| Next changeset 1:c7bed3fe0e23 (2017-08-19) |
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Commit message:
planemo upload for repository https://github.com/joachimwolff/galaxytools/tree/hicup/tools/hicup commit b77cbc104261f8aa1524922f41c2a9a23052f5da |
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added:
hicup_deduplicator.xml hicup_macros.xml test-data/HiCUP_summary_report.txt test-data/chr1.fa test-data/dataset.contiguous.filter.sam test-data/dataset.filt.sam test-data/dataset.hicup.sam test-data/dataset.invalid.filter.sam test-data/dataset.re_ligation.filter.sam test-data/dataset.same_circularised.filter.sam test-data/dataset.same_dangling_ends.filter.sam test-data/dataset.same_internal.filter.sam test-data/dataset1.fastq test-data/dataset1.mapper_barchart.svg test-data/dataset1.trunc.fastq test-data/dataset1.truncation_barchart.svg test-data/dataset2.fastq test-data/dataset2.mapper_barchart.svg test-data/dataset2.trunc.fastq test-data/dataset2.truncation_barchart.svg test-data/deduplicator_cis_trans_piechart.svg test-data/deduplicator_uniques_barchart.svg test-data/digester_file.txt test-data/filter_piechart.svg test-data/hicup_deduplicator_summary.txt test-data/hicup_filter_summary.txt test-data/hicup_mapper_summary.txt test-data/hicup_truncater_summary.txt test-data/result.pair.sam test-data/results.html tool-data/bowtie2_indices.loc.sample tool_data_table_conf.xml.sample |
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| diff -r 000000000000 -r d515a0639f8e hicup_deduplicator.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/hicup_deduplicator.xml Thu Mar 09 09:30:33 2017 -0500 |
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| @@ -0,0 +1,39 @@ +<tool id="hicup_deduplicator" name="Hicup Deduplicator" version="0.1.0"> + <description>removes duplicated di-tags (retaining one copy of each) from the data set.</description> + <macros> + <import>hicup_macros.xml</import> + </macros> + <expand macro="requirements_hicup" /> + <expand macro="stdio" /> + + <command><![CDATA[ + hicup_deduplicator --quiet '$input_file' + && mv *.dedup.* dataset.dedup_result + && mv hicup_deduplicator_summary*.txt hicup_deduplicator_summary.txt + && mv *deduplicator_cis_trans_piechart.svg deduplicator_cis_trans_piechart.svg + && mv *deduplicator_uniques_barchart.svg deduplicator_uniques_barchart.svg + ]]></command> + <inputs> + <param name="input_file" type="data" format="bam,sam" label="Input file(s)" help="Input files in bam or sam format."/> + </inputs> + <outputs> + <data name="dedup_result" format="bam,sam" label="Deduplicator Result" from_work_dir="dataset.dedup_result" /> + <expand macro="deduplicator_output" /> + </outputs> + <tests> + <test> + <param name="input_file" value="dataset.filt.sam" ftype="sam"/> + <output name="dataset_hicup" file="dataset.hicup.sam" lines_diff="5" /> + <output name="cis_trans_piechart" file="deduplicator_cis_trans_piechart.svg" ftype="svg" lines_diff="1000"/> + <output name="uniques_barchart" file="deduplicator_uniques_barchart.svg" ftype="svg" lines_diff="1000"/> + <output name="hicup_deduplicator_summary" file="hicup_deduplicator_summary.txt" lines_diff="2"/> + </test> + </tests> + <help><![CDATA[ + + For help please consult the documentation of HiCUP: http://www.bioinformatics.babraham.ac.uk/projects/hicup/overview/ + + To get more information about the deduplicator visit: http://www.bioinformatics.babraham.ac.uk/projects/hicup/scripts_description/#Deduplicator + ]]></help> + <expand macro="citation_hicup" /> +</tool> \ No newline at end of file |
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| diff -r 000000000000 -r d515a0639f8e hicup_macros.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/hicup_macros.xml Thu Mar 09 09:30:33 2017 -0500 |
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| @@ -0,0 +1,94 @@ + +<macros> + <xml name="requirements_hicup"> + <requirements> + <requirement type="package" version="0.5.9">hicup</requirement> + <requirement type="package" version="2.2.6">bowtie2</requirement> + <requirement type="package" version="1.2">samtools</requirement> + <requirement type="package" version="0.13.1">docutils</requirement> + </requirements> + </xml> + <xml name="stdio"> + <stdio> + <exit_code range="1:" /> + </stdio> + </xml> + <xml name="citation_hicup"> + <citations> + <citation type="doi">10.12688/f1000research.7334.1</citation> + </citations> + </xml> + <xml name="reference_genome_macro"> + <conditional name="reference_genome"> + <param name="source" type="select" label="Will you select a reference genome from your history or use a built-in index?" help="Built-ins were indexed using default options. See `Indexes` section of help below"> + <option value="indexed">Use a built-in genome index</option> + <option value="history">Use a genome from the history and build index</option> + </param> + <when value="indexed"> + <param name="index" type="select" label="Select reference genome" help="If your genome of interest is not listed, contact the Galaxy team"> + <options from_data_table="bowtie2_indices"> + <filter type="sort_by" column="2"/> + <validator type="no_options" message="No indexes are available for the selected input dataset"/> + </options> + </param> + </when> + <when value="history"> + <param name="own_file" type="data" format="fasta" label="Select reference genome" /> + <!--<param name="own_file" type="data" format="fasta" metadata_name="dbkey" label="Select reference genome" />--> + </when> + </conditional> + </xml> + <xml name="filter_output"> + <data name="dataset_filt" format="sam" from_work_dir="dataset.filt.sam" label="filt.sam" /> + <data name="hicup_filter_summary" format="txt" from_work_dir="hicup_filter_summary.txt" label="hicup_filter_summary.txt" /> + <data name="contiguous_filter" format="sam" from_work_dir="hicup_filter_ditag_rejects/dataset.contiguous.filter.sam" label="contiguous.filter.sam" /> + <data name="re_ligation_filter" format="sam" from_work_dir="hicup_filter_ditag_rejects/dataset.re_ligation.filter.sam" label="re_ligation.filter.sam" /> + <data name="same_dangling_ends_filter" format="sam" from_work_dir="hicup_filter_ditag_rejects/dataset.same_dangling_ends.filter.sam" label="same_dangling_ends.filter.sam" /> + <data name="invalid_filter" format="sam" from_work_dir="hicup_filter_ditag_rejects/dataset.invalid.filter.sam" label="invalid.filter.sam" /> + <data name="same_circularised_filter" format="sam" from_work_dir="hicup_filter_ditag_rejects/dataset.same_circularised.filter.sam" label="same_circularised.filter.sam" /> + <data name="same_internal_filter" format="sam" from_work_dir="hicup_filter_ditag_rejects/dataset.same_internal.filter.sam" label="same_internal.filter.sam" /> + <data name="wrong_size_filter" format="sam" from_work_dir="hicup_filter_ditag_rejects/dataset.wrong_size.filter.sam" label="wrong_size.filter.sam"/> + <data name="filter_piechart" format="svg" from_work_dir="filter_piechart.svg" label="Filter piechart.svg" /> + </xml> + <xml name="mapper_output"> + <data name="hicup_mapper_summary" format="txt" from_work_dir="hicup_mapper_summary.txt" label="hicup_mapper_summary.txt"/> + <data name="result_pair" format="sam" from_work_dir="result.pair.sam" label="pair.sam"/> + <data name="dataset1_mapper_barchart" format="svg" from_work_dir="dataset1.mapper_barchart.svg" label="Mapper Dataset1 Barchart.svg" /> + <data name="dataset2_mapper_barchart" format="svg" from_work_dir="dataset2.mapper_barchart.svg" label="Mapper Dataset2 Barchart.svg" /> + </xml> + <xml name="truncater_output"> + <data