| Next changeset 1:38c9f9a680f0 (2019-09-30) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit b395fa36fa826e26085820ba3a9faacaeddcb460 |
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added:
macros.xml macros_process.xml stacks_kmerfilter.xml test-data/clonefilter/R1_0001.1.fq.gz test-data/clonefilter/R2_0001.2.fq.gz test-data/clonefilter/Removed1_0001.1.1.fq.gz test-data/clonefilter/Removed1_0001.1.1.fq.single.gz test-data/clonefilter/Removed2_0001.2.2.fq.gz test-data/clonefilter/clonefilter.log test-data/cstacks/catalog.alleles.tsv test-data/cstacks/catalog.snps.tsv test-data/cstacks/catalog.tags.tsv test-data/cstacks/cstacks.log test-data/demultiplexed/PopA_01.1.fa test-data/demultiplexed/PopA_01.1.fa.gz test-data/demultiplexed/PopA_01.1.fq test-data/demultiplexed/PopA_01.2.fa test-data/demultiplexed/PopA_01.2.fa.gz test-data/demultiplexed/PopA_01.2.fq test-data/demultiplexed/PopA_01.fq test-data/demultiplexed/PopA_01.rem.1.fa test-data/demultiplexed/PopA_01.rem.1.fa.gz test-data/demultiplexed/PopA_01.rem.2.fa test-data/demultiplexed/PopA_01.rem.2.fa.gz test-data/demultiplexed/PopA_02.1.fq test-data/demultiplexed/PopA_02.2.fq test-data/denovo_map/denovo_map.log test-data/denovo_map/popmap_cstacks.tsv test-data/gentest.sh test-data/gstacks/PopA_01.alns.bam test-data/gstacks/PopA_02.alns.bam test-data/gstacks/alignments.bam test-data/gstacks/catalog.calls.vcf test-data/gstacks/catalog.fa.gz test-data/gstacks/gstacks.log test-data/gstacks/gstacks.log.distribs test-data/kmerfilter/kfreq.tsv test-data/kmerfilter/kfreqdist.tsv test-data/kmerfilter/kmerfilter.log test-data/populations/blacklist.tsv test-data/populations/populations.fixed.phylip test-data/populations/populations.fixed.phylip.log test-data/populations/populations.fst_summary.tsv test-data/populations/populations.haplotypes.tsv test-data/populations/populations.haps.genepop test-data/populations/populations.haps.radpainter test-data/populations/populations.haps.vcf test-data/populations/populations.hapstats.tsv test-data/populations/populations.hzar.csv test-data/populations/populations.loci.fa test-data/populations/populations.log test-data/populations/populations.log.distribs test-data/populations/populations.markers.tsv test-data/populations/populations.phistats.tsv test-data/populations/populations.phistats_summary.tsv test-data/populations/populations.plink.map test-data/populations/populations.plink.ped test-data/populations/populations.samples-raw.fa test-data/populations/populations.samples.fa test-data/populations/populations.snps.genepop test-data/populations/populations.snps.vcf test-data/populations/populations.structure test-data/populations/populations.sumstats.tsv test-data/populations/populations.sumstats_summary.tsv test-data/populations/populations.treemix test-data/populations/populations.var.phylip test-data/populations/populations.var.phylip.log test-data/procrad/R1.fa.discards test-data/procrad/R1.fq test-data/procrad/R1.fq.discards test-data/procrad/R1.fq.gzip test-data/procrad/R2.fa.discards test-data/procrad/R2.fq test-data/procrad/R2.fq.discards test-data/procrad/R2.fq.gzip test-data/procrad/barcodes test-data/procrad/process_radtags.out test-data/procrad/process_radtags_paired.out test-data/refmap/PopA_01.bam test-data/refmap/PopA_02.bam test-data/refmap/catalog.calls.vcf test-data/refmap/catalog.fa.gz test-data/refmap/populations.haplotypes.tsv test-data/refmap/populations.hapstats.tsv test-data/refmap/populations.log.distribs test-data/refmap/populations.markers.tsv test-data/refmap/populations.sumstats.tsv test-data/refmap/populations.sumstats_summary.tsv test-data/shortreads/PopA_01.forward.fq.gz test-data/shortreads/PopA_01.fq test-data/shortreads/PopA_01.rem.forward.fq.gz test-data/shortreads/PopA_01.rem.reverse.fq.gz test-data/shortreads/PopA_01.reverse.fq.gz test-data/shortreads/process_shortreads.out test-data/shortreads/reads.forward.fq test-data/shortreads/reads.reverse.fq test-data/sstacks/PopA_01.matches.tsv test-data/sstacks/PopA_02.matches.tsv test-data/sstacks/sstacks.log test-data/stacks_outputs/catalog.calls test-data/stacks_outputs/tsv2bam.log test-data/tsv2bam/PopA_01.bam test-data/tsv2bam/PopA_01.matches.bam test-data/tsv2bam/PopA_02.bam test-data/tsv2bam/PopA_02.matches.bam test-data/tsv2bam/tsv2bam.log test-data/ustacks/PopA_01.alleles.tsv test-data/ustacks/PopA_01.snps.tsv test-data/ustacks/PopA_01.tags.tsv test-data/ustacks/PopA_02.alleles.tsv test-data/ustacks/PopA_02.snps.tsv test-data/ustacks/PopA_02.tags.tsv test-data/ustacks/ustacks.log |
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| diff -r 000000000000 -r b2e3553e1be2 macros.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros.xml Mon Jul 01 10:58:28 2019 -0400 |
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| b'@@ -0,0 +1,596 @@\n+<?xml version="1.0"?>\n+<macros>\n+ <xml name="requirements">\n+ <requirements>\n+ <requirement type="package" version="@STACKS_VERSION@">stacks</requirement>\n+ <yield/>\n+ </requirements>\n+ </xml>\n+\n+ <token name="@STACKS_VERSION@">2.4</token>\n+ <token name="@WRAPPER_VERSION@">0</token>\n+ <!-- fix to 18.01 since https://github.com/galaxyproject/galaxy/pull/7032 -->\n+ <token name="@PROFILE@">18.01</token>\n+\n+ <xml name="citation">\n+ <citations>\n+ <citation type="doi">10.1111/mec.12354</citation>\n+ <citation type="doi">10.1111/mec.12330</citation>\n+ <citation type="doi">10.1534/g3.111.000240</citation>\n+ <citation type="doi">10.1534/genetics.111.127324</citation>\n+ <citation type="doi">10.1111/j.1755-0998.2010.02967.x</citation>\n+ <citation type="doi">10.1073/pnas.1006538107</citation>\n+ </citations>\n+ </xml>\n+\n+ <xml name="version_cmd">\n+ <version_command><![CDATA[\n+ process_radtags -h |& grep process_radtags | head -n 1 | cut -d" " -f 2\n+ ]]>\n+ </version_command>\n+ </xml>\n+\n+ <token name="@STACKS_INFOS@">\n+<![CDATA[\n+--------\n+\n+**Created by:**\n+\n+Stacks was developed by Julian Catchen with contributions from Angel Amores, Paul Hohenlohe, and Bill Cresko\n+\n+**Project links:**\n+\n+`Stacks website <http://catchenlab.life.illinois.edu/stacks/>`_\n+\n+`Stacks manual <http://catchenlab.life.illinois.edu/stacks/manual/>`_\n+\n+`Stacks google group <http://groups.google.com/group/stacks-users>`_\n+]]></token>\n+\n+ <!-- enzyme list for procrad and denovo -->\n+ <xml name="enzymes">\n+ <option value="">Unspecified</option>\n+ <option value="aciI">aciI</option>\n+ <option value="ageI">ageI</option>\n+ <option value="aluI">aluI</option>\n+ <option value="apaLI">apaLI</option>\n+ <option value="apeKI">apeKI</option>\n+ <option value="apoI">apoI</option>\n+ <option value="aseI">aseI</option>\n+ <option value="bamHI">bamHI</option>\n+ <option value="bbvCI">bbvCI</option>\n+ <option value="bfaI">bfaI</option>\n+ <option value="bfuCI">bfuCI</option>\n+ <option value="bgIII">bgIII</option>\n+ <option value="bsaHI">bsaHI</option>\n+ <option value="bspDI">bspDI</option>\n+ <option value="bstYI">bstYI</option>\n+ <option value="cac8I">cac8I</option>\n+ <option value="claI">claI</option>\n+ <option value="csp6I">csp6I</option>\n+ <option value="ddeI">ddeI</option>\n+ <option value="dpnII">dpnII</option>\n+ <option value="eaeI">eaeI</option>\n+ <option value="ecoRI">ecoRI</option>\n+ <option value="ecoRV">ecoRV</option>\n+ <option value="ecoT22I">ecoT22I</option>\n+ <option value="haeIII">haeIII</option>\n+ <option value="hindIII">hindIII</option>\n+ <option value="hinP1I">hinP1I</option>\n+ <option value="hpaII">hpaII</option>\n+ <option value="kpnI">kpnI</option>\n+ <option value="mluCI">mluCI</option>\n+ <option value="mseI">mseI</option>\n+ <option value="mslI">mslI</option>\n+ <option value="mspI">mspI</option>\n+ <option value="ncoI">ncoI</option>\n+ <option value="ndeI">ndeI</option>\n+ <option value="nheI">nheI</option>\n+ <option value="nlaIII">nlaIII</option>\n+ <option value="notI">notI</option>\n+ <option value="nsiI">nsiI</option>\n+ <option value="nspI">nspI</option>\n+ <option value="pstI">pstI</option>\n+ <option value="rsaI">rsaI</option>\n+ <option value="sacI">sacI</option>\n+ <option value="sau3AI">sau3AI</option>\n+ <option value="sbfI">sbfI</option>\n+ <option value="sexAI">sexAI</option>\n+ <option value="sgrAI">sgrAI</option>\n+ <option value="speI">speI</option>\n+ <option value="sphI">sphI</option>\n+ <option value="taqI">taqI</option'..b' <filter>populations_output[\'treemix\']</filter>\n+ </data>\n+ </xml>\n+\n+ <xml name="snp_options_alpha">\n+ <param argument="--alpha" type="select" label="Chi