\n+chrom_1\t69054\t69081\t0\n+chrom_1\t69081\t69102\t25.6148\n+chrom_1\t69102\t69347\t0\n+chrom_1\t69347\t69368\t25.6148\n+chrom_1\t69368\t69803\t0\n+chrom_1\t69803\t69824\t51.2295\n+chrom_1\t69824\t70110\t0\n+chrom_1\t70110\t70131\t25.6148\n+chrom_1\t70131\t70209\t0\n+chrom_1\t70209\t70230\t25.6148\n+chrom_1\t70230\t70362\t0\n+chrom_1\t70362\t70383\t25.6148\n+chrom_1\t70383\t71173\t0\n+chrom_1\t71173\t71194\t25.6148\n+chrom_1\t71194\t71558\t0\n+chrom_1\t71558\t71579\t25.6148\n+chrom_1\t71579\t72261\t0\n+chrom_1\t72261\t72282\t25.6148\n+chrom_1\t72282\t72667\t0\n+chrom_1\t72667\t72688\t25.6148\n+chrom_1\t72688\t72996\t0\n+chrom_1\t72996\t73017\t25.6148\n+chrom_1\t73017\t73254\t0\n+chrom_1\t73254\t73275\t25.6148\n+chrom_1\t73275\t73572\t0\n+chrom_1\t73572\t73593\t25.6148\n+chrom_1\t73593\t73976\t0\n+chrom_1\t73976\t73997\t25.6148\n+chrom_1\t73997\t74302\t0\n+chrom_1\t74302\t74323\t25.6148\n+chrom_1\t74323\t74487\t0\n+chrom_1\t74487\t74508\t25.6148\n+chrom_1\t74508\t75553\t0\n+chrom_1\t75553\t75574\t25.6148\n+chrom_1\t75574\t77140\t0\n+chrom_1\t77140\t77161\t25.6148\n+chrom_1\t77161\t77234\t0\n+chrom_1\t77234\t77255\t25.6148\n+chrom_1\t77255\t77443\t0\n+chrom_1\t77443\t77464\t25.6148\n+chrom_1\t77464\t80012\t0\n+chrom_1\t80012\t80033\t25.6148\n+chrom_1\t80033\t82019\t0\n+chrom_1\t82019\t82040\t25.6148\n+chrom_1\t82040\t82623\t0\n+chrom_1\t82623\t82644\t25.6148\n+chrom_1\t82644\t82981\t0\n+chrom_1\t82981\t83002\t25.6148\n+chrom_1\t83002\t83100\t0\n+chrom_1\t83100\t83121\t25.6148\n+chrom_1\t83121\t83268\t0\n+chrom_1\t83268\t83289\t25.6148\n+chrom_1\t83289\t83437\t0\n+chrom_1\t83437\t83458\t25.6148\n+chrom_1\t83458\t84524\t0\n+chrom_1\t84524\t84545\t25.6148\n+chrom_1\t84545\t84948\t0\n+chrom_1\t84948\t84969\t25.6148\n+chrom_1\t84969\t85094\t0\n+chrom_1\t85094\t85115\t51.2295\n+chrom_1\t85115\t85355\t0\n+chrom_1\t85355\t85376\t25.6148\n+chrom_1\t85376\t85407\t0\n+chrom_1\t85407\t85428\t25.6148\n+chrom_1\t85428\t85513\t0\n+chrom_1\t85513\t85534\t25.6148\n+chrom_1\t85534\t86344\t0\n+chrom_1\t86344\t86362\t51.2295\n+chrom_1\t86362\t86365\t76.8443\n+chrom_1\t86365\t86383\t25.6148\n+chrom_1\t86383\t86432\t0\n+chrom_1\t86432\t86453\t25.6148\n+chrom_1\t86453\t86950\t0\n+chrom_1\t86950\t86971\t25.6148\n+chrom_1\t86971\t87113\t0\n+chrom_1\t87113\t87134\t25.6148\n+chrom_1\t87134\t88633\t0\n+chrom_1\t88633\t88654\t25.6148\n+chrom_1\t88654\t89597\t0\n+chrom_1\t89597\t89618\t25.6148\n+chrom_1\t89618\t89999\t0\n+chrom_4\t0\t1151\t0\n+chrom_4\t1151\t1172\t25.6148\n+chrom_4\t1172\t2000\t0\n+chrom_5\t0\t1648\t0\n+chrom_5\t1648\t1669\t25.6148\n+chrom_5\t1669\t1782\t0\n+chrom_5\t1782\t1803\t25.6148\n+chrom_5\t1803\t1999\t0\n+chrom_6\t0\t885\t0\n+chrom_6\t885\t906\t25.6148\n+chrom_6\t906\t1109\t0\n+chrom_6\t1109\t1115\t25.6148\n+chrom_6\t1115\t1130\t51.2295\n+chrom_6\t1130\t1136\t25.6148\n+chrom_6\t1136\t3999\t0\n' |
| b |
| diff -r 9645d995fb3c -r 9185ca0a7b43 test-data/res_files/reads-sample-small.fastq/subgroups/siRNAs/siRNAs-genome_unique_sorted.bam |
| b |
| Binary file test-data/res_files/reads-sample-small.fastq/subgroups/siRNAs/siRNAs-genome_unique_sorted.bam has changed |
| b |
| diff -r 9645d995fb3c -r 9185ca0a7b43 test-data/res_files/reads-sample-small.fastq/subgroups/siRNAs/siRNAs-transcripts_reads_counts.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/res_files/reads-sample-small.fastq/subgroups/siRNAs/siRNAs-transcripts_reads_counts.txt Wed Jan 16 08:18:13 2019 -0500 |