name="hicup_truncater_summary" format="txt" label="hicup_truncater_summary.txt" from_work_dir="hicup_truncater_summary.txt" /> + <data name="dataset1_trunc" format="fastq" label="Hicup Dataset1 Truncation" from_work_dir="dataset1.trunc.fastq" /> + <data name="dataset2_trunc" format="fastq" label="Hicup Dataset2 Truncation" from_work_dir="dataset2.trunc.fastq" /> + <data name="dataset1_truncater_barchart" format="svg" label="Hicup Dataset1 Truncation Barchart.svg" from_work_dir="dataset1.truncation_barchart.svg" /> + <data name="dataset2_truncater_barchart" format="svg" label="Hicup Dataset2 Truncation Barchart.svg" from_work_dir="dataset2.truncation_barchart.svg" /> + + </xml> + <xml name="input_files"> + <param name="input_first_sequence" type="data" format="fastq" label="First input sequence" help="The first sequence:"/> + <param name="input_second_sequence" type="data" format="fastq" label="Second input sequence" help="The second sequence:"/> + </xml> + <xml name="re1"> + <param argument="--re1" type="text" value="" label="Restriction enzyme recognition sequence" help="Restriction enzyme recognition sequence"/> + </xml> + <xml name="re2"> + <param argument="--re2" type="text" value="" label="Restriction enzyme instead of sonication to shorten di-tags." help="To specify a restriction enzyme instead of sonication to shorten di-tags. This restriction site does NOT form a Hi-C ligation junction. 2 .g. AG^CT,AluI. Typically the sonication protocol is followed."/> + </xml> + <xml name="digester_input"> + <param name="input_files_digest" type="data" multiple="true" format="fa" label="Input DNA sequence files that should be digested"/> + <param argument="--genome" type="text" label="Genome" help="Name of the genome to be digested (not the path to the genome + file or files, but the genome name to include in the output file)"/> + </xml> + <xml name="filter_longest_shortest"> + <param argument="--longest" type="text" value="" label="Max insert size" help="Maximum allowable insert size (bps)"/> + <param argument="--shortest" type="text" value="" label="Min insert size" help="Minimum allowable insert size (bps)"/> + </xml> + <xml name="no_fill"> + <param argument="--nofill" type="boolean" value="false" truevalue="--nofill" falsevalue="" label="No fill" help="Hi-C protocol did NOT include a fill-in of sticky ends prior to re-ligation and therefore reads shall be truncated at the restriction site sequence"/> + </xml> + <xml name="deduplicator_output"> + <data name="cis_trans_piechart" format="svg" from_work_dir="deduplicator_cis_trans_piechart.svg" label="Hicup Deduplicator Cis Trans Piechart.svg"/> + <data name="uniques_barchart" format="svg" from_work_dir="deduplicator_uniques_barchart.svg" label="Hicup Deduplicator Uniques Barchart.svg" /> + <data name="hicup_deduplicator_summary" format="txt" from_work_dir="hicup_deduplicator_summary.txt" label="Hicup Deduplicator Summary" /> + </xml> +</macros> \ No newline at end of file |
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| diff -r 000000000000 -r d515a0639f8e test-data/HiCUP_summary_report.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/HiCUP_summary_report.txt Thu Mar 09 09:30:33 2017 -0500 |
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| @@ -0,0 +1,2 @@ +File Total_Reads_1 Total_Reads_2 Not_Truncated_Reads_1 Not_Truncated_Reads_2 Truncated_Read_1 Truncated_Read_2 Average_Length_Truncated_1 Average_Length_Truncated_2 Too_Short_To_Map_Read_1 Too_Short_To_Map_Read_2 Unique_Alignments_Read_1 Unique_Alignments_Read_2 Multiple_Alignments_Read_1 Multiple_Alignments_Read_2 Failed_To_Align_Read_1 Failed_To_Align_Read_2 Paired_Read_1 Paired_Read_2 Valid_Pairs Invalid_Pairs Same_Circularised Same_Dangling_Ends Same_Fragment_Internal Re_Ligation Contiguous_Sequence Wrong_Size Deduplication_Read_Pairs_Uniques Deduplication_Cis_Close_Uniques Deduplication_Cis_Far_Uniques Deduplication_Trans_Uniques Percentage_Mapped Percentage_Valid Percentage_Uniques Percentage_Unique_Trans Percentage_Ditags_Passed_Through_HiCUP +dataset_1265_4.dat.hicup.sam 1000 1000 923 939 77 61 21.39 22.21 35 24 14 23 13 7 938 946 1 1 1 0 0 0 0 0 0 0 1 0 1 0 0.10 100.00 100.00 0.00 0.10 |
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| diff -r 000000000000 -r d515a0639f8e test-data/chr1.fa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/chr1.fa Thu Mar 09 09:30:33 2017 -0500 |
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| b'@@ -0,0 +1,4000 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| diff -r 000000000000 -r d515a0639f8e test-data/dataset.contiguous.filter.sam --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/dataset.contiguous.filter.sam Thu Mar 09 09:30:33 2017 -0500 |
| b |
| @@ -0,0 +1,6 @@ +@HD VN:1.0 SO:unsorted +@SQ SN:chr1 LN:199950 +@PG ID:bowtie2 PN:bowtie2 VN:2.3.0 CL:"/home/wolffj/miniconda2/envs/hicup/bin/bowtie2-align-s --wrapper basic-0 --very-sensitive -x genome -p 1 - --passthrough" +@PG ID:HiCUP Mapper VN:0.5.9 +@PG ID:HiCUP Truncater VN:0.5.9 DS:"Restriction enzyme --re1 A^AGCTT" +@PG ID:HiCUP Filter VN:0.5.9 DS:"Max insert 0 Min insert 0 Digest file digest_file.txt" |
| b |
| diff -r 000000000000 -r d515a0639f8e test-data/dataset.filt.sam --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/dataset.filt.sam Thu Mar 09 09:30:33 2017 -0500 |
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| @@ -0,0 +1,8 @@ +@HD VN:1.0 SO:unsorted +@SQ SN:chr1 LN:199950 +@PG ID:bowtie2 PN:bowtie2 VN:2.3.0 CL:"/home/wolffj/miniconda2/envs/hicup/bin/bowtie2-align-s --wrapper basic-0 --very-sensitive -x genome -p 1 - --passthrough" +@PG ID:HiCUP Mapper VN:0.5.9 +@PG ID:HiCUP Truncater VN:0.5.9 DS:"Restriction enzyme --re1 A^AGCTT" +@PG ID:HiCUP Filter VN:0.5.9 DS:"Max insert 0 Min insert 0 Digest file digest_file.txt" +SRR071233.43293 83 chr1 35433 3 40M = 75323 0 GAGTCCAGGAGTTCAAGACCAGCCTGGGTAACATAGTGAG CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC AS:i:-15 XN:i:0 XM:i:3 XO:i:0 XG:i:0 NM:i:3 MD:Z:3G22A1C11 YT:Z:UU CT:Z:FAR +SRR071233.43293 163 chr1 75323 23 40M = 35433 0 CTCAATAAAATACTGGCAAACCGAATCCAGCAGCACATCG CCBCCCCCCBBCCCCCCCCCCCCCCCCCCCCCCCCCCCCC AS:i:-10 XN:i:0 XM:i:2 XO:i:0 XG:i:0 NM:i:2 MD:Z:20A18A0 YT:Z:UU CT:Z:FAR |
| b |
| diff -r 000000000000 -r d515a0639f8e test-data/dataset.hicup.sam --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/dataset.hicup.sam Thu Mar 09 09:30:33 2017 -0500 |
| b |
| @@ -0,0 +1,9 @@ +@HD VN:1.0 SO:unsorted +@SQ SN:chr1 LN:199950 +@PG ID:bowtie2 PN:bowtie2 VN:2.3.0 CL:"/home/wolffj/miniconda2/envs/hicup/bin/bowtie2-align-s --wrapper basic-0 --very-sensitive -x genome -p 1 - --passthrough" +@PG ID:HiCUP Mapper VN:0.5.9 +@PG ID:HiCUP Truncater VN:0.5.9 DS:"Restriction enzyme --re1 A^AGCTT" +@PG ID:HiCUP Filter VN:0.5.9 DS:"Max insert 0 Min insert 0 Digest file digest_file.txt" +@PG HiCUP Deduplicator VN:0.5.9 +SRR071233.43293 83 chr1 35433 3 40M = 75323 0 GAGTCCAGGAGTTCAAGACCAGCCTGGGTAACATAGTGAG CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC AS:i:-15 XN:i:0 XM:i:3 XO:i:0 XG:i:0 NM:i:3 MD:Z:3G22A1C11 YT:Z:UU CT:Z:FAR +SRR071233.43293 163 chr1 75323 23 40M = 35433 0 CTCAATAAAATACTGGCAAACCGAATCCAGCAGCACATCG CCBCCCCCCBBCCCCCCCCCCCCCCCCCCCCCCCCCCCCC AS:i:-10 XN:i:0 XM:i:2 XO:i:0 XG:i:0 NM:i:2 MD:Z:20A18A0 YT:Z:UU CT:Z:FAR |
| b |
| diff -r 000000000000 -r d515a0639f8e test-data/dataset.invalid.filter.sam --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/dataset.invalid.filter.sam Thu Mar 09 09:30:33 2017 -0500 |
| b |