square significance level required to call a heterozygote or homozygote" >\n+ <option value="0.1">0.1</option>\n+ <option value="0.05" selected="True">0.05</option>\n+ <option value="0.01">0.01</option>\n+ <option value="0.001">0.001</option>\n+ </param>\n+ </xml>\n+\n+ <xml name="snp_options">\n+ <conditional name="select_model">\n+ <param argument="--model_type" type="select" label="Choose the model">\n+ <option value="snp" selected="true">SNP</option>\n+ <option value="bounded">Bounded SNP</option>\n+ <option value="fixed">Fixed</option>\n+ </param>\n+ <when value="snp">\n+ <expand macro="snp_options_alpha"/>\n+ </when>\n+ <when value="bounded">\n+ <param argument="--bound_low" type="float" value="0.0" min="0.0" max="1.0" label="Lower bound for epsilon, the error rate" help="between 0 and 1.0"/>\n+ <param argument="--bound_high" type="float" value="1.0" min="0.0" max="1.0" label="Upper bound for epsilon, the error rate" help="between 0 and 1.0" />\n+ <expand macro="snp_options_alpha"/>\n+ </when>\n+ <when value="fixed">\n+ <yield/>\n+ </when>\n+ </conditional>\n+ </xml>\n+ <xml name="snp_options_full">\n+ <expand macro="snp_options">\n+ <param argument="--bc_err_freq" type="float" value="0.1" min="0.0" max="1.0" label="Barcode error frequency" help="between 0 and 1.0"/>\n+ </expand>\n+ </xml>\n+\n+\t<!-- variant calling option for use in gstacks and denovomap \n+ default for var_alpha is 0.01 if model == marukilow (which is the case in denovomap and refmap)\n+ otherwise no default is is available and gstacks will output and error\n+ "Error: No value was provided for \\-\\-var-alpha and there is no default for this model)" \n+\t-->\n+ <xml name="variant_calling_options_vg" token_varalpha_default="">\n+ <param argument="--var-alpha" name="var_alpha" type="float" value="@VARALPHA_DEFAULT@" min="0" label="Alpha threshold for discovering SNPs" help="Default is 0.01 if the marukilow model is used (which is the case in refmap and denovomap), otherwise no default value is available." />\n+ <param argument="--gt-alpha" name="gt_alpha" type="float" value="0.05" min="0" label="Alpha threshold for calling genotypes" />\n+ </xml>\n+\n+ <xml name="barcode_encoding_single" token_type="">\n+ <option value="--inline_null" selected="True">@TYPE@ is inline with sequence, occurs only on single-end read (--inline_null)</option>\n+ <option value="--index_null">@TYPE@ is provded in FASTQ header (Illumina i5 or i7 read) (--index_null)</option>\n+ <yield/>\n+ </xml>\n+\n+ <xml name="barcode_encoding_pair" token_type="">\n+ <expand macro="barcode_encoding_single" type="@TYPE@">\n+ <option value="--null_index">@TYPE@ is provded in FASTQ header (Illumina i7 read if both i5 and i7 read are provided) (--null_index)</option>\n+ <option value="--inline_inline">@TYPE@ is inline with sequence, occurs on single and paired-end read (--inline_inline)</option>\n+ <option value="--index_index">@TYPE@ is provded in FASTQ header (Illumina i5 and i7 reads) (--index_index)</option>\n+ <option value="--inline_index">@TYPE@ is inline with sequence on single-end read and occurs in FASTQ header (from either i5 or i7 read) (--inline_index)</option>\n+ <option value="--index_inline">@TYPE@ occurs in FASTQ header (Illumina i5 or i7 read) and is inline with sequence on single-end read (if single read data) or paired-end read (if paired data) (--index_inline)</option>\n+ </expand>\n+ </xml>\n+</macros>\n' |
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| diff -r 000000000000 -r b2e3553e1be2 macros_process.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros_process.xml Mon Jul 01 10:58:28 2019 -0400 |
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| b'@@ -0,0 +1,183 @@\n+<?xml version="1.0"?>\n+\n+<!-- macros and tokens for process_radtags and process_short_reads -->\n+\n+<macros>\n+\n+ <token name="@PROCESS_IOOPTIONS@"><![CDATA[\n+ -p stacks_inputs/\n+ #if $input_type.input_type_select == "paired"\n+ --paired\n+ #end if\n+ -i $inputype\n+ -b \'$barcode\'\n+ $input_type.barcode_encoding\n+ #if str( $outype ) != "auto"\n+ -y $outype\n+ #end if\n+ -o stacks_outputs\n+ ]]></token>\n+ <xml name="process_output_types">\n+ <param name="outype" argument="-y" type="select" label="Output format" >\n+ <option value="auto" selected="True">Same as input</option>\n+ <option value="fastq">fastq</option>\n+ <option value="fasta">fasta</option>\n+ <option value="gzfastq">gzipped fastq</option>\n+ <option value="gzfasta">gzipped fasta</option>\n+ </param>\n+ </xml>\n+\n+ <xml name="discover_faqgz_output_macro" token_pattern="" token_dir="">\n+ <expand macro="discover_faq_output_macro" pattern="@PATTERN@" dir="@DIR@"/>\n+ <discover_datasets pattern="@PATTERN@\\.fq\\.gz$" ext="fastqsanger.gz" directory="@DIR@/" />\n+ <discover_datasets pattern="@PATTERN@\\.fa\\.gz$" ext="fasta.gz" directory="@DIR@/" />\n+ </xml>\n+ <xml name="discover_faq_output_macro" token_pattern="" token_dir="">\n+ <discover_datasets pattern="@PATTERN@\\.fq$" ext="fastqsanger" directory="@DIR@/" />\n+ <discover_datasets pattern="@PATTERN@\\.fa$" ext="fasta" directory="@DIR@/" />\n+ </xml>\n+\n+ <xml name="process_outputs">\n+ <collection name="demultiplexed" type="list" label="${tool.name} on ${on_string} Demultiplexed reads">\n+ <filter>input_type[\'input_type_select\'] == "single"</filter>\n+ <expand macro="discover_faqgz_output_macro" pattern="(?P<name>.+)" dir="stacks_outputs"/>\n+ </collection>\n+ <collection name="demultiplexed_paired" type="list:paired" label="${tool.name} on ${on_string} Demultiplexed reads">\n+ <filter>input_type[\'input_type_select\'] == "paired"</filter>\n+ <expand macro="discover_faqgz_output_macro" pattern="(?P<identifier_0>.+)\\.(?P<identifier_1>[^.]+)" dir="stacks_outputs"/>\n+ </collection>\n+\n+ <collection name="remaining" type="list:paired" label="${tool.name} on ${on_string} Remaining orphan reads">\n+ <filter>input_type[\'input_type_select\'] == "paired"</filter>\n+ <expand macro="discover_faqgz_output_macro" pattern="(?P<identifier_0>.+)\\.rem\\.(?P<identifier_1>[^.]+)" dir="stacks_outputs/remaining"/>\n+ </collection>\n+\n+ <!-- note irrespective of -y output is always named fastq and are never zipped -->\n+ <collection name="discarded" type="list" label="${tool.name} on ${on_string} Discarded reads">\n+ <filter>capture is True and input_type[\'input_type_select\'] == "single"</filter>\n+ <expand macro="discover_faq_output_macro" pattern="(?P<name>.*)" dir="stacks_outputs/discarded"/>\n+ </collection>\n+ <collection name="discarded_paired" type="list:paired" label="${tool.name} on ${on_string} Discarded reads">\n+ <filter>capture is True and input_type[\'input_type_select\'] == "paired"</filter>\n+ <expand macro="discover_faq_output_macro" pattern="(?P<identifier_0>.+)\\.(?P<identifier_1>[^.]+)" dir="stacks_outputs/discarded"/>\n+ </collection>\n+ </xml>\n+\n+ <!-- FASTQ filtering options -->\n+ <xml name="process_filter">\n+ <conditional name="filter_cond" >\n+ <param name="filter_select" type="select" label="Do quality filtering">\n+ <option value="yes">Yes</option>\n+ <option value="no" selected="true">No</option>\n+ </param>\n+ <when value="yes">\n+ <param name="sliding" type="float" value="0.15" min="0" max="1" argument="-w" label="Set the size of the sliding window as a fraction'..b' -type f -iname "*.gz.discards" | while read file; do mv "\\$file" "\\$(echo \\$file | sed \'s/.gz.discards$/.discards/;\')"; done\n+\n+ ## the discard files are named fastq even if the output is fasta\n+ #if str($outype).endswith("fasta"):\n+ && find stacks_outputs/discarded/ -type f | while read file; do mv "\\$file" "\\$(echo \\$file | sed \'s/\\.fastq.discards/.fa/;\')"; done\n+ #else\n+ && find stacks_outputs/discarded/ -type f | while read file; do mv "\\$file" "\\$(echo \\$file | sed \'s/\\.fastq.discards/.fq/;\')"; done\n+ #end if\n+ #end if\n+ ## prepare paired read output for processing in galaxy\n+ #if $input_type.input_type_select == \'paired\':\n+ && mkdir stacks_outputs/remaining\n+ && find stacks_outputs -iregex ".*\\.rem\\.[12]\\.f[aq]\\(\\.gz\\)?" | while read file; do mv "\\$file" stacks_outputs/remaining/; done\n+ && find stacks_outputs/ -iregex ".*.f[aq]\\(\\.gz\\)?" | while read file; do mv "\\$file" "\\$(echo \\$file | sed \'s/\\.1\\./.forward./; s/\\.2\\./.reverse./\')"; done\n+ #end if\n+ ]]></token>\n+\n+ <!