| b |
| @@ -0,0 +1,14 @@ +ID reads counts RPKM per million of piRNAs per million of miRNAs per million of bonafide reads sense reads counts reverse reads counts % of sense 1U % of sense 10A % of reverse 1U % of reverse 10A +FBtr0073689 5 33.75 216.86 79365.08 163.77 2 3 50 100 0 33.3333333333333 +FBtr0078666 22 232.29 954.20 349206.35 720.60 11 11 81.8181818181818 18.1818181818182 18.1818181818182 0 +FBtr0086080 12 77.64 520.47 190476.19 393.06 4 8 75 75 0 75 +FBtr0089125 6 21.25 260.24 95238.10 196.53 0 6 0 0 16.6666666666667 66.6666666666667 +FBtr0089196 17 99.51 737.34 269841.27 556.83 11 6 81.8181818181818 18.1818181818182 16.6666666666667 33.3333333333333 +FBtr0113825 2 17.53 86.75 31746.03 65.51 1 1 0 0 0 0 +FBtr0114365 16 64.07 693.96 253968.25 524.07 8 8 37.5 12.5 0 12.5 +FBtr0310270 36 300.47 1561.42 571428.57 1179.17 0 36 0 0 0 16.6666666666667 +FBtr0332656 1 7.35 43.37 15873.02 32.75 1 0 100 0 0 0 +FBtr0345361 10 198.72 433.73 158730.16 327.55 10 0 100 0 0 0 +FBtr0345575 16 138.50 693.96 253968.25 524.07 4 12 75 50 16.6666666666667 33.3333333333333 +FBtr0345650 11 34.06 477.10 174603.17 360.30 9 2 44.4444444444444 0 0 50 +FBtr0346343 3 12.31 130.12 47619.05 98.26 3 0 66.6666666666667 33.3333333333333 0 0 |
| b |
| diff -r 9645d995fb3c -r 9185ca0a7b43 test-data/res_files/reads-sample-small.fastq/subgroups/siRNAs/siRNAs-transcripts_sorted.bam |
| b |
| Binary file test-data/res_files/reads-sample-small.fastq/subgroups/siRNAs/siRNAs-transcripts_sorted.bam has changed |
| b |
| diff -r 9645d995fb3c -r 9185ca0a7b43 test-data/res_files/reads-sample-small.fastq/subgroups/siRNAs/siRNAs-transcripts_unique_sorted.bam |
| b |
| Binary file test-data/res_files/reads-sample-small.fastq/subgroups/siRNAs/siRNAs-transcripts_unique_sorted.bam has changed |
| b |
| diff -r 9645d995fb3c -r 9185ca0a7b43 test-data/res_files/reads-sample-small.fastq/subgroups/transcripts.fai --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/res_files/reads-sample-small.fastq/subgroups/transcripts.fai Wed Jan 16 08:18:13 2019 -0500 |
| b |
| @@ -0,0 +1,13 @@ +FBtr0078666 2426 +FBtr0345575 2959 +FBtr0089125 7231 +FBtr0086080 3959 +FBtr0089196 4376 +FBtr0113825 2923 +FBtr0346343 6243 +FBtr0345361 1289 +FBtr0114365 6397 +FBtr0345650 8272 +FBtr0332656 3483 +FBtr0073689 3795 +FBtr0310270 3069 |
| b |
| diff -r 9645d995fb3c -r 9185ca0a7b43 test-data/res_files/reads-sample-small.fastq/subgroups/transcripts.sam_aln.err --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/res_files/reads-sample-small.fastq/subgroups/transcripts.sam_aln.err Wed Jan 16 08:18:13 2019 -0500 |
| [ |
| @@ -0,0 +1,6 @@ +[bwa_aln_core] calculate SA coordinate... 0.26 sec +[bwa_aln_core] write to the disk... 0.00 sec +[bwa_aln_core] 30530 sequences have been processed. +[main] Version: 0.7.12-r1039 +[main] CMD: bwa aln -t 8 -n 0 /data/galaxy/galaxy-server/database/jobs_directory/015/15696/dataset_35119_files/dataset_35118.dat_symlink.fa /data/galaxy/galaxy-server/database/jobs_directory/015/15696/dataset_35119_files/reads-sample-small.fastq/subgroups/bonafide_reads.fastq +[main] Real time: 0.120 sec; CPU: 0.308 sec |
| b |