| @@ -0,0 +1,6 @@ +@HD VN:1.0 SO:unsorted +@SQ SN:chr1 LN:199950 +@PG ID:bowtie2 PN:bowtie2 VN:2.3.0 CL:"/home/wolffj/miniconda2/envs/hicup/bin/bowtie2-align-s --wrapper basic-0 --very-sensitive -x genome -p 1 - --passthrough" +@PG ID:HiCUP Mapper VN:0.5.9 +@PG ID:HiCUP Truncater VN:0.5.9 DS:"Restriction enzyme --re1 A^AGCTT" +@PG ID:HiCUP Filter VN:0.5.9 DS:"Max insert 0 Min insert 0 Digest file digest_file.txt" |
| b |
| diff -r 000000000000 -r d515a0639f8e test-data/dataset.re_ligation.filter.sam --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/dataset.re_ligation.filter.sam Thu Mar 09 09:30:33 2017 -0500 |
| b |
| @@ -0,0 +1,6 @@ +@HD VN:1.0 SO:unsorted +@SQ SN:chr1 LN:199950 +@PG ID:bowtie2 PN:bowtie2 VN:2.3.0 CL:"/home/wolffj/miniconda2/envs/hicup/bin/bowtie2-align-s --wrapper basic-0 --very-sensitive -x genome -p 1 - --passthrough" +@PG ID:HiCUP Mapper VN:0.5.9 +@PG ID:HiCUP Truncater VN:0.5.9 DS:"Restriction enzyme --re1 A^AGCTT" +@PG ID:HiCUP Filter VN:0.5.9 DS:"Max insert 0 Min insert 0 Digest file digest_file.txt" |
| b |
| diff -r 000000000000 -r d515a0639f8e test-data/dataset.same_circularised.filter.sam --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/dataset.same_circularised.filter.sam Thu Mar 09 09:30:33 2017 -0500 |
| b |
| @@ -0,0 +1,6 @@ +@HD VN:1.0 SO:unsorted +@SQ SN:chr1 LN:199950 +@PG ID:bowtie2 PN:bowtie2 VN:2.3.0 CL:"/home/wolffj/miniconda2/envs/hicup/bin/bowtie2-align-s --wrapper basic-0 --very-sensitive -x genome -p 1 - --passthrough" +@PG ID:HiCUP Mapper VN:0.5.9 +@PG ID:HiCUP Truncater VN:0.5.9 DS:"Restriction enzyme --re1 A^AGCTT" +@PG ID:HiCUP Filter VN:0.5.9 DS:"Max insert 0 Min insert 0 Digest file digest_file.txt" |
| b |
| diff -r 000000000000 -r d515a0639f8e test-data/dataset.same_dangling_ends.filter.sam --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/dataset.same_dangling_ends.filter.sam Thu Mar 09 09:30:33 2017 -0500 |
| b |
| @@ -0,0 +1,6 @@ +@HD VN:1.0 SO:unsorted +@SQ SN:chr1 LN:199950 +@PG ID:bowtie2 PN:bowtie2 VN:2.3.0 CL:"/home/wolffj/miniconda2/envs/hicup/bin/bowtie2-align-s --wrapper basic-0 --very-sensitive -x genome -p 1 - --passthrough" +@PG ID:HiCUP Mapper VN:0.5.9 +@PG ID:HiCUP Truncater VN:0.5.9 DS:"Restriction enzyme --re1 A^AGCTT" +@PG ID:HiCUP Filter VN:0.5.9 DS:"Max insert 0 Min insert 0 Digest file digest_file.txt" |
| b |
| diff -r 000000000000 -r d515a0639f8e test-data/dataset.same_internal.filter.sam --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/dataset.same_internal.filter.sam Thu Mar 09 09:30:33 2017 -0500 |
| b |
| @@ -0,0 +1,6 @@ +@HD VN:1.0 SO:unsorted +@SQ SN:chr1 LN:199950 +@PG ID:bowtie2 PN:bowtie2 VN:2.3.0 CL:"/home/wolffj/miniconda2/envs/hicup/bin/bowtie2-align-s --wrapper basic-0 --very-sensitive -x genome -p 1 - --passthrough" +@PG ID:HiCUP Mapper VN:0.5.9 +@PG ID:HiCUP Truncater VN:0.5.9 DS:"Restriction enzyme --re1 A^AGCTT" +@PG ID:HiCUP Filter VN:0.5.9 DS:"Max insert 0 Min insert 0 Digest file digest_file.txt" |
| b |
| diff -r 000000000000 -r d515a0639f8e test-data/dataset1.fastq --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/dataset1.fastq Thu Mar 09 09:30:33 2017 -0500 |
| b |
| b'@@ -0,0 +1,4000 @@\n+@SRR071233.1 NRTG514-16_0001:3:1:1012:18280 length=40\n+NAAGATACCTTGACCGCTCATCCCCTGNNTTCATGAAAGA\n++SRR071233.1 NRTG514-16_0001:3:1:1012:18280 length=40\n+!##########################!!###########\n+@SRR071233.159 NRTG514-16_0001:3:1:1035:1632 length=40\n+AGCTTTCTCCTTCTTTTGTCTTTCCCTCCTTTCTGTTGGG\n++SRR071233.159 NRTG514-16_0001:3:1:1035:1632 length=40\n+:BBBBBA??BABBB@<:;A?@B@BBB?BB?6;9<9AA?:0\n+@SRR071233.317 NRTG514-16_0001:3:1:1055:11563 length=40\n+CATAGACAATACAATGGCAGCATTGAATAGTTGTGGCAGA\n++SRR071233.317 NRTG514-16_0001:3:1:1055:11563 length=40\n+C@CCB@CCCCCCCACC@BCAC?CC@?;:?BAAC@A=A<A5\n+@SRR071233.475 NRTG514-16_0001:3:1:1078:18960 length=40\n+AGATCAAGCTCAGGACAGTCTTGATCTCCTGACCTCATGA\n++SRR071233.475 NRTG514-16_0001:3:1:1078:18960 length=40\n+ACCAACCCACCCCCCCCCCCCBCCCCCCCCCCCCCBCCCC\n+@SRR071233.633 NRTG514-16_0001:3:1:1100:20149 length=40\n+ATACTGGCAAACTGAATCCAGCAGCACATCAAAAAGCTAG\n++SRR071233.633 NRTG514-16_0001:3:1:1100:20149 length=40\n+CCCCCCCBCCCCCCCCCCCCCCCCCCCCCCC@C@CBCACC\n+@SRR071233.791 NRTG514-16_0001:3:1:1122:17791 length=40\n+AGAAAACTGGAGAAGAAAGAGCCAGGGTAGTCAAAGGACT\n++SRR071233.791 NRTG514-16_0001:3:1:1122:17791 length=40\n+C?<CCCCCCCCCCCCCBCCCCCCCCCCC?CCCCC@CCCCC\n+@SRR071233.949 NRTG514-16_0001:3:1:1144:10543 length=40\n+AAAAAACCCTTCCTATTTGAAGAGCAAGCTACATAAGCAA\n++SRR071233.949 NRTG514-16_0001:3:1:1144:10543 length=40\n+CCCCBCCCCCCCCCBCCCCCCABCCC?BCCCCACCCBCC?\n+@SRR071233.1107 NRTG514-16_0001:3:1:1167:14820 length=40\n+GGACTGAATGAAATAATATATGCATAAAGTACATAAAAAT\n++SRR071233.1107 NRTG514-16_0001:3:1:1167:14820 length=40\n+CCCCCCCCCCCBACC<7<<:CCCCCCCCC@CCCCBCCC=>\n+@SRR071233.1265 NRTG514-16_0001:3:1:1186:18084 length=40\n+GCTTTCATCAAATGCCTTTGTCTTGGCATCTGAATTCCAG\n++SRR071233.1265 NRTG514-16_0001:3:1:1186:18084 length=40\n+CCCCCCCCCCCCCCCCCCCCCCCCCACCACCCCCCBCCCC\n+@SRR071233.1423 NRTG514-16_0001:3:1:1207:3079 length=40\n+CTATGAAAAGAAAAGAAGAAAAGCTAGCTTGTTTACATTG\n++SRR071233.1423 NRTG514-16_0001:3:1:1207:3079 length=40\n+CCCCCCCCCCCBBBBCBBCCCBBCCCCCCCCCCCCCCCCC\n+@SRR071233.1581 NRTG514-16_0001:3:1:1228:11045 length=40\n+AGAAGAGACACCTGCACACTTCCCTCCAAGAAGCTAGCTT\n++SRR071233.1581 NRTG514-16_0001:3:1:1228:11045 length=40\n+CCCCCCCCCCCCCCCCCCBCCCCCCCCCCCCCCCCCCCCC\n+@SRR071233.1739 NRTG514-16_0001:3:1:1250:19031 length=40\n+CGCATCACAAAGCTAGCTTAAGATTCCTTGTTGTTTCATC\n++SRR071233.1739 NRTG514-16_0001:3:1:1250:19031 length=40\n+CACCCCCCDCCCCCCCCCCCBCCCBCCCCCCCCCCCCCCC\n+@SRR071233.1897 NRTG514-16_0001:3:1:1270:19952 length=40\n+CATGCACACAATGGACAATCCCAGCAGAATTTGCTTTTCA\n++SRR071233.1897 NRTG514-16_0001:3:1:1270:19952 length=40\n+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC\n+@SRR071233.2055 NRTG514-16_0001:3:1:1291:5369 length=40\n+AGTTTTTCCTTGCATATGTGAAGCTAGCTTTCTCATCATC\n++SRR071233.2055 NRTG514-16_0001:3:1:1291:5369 length=40\n+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC\n+@SRR071233.2213 NRTG514-16_0001:3:1:1310:6855 length=40\n+GGCTTGGCTTAACCAATAACTTTTGTAGAAACCTTTATGA\n++SRR071233.2213 NRTG514-16_0001:3:1:1310:6855 length=40\n+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC\n+@SRR071233.2371 NRTG514-16_0001:3:1:1329:13048 length=40\n+AGCTTGGGCAGGAAGATGACCTACATGAATGAGGTGAGGA\n++SRR071233.2371 NRTG514-16_0001:3:1:1329:13048 length=40\n+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCDCCCCC\n+@SRR071233.2529 NRTG514-16_0001:3:1:1349:10964 length=40\n+TTGGTGTGTGGCCAGTGCTGACAACAGCATTTTGAACTAC\n++SRR071233.2529 NRTG514-16_0001:3:1:1349:10964 length=40\n+CCCCCCCCCCCCCBCCCCCCACCCCCCCCCCCCCCCCCCC\n+@SRR071233.2687 NRTG514-16_0001:3:1:1370:10692 length=40\n+ATAATTCTGCAAAAGGCCATAAGCTAGCTTGCACACTGCC\n++SRR071233.2687 NRTG514-16_0001:3:1:1370:10692 length=40\n+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC\n+@SRR071233.2845 NRTG514-16_0001:3:1:1387:3351 length=40\n+TGTGTTCCATTTGATGTCAAACAATAGGTTGAAAAATTAG\n++SRR071233.2845 NRTG514-16_0001:3:1:1387:3351 length=40\n+00///9;<;;BBBBBB@@B@BABBBBBB@BBBBBBBBBBB\n+@SRR071233.3003 NRTG514-16_0001:3:1:1407:3953 length=40\n+TGTGGGACCAGTGCAGCATTTAGTCTAGGAATAAATTTGT\n++SRR071233.3003 NRTG514-16_0001:3:1:1407:3953 length=40\n+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC\n+@SRR07123'..b'GAGGGTTTTTTCCTCGCTTGGGTTCATTAAGCTAGC\n++SRR071233.154841 NRTG514-16_0001:3:2:1055:18658 length=40\n+CBCCCCCCACCCCCCBC@?CBB@BB@BBBBBB<B>B9BBB\n+@SRR071233.154999 NRTG514-16_0001:3:2:1077:20120 length=40\n+AGCTTAGAATATACTATTATTGAAGAAGGAAAGCCTTAGA\n++SRR071233.154999 NRTG514-16_0001:3:2:1077:20120 