-- adapter trimming options -->\n+ <xml name="process_adapter">\n+ <param argument="--adapter_1" type="text" value="" optional="true" label="Adaptor sequence that may occur on the first read" />\n+ <param argument="--adapter_2" type="text" value="" optional="true" label="Adaptor sequence that may occur on the paired-read" />\n+ <param argument="--adapter_mm" type="integer" value="" optional="true" label="Number of mismatches allowed in the adapter sequence"/>\n+ </xml>\n+ <token name="@PROCESS_ADAPTER@"><![CDATA[\n+ ## Adapter options\n+ #if str($options_advanced.adapter_1) != "":\n+ --adapter_1 $options_advanced.adapter_1\n+ #end if\n+ #if str($options_advanced.adapter_2) != "":\n+ --adapter_2 $options_advanced.adapter_2\n+ #end if\n+ #if str($options_advanced.adapter_mm) != "":\n+ --adapter_mm $options_advanced.adapter_mm\n+ #end if\n+ ]]></token>\n+\n+ <!-- barcode rescue options -->\n+ <xml name="rescue_barcode">\n+ <conditional name="rescue_cond">\n+ <param name="rescue" type="select" argument="-r" label="Rescue mutated barcodes and RAD-Tags?">\n+ <option value="-r">yes</option>\n+ <option value="" selected="true">no</option>\n+ </param>\n+ <when value="-r">\n+ <param argument="--barcode_dist_1" type="integer" value="" optional="true" label="Number of allowed mismatches when rescuing first read barcodes" help="(default 1)"/>\n+ <param argument="--barcode_dist_2" type="integer" value="" optional="true" label="Number of allowed mismatches when rescuing paired read barcodes" help="(default value for single end barcodes)"/>\n+ </when>\n+ <when value=""/>\n+ </conditional>\n+ </xml>\n+ <token name="@RESCUE_BARCODE@"><![CDATA[\n+ #if str($options_advanced.rescue_cond.rescue) != ""\n+ $options_advanced.rescue_cond.rescue\n+ #if str($options_advanced.rescue_cond.barcode_dist_1) != "":\n+ --barcode_dist_1 $options_advanced.rescue_cond.barcode_dist_1\n+ #end if\n+ #if str($options_advanced.rescue_cond.barcode_dist_2) != "":\n+ --barcode_dist_2 $options_advanced.rescue_cond.barcode_dist_2\n+ #end if\n+ #end if\n+ ]]></token>\n+\n+ <!-- advanced options that are shared -->\n+ <xml name="common_advanced">\n+ <param name="truncate" type="integer" value="" optional="True" argument="-t" label="Truncate final read length to this value" />\n+ <param argument="--retain_header" type="boolean" checked="false" truevalue="--retain_header" falsevalue="" label="Retain unmodified FASTQ headers in the output" />\n+ </xml>\n+ <token name="@COMMON_ADVANCED@"><![CDATA[\n+ #if str($options_advanced.truncate)\n+ -t $options_advanced.truncate\n+ #end if\n+ $options_advanced.retain_header\n+ ]]></token>\n+</macros>\n' |
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| diff -r 000000000000 -r b2e3553e1be2 stacks_kmerfilter.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/stacks_kmerfilter.xml Mon Jul 01 10:58:28 2019 -0400 |
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| b'@@ -0,0 +1,200 @@\n+<tool id="stacks2_kmerfilter" name="Stacks2: kmer filter" profile="@PROFILE@" version="@STACKS_VERSION@+galaxy@WRAPPER_VERSION@">\n+<description>Identify PCR clones</description>\n+ <macros>\n+ <import>macros.xml</import>\n+ </macros>\n+ <expand macro="requirements"/>\n+ <expand macro="version_cmd"/>\n+ <command detect_errors="aggressive"><![CDATA[\n+@FASTQ_INPUT_FUNCTIONS@\n+\n+mkdir stacks_inputs stacks_outputs &&\n+\n+#set ($link_command, $fwd_path, $rev_path, $inputype) = $fastq_input_batch($input_type.fqinputs, $input_type.input_type_select)\n+$link_command\n+\n+kmer_filter\n+#if $input_type.input_type_select == \'single\':\n+ -f \'$fwd_path\'\n+#else\n+ -1 \'$fwd_path\'\n+ -2 \'$rev_path\'\n+#end if\n+## TODO $options_kmer_char.read_k_freq\n+-i $inputype\n+-o stacks_outputs\n+$capture\n+-y fastq\n+$options_filtering.rare\n+$options_filtering.abundant\n+--k_len $options_filtering.k_len\n+--max_k_freq $options_advanced_filtering.max_k_freq\n+#if str($options_advanced_filtering.min_lim)!="":\n+ --min_lim $options_advanced_filtering.min_lim\n+#end if\n+#if str($options_advanced_filtering.max_lim)!="":\n+ --max_lim $options_advanced_filtering.max_lim\n+#end if\n+#if str($options_normalization.normalize)!="":\n+ --normalize $options_normalization.normalize\n+#end if\n+#if $options_kmer_char.write_k_freq\n+ --read_k_freq $kfreq\n+#end if\n+$options_kmer_char.k_dist\n+#if $options_kmer_char.k_dist\n+ | sed \'s/KmerFrequency/# KmerFrequency/\' > $kfreqdist\n+#end if\n+@TEE_APPEND_LOG@\n+@CAT_LOG_TO_STDERR@\n+\n+## move outputs such that Galaxy can find them\n+## if filtering is on then ...filt...fq is created\n+## if normalization is on then ...norm...fq is created\n+## if both are active then both files are created, but only norm is needed\n+#if str($options_filtering.rare)!="" or str($options_filtering.abundant)!="" or str($options_normalization.normalize)!="":\n+ #if str($options_normalization.normalize)!="":\n+ #set infix="norm"\n+ #else\n+ #set infix="fil"\n+ #end if\n+ #if $capture:\n+ #if $input_type.input_type_select == "single"\n+ && mv stacks_outputs/*.discards.fastq \'$discarded\'\n+ #else\n+ && mv stacks_outputs/*.1.discards.fastq \'$discarded_pair.forward\'\n+ && mv stacks_outputs/*.2.discards.fastq \'$discarded_pair.reverse\'\n+ #end if\n+ #end if\n+ #if $input_type.input_type_select == "single"\n+ && mv stacks_outputs/*.${infix}.fastq \'$clean\'\n+ #else\n+ && mv stacks_outputs/*.1.${infix}.fastq \'$clean_pair.forward\'\n+ && mv stacks_outputs/*.2.${infix}.fastq \'$clean_pair.reverse\'\n+ #end if\n+#end if\n+\n+ ]]></command>\n+ <inputs>\n+ <expand macro="fastq_input_bc"/>\n+ <param name="capture" type="boolean" checked="false" truevalue="-D" falsevalue="" argument="-D" label="Capture discarded reads to a file" />\n+ <section name="options_filtering" title="Filtering options" expanded="False">\n+ <param argument="--rare" type="boolean" checked="false" truevalue="--rare" falsevalue="" label="Turn on filtering based on rare k-mers" />\n+ <param argument="--abundant" type="boolean" checked="false" truevalue="--abundant" falsevalue="" label="Turn on filtering based on abundant k-mers" />\n+ <param argument="--k_len" type="integer" value="15" label="K-mer size" />\n+ </section>\n+ <section name="options_advanced_filtering" title="Advanced fitering options" expanded="False">\n+ <param argument="--max_k_freq" type="integer" value="20000" label="Number of times a kmer must occur to be considered abundant" />\n+ <param argument="--min_lim" type="integer" value="" optional="true" label="Number of rare kmers occuring in a row required to discard a read" help="(default: 80% of the k-mer length)." />\n+ <param argument="--max_lim" type="integer" value="" optional="true" label="Number of abundant kmers required to discard a read" help="(default: 80% of '..b'ular" name="kfreq" label="${tool.name} on ${on_string} kmer frequencies">\n+ <filter>options_kmer_char[\'write_k_freq\']</filter>\n+ </data>\n+ <data format="tabular" name="kfreqdist" label="${tool.name} on ${on_string} kmer frequency distribution">\n+ <filter>options_kmer_char[\'k_dist\']</filter>\n+ </data>\n+ </outputs>\n+ <tests>\n+ <!-- default output for filtering -->\n+ <test>\n+ <conditional name="input_type">\n+ <param name="input_type_select" value="single" />\n+ <param name="fqinputs" ftype="fastqsanger.gz" value="clonefilter/R1_0001.1.fq.gz" />\n+ </conditional>\n+ <param name="add_log" value="yes" />\n+\t\t\t<output name="output_log" ftype="txt" file="kmerfilter/kmerfilter.log" lines_diff="8"/>\n+ <param name="rare" value="--rare"/>\n+ <param name="abundant" value="--abundant" />\n+ <param name="k_len" value="16" />\n+ <assert_command>\n+ <has_text text="--rare" />\n+ <has_text text="--abundant" />\n+ <has_text text="--k_len 16" />\n+ </assert_command>\n+ <output name="clean" compare="sim_size" file="clonefilter/Removed1_0001.1.1.fq.single.gz"/>\n+ </test>\n+ <test>\n+ <conditional name="input_type">\n+ <param name="input_type_select" value="paired" />\n+ <param name="fqinputs">\n+ <collection type="paired">\n+ <element name="forward" value="clonefilter/R1_0001.1.fq.gz" />\n+ <element name="reverse" value="clonefilter/R2_0001.2.fq.gz" />\n+ </collection>\n+ </param>\n+ </conditional>\n+ <param name="capture" value="-D" />\n+ <param name="normalize" value="1" />\n+ <assert_command>\n+ <has_text text="--normalize 1" />\n+ </assert_command>\n+ <output_collection name="clean_pair" type="paired">\n+ <element name="forward" compare="sim_size" file="clonefilter/Removed1_0001.1.1.fq.gz" />\n+ <element name="reverse" compare="sim_size" file="clonefilter/Removed2_0001.2.2.fq.gz" />\n+ </output_collection>\n+ <output_collection name="discarded_pair" type="paired">\n+ <element name="forward" compare="sim_size" file="clonefilter/Removed1_0001.1.1.fq.gz" />\n+ <element name="reverse" compare="sim_size" file="clonefilter/Removed2_0001.2.2.fq.gz" />\n+ </output_collection>\n+ </test>\n+ <!