| diff -r 9645d995fb3c -r 9185ca0a7b43 test-data/res_files/reads-sample-small.fastq/subgroups/transcripts.sam_samse.err --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/res_files/reads-sample-small.fastq/subgroups/transcripts.sam_samse.err Wed Jan 16 08:18:13 2019 -0500 |
| [ |
| @@ -0,0 +1,7 @@ +[bwa_aln_core] convert to sequence coordinate... 0.01 sec +[bwa_aln_core] refine gapped alignments... 0.00 sec +[bwa_aln_core] print alignments... 0.02 sec +[bwa_aln_core] 30530 sequences have been processed. +[main] Version: 0.7.12-r1039 +[main] CMD: bwa samse /data/galaxy/galaxy-server/database/jobs_directory/015/15696/dataset_35119_files/dataset_35118.dat_symlink.fa /dev/stdin /data/galaxy/galaxy-server/database/jobs_directory/015/15696/dataset_35119_files/reads-sample-small.fastq/subgroups/bonafide_reads.fastq +[main] Real time: 0.225 sec; CPU: 0.080 sec |
| b |
| diff -r 9645d995fb3c -r 9185ca0a7b43 test-data/res_files/report.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/res_files/report.txt Wed Jan 16 08:18:13 2019 -0500 |
| b |
| b"@@ -0,0 +1,74 @@\n+Creating index for /data/galaxy/galaxy-server/database/jobs_directory/015/15696/dataset_35119_files/dataset_35115.dat_symlink.fa\n+Creating index for /data/galaxy/galaxy-server/database/jobs_directory/015/15696/dataset_35119_files/dataset_35114.dat_symlink.fa\n+Creating index for /data/galaxy/galaxy-server/database/jobs_directory/015/15696/dataset_35119_files/dataset_35112.dat_symlink.fa\n+Creating index for /data/galaxy/galaxy-server/database/jobs_directory/015/15696/dataset_35119_files/dataset_35113.dat_symlink.fa\n+Creating index for /data/galaxy/galaxy-server/database/jobs_directory/015/15696/dataset_35119_files/dataset_35116.dat_symlink.fa\n+Creating index for /data/galaxy/galaxy-server/database/jobs_directory/015/15696/dataset_35119_files/dataset_35118.dat_symlink.fa\n+Creating index for /data/galaxy/galaxy-server/database/jobs_directory/015/15696/dataset_35119_files/dataset_35111.dat_symlink.fa\n+-----------------------------\n+bwa aln -t 8 -n 0 '/data/galaxy/galaxy-server/database/jobs_directory/015/15696/dataset_35119_files/dataset_35115.dat_symlink.fa' '/data/galaxy/galaxy-server/database/jobs_directory/015/15696/dataset_35119_files/reads-sample-small.fastq/dataset_35117_18-29.fastq' 2> '/data/galaxy/galaxy-server/database/jobs_directory/015/15696/dataset_35119_files/reads-sample-small.fastq/genome/reads-sample-small.fastq_18-29.sam_aln.err' | bwa samse /data/galaxy/galaxy-server/database/jobs_directory/015/15696/dataset_35119_files/dataset_35115.dat_symlink.fa /dev/stdin '/data/galaxy/galaxy-server/database/jobs_directory/015/15696/dataset_35119_files/reads-sample-small.fastq/dataset_35117_18-29.fastq' 2> '/data/galaxy/galaxy-server/database/jobs_directory/015/15696/dataset_35119_files/reads-sample-small.fastq/genome/reads-sample-small.fastq_18-29.sam_samse.err' > '/data/galaxy/galaxy-server/database/jobs_directory/015/15696/dataset_35119_files/reads-sample-small.fastq/genome/reads-sample-small.fastq_18-29.sam'\n+Parsing /data/galaxy/galaxy-server/database/jobs_directory/015/15696/dataset_35119_files/reads-sample-small.fastq/genome/reads-sample-small.fastq_18-29.sam file\n+\treads: 45570\n+\tmappers: 39040\n+\tunique mappers: 38991\n+-----------------------------\n+----------------------------\n+Create