length=40\n+CCCCCCCCACCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC\n+@SRR071233.155157 NRTG514-16_0001:3:2:1097:19808 length=40\n+TCTGAGAGTTCCAGTAGCTTCACATGCTCCAGTAATTGGT\n++SRR071233.155157 NRTG514-16_0001:3:2:1097:19808 length=40\n+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCDCDCCCC>\n+@SRR071233.155315 NRTG514-16_0001:3:2:1116:16443 length=40\n+CATGGAAGACAGCCCTGCAGAGCTAAATTTAGGCAGAGAC\n++SRR071233.155315 NRTG514-16_0001:3:2:1116:16443 length=40\n+CCCCCCBCCCCCCCCCCDCCCACCCCACCCCCCCDCDCCB\n+@SRR071233.155473 NRTG514-16_0001:3:2:1139:18586 length=40\n+ATCCACCCACCTTGGCCTCCCAAAGTGCTAGAATTACAGG\n++SRR071233.155473 NRTG514-16_0001:3:2:1139:18586 length=40\n+CCCCCCCCCCCCCCCCCCCCCCCCC?CCCACCCCCCCCCC\n+@SRR071233.155631 NRTG514-16_0001:3:2:1160:21064 length=40\n+ACTCATCTTGGACCTTGTTCTTCTTCTAATTCCACCATCA\n++SRR071233.155631 NRTG514-16_0001:3:2:1160:21064 length=40\n+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC\n+@SRR071233.155789 NRTG514-16_0001:3:2:1180:19951 length=40\n+AGCAGTGGTTCTCCCAGCACAGCATTTGAGCTCCAACAAC\n++SRR071233.155789 NRTG514-16_0001:3:2:1180:19951 length=40\n+CCCCCCCBCCCCCCCCCCCCCCC@CCCCCCCCCCCCCCCC\n+@SRR071233.155947 NRTG514-16_0001:3:2:1202:5247 length=40\n+CCTCTGAGACAAAGCTAGCTTCCTTTCACAGCTTGCTCCA\n++SRR071233.155947 NRTG514-16_0001:3:2:1202:5247 length=40\n+CCCCCCDCCCBCCCCCCCCCCCBCCCCCCCCCCCCCCCCC\n+@SRR071233.156105 NRTG514-16_0001:3:2:1222:1582 length=40\n+TCTTTAAAGTTCGCACAGAGTTTGGGGTATTCATTTTCAG\n++SRR071233.156105 NRTG514-16_0001:3:2:1222:1582 length=40\n+CCCCCCCCCCCCCCCCCCCCCCCCCCCBCCCACCCBCCCB\n+@SRR071233.156263 NRTG514-16_0001:3:2:1244:2002 length=40\n+TAGGTAGAGGGATTAGTTGAGGCCAAGGCCTTGATCTGGG\n++SRR071233.156263 NRTG514-16_0001:3:2:1244:2002 length=40\n+CCCCBCCACCC@CCCCCCCCCCCCCCCCCCCBCC@CCC@=\n+@SRR071233.156421 NRTG514-16_0001:3:2:1264:4614 length=40\n+TCAGATGAGTAGGTTGCGAAAATTTTCTCCCATTTTGTAG\n++SRR071233.156421 NRTG514-16_0001:3:2:1264:4614 length=40\n+CCCCCBCCCCCCBACCCCCCC@BCCBCCCCCCCCCCCCCC\n+@SRR071233.156579 NRTG514-16_0001:3:2:1286:4483 length=40\n+TTGGGGAGGTGGCTGGGGAAGACCAGGGGCTACCTAAAAA\n++SRR071233.156579 NRTG514-16_0001:3:2:1286:4483 length=40\n+DCCCCCCCBBCCDCCCCBCCBCCCBABCCC@CCCBCC?CC\n+@SRR071233.156737 NRTG514-16_0001:3:2:1303:9680 length=40\n+GGAGAGATGAAAGAGTCAGACAGCTCTACAAAGCCTCTTT\n++SRR071233.156737 NRTG514-16_0001:3:2:1303:9680 length=40\n+CCCCCCCCCCCCCCCDCCCCCCCCCCCCCCCCCCCCCBCC\n+@SRR071233.156895 NRTG514-16_0001:3:2:1322:14192 length=40\n+TAAACACTATGACCATTTCCATCTTTCAGCCCTCTTGATT\n++SRR071233.156895 NRTG514-16_0001:3:2:1322:14192 length=40\n+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC?CC\n+@SRR071233.157053 NRTG514-16_0001:3:2:1342:21359 length=40\n+TTAAAGACTAAATGCTTACCATGTGTATGCTAGGTGTACA\n++SRR071233.157053 NRTG514-16_0001:3:2:1342:21359 length=40\n+CC@CCBCCCCCCCCCCCCCCCCCCCCCCCCCBCCDCDCCC\n+@SRR071233.157211 NRTG514-16_0001:3:2:1360:17441 length=40\n+ACGTTACACAGTGCATGACTATGCATGGTTTTTGGATTAA\n++SRR071233.157211 NRTG514-16_0001:3:2:1360:17441 length=40\n+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCBCCCC\n+@SRR071233.157369 NRTG514-16_0001:3:2:1379:4266 length=40\n+AAAGTTTTCCCGTTTAATATTATAAAATGGAATCATGTAA\n++SRR071233.157369 NRTG514-16_0001:3:2:1379:4266 length=40\n+00//0+AAAACCCCCCBCCCCCCCCCCCCCCCCCCCCCCC\n+@SRR071233.157527 NRTG514-16_0001:3:2:1398:4540 length=40\n+TTTGGTAAGATTCTGAATGATTTTTCTGGTTTTATTTTTT\n++SRR071233.157527 NRTG514-16_0001:3:2:1398:4540 length=40\n+CCCCCCCCCCCCCCCCCCC@CCCCCCBBCCCCCCCBBBBB\n+@SRR071233.157685 NRTG514-16_0001:3:2:1418:10945 length=40\n+TCATTAAATGTACTCTAATGGAATCATGGAATGGACTCGA\n++SRR071233.157685 NRTG514-16_0001:3:2:1418:10945 length=40\n+ABCCBCC@CCCCCCCCCBCCCACCCCCCCC=B@B@CCCCC\n+@SRR071233.157843 NRTG514-16_0001:3:2:1438:19334 length=40\n+TCATAAAATCATTTGTAGATTGAAGCTAGCTTCTCAGTTG\n++SRR071233.157843 NRTG514-16_0001:3:2:1438:19334 length=40\n+CCCACCCCCCCCCCCCCCCCCCCCBCC?CCCCCCCCCCCC\n' |
| b |
| diff -r 000000000000 -r d515a0639f8e test-data/dataset1.mapper_barchart.svg --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/dataset1.mapper_barchart.svg Thu Mar 09 09:30:33 2017 -0500 |
| b |
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| b |
| diff -r 000000000000 -r d515a0639f8e test-data/dataset1.trunc.fastq --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/dataset1.trunc.fastq Thu Mar 09 09:30:33 2017 -0500 |
| b |
| b'@@ -0,0 +1,4000 @@\n+@SRR071233.1 NRTG514-16_0001:3:1:1012:18280 length=40\n+NAAGATACCTTGACCGCTCATCCCCTGNNTTCATGAAAGA\n++SRR071233.1 NRTG514-16_0001:3:1:1012:18280 length=40\n+!##########################!!###########\n+@SRR071233.159 NRTG514-16_0001:3:1:1035:1632 length=40\n+AGCTTTCTCCTTCTTTTGTCTTTCCCTCCTTTCTGTTGGG\n++SRR071233.159 NRTG514-16_0001:3:1:1035:1632 length=40\n+:BBBBBA??BABBB@<:;A?@B@BBB?BB?6;9<9AA?:0\n+@SRR071233.317 NRTG514-16_0001:3:1:1055:11563 length=40\n+CATAGACAATACAATGGCAGCATTGAATAGTTGTGGCAGA\n++SRR071233.317 NRTG514-16_0001:3:1:1055:11563 length=40\n+C@CCB@CCCCCCCACC@BCAC?CC@?;:?BAAC@A=A<A5\n+@SRR071233.475 NRTG514-16_0001:3:1:1078:18960 length=40\n+AGATCAAGCTCAGGACAGTCTTGATCTCCTGACCTCATGA\n++SRR071233.475 NRTG514-16_0001:3:1:1078:18960 length=40\n+ACCAACCCACCCCCCCCCCCCBCCCCCCCCCCCCCBCCCC\n+@SRR071233.633 NRTG514-16_0001:3:1:1100:20149 length=40\n+ATACTGGCAAACTGAATCCAGCAGCACATCAAAAAGCTAG\n++SRR071233.633 NRTG514-16_0001:3:1:1100:20149 length=40\n+CCCCCCCBCCCCCCCCCCCCCCCCCCCCCCC@C@CBCACC\n+@SRR071233.791 NRTG514-16_0001:3:1:1122:17791 length=40\n+AGAAAACTGGAGAAGAAAGAGCCAGGGTAGTCAAAGGACT\n++SRR071233.791 NRTG514-16_0001:3:1:1122:17791 length=40\n+C?<CCCCCCCCCCCCCBCCCCCCCCCCC?CCCCC@CCCCC\n+@SRR071233.949 NRTG514-16_0001:3:1:1144:10543 length=40\n+AAAAAACCCTTCCTATTTGAAGAGCAAGCTACATAAGCAA\n++SRR071233.949 NRTG514-16_0001:3:1:1144:10543 length=40\n+CCCCBCCCCCCCCCBCCCCCCABCCC?BCCCCACCCBCC?\n+@SRR071233.1107 NRTG514-16_0001:3:1:1167:14820 length=40\n+GGACTGAATGAAATAATATATGCATAAAGTACATAAAAAT\n++SRR071233.1107 NRTG514-16_0001:3:1:1167:14820 length=40\n+CCCCCCCCCCCBACC<7<<:CCCCCCCCC@CCCCBCCC=>\n+@SRR071233.1265 NRTG514-16_0001:3:1:1186:18084 length=40\n+GCTTTCATCAAATGCCTTTGTCTTGGCATCTGAATTCCAG\n++SRR071233.1265 NRTG514-16_0001:3:1:1186:18084 length=40\n+CCCCCCCCCCCCCCCCCCCCCCCCCACCACCCCCCBCCCC\n+@SRR071233.1423 NRTG514-16_0001:3:1:1207:3079 length=40\n+CTATGAAAAGAAAAGAAGAAAAGCTT\n++SRR071233.1423 NRTG514-16_0001:3:1:1207:3079 length=40\n+CCCCCCCCCCCBBBBCBBCCCBBCCC\n+@SRR071233.1581 NRTG514-16_0001:3:1:1228:11045 length=40\n+AGAAGAGACACCTGCACACTTCCCTCCAAGAAGCTT\n++SRR071233.1581 NRTG514-16_0001:3:1:1228:11045 length=40\n+CCCCCCCCCCCCCCCCCCBCCCCCCCCCCCCCCCCC\n+@SRR071233.1739 NRTG514-16_0001:3:1:1250:19031 length=40\n+CGCATCACAAAGCTT\n++SRR071233.1739 NRTG514-16_0001:3:1:1250:19031 length=40\n+CACCCCCCDCCCCCC\n+@SRR071233.1897 NRTG514-16_0001:3:1:1270:19952 length=40\n+CATGCACACAATGGACAATCCCAGCAGAATTTGCTTTTCA\n++SRR071233.1897 NRTG514-16_0001:3:1:1270:19952 length=40\n+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC\n+@SRR071233.2055 NRTG514-16_0001:3:1:1291:5369 length=40\n+AGTTTTTCCTTGCATATGTGAAGCTT\n++SRR071233.2055 NRTG514-16_0001:3:1:1291:5369 length=40\n+CCCCCCCCCCCCCCCCCCCCCCCCCC\n+@SRR071233.2213 NRTG514-16_0001:3:1:1310:6855 length=40\n+GGCTTGGCTTAACCAATAACTTTTGTAGAAACCTTTATGA\n++SRR071233.2213 NRTG514-16_0001:3:1:1310:6855 length=40\n+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC\n+@SRR071233.2371 NRTG514-16_0001:3:1:1329:13048 length=40\n+AGCTTGGGCAGGAAGATGACCTACATGAATGAGGTGAGGA\n++SRR071233.2371 NRTG514-16_0001:3:1:1329:13048 length=40\n+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCDCCCCC\n+@SRR071233.2529 