-- kfreq output -->\n+ <test>\n+ <conditional name="input_type">\n+ <param name="input_type_select" value="single" />\n+ <param name="fqinputs" ftype="fastqsanger.gz" value="clonefilter/R1_0001.1.fq.gz" />\n+ </conditional>\n+ <section name="options_kmer_char">\n+ <param name="write_k_freq" value="--write_k_freq" />\n+ </section>\n+ <output name="kfreq" file="kmerfilter/kfreq.tsv"/>\n+ </test>\n+ <!-- kfreqdist output -->\n+ <test>\n+ <conditional name="input_type">\n+ <param name="input_type_select" value="single" />\n+ <param name="fqinputs" ftype="fastqsanger.gz" value="clonefilter/R1_0001.1.fq.gz" />\n+ </conditional>\n+ <section name="options_kmer_char">\n+ <param name="k_dist" value="--k_dist" />\n+ </section>\n+ <output name="kfreqdist" file="kmerfilter/kfreqdist.tsv"/>\n+ </test>\n+ </tests>\n+ <help>\n+<![CDATA[\n+.. class:: infomark\n+\n+Allows paired or single-end reads to be filtered according to the number or rare or abundant kmers they contain. Useful for both RAD datasets as well as randomly sheared genomic or transcriptomic data.\n+\n+@STACKS_INFOS@\n+]]>\n+ </help>\n+ <expand macro="citation" />\n+</tool>\n' |
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| diff -r 000000000000 -r b2e3553e1be2 test-data/clonefilter/Removed1_0001.1.1.fq.single.gz |
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| diff -r 000000000000 -r b2e3553e1be2 test-data/clonefilter/clonefilter.log --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/clonefilter/clonefilter.log Mon Jul 01 10:58:28 2019 -0400 |
| [ |
| @@ -0,0 +1,8 @@ +Processing single-end data. +Searching for inline oligo on single-end read. +Found 1 input file(s). +Processing file 1 of 1 [R1_0001.fastq.gz] + Reading data from: + stacks_inputs/R1_0001.fastq.gz +Calculating the distribution of cloned read pairs... +5 pairs of reads input. 4 pairs of reads output, discarded 0 pairs of reads, 20.00% clone reads. |
| b |
| diff -r 000000000000 -r b2e3553e1be2 test-data/cstacks/catalog.alleles.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/cstacks/catalog.alleles.tsv Mon Jul 01 10:58:28 2019 -0400 |
| b |
| @@ -0,0 +1,3 @@ +# cstacks version 2.4; catalog generated on 2019-06-18 10:34:45 +0 1 AC 0 0 +0 1 CA 0 0 |
| b |
| diff -r 000000000000 -r b2e3553e1be2 test-data/cstacks/catalog.snps.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/cstacks/catalog.snps.tsv Mon Jul 01 10:58:28 2019 -0400 |
| b |
| @@ -0,0 +1,3 @@ +# cstacks version 2.4; catalog generated on 2019-06-18 10:34:45 +0 1 33 E 0 A C - - +0 1 88 E 0 A C - - |
| b |
| diff -r 000000000000 -r b2e3553e1be2 test-data/cstacks/catalog.tags.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/cstacks/catalog.tags.tsv Mon Jul 01 10:58:28 2019 -0400 |
| b |
| @@ -0,0 +1,4 @@ +# cstacks version 2.4; catalog generated on 2019-06-18 10:34:45 +0 1 consensus 0 1_1,2_1 AATTCGTTTGCTGCTTCAGGAATCTCTCGTATAATCTGAGTATGTGCGTACGTACGCTATTTAGATGGATAACCGACGCTGCCAGACGAGAGAC 0 0 0 +0 2 consensus 0 1_2,2_2 AATTCGGCTTGCAACGCAAGTGACGATTCCCACGGACATAACTGATCTAAGTAACTTCCAAATCTGGGAATGGGATTTCATAATTAAGGACTAT 0 0 0 +0 3 consensus 0 1_3,2_3 AATTCTCTACACCACAGCATCAATTCTAAAAATGACTACCAGAGAGACAACTCCGCAGTTAAACACTCTGACTGCCACGCCAGCTACCTCTAGA 0 0 0 |
| b |
| diff -r 000000000000 -r b2e3553e1be2 test-data/cstacks/cstacks.log --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/cstacks/cstacks.log Mon Jul 01 10:58:28 2019 -0400 |
| [ |
| @@ -0,0 +1,29 @@ +cstacks parameters selected: + Loci matched based on sequence identity. + Number of mismatches allowed between stacks: 1 + Gapped alignments: enabled +Constructing catalog from 2 samples. + +Initializing new catalog... + Parsing stacks_inputs/PopA_01.tags.tsv + Parsing stacks_inputs/PopA_01.snps.tsv + Parsing stacks_inputs/PopA_01.alleles.tsv + 3 loci were newly added to the catalog. + +Processing sample stacks_inputs/PopA_02 [2 of 2] + Parsing stacks_inputs/PopA_02.tags.tsv + Parsing stacks_inputs/PopA_02.snps.tsv + Parsing stacks_inputs/PopA_02.alleles.tsv +Searching for sequence matches... + 3 loci in the catalog, 184 kmers in the catalog hash. +Searching for gapped alignments... +Merging matches into catalog... + 3 loci were matched to a catalog locus. + 0 loci were matched to a catalog locus using gapped alignments. + 0 loci were newly added to the catalog. + 0 loci matched more than one catalog locus, linking them. + 0 linked catalog loci were merged into 0 loci. + +Writing catalog in directory 'stacks_inputs/'. +Final catalog contains 3 loci. +cstacks is done. |
| b |
| diff -r 000000000000 -r b2e3553e1be2 test-data/demultiplexed/PopA_01.1.fa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/demultiplexed/PopA_01.1.fa Mon Jul 01 10:58:28 2019 -0400 |
| b |
| b'@@ -0,0 +1,320 @@\n+>lane1_fakedata0_0 1:N:0:\n+AATTCGGCTTGCAACGCAAGTGACGATTCCCACGGACATAACTGATCTAAGTAACTTCCAAATCTGGGAA\n+>lane1_fakedata0_1 1:N:0:\n+AATTCGGCTTGCAACGCAAGTGACGATTCCCACGGACATAACTGATCTAAGTAACTTCCAAATCTGGGAA\n+>lane1_fakedata0_2 1:N:0:\n+AATTCGGCTTGCAACGCAAGTGACGATTCCCACGGACATAACTGATCTAAGTAACTTCCAAATCTGGGAA\n+>lane1_fakedata0_3 1:N:0:\n+AATTCGGCTTGCAACGCAAGTGACGATTCCCACGGACATAACTGATCTAAGTAACTTCCAAATCTGGGAA\n+>lane1_fakedata0_4 1:N:0:\n+AATTCGGCTTGCAACGCAAGTGACGATTCCCACGGACATAACTGATCTAAGTAACTTCCAAATCTGGGAA\n+>lane1_fakedata0_5 1:N:0:\n+AATTCGGCTTGCAACGCAAGTGACGATTCCCACGGACATAACTGATCTAAGTAACTTCCAAATCTGGGAA\n+>lane1_fakedata0_6 1:N:0:\n+AATTCGGCTTGCAACGCAAGTGACGATTCCCACGGACATAACTGATCTAAGTAACTTCCAAATCTGGGAA\n+>lane1_fakedata0_7 1:N:0:\n+AATTCGGCTTGCAACGCAAGTGACGATTCCCACGGACATAACTGATCTAAGTAACTTCCAAATCTGGGAA\n+>lane1_fakedata0_8 1:N:0:\n+AATTCGGCTTGCAACGCAAGTGACGATTCCCACGGACATAACTGATCTAAGTAACTTCCAAATCTGGGAA\n+>lane1_fakedata0_9 1:N:0:\n+AATTCGGCTTGCAACGCAAGTGACGATTCCCACGGACATAACTGATCTAAGTAACTTCCAAATCTGGGAA\n+>lane1_fakedata0_10 1:N:0:\n+AATTCGGCTTGCAACGCAAGTGACGATTCCCACGGACATAACTGATCTAAGTAACTTCCAAATCTGGGAA\n+>lane1_fakedata0_11 1:N:0:\n+AATTCGGCTTGCAACGCAAGTGACGATTCCCACGGACATAACTGATCTAAGTAACTTCCAAATCTGGGAA\n+>lane1_fakedata0_12 1:N:0:\n+AATTCGGCTTGCAACGCAAGTGACGATTCCCACGGACATAACTGATCTAAGTAACTTCCAAATCTGGGAA\n+>lane1_fakedata0_13 1:N:0:\n+AATTCGGCTTGCAACGCAAGTGACGATTCCCACGGACATAACTGATCTAAGTAACTTCCAAATCTGGGAA\n+>lane1_fakedata0_14 1:N:0:\n+AATTCGGCTTGCAACGCAAGTGACGATTCCCACGGACATAACTGATCTAAGTAACTTCCAAATCTGGGAA\n+>lane1_fakedata0_15 1:N:0:\n+AATTCGGCTTGCAACGCAAGTGACGATTCCCACGGACATAACTGATCTAAGTAACTTCCAAGTCTGGGAA\n+>lane1_fakedata0_16 1:N:0:\n+AATTCGGCTTGCAACGCAAGTGACGATTCCCACGGACATAACTGATCTAAGTAACTTCCAAATCTGGGAA\n+>lane1_fakedata0_17 1:N:0:\n+AATTCGGCTTGCAACGCAAGTGACGATTCCCACGGACATAACTGATCTAAGTAACTTCCAAATCTGGGAA\n+>lane1_fakedata0_18 1:N:0:\n+AATTCGGCTTGCAACGCAAGTGACGATTCCCACGGACATAACTGATCTAAGTAACTTCCAAATCTGGGAA\n+>lane1_fakedata0_19 1:N:0:\n+AATTCGGCTTGCAACGCAAGTGACGATTCCCACGGACATAACTGATCTAAGTAACTTCCAAATCTGGGAA\n+>lane1_fakedata0_20 1:N:0:\n+AATTCGGCTTGCAACGCAAGTGACGATTCCCACGGACATAACTGATCTAAGTAACTTCCAAATCTGGGAA\n+>lane1_fakedata0_21 1:N:0:\n+AATTCGGCTTGCAACGCAAGTGACGATTCCCACGGACATAACTGATCTAAGTAACTTCCAAATCTGGGAA\n+>lane1_fakedata0_22 1:N:0:\n+AATTCGGCTTGCAACGCAAGTGACGATTCCCACGGACATAACTGATCTAAGTAACTTCCAAATCTGGGAA\n+>lane1_fakedata0_23 1:N:0:\n+AATTCGGCTTGCAACGCAAGTGACGATTCCCACGGACATAACTGATCTAAGTAACTTCCAAATCTGGGAA\n+>lane1_fakedata0_24 1:N:0:\n+AATTCGGCTTGCAACGCAAGTGACGATTCCCACGGACATAACTGATCTAAGTAACTTCCAAATCTGGGAA\n+>lane1_fakedata0_25 1:N:0:\n+AATTCGGCTTGCAACGCAAGTGACGATTCCCACGGACATAACTGATCTAAGTAACTTCCAAATCTGGGAA\n+>lane1_fakedata0_26 1:N:0:\n+AATTCGGCTTGCAACGCAAGTGACGATTCCCACGGACATAACTGATCTAAGTAACTTCCAAATCTGGGAA\n+>lane1_fakedata0_27 1:N:0:\n+AATTCGGCTTGCAACGCAAGTGACGATTCCCACGGACATAACTGATCTAAGTAACTTCCAAATCTGGGAA\n+>lane1_fakedata2_0 1:N:0:\n+AATTCTCTACACCACAGCATCAATTCTAAAAATGACTACCAGAGAGACAACTCCGCAGTTAAACACTCTG\n+>lane1_fakedata2_1 1:N:0:\n+AATTCTCTACACCACAGCATCAATTCTAAAAATGACTACCAGAGAGACAACTCCGCAGTTAAACACTCTG\n+>lane1_fakedata2_2 1:N:0:\n+AATTCTCTACACCACAGCATCAATTCTAAAAATGACTACCAGAGAGACAACTCCGCAGTTAAACACTCTG\n+>lane1_fakedata2_3 1:N:0:\n+AATTCTCTACACCACAGCATCAATTCTAAAAATGACTACCAGAGAGACAACTCCGCAGTTAAACACTCTG\n+>lane1_fakedata2_4 1:N:0:\n+AATTCTCTACACCACAGCATCAATTCTAAAAATGACTACCAGAGAGACAACTCCGCAGTTAAACACTCTG\n+>lane1_fakedata2_5 1:N:0:\n+AATTCTCTACACCACAGCATCAATTCTAAAAATGACTACCAGAGAGACAACTCCGCAGTAAAACACTCTG\n+>lane1_fakedata2_6 1:N:0:\n+AATTCTCTACACCACAGCATCAATTCTAAAAATGACTACCAGAGAGACAACTCCGCAGTTAAACACTCTG\n+>lane1_fakedata2_7 