subgroups:\n+fastq_in: fastq_dir/reads-sample-small.fastq_all_mappers.fastq\n+directory_out: /data/galaxy/galaxy-server/database/jobs_directory/015/15696/dataset_35119_files/reads-sample-small.fastq/subgroups/\n+mismatches: 0\n+mismatches TE: 3\n+-----------------------------\n+bwa aln -t 8 -n 0 '/data/galaxy/galaxy-server/database/jobs_directory/015/15696/dataset_35119_files/dataset_35116.dat_symlink.fa' 'fastq_dir/reads-sample-small.fastq_all_mappers.fastq' 2> '/data/galaxy/galaxy-server/database/jobs_directory/015/15696/dataset_35119_files/reads-sample-small.fastq/subgroups/miRNAs.sam_aln.err' | bwa samse /data/galaxy/galaxy-server/database/jobs_directory/015/15696/dataset_35119_files/dataset_35116.dat_symlink.fa /dev/stdin 'fastq_dir/reads-sample-small.fastq_all_mappers.fastq' 2> '/data/galaxy/galaxy-server/database/jobs_directory/015/15696/dataset_35119_files/reads-sample-small.fastq/subgroups/miRNAs.sam_samse.err' > '/data/galaxy/galaxy-server/database/jobs_directory/015/15696/dataset_35119_files/reads-sample-small.fastq/subgroups/miRNAs.sam'\n+\treads: 39040\n+\tmappers: 63\n+\tunmapped: 38977\n+-----------------------------\n+-----------------------------\n+bwa aln -t 8 -n 0 '/data/galaxy/galaxy-server/database/jobs_directory/015/15696/dataset_35119_files/dataset_35112.dat_symlink.fa' '/data/galaxy/galaxy-server/database/jobs_directory/015/15696/dataset_35119_files/reads-sample-small.fastq/subgroups/miRNAs_rejected.fastq' 2> 'SLupcxhh_aln.err' | bwa samse /data/galaxy/galaxy-server/database/jobs_directory/015/15696/dataset_35119_files/dataset_35112.dat_symlink.fa /dev/stdin '/data/galaxy/galaxy-server/database/jobs_directory/015/15696/dataset_35119_files/reads-sample-small.fastq/subgroups/miRNAs_rejected.fastq' 2> 'SLupcxhh"..b"miRNAs-TEs.sam_samse.err' > '/data/galaxy/galaxy-server/database/jobs_directory/015/15696/dataset_35119_files/reads-sample-small.fastq/subgroups/miRNAs/miRNAs-TEs.sam'\n+-----------------------------\n+bwa aln -t 8 -n 0 '/data/galaxy/galaxy-server/database/jobs_directory/015/15696/dataset_35119_files/dataset_35118.dat_symlink.fa' '/data/galaxy/galaxy-server/database/jobs_directory/015/15696/dataset_35119_files/reads-sample-small.fastq/subgroups/miRNAs.fastq' 2> '/data/galaxy/galaxy-server/database/jobs_directory/015/15696/dataset_35119_files/reads-sample-small.fastq/subgroups/miRNAs/miRNAs-transcripts.sam_aln.err' | bwa samse /data/galaxy/galaxy-server/database/jobs_directory/015/15696/dataset_35119_files/dataset_35118.dat_symlink.fa /dev/stdin '/data/galaxy/galaxy-server/database/jobs_directory/015/15696/dataset_35119_files/reads-sample-small.fastq/subgroups/miRNAs.fastq' 2> '/data/galaxy/galaxy-server/database/jobs_directory/015/15696/dataset_35119_files/reads-sample-small.fastq/subgroups/miRNAs/miRNAs-transcripts.sam_samse.err' > '/data/galaxy/galaxy-server/database/jobs_directory/015/15696/dataset_35119_files/reads-sample-small.fastq/subgroups/miRNAs/miRNAs-transcripts.sam'\n+-----------------------------\n+bwa aln -t 8 -n 0 '/data/galaxy/galaxy-server/database/jobs_directory/015/15696/dataset_35119_files/dataset_35115.dat_symlink.fa' '/data/galaxy/galaxy-server/database/jobs_directory/015/15696/dataset_35119_files/reads-sample-small.fastq/subgroups/miRNAs.fastq' 