NRTG514-16_0001:3:1:1349:10964 length=40\n+TTGGTGTGTGGCCAGTGCTGACAACAGCATTTTGAACTAC\n++SRR071233.2529 NRTG514-16_0001:3:1:1349:10964 length=40\n+CCCCCCCCCCCCCBCCCCCCACCCCCCCCCCCCCCCCCCC\n+@SRR071233.2687 NRTG514-16_0001:3:1:1370:10692 length=40\n+ATAATTCTGCAAAAGGCCATAAGCTT\n++SRR071233.2687 NRTG514-16_0001:3:1:1370:10692 length=40\n+CCCCCCCCCCCCCCCCCCCCCCCCCC\n+@SRR071233.2845 NRTG514-16_0001:3:1:1387:3351 length=40\n+TGTGTTCCATTTGATGTCAAACAATAGGTTGAAAAATTAG\n++SRR071233.2845 NRTG514-16_0001:3:1:1387:3351 length=40\n+00///9;<;;BBBBBB@@B@BABBBBBB@BBBBBBBBBBB\n+@SRR071233.3003 NRTG514-16_0001:3:1:1407:3953 length=40\n+TGTGGGACCAGTGCAGCATTTAGTCTAGGAATAAATTTGT\n++SRR071233.3003 NRTG514-16_0001:3:1:1407:3953 length=40\n+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC\n+@SRR071233.3161 NRTG514-16_0001:3:1:1426:3923 length=40\n+TGAAAAAGCCAAACATAGAAAACGAAACTTTAAAACAGCA\n++SRR071233.3161 NRTG514-16_0001:3:1:1426:3923 length'..b'===:\n+@SRR071233.154841 NRTG514-16_0001:3:2:1055:18658 length=40\n+TGTGGAGGGTTTTTTCCTCGCTTGGGTTCATTAAGCTAGC\n++SRR071233.154841 NRTG514-16_0001:3:2:1055:18658 length=40\n+CBCCCCCCACCCCCCBC@?CBB@BB@BBBBBB<B>B9BBB\n+@SRR071233.154999 NRTG514-16_0001:3:2:1077:20120 length=40\n+AGCTTAGAATATACTATTATTGAAGAAGGAAAGCCTTAGA\n++SRR071233.154999 NRTG514-16_0001:3:2:1077:20120 length=40\n+CCCCCCCCACCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC\n+@SRR071233.155157 NRTG514-16_0001:3:2:1097:19808 length=40\n+TCTGAGAGTTCCAGTAGCTTCACATGCTCCAGTAATTGGT\n++SRR071233.155157 NRTG514-16_0001:3:2:1097:19808 length=40\n+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCDCDCCCC>\n+@SRR071233.155315 NRTG514-16_0001:3:2:1116:16443 length=40\n+CATGGAAGACAGCCCTGCAGAGCTAAATTTAGGCAGAGAC\n++SRR071233.155315 NRTG514-16_0001:3:2:1116:16443 length=40\n+CCCCCCBCCCCCCCCCCDCCCACCCCACCCCCCCDCDCCB\n+@SRR071233.155473 NRTG514-16_0001:3:2:1139:18586 length=40\n+ATCCACCCACCTTGGCCTCCCAAAGTGCTAGAATTACAGG\n++SRR071233.155473 NRTG514-16_0001:3:2:1139:18586 length=40\n+CCCCCCCCCCCCCCCCCCCCCCCCC?CCCACCCCCCCCCC\n+@SRR071233.155631 NRTG514-16_0001:3:2:1160:21064 length=40\n+ACTCATCTTGGACCTTGTTCTTCTTCTAATTCCACCATCA\n++SRR071233.155631 NRTG514-16_0001:3:2:1160:21064 length=40\n+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC\n+@SRR071233.155789 NRTG514-16_0001:3:2:1180:19951 length=40\n+AGCAGTGGTTCTCCCAGCACAGCATTTGAGCTCCAACAAC\n++SRR071233.155789 NRTG514-16_0001:3:2:1180:19951 length=40\n+CCCCCCCBCCCCCCCCCCCCCCC@CCCCCCCCCCCCCCCC\n+@SRR071233.155947 NRTG514-16_0001:3:2:1202:5247 length=40\n+CCTCTGAGACAAAGCTT\n++SRR071233.155947 NRTG514-16_0001:3:2:1202:5247 length=40\n+CCCCCCDCCCBCCCCCC\n+@SRR071233.156105 NRTG514-16_0001:3:2:1222:1582 length=40\n+TCTTTAAAGTTCGCACAGAGTTTGGGGTATTCATTTTCAG\n++SRR071233.156105 NRTG514-16_0001:3:2:1222:1582 length=40\n+CCCCCCCCCCCCCCCCCCCCCCCCCCCBCCCACCCBCCCB\n+@SRR071233.156263 NRTG514-16_0001:3:2:1244:2002 length=40\n+TAGGTAGAGGGATTAGTTGAGGCCAAGGCCTTGATCTGGG\n++SRR071233.156263 NRTG514-16_0001:3:2:1244:2002 length=40\n+CCCCBCCACCC@CCCCCCCCCCCCCCCCCCCBCC@CCC@=\n+@SRR071233.156421 NRTG514-16_0001:3:2:1264:4614 length=40\n+TCAGATGAGTAGGTTGCGAAAATTTTCTCCCATTTTGTAG\n++SRR071233.156421 NRTG514-16_0001:3:2:1264:4614 length=40\n+CCCCCBCCCCCCBACCCCCCC@BCCBCCCCCCCCCCCCCC\n+@SRR071233.156579 NRTG514-16_0001:3:2:1286:4483 length=40\n+TTGGGGAGGTGGCTGGGGAAGACCAGGGGCTACCTAAAAA\n++SRR071233.156579 NRTG514-16_0001:3:2:1286:4483 length=40\n+DCCCCCCCBBCCDCCCCBCCBCCCBABCCC@CCCBCC?CC\n+@SRR071233.156737 NRTG514-16_0001:3:2:1303:9680 length=40\n+GGAGAGATGAAAGAGTCAGACAGCTCTACAAAGCCTCTTT\n++SRR071233.156737 NRTG514-16_0001:3:2:1303:9680 length=40\n+CCCCCCCCCCCCCCCDCCCCCCCCCCCCCCCCCCCCCBCC\n+@SRR071233.156895 NRTG514-16_0001:3:2:1322:14192 length=40\n+TAAACACTATGACCATTTCCATCTTTCAGCCCTCTTGATT\n++SRR071233.156895 NRTG514-16_0001:3:2:1322:14192 length=40\n+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC?CC\n+@SRR071233.157053 NRTG514-16_0001:3:2:1342:21359 length=40\n+TTAAAGACTAAATGCTTACCATGTGTATGCTAGGTGTACA\n++SRR071233.157053 NRTG514-16_0001:3:2:1342:21359 length=40\n+CC@CCBCCCCCCCCCCCCCCCCCCCCCCCCCBCCDCDCCC\n+@SRR071233.157211 NRTG514-16_0001:3:2:1360:17441 length=40\n+ACGTTACACAGTGCATGACTATGCATGGTTTTTGGATTAA\n++SRR071233.157211 NRTG514-16_0001:3:2:1360:17441 length=40\n+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCBCCCC\n+@SRR071233.157369 NRTG514-16_0001:3:2:1379:4266 length=40\n+AAAGTTTTCCCGTTTAATATTATAAAATGGAATCATGTAA\n++SRR071233.157369 NRTG514-16_0001:3:2:1379:4266 length=40\n+00//0+AAAACCCCCCBCCCCCCCCCCCCCCCCCCCCCCC\n+@SRR071233.157527 NRTG514-16_0001:3:2:1398:4540 length=40\n+TTTGGTAAGATTCTGAATGATTTTTCTGGTTTTATTTTTT\n++SRR071233.157527 NRTG514-16_0001:3:2:1398:4540 length=40\n+CCCCCCCCCCCCCCCCCCC@CCCCCCBBCCCCCCCBBBBB\n+@SRR071233.157685 NRTG514-16_0001:3:2:1418:10945 length=40\n+TCATTAAATGTACTCTAATGGAATCATGGAATGGACTCGA\n++SRR071233.157685 NRTG514-16_0001:3:2:1418:10945 length=40\n+ABCCBCC@CCCCCCCCCBCCCACCCCCCCC=B@B@CCCCC\n+@SRR071233.157843 NRTG514-16_0001:3:2:1438:19334 length=40\n+TCATAAAATCATTTGTAGATTGAAGCTT\n++SRR071233.157843 NRTG514-16_0001:3:2:1438:19334 length=40\n+CCCACCCCCCCCCCCCCCCCCCCCBCC?\n' |
| b |
| diff -r 000000000000 -r d515a0639f8e test-data/dataset1.truncation_barchart.svg --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/dataset1.truncation_barchart.svg Thu Mar 09 09:30:33 2017 -0500 |
| b |
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| b |
| diff -r 000000000000 -r d515a0639f8e test-data/dataset2.fastq --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/dataset2.fastq Thu Mar 09 09:30:33 2017 -0500 |
| b |
| b'@@ -0,0 +1,4000 @@\n+@SRR071233.1 NRTG514-16_0001:3:1:1012:18280 length=40\n+AGAACCCATTCACACTCCCGCCAGCAGCAGGTTCGTGCCA\n++SRR071233.1 NRTG514-16_0001:3:1:1012:18280 length=40\n+@BABA@BBBBBBBB?BBBB@:?AAAB5<BAA92A=2:;77\n+@SRR071233.159 NRTG514-16_0001:3:1:1035:1632 length=40\n+GTTGGAAACGGGATAAACCGCACAGAACTAAACAGAAGCA\n++SRR071233.159 NRTG514-16_0001:3:1:1035:1632 length=40\n+?????<B???A:5>-794<4<7>>97?9?;BAB@@7895;\n+@SRR071233.317 NRTG514-16_0001:3:1:1055:11563 length=40\n+GATGCAGCTAGCAAGCAGGAGGGCCAGGTTTCCAACCGCG\n++SRR071233.317 NRTG514-16_0001:3:1:1055:11563 length=40\n+BCCCBCC@CCCCCCC=CBBACCAACCCCCBCCB;CCCCC?\n+@SRR071233.475 NRTG514-16_0001:3:1:1078:18960 length=40\n+GACCATGCTCCCTATTATTCTTGTTGAGTAACTGTAAGAC\n++SRR071233.475 NRTG514-16_0001:3:1:1078:18960 length=40\n+CCCCCCCB8CCCCCCCCCCCCCCCCBCCCCBBACCCBCCC\n+@SRR071233.633 NRTG514-16_0001:3:1:1100:20149 length=40\n+CTAGTGGGAAAGTGAAATGGTGTTGCATGTATGCAAGCTT\n++SRR071233.633 NRTG514-16_0001:3:1:1100:20149 length=40\n+CCCC>CCCCCCCBCC@CCCC@CCCCCCCCCCCCCCCCC@C\n+@SRR071233.791 NRTG514-16_0001:3:1:1122:17791 length=40\n+GCAAGAGGCCTAGCTTTAAGGCTATCTCAGTTTTTGACAT\n++SRR071233.791 NRTG514-16_0001:3:1:1122:17791 length=40\n+CCC@CCCCCCCCCB?CCCCC@CC?@@@@@?C@CC?C?CC@\n+@SRR071233.949 NRTG514-16_0001:3:1:1144:10543 length=40\n+GGTAGCCATCCCAACAGCCTTGGACCTCACTGCAGATCTA\n++SRR071233.949 NRTG514-16_0001:3:1:1144:10543 length=40\n+CCCCCCC>CCCCACCBCBACBCCCCCCCBCCCCCCCCC@B\n+@SRR071233.1107 NRTG514-16_0001:3:1:1167:14820 length=40\n+GCTCCCAACTCAGAGGAGTTGGCCGGGTAAGCTGTTTTCA\n++SRR071233.1107 NRTG514-16_0001:3:1:1167:14820 length=40\n+BCCCCC@CBBCC@?