1:N:0:\n+AATTCTCTACACCACAGCATCAATTCTAAAAATGACTACCAGAGAGACAACTCCGCAGTTAAACACTCTG\n+>lane1_fakedata2_8 1:N:0:\n+AATTCTCTACACCACAGCATCAATTCTAAAAATGACTACCAGAGAGACAACTCCGCAGTTAAACACTCTG\n+>lane1_fakedata2_9 1:N:0:\n+AATTCTCTACACCACAGCATCAATTCTAAAAATGACTACCAGAGAGACAACTCCGCAGTTAAACACTCTG\n+>lane1_fakedata2_10 1:N:0:\n+AATTCTCTACACCACAGCATCAATTCTAAAAATGACTACCAGAGAGACAACTCCGCAGTTAAACACTCTG\n+>lane1_fakedata2_11 1:N:0:\n+AATTCTCTACACCACAGCATCAATTCTAAAAATGACTACCAGAGAGACAACTCCGCAGTTAAACACTCTG\n+'..b'CGTACGCTATTTAGATGGAT\n+>lane1_fakedata7_8 1:N:0:\n+AATTCGTTTGCTGCTTCAGGAATCTCTCGTATACTCTGAGTATGTGCGTACGTACGCTATTTAGATGGAT\n+>lane1_fakedata7_9 1:N:0:\n+AATTCGTTTGCTGCTTCAGGAATCTCTCGTATAATCTGAGTATGTGCGTACGTACGCTATTTAGATGGAT\n+>lane1_fakedata7_10 1:N:0:\n+AATTCGTTTGCTGCTTCAGGAATCTCTCGTATAATCTGAGTATGTGCGTACGTACGCTATTTAGATGGAT\n+>lane1_fakedata7_11 1:N:0:\n+AATTCGTTTGCTGCTTCAGGAATCTCTCGTATAATCTGAGTATGTGCGTACGTACGCTATTTAGATGGAT\n+>lane1_fakedata7_12 1:N:0:\n+AATTCGTTTGCTGCTTCAGGAATCTCTCGTATAATCTGAGTATGTGCGTACGTACGCTATTTAGATGGAT\n+>lane1_fakedata7_13 1:N:0:\n+AATTCGTTTGCTGCTTCAGGAATCTCTCGTATAATCTGAGTATGTGCGTACGTACGCTATTTAGATGGAT\n+>lane1_fakedata7_14 1:N:0:\n+AATTCGTTTGCTGCTTCAGGAATCTCTCGTATAATCTGAGTATGTGCGTACGTACGCTATTTAGATGGAT\n+>lane1_fakedata7_15 1:N:0:\n+AATTCGTTTGCTGCTTCAGGAATCTCTCGTATAATCTGAGTATGTGCGTACGTACGCTATTTAGATGGAT\n+>lane1_fakedata7_16 1:N:0:\n+AATTCGTTTGCTGCTTCAGGAATCTCTCGTATAATCTGAGTATGTGCGTACGTACGCTATTTAGATGGAT\n+>lane1_fakedata7_17 1:N:0:\n+AATTCGTTTGCTGCTTCAGGAATCTCTCGTATAATCTGAGTATGTGCGTACGTACGCTATTTAGATGGAT\n+>lane1_fakedata8_0 1:N:0:\n+AATTGTGACACGCAGCCTGGGTGACGTCTCTTCTGATAGGCATTGGCAGATTGACTACGCATAGGCGCTC\n+>lane1_fakedata8_1 1:N:0:\n+AATTGTGACACGCAGCCTGGGTGACGTCTCTTCTGATAGGCATTGGCAGATTGACTACGCATAGGCGCTC\n+>lane1_fakedata8_2 1:N:0:\n+AATTGTGACACGCAGCCTGGGTGACGTCTCTTCTGATAGGCATTGGCAGATTGACTACGCATAGGCGCTC\n+>lane1_fakedata8_3 1:N:0:\n+AATTGTGACACGCAGCCTGGGTGACGTCTCTTCTGATAGGCATTGGCAGATCGACTACGCATAGGCGCTC\n+>lane1_fakedata8_4 1:N:0:\n+AATTGTGACACGCAGCCTGGGTGACGTCTCTTCTGATAGGCATTGGCAGATTGACTACGCATAGGCGCTC\n+>lane1_fakedata8_5 1:N:0:\n+AATTGTGACACGCAGCCTGGGTGACGTCACTTCTGATAGGCATTGGCAGATTGACTACGCATAGGCGCTC\n+>lane1_fakedata8_6 1:N:0:\n+AATTGTGACACGCAGCCTGGGTGACGTCTCTTCTGATAGGCATTGGCAGATTGACTACGCATAGGCGCTC\n+>lane1_fakedata8_7 1:N:0:\n+AATTGTGACACGCAGCCTGGGTGACGTCTCTTCTGTTAGGCATTGGCAGATTGACTACGCATAGGCGCTC\n+>lane1_fakedata8_8 1:N:0:\n+AATTGTGACACGCAGCCTGGGTGACGTCTCTTCTGATAGGCATTGGCAGATTGACTACGCATAGGCGCTC\n+>lane1_fakedata8_9 1:N:0:\n+AATTGTGACACGCAGCCTGGGTGACGTCTCTTCTGATAGGCATTGGCAGATTGACTACGCATAGGCGCTC\n+>lane1_fakedata9_0 1:N:0:\n+AATTATAACAAAGGTCGACCTGACTCAGCCATTGTTGATAGACGCGAAAATAACGAAGCAGGATGACCGC\n+>lane1_fakedata9_1 1:N:0:\n+AATTATAACAAAGGTCGACCTGACTCAGCCATTGTTGATAGACGCGAAAATAACGAAGCAGGATGACCGC\n+>lane1_fakedata9_2 1:N:0:\n+AATTATAACAAAGGTCGACCTGACTCAGCCATTGTTGATAGACGCGAAAATAACGAAGCAGGATGACCGC\n+>lane1_fakedata9_3 1:N:0:\n+AATTATAACAAAGGTCGACCTGACTCAGCCATTGTTGATAGACGCGAAAATAACGAAGCAGGATGACCGC\n+>lane1_fakedata9_4 1:N:0:\n+AATTATAACAAAGGTCGACCTGACTCAGCCATTGTTGATAGACGCGAAAATAACGAAGCAGGATGACCGC\n+>lane1_fakedata9_5 1:N:0:\n+AATTATAACAAAGGTCGACCTGACTCAGCCATTGTTGATAGACGCGAAAATAACGAAGCAGGATGACCGC\n+>lane1_fakedata9_6 1:N:0:\n+AATTATAACAAAGGTCGACCTGACTCAGCCATTGTTGATAGACGCGAAAATAACGAAGCAGGATGACCGC\n+>lane1_fakedata9_7 1:N:0:\n+AATTATAACAAAGGTCGACCTGACTCAGCCATTGTTGATAGACGCGAAAATAACGAAGCAGGATGACCGC\n+>lane1_fakedata9_8 1:N:0:\n+AATTATAACAAAGGTCGACCTGACTCAGCCATTGTTGATAGACGCGAAAATAACGAAGCAGGATGACCGC\n+>lane1_fakedata9_9 1:N:0:\n+AATTATAACAAAGGTCGACCTGACTCAGCCATTGTTGATAGACGCGAAAATAACGAAGCAGGATGACCGC\n+>lane1_fakedata9_10 1:N:0:\n+AATTATAACAAAGGTCGACCTGACTCAGCCATTGTTGATAGACGCGAAAATAACGAAGCAGGATGACCGC\n+>lane1_fakedata9_11 1:N:0:\n+AATTATAACAAAGGTCGACCTGACTCAGCCATTGTTGATAGACGCGAAAATAACGAAGCAGGATGACCGC\n+>lane1_fakedata9_12 1:N:0:\n+AATTATAACAAAGGTCGACCTGACTCAGCCATTGTTGATAGACGCGAAAATAACGAAGCAGGATGACCGC\n+>lane1_fakedata9_13 1:N:0:\n+AATTATAACAAAGGTCGACCTGACTCAGCCATTGTTGATAGACGCGAAAATAACGAAGCAGGATGACCGC\n+>lane1_fakedata9_14 1:N:0:\n+AATTATAACAAAGGTCGACCTGACTCAGCCATTGTTGATAGACGCGAAAATAACGAAGCAGGATGACCGC\n+>lane1_fakedata9_15 1:N:0:\n+AATTATAACAAAGGTCGACCTGACTCAGCCATTGTTGATAGACGCGAAAATAACGAAGCAGGATGACCGC\n+>lane1_fakedata9_16 1:N:0:\n+AATTATAACAAAGGTCGACCTGACTCAGCCATTGTTGATAGACGCGAAAATAACGAAGCAGGATGACCGC\n+>lane1_fakedata9_17 1:N:0:\n+AATTATAACAAAGGTCGACCTGACTCAGCCATTGTTGATAGACGCGAAAATAACGAAGCAGGATGACCGC\n+>lane1_fakedata9_18 1:N:0:\n+AATTATAACAAAGGTCGACCTGACTCAGCCATTGTTGATAGACGCGAAAATAACGAAGCAGGATGACCGC\n+>lane1_fakedata9_19 1:N:0:\n+AATTATAACAAAGGTCGACCTGACTCAGCCATTGTTGATAGACGCGAAAATAACGAAGCAGGATGACCGC\n' |
| b |
| diff -r 000000000000 -r b2e3553e1be2 test-data/demultiplexed/PopA_01.1.fa.gz |
| b |
| Binary file test-data/demultiplexed/PopA_01.1.fa.gz has changed |
| b |
| diff -r 000000000000 -r b2e3553e1be2 test-data/demultiplexed/PopA_01.1.fq --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/demultiplexed/PopA_01.1.fq Mon Jul 01 10:58:28 2019 -0400 |
| b |
| b'@@ -0,0 +1,264 @@\n+@lane1_fakedata0_0 1:N:0:/1\n+AATTCGGCTTGCAACGCAAGTGACGATTCCCACGGACATAACTGATCTAAGTAACTTCCAAATCTGGGAATGGGATTTCATAATTAAGGACTAT\n++\n+BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB\n+@lane1_fakedata0_1 1:N:0:/1\n+AATTCGGCTTGCAACGCAAGTGACGATTCCCACGGACATAACTGATCTAAGTAACTTCCAAATCTGGGAATGGGATTTCATAATTAAGGACTAT\n++\n+BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB\n+@lane1_fakedata0_2 1:N:0:/1\n+AATTCGGCTTGCAACGCAAGTGACGATTCCCACGGACATAACTGATCTAAGTAACTTCCAAATCTGGGAATGGGATTTCATAATTAAGGACTAT\n++\n+BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB\n+@lane1_fakedata0_3 1:N:0:/1\n+AATTCGGCTTGCAACGCAAGTGACGATTCCCACGGACATAACTGATCTAAGTAACTTCCAAATCTGGGAATGGGATTTCATAATTAAGGACTAT\n++\n+BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB\n+@lane1_fakedata0_4 1:N:0:/1\n+AATTCGGCTTGCAACGCAAGTGACGATTCCCACGGACATAACTGATCTAAGTAACTTCCAAATCTGGGAATGGGATTTCATAATTAAGGACTAT\n++\n+BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB\n+@lane1_fakedata0_5 1:N:0:/1\n+AATTCGGCTTGCAACGCAAGTGACGATTCCCACGGACATAACTGATCTAAGTAACTTCCAAATCTGGGAATGGGATTTCATAATTAAGGACTAT\n++\n+BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB\n+@lane1_fakedata0_6 1:N:0:/1\n+AATTCGGCTTGCAACGCAAGTGACGATTCCCACGGACATAACTGATCTAAGTAACTTCCAAATCTGGGAATGGGATTTCATAATTAAGGACTAT\n++\n+BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB\n+@lane1_fakedata0_7 1:N:0:/1\n+AATTCGGCTTGCAACGCAAGTGACGATTCCCACGGACATAACTGATCTAAGTAACTTCCAAATCTGGGAATGGGATTTCATAATTAAGGACTAT\n++\n+BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB\n+@lane1_fakedata0_8 1:N:0:/1\n+AATTCGGCTTGCAACGCAAGTGACGATTCCCACGGACATAACTGATCTAAGTAACTTCCAAATCTGGGAATGGGATTTCATAATTAAGGACTAT\n++\n+BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB\n+@lane1_fakedata0_9 1:N:0:/1\n+AATTCGGCTTGCAACGCAAGTGACGATTCCCACGGACATAACTGATCTAAGTAACTTCCAAATCTGGGAATGGGATTTCATAATTAAGGACTAT\n++\n+BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB\n+@lane1_fakedata0_10 1:N:0:/1\n+AATTCGGCTTGCAACGCAAGTGACGATTCCCACGGACATAACTGATCTAAGTAACTTCCAAATCTGGGAATGGGATTTCATAATTAAGGACTAT\n++\n+BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB\n+@lane1_fakedata0_11 1:N:0:/1\n+AATTCGGCTTGCAACGCAAGTGACGATTCCCACGGACATAACTGATCTAAGTAACTTCCAAATCTGGGAATGGGATTTCATAATTAAGGACTAT\n++\n+BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB\n+@lane1_fakedata0_12 1:N:0:/1\n+AATTCGGCTTGCAACGCAAGTGACGATTCCCACGGACATAACTGATCTAAGTAACTTCCAAATCTGGGAATGGGATTTCATAATTAAGGACTAT\n++\n+BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB\n+@lane1_fakedata0_13 1:N:0:/1\n+AATTCGGCTTGCAACGCAAGTGACGATTCCCACGGACATAACTGATCTAAGTAACTTCCAAATCTGGGAATGGGATTTCATAATTAAGGACTAT\n++\n+BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB\n+@lane1_fakedata0_14 1:N:0:/1\n+AATTCGGCTTGCAACGCAAGTGACGATTCCCACGGACATAACTGATCTAAGTAACTTCCAAATCTGGGAATGGGATTTCATAATTAAGGACTAT\n++\n+BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB\n+@lane1_fakedata0_15 1:N:0:/1\n+AATTCGGCTTGCAACGCAAGTGACGATTCCCACGGACATAACTGATCTAAGTAACTTCCAAGTCTGGGAATGGGATTTCATAATTAAGGACTAT\n++\n+BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB\n+@lane1_fakedata0_16 1:N:0:/1\n+AATTCGGCTTGCAACGCAAGTGACGATTCCCACGGACATAACTGATCTAAGTAACTTCCAAATCTGGGAATGGGATTTCATAATTAAGGACTAT\n++\n+BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB\n+@lane1_fakedata0_17 1:N:0:/1\n+AATTCGGCTTGCAACGCAAGTGACGATTCCCACGGACATAACTGATCTAAGTAACTTCCAAATCTGGGAATGGGATTTCATAATTAAGGACTAT\n++\n+BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB'..b'TGCTTCAGGAATCTCTCGTATACTCTGAGTATGTGCGTACGTACGCTATTTAGATGGATAACCGACGCTGCCAGACGAGAGAC\n++\n+BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB\n+@lane1_fakedata7_1 