2> '/data/galaxy/galaxy-server/database/jobs_directory/015/15696/dataset_35119_files/reads-sample-small.fastq/subgroups/miRNAs/miRNAs-genome.sam_aln.err' | bwa samse /data/galaxy/galaxy-server/database/jobs_directory/015/15696/dataset_35119_files/dataset_35115.dat_symlink.fa /dev/stdin '/data/galaxy/galaxy-server/database/jobs_directory/015/15696/dataset_35119_files/reads-sample-small.fastq/subgroups/miRNAs.fastq' 2> '/data/galaxy/galaxy-server/database/jobs_directory/015/15696/dataset_35119_files/reads-sample-small.fastq/subgroups/miRNAs/miRNAs-genome.sam_samse.err' > '/data/galaxy/galaxy-server/database/jobs_directory/015/15696/dataset_35119_files/reads-sample-small.fastq/subgroups/miRNAs/miRNAs-genome.sam'\n+** Subgroup fork /data/galaxy/galaxy-server/database/jobs_directory/015/15696/dataset_35119_files/reads-sample-small.fastq/subgroups/miRNAs.fastq started, pid: 14244\n+** Subgroup fork /data/galaxy/galaxy-server/database/jobs_directory/015/15696/dataset_35119_files/reads-sample-small.fastq/subgroups/miRNAs.fastq just finished with PID 14244 and exit code: 0\n+** Subgroup fork /data/galaxy/galaxy-server/database/jobs_directory/015/15696/dataset_35119_files/reads-sample-small.fastq/subgroups/siRNAs.fastq started, pid: 14405\n+** Subgroup fork /data/galaxy/galaxy-server/database/jobs_directory/015/15696/dataset_35119_files/reads-sample-small.fastq/subgroups/bonafide_reads.fastq just finished with PID 14243 and exit code: 0\n+** Subgroup fork /data/galaxy/galaxy-server/database/jobs_directory/015/15696/dataset_35119_files/reads-sample-small.fastq/subgroups/piRNAs.fastq started, pid: 14463\n+** Subgroup fork /data/galaxy/galaxy-server/database/jobs_directory/015/15696/dataset_35119_files/reads-sample-small.fastq/subgroups/siRNAs.fastq just finished with PID 14405 and exit code: 0\n+** Subgroup fork /data/galaxy/galaxy-server/database/jobs_directory/015/15696/dataset_35119_files/reads-sample-small.fastq/subgroups/piRNAs.fastq just finished with PID 14463 and exit code: 0\n+ping_pong_partners /data/galaxy/galaxy-server/database/jobs_directory/015/15696/dataset_35119_files/reads-sample-small.fastq/subgroups//piRNAs/TEs.sam /data/galaxy/galaxy-server/database/jobs_directory/015/15696/dataset_35119_files/reads-sample-small.fastq/subgroups/PPPartners/\n+Fastq fork : /data/galaxy/galaxy-server/database/files/035/dataset_35117.dat started, pid: 14070\n+Fastq fork /data/galaxy/galaxy-server/database/files/035/dataset_35117.dat just finished with PID 14070 and exit code: 0\n+Job done!\n" |
| b |
| diff -r 9645d995fb3c -r 9185ca0a7b43 test-data/transcripts-file-small.fa --- a/test-data/transcripts-file-small.fa Wed Oct 24 07:40:20 2018 -0400 +++ b/test-data/transcripts-file-small.fa Wed Jan 16 08:18:13 2019 -0500 |
| b |
| b'@@ -1,26 +1,26 @@\n->FBtr0078666 type=mRNA; loc=3R:complement(join(5822026..5824307,5824361..5824504)); ID=FBtr0078666; name=CG2023-RA; dbxref=FlyBase:FBtr0078666,FlyBase_Annotation_IDs:CG2023-RA,REFSEQ:NM_141338,REFSEQ:NM_141338,REFSEQ:NM_141338; score=11; score_text=Strongly