@C?C=@BBBB>CC;?CC@CC=CB>C@\n+@SRR071233.1265 NRTG514-16_0001:3:1:1186:18084 length=40\n+GAATTTCATATCCAGCCAAACTAAGCTACCTTTGCTATCA\n++SRR071233.1265 NRTG514-16_0001:3:1:1186:18084 length=40\n+CCCCCCCCDCCCCCCDCCCCCCCCCBACCCCC@CCCCCCC\n+@SRR071233.1423 NRTG514-16_0001:3:1:1207:3079 length=40\n+GCCATGGTGAGCATTTACACCATGGACACTGGCAAACTCC\n++SRR071233.1423 NRTG514-16_0001:3:1:1207:3079 length=40\n+CCCCCCCCCBCC@CCCCCCCCCCCCACCCCCCC@CCDCCC\n+@SRR071233.1581 NRTG514-16_0001:3:1:1228:11045 length=40\n+TAGTATTTTTATCATTTTATCTAAAGATCTTTACTTTTCG\n++SRR071233.1581 NRTG514-16_0001:3:1:1228:11045 length=40\n+CCCCCCCCCBBBBCCCCCCCCCCCCCCCCCCCCCCCCCCC\n+@SRR071233.1739 NRTG514-16_0001:3:1:1250:19031 length=40\n+TAAAAGACTTGGGTGGCATGTGGTTTTTAGAAGAAATTTA\n++SRR071233.1739 NRTG514-16_0001:3:1:1250:19031 length=40\n+@CCCCCCCCCCBCBCCCCCCCCCBCCCCCCC:CCC?BCCC\n+@SRR071233.1897 NRTG514-16_0001:3:1:1270:19952 length=40\n+AACCCCAGGAAAGCTAGCTTTCGTGGATTTTCTGAGGTCA\n++SRR071233.1897 NRTG514-16_0001:3:1:1270:19952 length=40\n+CCCCCCCCCCCCCCCCCCCCCCCDCCCCCCCCCCCCCBCC\n+@SRR071233.2055 NRTG514-16_0001:3:1:1291:5369 length=40\n+AGCTTTTCGGAGCTAAATCATGCCCCAACAAAGGATAGCA\n++SRR071233.2055 NRTG514-16_0001:3:1:1291:5369 length=40\n+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCBCCC\n+@SRR071233.2213 NRTG514-16_0001:3:1:1310:6855 length=40\n+TACTAACTGTTTTAGTTTACCTCTTAGTTTTCCGCATGTC\n++SRR071233.2213 NRTG514-16_0001:3:1:1310:6855 length=40\n+CCCCCCCCCCCCCACCCCCCCCCCCDCCCCCCCCCCCCCC\n+@SRR071233.2371 NRTG514-16_0001:3:1:1329:13048 length=40\n+CGCATTTAAGCTTCTCAAAGATGGTCATGCCTCCCTCACC\n++SRR071233.2371 NRTG514-16_0001:3:1:1329:13048 length=40\n+CCCCCCCCCCCCCCCCC6CCCCCCCCCCCCCCCCCCCCCC\n+@SRR071233.2529 NRTG514-16_0001:3:1:1349:10964 length=40\n+GGTCAAATCTAAGCTAGCTTACTTAGAATTACAGCTCTTT\n++SRR071233.2529 NRTG514-16_0001:3:1:1349:10964 length=40\n+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC\n+@SRR071233.2687 NRTG514-16_0001:3:1:1370:10692 length=40\n+AATAAATAAAGTATTTAGGAAACAGATCTTACCTCACTTG\n++SRR071233.2687 NRTG514-16_0001:3:1:1370:10692 length=40\n+CCCCCCCCCBBCCCCCCCCCCCCCCCCCCCCCCCCCCCCC\n+@SRR071233.2845 NRTG514-16_0001:3:1:1387:3351 length=40\n+CAAGGCTCTGATTTATCTCTTGATTTTTATTCTTACTTTT\n++SRR071233.2845 NRTG514-16_0001:3:1:1387:3351 length=40\n+BBBBBBBBBB>BBBBBAB@B?@3>@BBBB===BBBBBBAB\n+@SRR071233.3003 NRTG514-16_0001:3:1:1407:3953 length=40\n+AATAGTTTGTGCCTCTAAAAACAGGCAGGCTAAATAAGCT\n++SRR071233.3003 NRTG514-16_0001:3:1:1407:3953 length=40\n+CDCCCCCCCCCCCCCCCCCCCCBBCCCCCCCACCCCCCCC\n+@SRR07123'..b'AAGGGCAAGGAAGACTTTTACAGGTGCTGGATCCGG\n++SRR071233.154841 NRTG514-16_0001:3:2:1055:18658 length=40\n+>>6>>@<@?@B>BBBBBBBBBB>BBBBBBBBBBBB8@B@B\n+@SRR071233.154999 NRTG514-16_0001:3:2:1077:20120 length=40\n+TCTCATATTTTTTGAAGTAAACATCAAAATCACCATCCAG\n++SRR071233.154999 NRTG514-16_0001:3:2:1077:20120 length=40\n+CCCCCCCCCCC@@@CCCCCCCCCACCCCCCCCCCCCCCCC\n+@SRR071233.155157 NRTG514-16_0001:3:2:1097:19808 length=40\n+AATGAGAGAAAACTTCAGTAATCACCTAACCCCAAAAAAT\n++SRR071233.155157 NRTG514-16_0001:3:2:1097:19808 length=40\n+CCCCCCCCCCCCCCBCCCCCCCCCCCCCCCCCCC@CCCCC\n+@SRR071233.155315 NRTG514-16_0001:3:2:1116:16443 length=40\n+CACACCACTGCCCTGCACACAAACCCTCCAGGAGGTTTAT\n++SRR071233.155315 NRTG514-16_0001:3:2:1116:16443 length=40\n+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCBCB>CCBC\n+@SRR071233.155473 NRTG514-16_0001:3:2:1139:18586 length=40\n+TGGATTTCTCATGAATGGTTGAGTACTATCCTTTTGCTAC\n++SRR071233.155473 NRTG514-16_0001:3:2:1139:18586 length=40\n+CCCCCCBCCCCCCCCCCCCCCCCCBCCCCCCCCCCCCCCC\n+@SRR071233.155631 NRTG514-16_0001:3:2:1160:21064 length=40\n+GGTGACGGATGTCCCAGGAGGACGACCCAAGCCCACCCGC\n++SRR071233.155631 NRTG514-16_0001:3:2:1160:21064 length=40\n+CCCCCCCCCBCCCCCBCCCCCCCCCCCCCCCCCB<CBB@?\n+@SRR071233.155789 NRTG514-16_0001:3:2:1180:19951 length=40\n+GGCCTTGATAAATTGTAACTACCATGATTAGACTTTTGTA\n++SRR071233.155789 NRTG514-16_0001:3:2:1180:19951 length=40\n+CCCCCBCCCCCACCCCCCCCCCCCCCCACCCCCCCCCCCC\n+@SRR071233.155947 NRTG514-16_0001:3:2:1202:5247 length=40\n+AGTCTCCTTACTAGGGCAGTTCAACTTCATAGTGGTGCAG\n++SRR071233.155947 NRTG514-16_0001:3:2:1202:5247 length=40\n+CCCCCCCCC;CBCCCCCCCCCCCCCCCDBCCCBCCCCCCC\n+@SRR071233.156105 NRTG514-16_0001:3:2:1222:1582 length=40\n+CCTACAATGCTCCCATCCAAGCTAGGGTGAAGGCAGATCC\n++SRR071233.156105 NRTG514-16_0001:3:2:1222:1582 length=40\n+CCCCCCCCCCCCCCCBCCCCCCCCCCA@CCCCC>@CACCC\n+@SRR071233.156263 NRTG514-16_0001:3:2:1244:2002 length=40\n+ATGCTCCTTTCTCAGTACTTTCATAGCACCTTCTTCATAC\n++SRR071233.156263 NRTG514-16_0001:3:2:1244:2002 length=40\n+CCACCCCCCCCCBCC@BCCCACBCCCCCCCACCCC@BCCC\n+@SRR071233.156421 NRTG514-16_0001:3:2:1264:4614 length=40\n+AAGAAAACCTAGGCATTACCATTCAGGACATAGGCATGGG\n++SRR071233.156421 NRTG514-16_0001:3:2:1264:4614 length=40\n+CCCCC?@@CBCCCCCCCBCCCCCCCCC@CCCC@CCCCCC?\n+@SRR071233.156579 NRTG514-16_0001:3:2:1286:4483 length=40\n+ACAGAGCGCAGGACAGAAAGTAAGGCATTTCAAGCAGAGA\n++SRR071233.156579 NRTG514-16_0001:3:2:1286:4483 length=40\n+CCCCCCCCCCCCCCCCCACB@CCCCCCCCCCCCC?A8AAA\n+@SRR071233.156737 NRTG514-16_0001:3:2:1303:9680 length=40\n+AACACTTAAAAAAAAAAAAAAAAAACCAAACCCCAGGCTC\n++SRR071233.156737 NRTG514-16_0001:3:2:1303:9680 length=40\n+BBCCCCCDCCCCC@BBBBBBBBBB################\n+@SRR071233.156895 NRTG514-16_0001:3:2:1322:14192 length=40\n+CTAAAACTGGACTGAGAAAAGGTGATCCCATTTGGCTTCA\n++SRR071233.156895 NRTG514-16_0001:3:2:1322:14192 length=40\n+CCCCCCCCCCCCCCCCCCCCCCBCCCCCCCCCCCCCCCCC\n+@SRR071233.157053 NRTG514-16_0001:3:2:1342:21359 length=40\n+TATAATTTCTGTTCTTTTACATTTGCTGAGGAGTGCTTTA\n++SRR071233.157053 NRTG514-16_0001:3:2:1342:21359 length=40\n+CCCCCCCCCCCCCCCCC@@CCCCCCCCCCCCCCCCCCCCC\n+@SRR071233.157211 NRTG514-16_0001:3:2:1360:17441 length=40\n+CTATCCTAAGGTTATGAATGTATTCTCCTATATTATATTC\n++SRR071233.157211 NRTG514-16_0001:3:2:1360:17441 length=40\n+CCCCCCCCCCCCCCCCCACCDCCCCCCCCCCACCCCCCCC\n+@SRR071233.157369 NRTG514-16_0001:3:2:1379:4266 length=40\n+TAAAATTCAAAATTTCTGCTCCCCTATCCAGACCACTGGC\n++SRR071233.157369 NRTG514-16_0001:3:2:1379:4266 length=40\n+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC\n+@SRR071233.157527 NRTG514-16_0001:3:2:1398:4540 length=40\n+AGCTTTGCCCATCATGAGGAATGAACCTAGCTCCTATTGC\n++SRR071233.157527 NRTG514-16_0001:3:2:1398:4540 length=40\n+CCCCACCCCCCCCCCCCCCCCCCCCCCCCCCCDCADCCCC\n+@SRR071233.157685 NRTG514-16_0001:3:2:1418:10945 length=40\n+ATTTGATTCCATTCAATGATGATTCCATTCTATTCCATTC\n++SRR071233.157685 NRTG514-16_0001:3:2:1418:10945 length=40\n+@BABAACCCCCCCCCCCCBB@=@AACBCCCCCCBCCC?CC\n+@SRR071233.157843 NRTG514-16_0001:3:2:1438:19334 length=40\n+AGGATGTATTGGCAAGAGGAACTATTAAGACCATTGTTAC\n++SRR071233.157843 NRTG514-16_0001:3:2:1438:19334 length=40\n+CCCBCCCCCCCCCCCCCCC?CCBCCCCCCCCCCCCCCCCC\n' |
| b |
| diff -r 000000000000 -r d515a0639f8e test-data/dataset2.mapper_barchart.svg --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/dataset2.mapper_barchart.svg Thu Mar 09 09:30:33 2017 -0500 |
| b |
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| b |
| diff -r 000000000000 -r d515a0639f8e test-data/dataset2.trunc.fastq --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/dataset2.trunc.fastq Thu Mar 09 09:30:33 2017 -0500 |
| b |