1:N:0:/1\n+AATTCGTTTGCTGCTTCAGGAATCTCTCGTATACTCTGAGTATGTGCGTACGTACGCTATTTAGATGGATAACCGACGCTGCCAGACGAGAGAC\n++\n+BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB\n+@lane1_fakedata7_2 1:N:0:/1\n+AATTCGTTTGCTGCTTCAGGAATCTCTCGTATACTCTGAGTATGTGCGTACGTACGCTATTTAGATGGATAACCGACGCTGCCAGACGAGAGAC\n++\n+BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB\n+@lane1_fakedata7_3 1:N:0:/1\n+AATTCGTTTGCTGCTTCAGGAATCTCTCGTATACTCTGAGTATGTGCGTACGTACGCTATTTAGATGGATAACCGACGCTGCCAGACGAGAGAC\n++\n+BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB\n+@lane1_fakedata7_4 1:N:0:/1\n+AATTCGTTTGCTGCTTCAGGAATCTCTCGTATACTCTGAGTATGTGCGTACGTACGCTATTTAGATGGATAACCGACGCTGCCAGACGAGAGAC\n++\n+BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB\n+@lane1_fakedata7_5 1:N:0:/1\n+AATTCGTTTGCTGCTTCAGGAATCTCTCGTATACTCTGAGTATGTGCGTACGTACGCTATTTAGATGGATAACCGACGCTGCCAGACGAGAGAC\n++\n+BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB\n+@lane1_fakedata7_6 1:N:0:/1\n+AATTCGTTTGCTGCTTCAGGAATCTCTCGTATACTCTGAGTATGTGCGTACGTACGCTATTTAGATGGATAACCGACGCTGCCAGACGAGAGAC\n++\n+BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB\n+@lane1_fakedata7_7 1:N:0:/1\n+AATTCGTTTGCTGCTTCAGGAATCTCTCGTATACTCTGAGTATGTGCGTACGTACGCTATTTAGATGGATAACCGACGCTGCCAGACGAGAGAC\n++\n+BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB\n+@lane1_fakedata7_8 1:N:0:/1\n+AATTCGTTTGCTGCTTCAGGAATCTCTCGTATACTCTGAGTATGTGCGTACGTACGCTATTTAGATGGATAACCGACGCTGCCAGACGAGAGAC\n++\n+BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB\n+@lane1_fakedata7_9 1:N:0:/1\n+AATTCGTTTGCTGCTTCAGGAATCTCTCGTATAATCTGAGTATGTGCGTACGTACGCTATTTAGATGGATAACCGACGCTGCCAGACGCGAGAC\n++\n+BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB\n+@lane1_fakedata7_10 1:N:0:/1\n+AATTCGTTTGCTGCTTCAGGAATCTCTCGTATAATCTGAGTATGTGCGTACGTACGCTATTTAGATGGATAACCGACGCTGCCAGACGCGAGAC\n++\n+BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB\n+@lane1_fakedata7_11 1:N:0:/1\n+AATTCGTTTGCTGCTTCAGGAATCTCTCGTATAATCTGAGTATGTGCGTACGTACGCTATTTAGATGGATAACCGACGCTGCCAGACGCGAGAC\n++\n+BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB\n+@lane1_fakedata7_12 1:N:0:/1\n+AATTCGTTTGCTGCTTCAGGAATCTCTCGTATAATCTGAGTATGTGCGTACGTACGCTATTTAGATGGATAACCGACGCTGCCAGACGCGAGAC\n++\n+BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB\n+@lane1_fakedata7_13 1:N:0:/1\n+AATTCGTTTGCTGCTTCAGGAATCTCTCGTATAATCTGAGTATGTGCGTACGTACGCTATTTAGATGGATAACCGACGCTGCCAGACGCGAGAC\n++\n+BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB\n+@lane1_fakedata7_14 1:N:0:/1\n+AATTCGTTTGCTGCTTCAGGAATCTCTCGTATAATCTGAGTATGTGCGTACGTACGCTATTTAGATGGATAACCGACGCTGCCAGACGCGAGAC\n++\n+BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB\n+@lane1_fakedata7_15 1:N:0:/1\n+AATTCGTTTGCTGCTTCAGGAATCTCTCGTATAATCTGAGTATGTGCGTACGTACGCTATTTAGATGGATAACCGACGCTGCCAGACGCGAGAC\n++\n+BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB\n+@lane1_fakedata7_16 1:N:0:/1\n+AATTCGTTTGCTGCTTCAGGAATCTCTCGTATAATCTGAGTATGTGCGTACGTACGCTATTTAGATGGATAACCGACGCTGCCAGACGCGAGAC\n++\n+BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB\n+@lane1_fakedata7_17 1:N:0:/1\n+AATTCGTTTGCTGCTTCAGGAATCTCTCGTATAATCTGAGTATGTGCGTACGTACGCTATTTAGATGGATAACCGACGCTGCCAGACGCGAGAC\n++\n+BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB\n' |
| b |
| diff -r 000000000000 -r b2e3553e1be2 test-data/demultiplexed/PopA_01.2.fa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/demultiplexed/PopA_01.2.fa Mon Jul 01 10:58:28 2019 -0400 |
| b |
| b'@@ -0,0 +1,320 @@\n+>lane1_fakedata0_0 1:N:0:\n+CCGTGTATTCTCCCATGCGACAGCAGGACCTCCCATCCCCCTCTGATGTTATCAATCATAAGACGCTTCG\n+>lane1_fakedata0_1 1:N:0:\n+CCGTGTATTCTCCCATGCGACAGCAGGACCTCCCATCCCCCTCTGATGTTATCAATCATAAGACGCTTCG\n+>lane1_fakedata0_2 1:N:0:\n+CCGTGTATTCTCCCATGCGACAGCAGGACCTCCCATCCCCCTCTGATGTTATCAATCATAAGACGCTTCG\n+>lane1_fakedata0_3 1:N:0:\n+CCGTGTATTCTCCCATGCGACAGCAGGACCTCCCATCCCCCTCTGATGTTATCAATCATAAGACGCTTCG\n+>lane1_fakedata0_4 1:N:0:\n+CCGTGTATTCTCCCATGCGACAGCAGGACCTCCCATCCCCCTCTGATGTTATCAATCATAAGACGCTTCG\n+>lane1_fakedata0_5 1:N:0:\n+CCGTGTATTCTCCCATGCGACAGCAGGACCTCCCATCCCCCTCTGATGTTATCAATCATAAGACGCTTCG\n+>lane1_fakedata0_6 1:N:0:\n+CCGTGTATTCTCCCATGCGACAGCAGGACCTCCCATCCCCCTCTGATGTTATCAATCATAAGACGCTTCG\n+>lane1_fakedata0_7 1:N:0:\n+CCGTGTATTCTCCCATGCGACAGCAGGACCTCCCATCCCCCTCTGATGTTATCAATCATAAGACGCTTCG\n+>lane1_fakedata0_8 1:N:0:\n+CCGTGTATTCTCCCATGCGACAGCAGGACCTCCCATCCCCCTCTGATGTTATCAATCATAAGACGCTTCG\n+>lane1_fakedata0_9 1:N:0:\n+CCGTGTATTCTCCCATGCGACAGCAGGACCTCCCATCCCCCTCTGATGTTATCAATCATAAGACGCTTCG\n+>lane1_fakedata0_10 1:N:0:\n+CCGTGTATTCTCCCATGCGACAGCAGGACCTCCCATCCCCCTCTGATGTTATCAATCATAAGACGCTTCG\n+>lane1_fakedata0_11 1:N:0:\n+CCGTGTATTCTCCCATGCGACAGCAGGACCTCCCATCCCCCTCTGATGTTATCAATCATAAGACGCTTCG\n+>lane1_fakedata0_12 1:N:0:\n+CCGTGTATTCTCCCATGCGACAGCAGGACCTCCCATCCCCCTCTGATGTTATCAATCATAAGACGCTTCG\n+>lane1_fakedata0_13 1:N:0:\n+CCGTGTATTCTCCCATGCGACAGCAGGACCTCCCATCCCCCTCTGATGTTATCAATCATAAGACGCTTCG\n+>lane1_fakedata0_14 1:N:0:\n+CCGTGTATTCTCCCATGCGACAGCAGGACCTCCCATCCCCCTCTGATGTTATCAATCATAAGACGCTTCG\n+>lane1_fakedata0_15 1:N:0:\n+CCGTGTATTCTCCCATGCGACAGCAGGACATCCCATCCCCCTCTGATGTTATCAATCATAAGACGCTTCG\n+>lane1_fakedata0_16 1:N:0:\n+CCGTGTATTCTCCCATGCGACAGCAGGACCTCCCATCCCCCTCTGATGTTATCAATCATAAGACGCTTCG\n+>lane1_fakedata0_17 1:N:0:\n+CCGTGTATTCTCCCATGCGACAGCAGGACCTCCCATCCCCCTCTGATGTTATCAATCATAAGACGCTTCG\n+>lane1_fakedata0_18 1:N:0:\n+CCGTGTATTCTCCCATGCGACAGCAGGACCTCCCATCCCCCTCTGATGTTATCAATTATAAGACGCTTCG\n+>lane1_fakedata0_19 1:N:0:\n+CCGTGTATTCTCCCATGCGACAGCAGGACCTCCCATCCCCCTCTGATGTTATCAATCATAAGACGCTTCG\n+>lane1_fakedata0_20 1:N:0:\n+CCGTGTATTCTCCCATGCGACAGCAGGACCTCCCATCCCCCTCTGATGTTATCAATCATAAGACGCTTCG\n+>lane1_fakedata0_21 1:N:0:\n+CCGTGTATTCTCCCATGCGACAGCAGGACCTCCCATCCCCCTCTGATGTTATCAATCATAAGACGCTTCG\n+>lane1_fakedata0_22 1:N:0:\n+CCGTGTATTCTCCCATGCGACAGCAGGACCTCCCATCCCCCTCTGATGTTATCAATCATAAGACGCTTCG\n+>lane1_fakedata0_23 1:N:0:\n+CCGTGTATTCTCCCATGCGACAGCAGGACCTCCCATCCCCCTCTGATGTTATCAATCATAAGACGCTTCG\n+>lane1_fakedata0_24 1:N:0:\n+CCGTGTATTCTCCCATGCGACAGCAGGACCTCCCATCCCCCTCTGATGTTATCAATCATAAGACGCTTCG\n+>lane1_fakedata0_25 1:N:0:\n+CCGTGTATTCTCCCATGCGACAGCAGGACCTCCCATCCCCCTCTGATGTTATCAATCATAAGACGCTTCG\n+>lane1_fakedata0_26 1:N:0:\n+CCGTGTATTCTCCCATGCGACAGCAGGACCTCCCATCCCCCTCTGATGTTATCAATCATAAGACGCTTCG\n+>lane1_fakedata0_27 1:N:0:\n+CCGTGTATTCTCCCATGCGACAGCAGGACCTCCCATCCCCCTCTGATGTTATCAATCATAAGACGCTTCG\n+>lane1_fakedata2_0 1:N:0:\n+CCGGTTCACTAAACTCACTCAACGGTTGGCGATATTGGCCGTGAACTCAGGAATGCTATGTAATCCAGTC\n+>lane1_fakedata2_1 1:N:0:\n+CCGGTTCACTAAACTCACTCAACGGTTGGCGATATTGGCCGTGAACTCAGGAATGCTATGTAATCCAGTC\n+>lane1_fakedata2_2 1:N:0:\n+CCGGTTCACTAAACTCACTCAACGGTTGGCGATATTGGCCGTGAACTCAGGAATGCTATGTAATCCAGTC\n+>lane1_fakedata2_3 1:N:0:\n+CCGGTTCACTAAACTCACTCAACGGTTGGCGATATTGGCCGTGAACTCAGGAATGCTATGTAATCCAGTC\n+>lane1_fakedata2_4 1:N:0:\n+CCGGTTCACTAAACTCACTCAACGGTTGGCGATATTGGCCGTGAACTCAGGAATGCTATGTAATCCAGTC\n+>lane1_fakedata2_5 1:N:0:\n+CCGGTTCACTAAACTCACTCAACGGTTGGCGATATTGGCCGTGAACTCAGGAATGCTATGTAATCCAGTC\n+>lane1_fakedata2_6 1:N:0:\n+CCGGTTCACTAAACTCACTCAACGGTTGGCGATATTGGCCGTGAACTCAGGAATGCTATGTAATCCAGTC\n+>lane1_fakedata2_7 1:N:0:\n+CCGGTTCACTAAACTCACTCAACGGTTGGCGATATTGGCCGTGAACTCAGGAATGCTATGTAATCCAGTC\n+>lane1_fakedata2_8 1:N:0:\n+CCGGTTCACTAAACTCACTCAACGGTTGGCGATATTGGCCGTGAACTCAGGAATGCTATGTAATCCAGTC\n+>lane1_fakedata2_9 1:N:0:\n+CCGGTTCACTAAACTCACTCAACGGTTGGCGATATTGGCCGTGAACTCAGGAATGCTATGTAATCCAGTC\n+>lane1_fakedata2_10 1:N:0:\n+CCGGTTCACTAAACTCACTCAACGGTTGGCGATATTGGCCGTGAACTAAGGAATGCTATATAATCCAGTC\n+>lane1_fakedata2_11 1:N:0:\n+CCGGTTCACTAAACTCACTCAACGGTTGGCGATATTGGCCGTGAACTAAGGAATGCTATATAATCCAGTC\n+'..b'TGTGGTAGAGAGAAACTGCT\n+>lane1_fakedata7_8 1:N:0:\n+CCGATCAGCATCAGTAGTTTTCAACGAGCTGGCCCAATGGTGTATAACTATGTGGTAGAGAGAAACTGCT\n+>lane1_fakedata7_9 1:N:0:\n+CCGATCAGCATCAGTAGTTTTCAACGAGCTGGCCCAATGGTGTATAACTATGTGGTAGAGAGAAACTGCT\n+>lane1_fakedata7_10 1:N:0:\n+CCGATCAGCATCAGTAGTTTTCAACGAGCTGGCCCAATGGTGTATAACTATGTGGTAGAGAGAAACTGCT\n+>lane1_fakedata7_11 1:N:0:\n+CCGATCAGCATCAGTAGTTTTCAACGAGCTGGCCCAATGGTGTATAACTATGTGGTAGAGAGAAACTGCT\n+>lane1_fakedata7_12 1:N:0:\n+CCGATCAGCATCAATAGTTTTCAACGAGCTGGCCCAATGGTGTATAACTATGTGGTAGAGAGAAACTGCT\n+>lane1_fakedata7_13 1:N:0:\n+CCGATCAGCATCAGTAGTTTTCAACGAGCTGGCCCAATGGTGTATAACTATGTGGTAGAGAGAAACTGCT\n+>lane1_fakedata7_14 1:N:0:\n+CCGATCAGCATCAGTAGTTTTCAACGAGCTGGCCCAATGGTGTATAACTATGTGGTAGAGAGAAACTGCT\n+>lane1_fakedata7_15 1:N:0:\n+CCGATCAGCATCAGTAGTTTTCAACGAGCTGGCCCAATGGTGTATAACTATGTGGTAGAGAGAAACTGCT\n+>lane1_fakedata7_16 1:N:0:\n+CCGATCAGCATCAGTAGTTTTCAACGAGCTGGCCCAATGGTGTATAACTATGTGGTAGAGAGAAACTGCT\n+>lane1_fakedata7_17 