Supported; MD5=d3ca07b9149e74faf0d15d708cb012db; length=2426; parent=FBgn0037383; release=r6.16; species=Dmel; \r\n-GTTAAATGCACGTCACCAAAGCAGAATAATAGAATATTTTCGAAACAAAACAAAGTTGGAGACATGGACAAGGATGCGTTTACATTACAGGCCATACGGCAGGACCTTATCGATAACAATCTGCAGGCTAAGGCAATAATACACGACATCCTGAACAGCCGCACCTCCATCGCCGAACTCGAGGAGCTGAACGAAGCGGGCCGCTCCAAACTGTCTGCTATCCGCAAAAGCATCGAGCGGCTGGACGACTGGGCGCGGGACACGGCAGACTCTGCGCTGGCCAATGAAGTGGACGACCACCGTGATCAGTTCTCCAAAACGCTGCAGGCGTTCCGAAAAGCAAACGTGTCCACGATGCTGGAGATCGAGAAGGCCAATCGGGAGGAGTTAATGGCCATTACCGGCGAGAGTGAGCTACGCCAACGAACCACAACACGGGCGCGGCACAACCAGGGCAGTCTGGTTTCGCAGGAGAACGACGTGACCGAGAAGATGCTGGCTATATCGCGGCACCTCTCGGAGACCACCCAGAAGAGCGCCATCACCCTGGAAACGCTCGTGGCCTCGTCGCAAAATGTGGAGGCCACCAGCGACGAACTGCACCACACGGCCGGCAGCATTAGCATGTCCGGCAAGCTGCTCAAAAAGTACGGACGACGCGAGTGCACTGACAAAATGCTGCTCTTCTTCGCCTTCTCCTTGTTCCTCGCCTGTGTCTTTTACATCGTCCAAAAGCGACTCTTCTAAGACTCCACAAATGGACAAAACCCGTTCCCAAAATAGCTTAAGGTTGTCGCTTCTGTTGTCTAGGTATAGCTAGATTAAGCTTAGCACATGACCATACCTTGTAAGCACAGCTCCTATATTTATATTATTTAGTGATTTGCCTAAGTTGTAAACGTGGTACAGCCAAAGACCCTAGAATAACAAGATGCGTAACGCCATACGATTTTTTGGCACACGATTTTTTGGCCGTGGCTCTAGAGGTGGCTCCAGGCTCTCTCGAATTTTTGTTAGAGAGCGAGAGAGCGAAGAGCGCTACAGCGAACAGCTCTTTTCAACGCACAAAGTGATAGCAGACATCTGTATGTGTGCACACGTATTCACATGCATTGTAAATTTGACAAAATATGCCCTTCACCTTAGAAGTTCTTTGGCTTTAAATCTATATTATTTTTTATCAATTGGCACCATGCGAAAAATTCTTGTTTTGCATTGCCTTAACGTTATTATTATTTGAAAATAGATTAGAAATAGTCAAATCTATGTACATATTATCACAAAAATAAATTTCAAAAATGAATTTATATAAGAATATTTGTCATTAGAGTATTCATCTTGCGGCGTGTGAAAAATTAATAAGGCAATGATTGTTGAGTGCTTGTGTCCGCACTTCGTGCCTCAAGATATGAACAAAGCAAAGACACTAGAATAATTCTATTGTCTTTGATATTACTTTTGCAATTTAATTTAATTGCATATTTAATTATTTAGTATATTTATTAAATCATTTGACTTAATATGATGTAACATTAACATTAAAAGTGTTTCAAAAAAAATATTTCGGTTTTAAAAAATTGTCAGATGAGAGACAAATTAGAATTAAACATAAATACAAATGTGTAAACGGTAGCTAATTCGAGCGGCGATTTTAACAAAGAAATTTAAAAAAGCTTTAAAATTATAATAGCCAGGGCGCGAATTTTTAAAAATTTTTTATTTTATCATATTGCTAGGAAATTGGCAAAAACTACCCTAATATGTACCATGTAAATTCGTTTCTTCGATCAGAATTGATTTCGGCCCGAAAATCGTCTTCTAGCACAACACGCACACTTATACGCGTTCTCGTCTCTTGTTTTTACTCACACAAGCAAGCAAATTATATTTTTAGATTTCTTACGCTCTAAGCGGGAGTGAGCGGAAAGAGAGTAATTTTGGCCGTCACCAAAAAAGTGGCTGCATAGTGCCAAACCAATGTATGGCCGTTACGCATCTTGTTATTCTAGTGTCTTTGGTACAGCCTAGTATAGTATGGTAAATGCAATTTATTTTTATTTAGAATATATGAGTGTTGTATATGTAGATAAAAATGTTAAGCAAGTTAGTAAGGGCACCTAGGCACTCCTCCGGGGTTTGTGAATCCGTTGGTGTTGACCAACCTGCAGATGTCCTTGTATGACCGCGCCGATTTTGCAGGCCTTTCTGGCTGTGGCTGGGAATAACCTCTGTTGTAATAGTCAGGATAGAACTGGAACCAAGAAGGCCTGTGGTAGTTGTAGTCGGGAAAAAATTCTTTAAGCACAGAGCTGCTGCAGAATCTGCTTAGCCCCAGAATCCACAGCAGAATGTATATAATCGACTTGCGCATGGCCACTTCGCCTGAGCTTAAGATTTGGAATAAAGCCGTACCCGATTCTCATTGT\r\n->FBtr0345575 type=mRNA; loc=2R:complement(join(8564187..8564768,8564826..8567202)); ID=FBtr0345575; name=Cyp6a14-RE; dbxref=FlyBase:FBtr0345575,FlyBase_Annotation_IDs:CG8687-RE,REFSEQ:NM_001299270; score=11; score_text=Strongly Supported; MD5=8174de0eb4bb4210648ec87219a6a80c; length=2959; parent=FBgn0033302; release=r6.16; species=Dmel; \r\n-AGTTGTCCCTAAACGCTGATTCAGTGAAGTCGTTTACGCGATAAGTTTACTGTGTGAAAAAGAAATAAAAGTTTCGTCAGCCTTTAGGTGGAATTCCCTCTATTGGTTGTCCGAAATCGGCAACATACATTTGTTTAACACCAACATTTGTCTTTGCTTTACCAAATAAATGATGTTTGAGGTGCCGTTACTCATTGACAGCAATATAGAACTTGGTACTACCAAAGACACTAGAATAACAAGATGCGTAACGGCCATACATTGGTTTGGCACTATGCAGCCACTTTTTTGGTGACGGCCAAAATTGCTCTCTTTCCGCTCGCTCACGCGCCCTTCTTATTATAATTTTAAAGCTGTTTAAATTTGTTTGTTAAAATCGCCGCTCGAATTATCTACCGTTTACACATTTATATTTATGTTTAATTCTAATTTGTCTCTCATCTGACAATTTTTTAAAAGCGAAATAATTTTTTTGAAACACTTTTAATGTTAATGTTACATCATATTAGGTCAAATGATTTAATAAATATACTAAATAATTAAATATGATAACTGTTTATTGCAAAAGTAATATCAAAGACACTAGAATTATTCTAGTGTCTTTGCTTTGTTCATATCTTGAGGCACGAAATGCGGACACAAGCACTCAACAATCATTGCCTTATTAATTTTTCACACGCCGCAAGATGAATACTCTAATGACAAATATTCTTATATAAAGTCATTTTTGAAATTGATTTTTGTGATAATATGTACATAGATTTGGCTTTTTCTAATCTATTTTCAAATAATAATAACGTTAAGGCAATGTAAAACAAGAATTTTTCGCATGGTGCC'..b'CACCAAATGATATGTAATTAAAATTAAATAAATATCTAAACACATATTGTGAATGACGACTAATCTTGCAAACGACATTACATACTTTATGTAGGGCGAATTCTGGTTGATTTTTACAATCGACCACTTGACGAGCAGTTAAGCCAGTTCTTTTTTTTTTGTTTAAAACAATACGTATTTTATTTTTACAAGACATTCCCTAACTAGGTTAGGGTTCCCATTTAAAGGTATTTCCTTACTCGCTTACAATTGAATCCCGAAATGGATTCAATGTACTATTTATCTAATATCACCTCATGGCATCTAAGGAATTTAAGGGATCTTTGAACTAACACCTACATATTTGTGTATTGTATTCAAATATATTGTGTATCTGTCTGGTAAAGTGTTAACTTAACTTTGTAAATACTATGCGGTTTACTTTAAAGACAAATCAAAGGCGATAGTGTGCGAAAGCAAAAGGAAACAATTAAATACGAGTATAATAAATATTTTTTTCAAAT\n+>FBtr0310270 type=mRNA; loc=X:join(15024436..15024954,15030586..15030847,15030911..15031068,15031178..15031467,15031543..15032573,15033606..15034414); ID=FBtr0310270; name=be-RF; dbxref=FlyBase:FBtr0310270,FlyBase_Annotation_IDs:CG32594-RF,REFSEQ:NM_001258745,REFSEQ:NM_001258745; score=15; score_text=Strongly Supported; MD5=5539c8fae56fdff6eb554e4ed9309709; length=3069; parent=FBgn0052594; release=r6.16; species=Dmel; \n+TTAGAGCTAAACGAACTGCCATCCGGTAAACACGTCTCACAACGTTATTTGTGTTGAATATATATATATTTTTTTGTTGTGGCTCTTTTTTTTTAATTTCTGCGGCCCCTAAAGTTCGACGATCGTGAGAAGGGAAAAAGAGTGTGAAGTGACCTAAGCGGTTTTGAAATATCTATCTTGGCAAAACGAAAACAAATTTGTTAAAGCACATATAAACAAAAACAAAATAACAAAAATAAAAGTGAAGCAAAGGTGAAGAAGACCAGAATGAATTCGCGACGGATTGCTCTGGTCCTCCTAATCGGCATAATCGTTTCGTTTTCTGGCCATGATGCACTAACCTATCCGGAGCGCTTCGATCGCCTGCCCACTTGGGGTGGTCATTCCCAAATTGGTGGGCCGCTGCTGGATACCGCCCACCGGGAGAATCGTGAGAAAAGGGAGAATAGGGTGGACCTGTGCCGGCACTGTTTCTGCATTCATCTCAAGGCAATCTGTGATTACAAGCTTAACAAAACGCTCCCGAACGAATTTAACGATAAACTATTGGTGCCGCTGAACATCAAATATATTGAGGTGCGACTGACTGTTGGCACCCAGTTCGTGATGTACGAGAACTTCTTCCAGGACAACCAGGTGAACTACTTTGGTGTAATCGGAGTGGGGAAAGATGACCAGGTGGAAATAACCAGCAATGCATTTAGCCACAACAAAGGCGGTTTTCCCAACATCGAAATACGAAATGTATTGCGAGTTTTTCTGCGTGAGAAATTCCTGACCGGTGCGGACTACAAGCTGCTGGTGGAGGATGTTACTCAGCTGTCCGTATTCTCCAATGCCCTTCAGATGACTAATCTAGACTGTTCTCTCAAGCGGATCAAGGAGCTGAATCTGATGAAGAACGCTTTCAATCCTGGGGTTGCCAAATATGGAATAAATCTCCGCATCGAGGATTCGAACATCAATCAGCTGGGTATATTCGGCGTGTCCATGGGCAAGGTGAGCCTGTTGCGCTGCCACATCGACATGATCATGAGCAACGCCTTTGACGTTACCAGCATCAAGGAGCTGATTATCGAGGGCTGCAATATCGAGGTGATCGAGAGCCAGGCGCTAACCAACAAATTGCATAGCGATAAGGTGGCCATCGTGGATACGGTGATCGGTACGATTGAGGGTCAGGCGATCAGTCAGAGCGGTATAACTACCATGATTATGTTTGGAAATACAATTACAAAAATACGTTCGAATGCCATTCAAATTGTTGCCGTTAGTCTGTTCATACGCAACAATTCAATGAGCCATGTGGAGCCCAATTGGTTGAGTGTCAGCCAGGCCGATCAAGTGGAGATTGCGAATAATCGCTTCGAGGACTACGGACGCTGTGAACTGAACATTGGCTCCTCGAACTGCAGTTTTCGCAACAATATACTGCAGAATCCGCAATCGGGTAGCCTCAATTTTACATGTCGCGTCCACCAGGTGCGCGTGGGCACCGAGTGCTCGTGCAACAAGTCCTGGCTATCGGAGCTAACCGATCATGATCTGGAATCGGAAATCATGTGTCAGGTGGCAAAGCGTGATGCCAACTGCTTTAATGCCACCAATACGGATGTCCGCCGGTATGTCAACGAGGCATGTGGCAGCAATGTGACCCGCTACTGTATGGGTGGCCAGTGGGTGACCAAGGCGGTCAGTGATCATTCTAGCGACTCCAGCAAATTGACCATCGGAATGATAGCCCTTGAGATTGTGATTTTAACACTCTTGCTTGTTGCGATTGTCTGTGTGTTGGCCAAAAACTGTGGCAGTGGAAGCTGCGCTCCTGCCGGTGGCCAGTCCACTGATAATTGCCTAATCGAGGAGGACATTCGCAACTCACTGCGCCAGCTCGCACTGCACAGCGAGAGCAATAAGACACGCAAGGCTATACTGAAGCTGATCAATGGTCATTTGAGCAAGGGGGAGTGCAACGATCGGATACTCTTTATAGTGGACAACATGCCGCAAAATCAGGCGATCGAAAGCCTGCTGTTTAGGCACATATCGCAGAGTCACATGGAGCCCAGTGATAGTGAGGCATATGCCAGCACCGCCTTAACAGCCAATGCAACAGCACCACCACTGCCGCCCAGTACCGATTCCAGTGAGCCCATCTACCAAGAGCTCGACCAGCAACGACTGATCATCGACGACAAGTACTCATTGCCGCTGAATTCCGACGAGGATCCGCCGTACTCGGAGCCGTCCAATATGATGAATACGAACGACATGCCACCGGCATATCAATATGCCACACCGATGCGCATCCTGCCATGCCACCAGATGCAGCATCAGCAGCCGTCGACGACGGCCAATTATGCCATCCCCGTTTGGAGGTCCACTCCAAGTGCCACGCCCACTAGCCGCCCACCCTCGGGCTCACAGGAGGGGTCGGCCACCGCCACAGCGCCCAGAGCTGTCAAGGATTTGCGGCAGGCTCTGCAGAACTCCCCACAGTTCCATCCCAACCAGCTGACCTCAACGCGCAACCAAAGACAAATCCTGCAGATTCTGCCGCCGCTTCAGCCGCCGCCGTACACTCAGAGGTCACAGGTCAGGGGTCAGCGGAGGCGCAGCTTCGAGTGCCTCGATGGCGCCGCCAGCTTGGCGGCCATGGAGCACATGGACTCCGGCTCGGATCACTCTGGCGGCAGTGATGTGACCGTCCAAATTGCTGATGTGATCGACTACGCGGATGCCTAAAAGTATGCAGAGCACTCAAATATATACTATACTATATATATATAGTACAGGTATATAGTAACATAATATGCTTCTCATATTACGTTTACATACTTACACTAATTGTACATACAATCTTGCACATGCATAAACACATGAAACCAGTTTACATTTTTACTTACACTTAAGCGCATAATTTGTTGTGCATCCATACCGTTATTTTTCCGTTTTTTTTTGTACACATATACTGATTAGACATTCCCGTTTCTCGCGACTCACTTCGAGCCGATCAAAAACTCTGTACAGTCAGTCTTAAGCCGACAACGAAGAAATAAAGATCTAAAC\n' |
| b |
| diff -r 9645d995fb3c -r 9185ca0a7b43 tool-data/bwa_index.loc.sample --- a/tool-data/bwa_index.loc.sample Wed Oct 24 07:40:20 2018 -0400 +++ b/tool-data/bwa_index.loc.sample Wed Jan 16 08:18:13 2019 -0500 |
| b |
| @@ -1,14 +1,14 @@ -#-rw-r--r-- 1 james universe 830134 2005-09-13 10:12 phiX.fa.amb -#-rw-r--r-- 1 james universe 527388 2005-09-13 10:12 phiX.fa.ann -#-rw-r--r-- 1 james universe 269808 2005-09-13 10:12 phiX.fa.bwt -#...etc... -# -#Your bwa_index.loc file should include an entry per line for each -#index set you have stored. The "file" in the path does not actually -#exist, but it is the prefix for the actual index files. For example: -# -#phiX174 phiX phiX174 /depot/data2/galaxy/phiX/base/phiX.fa -#hg18canon hg18 hg18 Canonical /depot/data2/galaxy/hg18/base/hg18canon.fa -#hg18full hg18 hg18 Full /depot/data2/galaxy/hg18/base/hg18full.fa -#/orig/path/hg19.fa hg19 hg19 /depot/data2/galaxy/hg19/base/hg19.fa +#-rw-r--r-- 1 james universe 830134 2005-09-13 10:12 phiX.fa.amb +#-rw-r--r-- 1 james universe 527388 2005-09-13 10:12 phiX.fa.ann +#-rw-r--r-- 1 james universe 269808 2005-09-13 10:12 phiX.fa.bwt +#...etc... +# +#Your bwa_index.loc file should include an entry per line for each +#index set you have stored. The "file" in the path does not actually +#exist, but it is the prefix for the actual index files. For example: +# +#phiX174 phiX phiX174 /depot/data2/galaxy/phiX/base/phiX.fa +#hg18canon hg18 hg18 Canonical /depot/data2/galaxy/hg18/base/hg18canon.fa +#hg18full hg18 hg18 Full /depot/data2/galaxy/hg18/base/hg18full.fa +#/orig/path/hg19.fa hg19 hg19 /depot/data2/galaxy/hg19/base/hg19.fa #...etc... \ No newline at end of file |
| b |
| diff -r 9645d995fb3c -r 9185ca0a7b43 tool_data_table_conf.xml.sample --- a/tool_data_table_conf.xml.sample Wed Oct 24 07:40:20 2018 -0400 +++ b/tool_data_table_conf.xml.sample Wed Jan 16 08:18:13 2019 -0500 |
| b |
| @@ -1,7 +1,7 @@ -<tables> - <!-- Locations of configurations --> - <table name="bwa_indexes" comment_char="#"> - <columns>value, dbkey, name, path</columns> - <file path="tool-data/bwa_index.loc" /> - </table> +<tables> + <!-- Locations of configurations --> + <table name="bwa_indexes" comment_char="#"> + <columns>value, dbkey, name, path</columns> + <file path="tool-data/bwa_index.loc" /> + </table> </tables> \ No newline at end of file |