| b'@@ -0,0 +1,4000 @@\n+@SRR071233.1 NRTG514-16_0001:3:1:1012:18280 length=40\n+AGAACCCATTCACACTCCCGCCAGCAGCAGGTTCGTGCCA\n++SRR071233.1 NRTG514-16_0001:3:1:1012:18280 length=40\n+@BABA@BBBBBBBB?BBBB@:?AAAB5<BAA92A=2:;77\n+@SRR071233.159 NRTG514-16_0001:3:1:1035:1632 length=40\n+GTTGGAAACGGGATAAACCGCACAGAACTAAACAGAAGCA\n++SRR071233.159 NRTG514-16_0001:3:1:1035:1632 length=40\n+?????<B???A:5>-794<4<7>>97?9?;BAB@@7895;\n+@SRR071233.317 NRTG514-16_0001:3:1:1055:11563 length=40\n+GATGCAGCTAGCAAGCAGGAGGGCCAGGTTTCCAACCGCG\n++SRR071233.317 NRTG514-16_0001:3:1:1055:11563 length=40\n+BCCCBCC@CCCCCCC=CBBACCAACCCCCBCCB;CCCCC?\n+@SRR071233.475 NRTG514-16_0001:3:1:1078:18960 length=40\n+GACCATGCTCCCTATTATTCTTGTTGAGTAACTGTAAGAC\n++SRR071233.475 NRTG514-16_0001:3:1:1078:18960 length=40\n+CCCCCCCB8CCCCCCCCCCCCCCCCBCCCCBBACCCBCCC\n+@SRR071233.633 NRTG514-16_0001:3:1:1100:20149 length=40\n+CTAGTGGGAAAGTGAAATGGTGTTGCATGTATGCAAGCTT\n++SRR071233.633 NRTG514-16_0001:3:1:1100:20149 length=40\n+CCCC>CCCCCCCBCC@CCCC@CCCCCCCCCCCCCCCCC@C\n+@SRR071233.791 NRTG514-16_0001:3:1:1122:17791 length=40\n+GCAAGAGGCCTAGCTTTAAGGCTATCTCAGTTTTTGACAT\n++SRR071233.791 NRTG514-16_0001:3:1:1122:17791 length=40\n+CCC@CCCCCCCCCB?CCCCC@CC?@@@@@?C@CC?C?CC@\n+@SRR071233.949 NRTG514-16_0001:3:1:1144:10543 length=40\n+GGTAGCCATCCCAACAGCCTTGGACCTCACTGCAGATCTA\n++SRR071233.949 NRTG514-16_0001:3:1:1144:10543 length=40\n+CCCCCCC>CCCCACCBCBACBCCCCCCCBCCCCCCCCC@B\n+@SRR071233.1107 NRTG514-16_0001:3:1:1167:14820 length=40\n+GCTCCCAACTCAGAGGAGTTGGCCGGGTAAGCTGTTTTCA\n++SRR071233.1107 NRTG514-16_0001:3:1:1167:14820 length=40\n+BCCCCC@CBBCC@?@C?C=@BBBB>CC;?CC@CC=CB>C@\n+@SRR071233.1265 NRTG514-16_0001:3:1:1186:18084 length=40\n+GAATTTCATATCCAGCCAAACTAAGCTACCTTTGCTATCA\n++SRR071233.1265 NRTG514-16_0001:3:1:1186:18084 length=40\n+CCCCCCCCDCCCCCCDCCCCCCCCCBACCCCC@CCCCCCC\n+@SRR071233.1423 NRTG514-16_0001:3:1:1207:3079 length=40\n+GCCATGGTGAGCATTTACACCATGGACACTGGCAAACTCC\n++SRR071233.1423 NRTG514-16_0001:3:1:1207:3079 length=40\n+CCCCCCCCCBCC@CCCCCCCCCCCCACCCCCCC@CCDCCC\n+@SRR071233.1581 NRTG514-16_0001:3:1:1228:11045 length=40\n+TAGTATTTTTATCATTTTATCTAAAGATCTTTACTTTTCG\n++SRR071233.1581 NRTG514-16_0001:3:1:1228:11045 length=40\n+CCCCCCCCCBBBBCCCCCCCCCCCCCCCCCCCCCCCCCCC\n+@SRR071233.1739 NRTG514-16_0001:3:1:1250:19031 length=40\n+TAAAAGACTTGGGTGGCATGTGGTTTTTAGAAGAAATTTA\n++SRR071233.1739 NRTG514-16_0001:3:1:1250:19031 length=40\n+@CCCCCCCCCCBCBCCCCCCCCCBCCCCCCC:CCC?BCCC\n+@SRR071233.1897 NRTG514-16_0001:3:1:1270:19952 length=40\n+AACCCCAGGAAAGCTT\n++SRR071233.1897 NRTG514-16_0001:3:1:1270:19952 length=40\n+CCCCCCCCCCCCCCCC\n+@SRR071233.2055 NRTG514-16_0001:3:1:1291:5369 length=40\n+AGCTTTTCGGAGCTAAATCATGCCCCAACAAAGGATAGCA\n++SRR071233.2055 NRTG514-16_0001:3:1:1291:5369 length=40\n+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCBCCC\n+@SRR071233.2213 NRTG514-16_0001:3:1:1310:6855 length=40\n+TACTAACTGTTTTAGTTTACCTCTTAGTTTTCCGCATGTC\n++SRR071233.2213 NRTG514-16_0001:3:1:1310:6855 length=40\n+CCCCCCCCCCCCCACCCCCCCCCCCDCCCCCCCCCCCCCC\n+@SRR071233.2371 NRTG514-16_0001:3:1:1329:13048 length=40\n+CGCATTTAAGCTTCTCAAAGATGGTCATGCCTCCCTCACC\n++SRR071233.2371 NRTG514-16_0001:3:1:1329:13048 length=40\n+CCCCCCCCCCCCCCCCC6CCCCCCCCCCCCCCCCCCCCCC\n+@SRR071233.2529 NRTG514-16_0001:3:1:1349:10964 length=40\n+GGTCAAATCTAAGCTT\n++SRR071233.2529 NRTG514-16_0001:3:1:1349:10964 length=40\n+CCCCCCCCCCCCCCCC\n+@SRR071233.2687 NRTG514-16_0001:3:1:1370:10692 length=40\n+AATAAATAAAGTATTTAGGAAACAGATCTTACCTCACTTG\n++SRR071233.2687 NRTG514-16_0001:3:1:1370:10692 length=40\n+CCCCCCCCCBBCCCCCCCCCCCCCCCCCCCCCCCCCCCCC\n+@SRR071233.2845 NRTG514-16_0001:3:1:1387:3351 length=40\n+CAAGGCTCTGATTTATCTCTTGATTTTTATTCTTACTTTT\n++SRR071233.2845 NRTG514-16_0001:3:1:1387:3351 length=40\n+BBBBBBBBBB>BBBBBAB@B?@3>@BBBB===BBBBBBAB\n+@SRR071233.3003 NRTG514-16_0001:3:1:1407:3953 length=40\n+AATAGTTTGTGCCTCTAAAAACAGGCAGGCTAAATAAGCT\n++SRR071233.3003 NRTG514-16_0001:3:1:1407:3953 length=40\n+CDCCCCCCCCCCCCCCCCCCCCBBCCCCCCCACCCCCCCC\n+@SRR071233.3161 NRTG514-16_0001:3:1:1426:3923 length=40\n+AACAAGGACTCCTGGGTTGATCTCCAGCCTCAAAAATCCT\n++SRR07'..b'AAGGGCAAGGAAGACTTTTACAGGTGCTGGATCCGG\n++SRR071233.154841 NRTG514-16_0001:3:2:1055:18658 length=40\n+>>6>>@<@?@B>BBBBBBBBBB>BBBBBBBBBBBB8@B@B\n+@SRR071233.154999 NRTG514-16_0001:3:2:1077:20120 length=40\n+TCTCATATTTTTTGAAGTAAACATCAAAATCACCATCCAG\n++SRR071233.154999 NRTG514-16_0001:3:2:1077:20120 length=40\n+CCCCCCCCCCC@@@CCCCCCCCCACCCCCCCCCCCCCCCC\n+@SRR071233.155157 NRTG514-16_0001:3:2:1097:19808 length=40\n+AATGAGAGAAAACTTCAGTAATCACCTAACCCCAAAAAAT\n++SRR071233.155157 NRTG514-16_0001:3:2:1097:19808 length=40\n+CCCCCCCCCCCCCCBCCCCCCCCCCCCCCCCCCC@CCCCC\n+@SRR071233.155315 NRTG514-16_0001:3:2:1116:16443 length=40\n+CACACCACTGCCCTGCACACAAACCCTCCAGGAGGTTTAT\n++SRR071233.155315 NRTG514-16_0001:3:2:1116:16443 length=40\n+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCBCB>CCBC\n+@SRR071233.155473 NRTG514-16_0001:3:2:1139:18586 length=40\n+TGGATTTCTCATGAATGGTTGAGTACTATCCTTTTGCTAC\n++SRR071233.155473 NRTG514-16_0001:3:2:1139:18586 length=40\n+CCCCCCBCCCCCCCCCCCCCCCCCBCCCCCCCCCCCCCCC\n+@SRR071233.155631 NRTG514-16_0001:3:2:1160:21064 length=40\n+GGTGACGGATGTCCCAGGAGGACGACCCAAGCCCACCCGC\n++SRR071233.155631 NRTG514-16_0001:3:2:1160:21064 length=40\n+CCCCCCCCCBCCCCCBCCCCCCCCCCCCCCCCCB<CBB@?\n+@SRR071233.155789 NRTG514-16_0001:3:2:1180:19951 length=40\n+GGCCTTGATAAATTGTAACTACCATGATTAGACTTTTGTA\n++SRR071233.155789 NRTG514-16_0001:3:2:1180:19951 length=40\n+CCCCCBCCCCCACCCCCCCCCCCCCCCACCCCCCCCCCCC\n+@SRR071233.155947 NRTG514-16_0001:3:2:1202:5247 length=40\n+AGTCTCCTTACTAGGGCAGTTCAACTTCATAGTGGTGCAG\n++SRR071233.155947 NRTG514-16_0001:3:2:1202:5247 length=40\n+CCCCCCCCC;CBCCCCCCCCCCCCCCCDBCCCBCCCCCCC\n+@SRR071233.156105 NRTG514-16_0001:3:2:1222:1582 length=40\n+CCTACAATGCTCCCATCCAAGCTAGGGTGAAGGCAGATCC\n++SRR071233.156105 NRTG514-16_0001:3:2:1222:1582 length=40\n+CCCCCCCCCCCCCCCBCCCCCCCCCCA@CCCCC>@CACCC\n+@SRR071233.156263 NRTG514-16_0001:3:2:1244:2002 length=40\n+ATGCTCCTTTCTCAGTACTTTCATAGCACCTTCTTCATAC\n++SRR071233.156263 NRTG514-16_0001:3:2:1244:2002 length=40\n+CCACCCCCCCCCBCC@BCCCACBCCCCCCCACCCC@BCCC\n+@SRR071233.156421 NRTG514-16_0001:3:2:1264:4614 length=40\n+AAGAAAACCTAGGCATTACCATTCAGGACATAGGCATGGG\n++SRR071233.156421 NRTG514-16_0001:3:2:1264:4614 length=40\n+CCCCC?@@CBCCCCCCCBCCCCCCCCC@CCCC@CCCCCC?\n+@SRR071233.156579 NRTG514-16_0001:3:2:1286:4483 length=40\n+ACAGAGCGCAGGACAGAAAGTAAGGCATTTCAAGCAGAGA\n++SRR071233.156579 NRTG514-16_0001:3:2:1286:4483 length=40\n+CCCCCCCCCCCCCCCCCACB@CCCCCCCCCCCCC?A8AAA\n+@SRR071233.156737 NRTG514-16_0001:3:2:1303:9680 length=40\n+AACACTTAAAAAAAAAAAAAAAAAACCAAACCCCAGGCTC\n++SRR071233.156737 NRTG514-16_0001:3:2:1303:9680 length=40\n+BBCCCCCDCCCCC@BBBBBBBBBB################\n+@SRR071233.156895 NRTG514-16_0001:3:2:1322:14192 length=40\n+CTAAAACTGGACTGAGAAAAGGTGATCCCATTTGGCTTCA\n++SRR071233.156895 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| b |
| diff -r 000000000000 -r d515a0639f8e test-data/dataset2.truncation_barchart.svg --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/dataset2.truncation_barchart.svg Thu Mar 09 09:30:33 2017 -0500 |
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| diff -r 000000000000 -r d515a0639f8e test-data/deduplicator_cis_trans_piechart.svg --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/deduplicator_cis_trans_piechart.svg Thu Mar 09 09:30:33 2017 -0500 |
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| b |
| diff -r 000000000000 -r d515a0639f8e test-data/deduplicator_uniques_barchart.svg --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/deduplicator_uniques_barchart.svg Thu Mar 09 09:30:33 2017 -0500 |
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| b |
| diff -r 000000000000 -r d515a0639f8e test-data/digester_file.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/digester_file.txt Thu Mar 09 09:30:33 2017 -0500 |
| [ |