1:N:0:\n+CCGATCAGCATCAGTAGTTTTCAACGAGCTGGCCCAATGGTGTATAACTATGTGGTAGAGAGAAACTGCT\n+>lane1_fakedata8_0 1:N:0:\n+CCGGTGGTATCGGATATGTATATGAATTAACCAAGCGCACCCGGGTTTCTGGCATACCAGTTCCATATAC\n+>lane1_fakedata8_1 1:N:0:\n+CCGGTGGTATCGGATATGTATATGAATTAACCAAGCGCACCCGGGTTTCTGGCATACCAGTTCCATATAC\n+>lane1_fakedata8_2 1:N:0:\n+CCGGTGGTATCGGATATGTATATGAATTAACCAAGCGCACCCGGGTTTCTGGCATACCAGTTCCATATAC\n+>lane1_fakedata8_3 1:N:0:\n+CCGGTGGTATCGGATATGTATATGAATTAACCAAGCGCACCCGGGTTTCTGGCATACCAGTTCCATATAC\n+>lane1_fakedata8_4 1:N:0:\n+CCGGTGGTATCGGATATGTATATGAATTAACCAAGCGCACCCGGGTTTCTGGCATACCAGTTCCATATAC\n+>lane1_fakedata8_5 1:N:0:\n+CCGGTGGTATCGGATATGTATAAGAATTAACCAAGCGCACCCGGGTTTCTAGCATACCAGTTCCATATAC\n+>lane1_fakedata8_6 1:N:0:\n+CCGGTGGTATCGGATATGTATAAGAATTAACCAAGCGCACCCGGGTTTCTAGCATACCAGTTCCATATAC\n+>lane1_fakedata8_7 1:N:0:\n+CCGGTGGTATCGGATATGTATAAGAATTAACCAAGCGCACCCGGGTTTCTAGCATACCAGTTCCATATAC\n+>lane1_fakedata8_8 1:N:0:\n+CCGGTGGTATCGGATATGTATAAGAATTAACCAAGCGCACCCGGGTTTCTAGCATACCAGTTCCATATAC\n+>lane1_fakedata8_9 1:N:0:\n+CCGGTGGTATCGGATATGTATAAGAATTAACCAAGCGCACCCGGGTTTCTAGCATACCAGTTCCATATAC\n+>lane1_fakedata9_0 1:N:0:\n+CCGCGGTTAAAATTGCTCAGTTCCGTCCAAGCAGGTTCTTTCCTCAACCGATGCGATTGGGTTCGCAACA\n+>lane1_fakedata9_1 1:N:0:\n+CCGCGGTTAAAATTGCTCAGTTCCGTCCAAGCAGGTTCTTTCCTCAACCGATGCGATTGGGTTCGCAACA\n+>lane1_fakedata9_2 1:N:0:\n+CCGCGGTTAAAATTGCTCAGTTCCGTCCAAGCAGGTTCTTTCCTCAACCGATGCGATTGGGTTCGCAACA\n+>lane1_fakedata9_3 1:N:0:\n+CCGCGGTTAAAATTGCTCAGTTCCGTCCAAGCAGGTTCTTTCCTCAACCGATGCGATTGGGTTCGCAACA\n+>lane1_fakedata9_4 1:N:0:\n+CCGCGGTTAAAATTGCTCAGTTCCGTCCAAGCAGGTTCTTTCCTCAACCGATGCGATTGGGTTCGCAACA\n+>lane1_fakedata9_5 1:N:0:\n+CCGCGGTTAAAATTGCTCAGTTCCGTCCAAGCAGGTTCTTTCCTCAACCGATGCGATTGGGTTCGCAACA\n+>lane1_fakedata9_6 1:N:0:\n+CCGCGGTTAAAATTGCTCAGTTCCGTCCAAGCAGGTTCTTTCCTCAACCGATGCGATTGGGTTCGCAACA\n+>lane1_fakedata9_7 1:N:0:\n+CCGCGGTTAAAATTGCTCAGTTCCGTCCAAGCAGGTTCTTTCCTCAACCGATGCGATTGGGTTCGCAACA\n+>lane1_fakedata9_8 1:N:0:\n+CCGCGGTTAAAATTGCTCAGTTCCGTCCAAGCAGGTTCTTTCCTCAACCGATGCGATTGGGTTCGCAACA\n+>lane1_fakedata9_9 1:N:0:\n+CCGCGGTTAAAATTGCTCAGTTCCGTCCAAGCAGGTTCTTTCCTCAACCGATGCGATTGGGTTCGCAACA\n+>lane1_fakedata9_10 1:N:0:\n+CCGCGGTTAAAATTGCTCAGTTCCGTCCAAGCAGGTTCTTTCCTCAACCGATGCGATTGGGTTCGCAACA\n+>lane1_fakedata9_11 1:N:0:\n+CCGCGGTTAAAATTGCTCAGTTCCGTCCAAGCAGGTTCTTTCCTCAACCGATGCGATTGGGTTCGCAACA\n+>lane1_fakedata9_12 1:N:0:\n+CCGCGGTTAAAATTGCTCAGTTCCGTCCAAGCAGGTTCTTTCCTCAACCGATGCGATTGGGTTCGCAACA\n+>lane1_fakedata9_13 1:N:0:\n+CCGCGGTTAAAATTGCTCAGTTCCGTCCAAGCAGGTTCTTTCCTCAACCGATGCGATTGGGTTCGCAACA\n+>lane1_fakedata9_14 1:N:0:\n+CCGCGGTTAAAATTGCTCAGTTCCGTCCAAGCAGGTTCTTTCCTCAACCGATGCGATTGGGTTCGCAACA\n+>lane1_fakedata9_15 1:N:0:\n+CCGCGGTTAAAATTGCTCAGTTCCGTCCAAGCAGGTTCTTTCCTCAACCGATGCGATTGGGTTCGCAACA\n+>lane1_fakedata9_16 1:N:0:\n+CCGCGGTTAAAATTGCTCAGTTCCGTCCAAGCAGGTTCTTTCCTCAACCGATGCGATTGGGTTCGCAACA\n+>lane1_fakedata9_17 1:N:0:\n+CCGCGGTTAAAATTGCTCAGTTCCGTCCAAGCAGGTTCTTTCCTCAACCGATGCGATTGGGTTCGCAACA\n+>lane1_fakedata9_18 1:N:0:\n+CCGCGGTTAAAATTGCTCAGTTCCGTCCAAGCAGGTTCTTTCCTCAACCGATGCGATTGGGTTCGCAACA\n+>lane1_fakedata9_19 1:N:0:\n+CCGCGGTTAAAATTGCTCAGTTCCGTGCAAGCAGGTTCTTTCCTCAACCGATGCGATTGGGTTCGCAACA\n' |
| b |
| diff -r 000000000000 -r b2e3553e1be2 test-data/demultiplexed/PopA_01.2.fa.gz |
| b |
| Binary file test-data/demultiplexed/PopA_01.2.fa.gz has changed |
| b |
| diff -r 000000000000 -r b2e3553e1be2 test-data/demultiplexed/PopA_01.2.fq --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/demultiplexed/PopA_01.2.fq Mon Jul 01 10:58:28 2019 -0400 |
| b |
| b'@@ -0,0 +1,264 @@\n+@lane1_fakedata0_0 1:N:0:/2\n+CCGTGTATTCTCCCATGCGACAGCAGGACCTCCCATCCCCCTCTGATGTTATCAATCATAAGACGCTTCGATGGGCCTAGGTCTGTGGATTGCTCGTCGT\n++\n+BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB\n+@lane1_fakedata0_1 1:N:0:/2\n+CCGTGTATTCTCCCATGCGACAGCAGGACCTCCCATCCCCCTCTGATGTTATCAATCATAAGACGCTTCGATGGGCCTAGGTCTGTGGATTGCTCGTCGT\n++\n+BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB\n+@lane1_fakedata0_2 1:N:0:/2\n+CCGTGTATTCTCCCATGCGACAGCAGGACCTCCCATCCCCCTCTGATGTTATCAATCATAAGACGCTTCGATGGGCCTAGGTCTGTGGATTGCTCGTCGT\n++\n+BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB\n+@lane1_fakedata0_3 1:N:0:/2\n+CCGTGTATTCTCCCATGCGACAGCAGGACCTCCCATCCCCCTCTGATGTTATCAATCATAAGACGCTTCGATGGGCCTAGGTCTGTGGATTGCTCGTCGT\n++\n+BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB\n+@lane1_fakedata0_4 1:N:0:/2\n+CCGTGTATTCTCCCATGCGACAGCAGGACCTCCCATCCCCCTCTGATGTTATCAATCATAAGACGCTTCGATGGGCCTAGGTCTGTGGATTGCTCGTCGT\n++\n+BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB\n+@lane1_fakedata0_5 1:N:0:/2\n+CCGTGTATTCTCCCATGCGACAGCAGGACCTCCCATCCCCCTCTGATGTTATCAATCATAAGACGCTTCGATGGGCCTAGGTCTGTGGATTGCTCGTCGT\n++\n+BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB\n+@lane1_fakedata0_6 1:N:0:/2\n+CCGTGTATTCTCCCATGCGACAGCAGGACCTCCCATCCCCCTCTGATGTTATCAATCATAAGACGCTTCGATGGGCCTAGGTCTGTGGATTGCTCGTCGT\n++\n+BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB\n+@lane1_fakedata0_7 1:N:0:/2\n+CCGTGTATTCTCCCATGCGACAGCAGGACCTCCCATCCCCCTCTGATGTTATCAATCATAAGACGCTTCGATGGGCCTAGGTCTGTGGATTGCTCGTCGT\n++\n+BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB\n+@lane1_fakedata0_8 1:N:0:/2\n+CCGTGTATTCTCCCATGCGACAGCAGGACCTCCCATCCCCCTCTGATGTTATCAATCATAAGACGCTTCGATGGGCCTAGGTCTGTGGATTGCTCGTCGT\n++\n+BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB\n+@lane1_fakedata0_9 1:N:0:/2\n+CCGTGTATTCTCCCATGCGACAGCAGGACCTCCCATCCCCCTCTGATGTTATCAATCATAAGACGCTTCGATGGGCCTAGGTCTGTGGATTGCTCGTCGT\n++\n+BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB\n+@lane1_fakedata0_10 1:N:0:/2\n+CCGTGTATTCTCCCATGCGACAGCAGGACCTCCCATCCCCCTCTGATGTTATCAATCATAAGACGCTTCGATGGGCCTAGGTCTGTGGATTGCTCGTCGT\n++\n+BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB\n+@lane1_fakedata0_11 1:N:0:/2\n+CCGTGTATTCTCCCATGCGACAGCAGGACCTCCCATCCCCCTCTGATGTTATCAATCATAAGACGCTTCGATGGGCCTAGGTCTGTGGATTGCTCGTCGT\n++\n+BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB\n+@lane1_fakedata0_12 1:N:0:/2\n+CCGTGTATTCTCCCATGCGACAGCAGGACCTCCCATCCCCCTCTGATGTTATCAATCATAAGACGCTTCGATGGGCCTAGGTCTGTGGATTGCTCGTCGT\n++\n+BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB\n+@lane1_fakedata0_13 1:N:0:/2\n+CCGTGTATTCTCCCATGCGACAGCAGGACCTCCCATCCCCCTCTGATGTTATCAATCATAAGACGCTTCGATGGGCCTAGGTCTGTGGATTGCTCGTCGT\n++\n+BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB\n+@lane1_fakedata0_14 1:N:0:/2\n+CCGTGTATTCTCCCATGCGACAGCAGGACCTCCCATCCCCCTCTGATGTTATCAATCATAAGACGCTTCGATGGGCCTAGGTCTGTGGATTGCTCGTCGT\n++\n+BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB\n+@lane1_fakedata0_15 1:N:0:/2\n+CCGTGTATTCTCCCATGCGACAGCAGGACATCCCATCCCCCTCTGATGTTATCAATCATAAGACGCTTCGATGGGCCTAGGTCTGTGGATTGCTCGTCGT\n++\n+BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB\n+@lane1_fakedata0_16 1:N:0:/2\n+CCGTGTATTCTCCCATGCGACAGCAGGACCTCCCATCCCCCTCTGATGTTATCAATCATAAGACGCTTCGATGGGCCTAGGTCTGTGGATTGCTCGTCGT\n++\n+BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB'..b':N:0:/2\n+CCGATCAGCATCAGTAGTTTTCAACGAGCTGGCCCAATGGTGTATAACTATGTGGTAGAGAGAAACTGCTGCTATCACTCACGATATAAGCCCTCTGACG\n++\n+BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB\n+@lane1_fakedata7_2 1:N:0:/2\n+CCGATCAGCATCAGTAGTTTTCAACGAGCTGGCCCAATGGTGTATAACTATGTGGTAGAGAGAAACTGCTGCTATCACTCACGATATAAGCCCTCTGACG\n++\n+BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB\n+@lane1_fakedata7_3 1:N:0:/2\n+CCGATCAGCATCAGTAGTTTTCAACGAGCTGGCCCAATGGTGTATAACTATGTGGTAGAGAGAAACTGCTGCTATCACTCACGATATAAGCCCTCTGACG\n++\n+BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB\n+@lane1_fakedata7_4 1:N:0:/2\n+CCGATCAGCATCAGTAGTTTTCAACGAGCTGGCCCAATGGTGTATAACTATGTGGTAGAGAGAAACTGCTGCTATCACTCACGATATAAGCCCTCTGACG\n++\n+BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB\n+@lane1_fakedata7_5 1:N:0:/2\n+CCGATCAGCATCAGTAGTTTTCAACGAGCTGGCCCAATGGTGTATAACTATGTGGTAGAGAGAAACTGCTGCTATCACTCACGATATAAGCCCTCTGACG\n++\n+BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB\n+@lane1_fakedata7_6 1:N:0:/2\n+CCGATCAGCATCAGTAGTTTTCAACGAGCTGGCCCAATGGTGTATAACTATGTGGTAGAGAGAAACTGCTGCTATCACTCACGATATAAGCCCTCTGACG\n++\n+BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB\n+@lane1_fakedata7_7 1:N:0:/2\n+CCGATCAGCATCAGTAGTTTTCAACGAGCTGGCCCAATGGTGTATAACTATGTGGTAGAGAGAAACTGCTGCTATCACTCACGATATAAGCCCTCTGACG\n++\n+BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB\n+@lane1_fakedata7_8 1:N:0:/2\n+CCGATCAGCATCAGTAGTTTTCAACGAGCTGGCCCAATGGTGTATAACTATGTGGTAGAGAGAAACTGCTGCTATCACTCACGATATAAGCCCTCTGACG\n++\n+BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB\n+@lane1_fakedata7_9 1:N:0:/2\n+CCGATCAGCATCAGTAGTTTTCAACGAGCTGGCCCAATGGTGTATAACTATGTGGTAGAGAGAAACTGCTGCTATCACTCACGATATAAGCCCTCTGACG\n++\n+BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB\n+@lane1_fakedata7_10 