| @@ -0,0 +1,56 @@ +Genome:genome Restriction_Enzyme1:re1_unspecified [A^AGCTT] Restriction_Enzyme2:None Hicup digester version 0.5.9 +Chromosome Fragment_Start_Position Fragment_End_Position Fragment_Number RE1_Fragment_Number 5'_Restriction_Site 3'_Restriction_Site +chr1 1 16007 1 1 None Re1 +chr1 16008 24571 2 2 Re1 Re1 +chr1 24572 27981 3 3 Re1 Re1 +chr1 27982 30429 4 4 Re1 Re1 +chr1 30430 32153 5 5 Re1 Re1 +chr1 32154 32774 6 6 Re1 Re1 +chr1 32775 37752 7 7 Re1 Re1 +chr1 37753 38369 8 8 Re1 Re1 +chr1 38370 38791 9 9 Re1 Re1 +chr1 38792 39255 10 10 Re1 Re1 +chr1 39256 43602 11 11 Re1 Re1 +chr1 43603 46455 12 12 Re1 Re1 +chr1 46456 52419 13 13 Re1 Re1 +chr1 52420 56815 14 14 Re1 Re1 +chr1 56816 58747 15 15 Re1 Re1 +chr1 58748 58954 16 16 Re1 Re1 +chr1 58955 59356 17 17 Re1 Re1 +chr1 59357 75365 18 18 Re1 Re1 +chr1 75366 83359 19 19 Re1 Re1 +chr1 83360 84049 20 20 Re1 Re1 +chr1 84050 90742 21 21 Re1 Re1 +chr1 90743 91319 22 22 Re1 Re1 +chr1 91320 91586 23 23 Re1 Re1 +chr1 91587 92457 24 24 Re1 Re1 +chr1 92458 97923 25 25 Re1 Re1 +chr1 97924 101016 26 26 Re1 Re1 +chr1 101017 102672 27 27 Re1 Re1 +chr1 102673 105557 28 28 Re1 Re1 +chr1 105558 106650 29 29 Re1 Re1 +chr1 106651 107958 30 30 Re1 Re1 +chr1 107959 108196 31 31 Re1 Re1 +chr1 108197 109517 32 32 Re1 Re1 +chr1 109518 114993 33 33 Re1 Re1 +chr1 114994 115427 34 34 Re1 Re1 +chr1 115428 116791 35 35 Re1 Re1 +chr1 116792 117059 36 36 Re1 Re1 +chr1 117060 118299 37 37 Re1 Re1 +chr1 118300 121955 38 38 Re1 Re1 +chr1 121956 124936 39 39 Re1 Re1 +chr1 124937 130392 40 40 Re1 Re1 +chr1 130393 130459 41 41 Re1 Re1 +chr1 130460 139816 42 42 Re1 Re1 +chr1 139817 140040 43 43 Re1 Re1 +chr1 140041 142850 44 44 Re1 Re1 +chr1 142851 155672 45 45 Re1 Re1 +chr1 155673 157485 46 46 Re1 Re1 +chr1 157486 157620 47 47 Re1 Re1 +chr1 157621 159124 48 48 Re1 Re1 +chr1 159125 159859 49 49 Re1 Re1 +chr1 159860 161088 50 50 Re1 Re1 +chr1 161089 173279 51 51 Re1 Re1 +chr1 173280 174257 52 52 Re1 Re1 +chr1 174258 175543 53 53 Re1 Re1 +chr1 175544 199950 54 54 Re1 None |
| b |
| diff -r 000000000000 -r d515a0639f8e test-data/filter_piechart.svg --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/filter_piechart.svg Thu Mar 09 09:30:33 2017 -0500 |
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| b |
| diff -r 000000000000 -r d515a0639f8e test-data/hicup_deduplicator_summary.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/hicup_deduplicator_summary.txt Thu Mar 09 09:30:33 2017 -0500 |
| b |
| @@ -0,0 +1,2 @@ +File Read_pairs_processed Unique_di-tags Cis_<10kbp_of_uniques Cis_>10kbp_of_uniques Trans_of_uniques +dataset_1265_4.dat.filt.sam 1 1 0 1 0 |
| b |
| diff -r 000000000000 -r d515a0639f8e test-data/hicup_filter_summary.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/hicup_filter_summary.txt Thu Mar 09 09:30:33 2017 -0500 |
| b |
| @@ -0,0 +1,2 @@ +File Total_pairs Valid_pairs Cis_<10kbp Cis_>10kbp Trans Invalid_pairs Same_circularised Same_dangling_ends Same_internal Re-ligation Contiguous_sequence Wrong_size +dataset_1265_4.dat.pair.sam 1 1 0 1 0 0 0 0 0 0 0 0 |
| b |
| diff -r 000000000000 -r d515a0639f8e test-data/hicup_mapper_summary.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/hicup_mapper_summary.txt Thu Mar 09 09:30:33 2017 -0500 |
| b |
| @@ -0,0 +1,3 @@ +File Total_reads_processed Reads_too_short_to_map %Reads_too_short_to_map Unique_alignments %Unique_alignments Multiple_alignments %Multiple_alignments Failed_to_align %failed_to_align Paired %Paired +dataset_1265.dat.trunc.fastq 1000 35 3.5 14 1.4 13 1.3 938 93.8 1 0.1 +dataset_1264.dat.trunc.fastq 1000 24 2.4 23 2.3 7 0.7 946 94.6 1 0.1 |
| b |
| diff -r 000000000000 -r d515a0639f8e test-data/hicup_truncater_summary.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/hicup_truncater_summary.txt Thu Mar 09 09:30:33 2017 -0500 |
| b |
| @@ -0,0 +1,3 @@ +File Total_Reads_Processed Truncated %Truncated Not_truncated %Not_truncated Average_length_truncated_sequence +dataset_1265.dat 1000 77 7.70 923 92.30 21.39 +dataset_1264.dat 1000 61 6.10 939 93.90 22.21 |
| b |
| diff -r 000000000000 -r d515a0639f8e test-data/result.pair.sam --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/result.pair.sam Thu Mar 09 09:30:33 2017 -0500 |
| b |
| @@ -0,0 +1,7 @@ +@HD VN:1.0 SO:unsorted +@SQ SN:chr1 LN:199950 +@PG ID:bowtie2 PN:bowtie2 VN:2.3.0 CL:"/home/wolffj/miniconda2/envs/hicup/bin/bowtie2-align-s --wrapper basic-0 --very-sensitive -x genome -p 1 - --passthrough" +@PG ID:HiCUP Mapper VN:0.5.9 +@PG ID:HiCUP Truncater VN:0.5.9 DS:"Restriction enzyme --re1 A^AGCTT" +SRR071233.43293 83 chr1 35433 3 40M = 75323 0 GAGTCCAGGAGTTCAAGACCAGCCTGGGTAACATAGTGAG CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC AS:i:-15 XN:i:0 XM:i:3 XO:i:0 XG:i:0 NM:i:3 MD:Z:3G22A1C11 YT:Z:UU +SRR071233.43293 163 chr1 75323 23 40M = 35433 0 CTCAATAAAATACTGGCAAACCGAATCCAGCAGCACATCG CCBCCCCCCBBCCCCCCCCCCCCCCCCCCCCCCCCCCCCC AS:i:-10 XN:i:0 XM:i:2 XO:i:0 XG:i:0 NM:i:2 MD:Z:20A18A0 YT:Z:UU |
| b |
| diff -r 000000000000 -r d515a0639f8e test-data/results.html --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/results.html Thu Mar 09 09:30:33 2017 -0500 |
| [ |
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/></a>\n+\t\t<p>Analysis produced by <a href="http://www.bioinformatics.babraham.ac.uk/projects/hicup/"><strong>HiCUP</strong></a> (0.5.9) - a tool for mapping and performing quality control on Hi-C data.</p>\n+\t\t<p>Report graphs rendered using <a href="http://jquery.com/">jQuery</a> and <a href="http://www.highcharts.com/">Highcharts</a>.</p>\n+\t</footer>\n+</div>\n+</body>\n+</html>\n+\n' |
| b |
| diff -r 000000000000 -r d515a0639f8e tool-data/bowtie2_indices.loc.sample --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool-data/bowtie2_indices.loc.sample Thu Mar 09 09:30:33 2017 -0500 |
| b |
| @@ -0,0 +1,37 @@ +#This is a sample file distributed with Galaxy that enables tools +#to use a directory of Bowtie2 indexed sequences data files. You will +#need to create these data files and then create a bowtie_indices.loc +#file similar to this one (store it in this directory) that points to +#the directories in which those files are stored. The bowtie2_indices.loc +#file has this format (longer white space characters are TAB characters): +# +#<unique_build_id> <dbkey> <display_name> <file_base_path> +# +#So, for example, if you had hg18 indexed stored in +#/depot/data2/galaxy/bowtie2/hg18/, +#then the bowtie2_indices.loc entry would look like this: +# +#hg18 hg18 hg18 /depot/data2/galaxy/bowtie2/hg18/hg18 +# +#and your /depot/data2/galaxy/bowtie2/hg18/ directory +#would contain hg18.*.ebwt files: +# +#-rw-r--r-- 1 james universe 830134 2005-09-13 10:12 hg18.1.ebwt +#-rw-r--r-- 1 james universe 527388 2005-09-13 10:12 hg18.2.ebwt +#-rw-r--r-- 1 james universe 269808 2005-09-13 10:12 hg18.3.ebwt +#...etc... +# +#Your bowtie2_indices.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: +# +#hg18canon hg18 hg18 Canonical /depot/data2/galaxy/bowtie2/hg18/hg18canon +#hg18full hg18 hg18 Full /depot/data2/galaxy/bowtie2/hg18/hg18full +#/orig/path/hg19 hg19 hg19 /depot/data2/galaxy/bowtie2/hg19/hg19 +#...etc... +# +#Note that for backwards compatibility with workflows, the unique ID of +#an entry must be the path that was in the original loc file, because that +#is the value stored in the workflow for that parameter. That is why the +#hg19 entry above looks odd. New genomes can be better-looking. +# |
| b |
| diff -r 000000000000 -r d515a0639f8e tool_data_table_conf.xml.sample --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_data_table_conf.xml.sample Thu Mar 09 09:30:33 2017 -0500 |
| b |
| @@ -0,0 +1,8 @@ +<!-- Use the file tool_data_table_conf.xml.oldlocstyle if you don't want to update your loc files as changed in revision 4550:535d276c92bc--> +<tables> + <!-- Locations of indexes in the Bowtie2 mapper format --> + <table name="bowtie2_indexes" comment_char="#"> + <columns>value, dbkey, name, path</columns> + <file path="tool-data/bowtie2_indices.loc" /> + </table> +</tables> |