1:N:0:/2\n+CCGATCAGCATCAGTAGTTTTCAACGAGCTGGCCCAATGGTGTATAACTATGTGGTAGAGAGAAACTGCTGCTATCACTCACGATATAAGCCCTCTGACG\n++\n+BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB\n+@lane1_fakedata7_11 1:N:0:/2\n+CCGATCAGCATCAGTAGTTTTCAACGAGCTGGCCCAATGGTGTATAACTATGTGGTAGAGAGAAACTGCTGCTATCACTCACGATATAAGCCCTCTGACG\n++\n+BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB\n+@lane1_fakedata7_12 1:N:0:/2\n+CCGATCAGCATCAATAGTTTTCAACGAGCTGGCCCAATGGTGTATAACTATGTGGTAGAGAGAAACTGCTGCTATCACTCACGATATAAGCCCTCTGACG\n++\n+BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB\n+@lane1_fakedata7_13 1:N:0:/2\n+CCGATCAGCATCAGTAGTTTTCAACGAGCTGGCCCAATGGTGTATAACTATGTGGTAGAGAGAAACTGCTGCTATCACTCACGATATAAGCCCTCTGACG\n++\n+BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB\n+@lane1_fakedata7_14 1:N:0:/2\n+CCGATCAGCATCAGTAGTTTTCAACGAGCTGGCCCAATGGTGTATAACTATGTGGTAGAGAGAAACTGCTGCTATCACTCACGATATAAGCCCTCTGACG\n++\n+BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB\n+@lane1_fakedata7_15 1:N:0:/2\n+CCGATCAGCATCAGTAGTTTTCAACGAGCTGGCCCAATGGTGTATAACTATGTGGTAGAGAGAAACTGCTGCTATCACTCACGATATAAGCCCTCTGACG\n++\n+BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB\n+@lane1_fakedata7_16 1:N:0:/2\n+CCGATCAGCATCAGTAGTTTTCAACGAGCTGGCCCAATGGTGTATAACTATGTGGTAGAGAGAAACTGCTGCTATCACTCACGATATAAGCCCTCTGACG\n++\n+BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB\n+@lane1_fakedata7_17 1:N:0:/2\n+CCGATCAGCATCAGTAGTTTTCAACGAGCTGGCCCAATGGTGTATAACTATGTGGTAGAGAGAAACTGCTGCTATCACTCACGATATAAGCCCTCTGACG\n++\n+BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB\n' |
| b |
| diff -r 000000000000 -r b2e3553e1be2 test-data/demultiplexed/PopA_01.fq --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/demultiplexed/PopA_01.fq Mon Jul 01 10:58:28 2019 -0400 |
| b |
| b'@@ -0,0 +1,264 @@\n+@lane1_fakedata0_0 1:N:0:/1\n+AATTCGGCTTGCAACGCAAGTGACGATTCCCACGGACATAACTGATCTAAGTAACTTCCAAATCTGGGAATGGGATTTCATAATTAAGGACTAT\n++\n+BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB\n+@lane1_fakedata0_1 1:N:0:/1\n+AATTCGGCTTGCAACGCAAGTGACGATTCCCACGGACATAACTGATCTAAGTAACTTCCAAATCTGGGAATGGGATTTCATAATTAAGGACTAT\n++\n+BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB\n+@lane1_fakedata0_2 1:N:0:/1\n+AATTCGGCTTGCAACGCAAGTGACGATTCCCACGGACATAACTGATCTAAGTAACTTCCAAATCTGGGAATGGGATTTCATAATTAAGGACTAT\n++\n+BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB\n+@lane1_fakedata0_3 1:N:0:/1\n+AATTCGGCTTGCAACGCAAGTGACGATTCCCACGGACATAACTGATCTAAGTAACTTCCAAATCTGGGAATGGGATTTCATAATTAAGGACTAT\n++\n+BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB\n+@lane1_fakedata0_4 1:N:0:/1\n+AATTCGGCTTGCAACGCAAGTGACGATTCCCACGGACATAACTGATCTAAGTAACTTCCAAATCTGGGAATGGGATTTCATAATTAAGGACTAT\n++\n+BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB\n+@lane1_fakedata0_5 1:N:0:/1\n+AATTCGGCTTGCAACGCAAGTGACGATTCCCACGGACATAACTGATCTAAGTAACTTCCAAATCTGGGAATGGGATTTCATAATTAAGGACTAT\n++\n+BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB\n+@lane1_fakedata0_6 1:N:0:/1\n+AATTCGGCTTGCAACGCAAGTGACGATTCCCACGGACATAACTGATCTAAGTAACTTCCAAATCTGGGAATGGGATTTCATAATTAAGGACTAT\n++\n+BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB\n+@lane1_fakedata0_7 1:N:0:/1\n+AATTCGGCTTGCAACGCAAGTGACGATTCCCACGGACATAACTGATCTAAGTAACTTCCAAATCTGGGAATGGGATTTCATAATTAAGGACTAT\n++\n+BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB\n+@lane1_fakedata0_8 1:N:0:/1\n+AATTCGGCTTGCAACGCAAGTGACGATTCCCACGGACATAACTGATCTAAGTAACTTCCAAATCTGGGAATGGGATTTCATAATTAAGGACTAT\n++\n+BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB\n+@lane1_fakedata0_9 1:N:0:/1\n+AATTCGGCTTGCAACGCAAGTGACGATTCCCACGGACATAACTGATCTAAGTAACTTCCAAATCTGGGAATGGGATTTCATAATTAAGGACTAT\n++\n+BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB\n+@lane1_fakedata0_10 1:N:0:/1\n+AATTCGGCTTGCAACGCAAGTGACGATTCCCACGGACATAACTGATCTAAGTAACTTCCAAATCTGGGAATGGGATTTCATAATTAAGGACTAT\n++\n+BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB\n+@lane1_fakedata0_11 1:N:0:/1\n+AATTCGGCTTGCAACGCAAGTGACGATTCCCACGGACATAACTGATCTAAGTAACTTCCAAATCTGGGAATGGGATTTCATAATTAAGGACTAT\n++\n+BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB\n+@lane1_fakedata0_12 1:N:0:/1\n+AATTCGGCTTGCAACGCAAGTGACGATTCCCACGGACATAACTGATCTAAGTAACTTCCAAATCTGGGAATGGGATTTCATAATTAAGGACTAT\n++\n+BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB\n+@lane1_fakedata0_13 1:N:0:/1\n+AATTCGGCTTGCAACGCAAGTGACGATTCCCACGGACATAACTGATCTAAGTAACTTCCAAATCTGGGAATGGGATTTCATAATTAAGGACTAT\n++\n+BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB\n+@lane1_fakedata0_14 1:N:0:/1\n+AATTCGGCTTGCAACGCAAGTGACGATTCCCACGGACATAACTGATCTAAGTAACTTCCAAATCTGGGAATGGGATTTCATAATTAAGGACTAT\n++\n+BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB\n+@lane1_fakedata0_15 1:N:0:/1\n+AATTCGGCTTGCAACGCAAGTGACGATTCCCACGGACATAACTGATCTAAGTAACTTCCAAGTCTGGGAATGGGATTTCATAATTAAGGACTAT\n++\n+BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB\n+@lane1_fakedata0_16 1:N:0:/1\n+AATTCGGCTTGCAACGCAAGTGACGATTCCCACGGACATAACTGATCTAAGTAACTTCCAAATCTGGGAATGGGATTTCATAATTAAGGACTAT\n++\n+BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB\n+@lane1_fakedata0_17 1:N:0:/1\n+AATTCGGCTTGCAACGCAAGTGACGATTCCCACGGACATAACTGATCTAAGTAACTTCCAAATCTGGGAATGGGATTTCATAATTAAGGACTAT\n++\n+BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB'..b'TGCTTCAGGAATCTCTCGTATACTCTGAGTATGTGCGTACGTACGCTATTTAGATGGATAACCGACGCTGCCAGACGAGAGAC\n++\n+BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB\n+@lane1_fakedata7_1 1:N:0:/1\n+AATTCGTTTGCTGCTTCAGGAATCTCTCGTATACTCTGAGTATGTGCGTACGTACGCTATTTAGATGGATAACCGACGCTGCCAGACGAGAGAC\n++\n+BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB\n+@lane1_fakedata7_2 1:N:0:/1\n+AATTCGTTTGCTGCTTCAGGAATCTCTCGTATACTCTGAGTATGTGCGTACGTACGCTATTTAGATGGATAACCGACGCTGCCAGACGAGAGAC\n++\n+BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB\n+@lane1_fakedata7_3 1:N:0:/1\n+AATTCGTTTGCTGCTTCAGGAATCTCTCGTATACTCTGAGTATGTGCGTACGTACGCTATTTAGATGGATAACCGACGCTGCCAGACGAGAGAC\n++\n+BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB\n+@lane1_fakedata7_4 1:N:0:/1\n+AATTCGTTTGCTGCTTCAGGAATCTCTCGTATACTCTGAGTATGTGCGTACGTACGCTATTTAGATGGATAACCGACGCTGCCAGACGAGAGAC\n++\n+BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB\n+@lane1_fakedata7_5 1:N:0:/1\n+AATTCGTTTGCTGCTTCAGGAATCTCTCGTATACTCTGAGTATGTGCGTACGTACGCTATTTAGATGGATAACCGACGCTGCCAGACGAGAGAC\n++\n+BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB\n+@lane1_fakedata7_6 1:N:0:/1\n+AATTCGTTTGCTGCTTCAGGAATCTCTCGTATACTCTGAGTATGTGCGTACGTACGCTATTTAGATGGATAACCGACGCTGCCAGACGAGAGAC\n++\n+BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB\n+@lane1_fakedata7_7 1:N:0:/1\n+AATTCGTTTGCTGCTTCAGGAATCTCTCGTATACTCTGAGTATGTGCGTACGTACGCTATTTAGATGGATAACCGACGCTGCCAGACGAGAGAC\n++\n+BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB\n+@lane1_fakedata7_8 1:N:0:/1\n+AATTCGTTTGCTGCTTCAGGAATCTCTCGTATACTCTGAGTATGTGCGTACGTACGCTATTTAGATGGATAACCGACGCTGCCAGACGAGAGAC\n++\n+BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB\n+@lane1_fakedata7_9 1:N:0:/1\n+AATTCGTTTGCTGCTTCAGGAATCTCTCGTATAATCTGAGTATGTGCGTACGTACGCTATTTAGATGGATAACCGACGCTGCCAGACGCGAGAC\n++\n+BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB\n+@lane1_fakedata7_10 1:N:0:/1\n+AATTCGTTTGCTGCTTCAGGAATCTCTCGTATAATCTGAGTATGTGCGTACGTACGCTATTTAGATGGATAACCGACGCTGCCAGACGCGAGAC\n++\n+BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB\n+@lane1_fakedata7_11 1:N:0:/1\n+AATTCGTTTGCTGCTTCAGGAATCTCTCGTATAATCTGAGTATGTGCGTACGTACGCTATTTAGATGGATAACCGACGCTGCCAGACGCGAGAC\n++\n+BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB\n+@lane1_fakedata7_12 1:N:0:/1\n+AATTCGTTTGCTGCTTCAGGAATCTCTCGTATAATCTGAGTATGTGCGTACGTACGCTATTTAGATGGATAACCGACGCTGCCAGACGCGAGAC\n++\n+BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB\n+@lane1_fakedata7_13 1:N:0:/1\n+AATTCGTTTGCTGCTTCAGGAATCTCTCGTATAATCTGAGTATGTGCGTACGTACGCTATTTAGATGGATAACCGACGCTGCCAGACGCGAGAC\n++\n+BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB\n+@lane1_fakedata7_14 1:N:0:/1\n+AATTCGTTTGCTGCTTCAGGAATCTCTCGTATAATCTGAGTATGTGCGTACGTACGCTATTTAGATGGATAACCGACGCTGCCAGACGCGAGAC\n++\n+BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB\n+@lane1_fakedata7_15 1:N:0:/1\n+AATTCGTTTGCTGCTTCAGGAATCTCTCGTATAATCTGAGTATGTGCGTACGTACGCTATTTAGATGGATAACCGACGCTGCCAGACGCGAGAC\n++\n+BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB\n+@lane1_fakedata7_16 1:N:0:/1\n+AATTCGTTTGCTGCTTCAGGAATCTCTCGTATAATCTGAGTATGTGCGTACGTACGCTATTTAGATGGATAACCGACGCTGCCAGACGCGAGAC\n++\n+BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB\n+@lane1_fakedata7_17 1:N:0:/1\n+AATTCGTTTGCTGCTTCAGGAATCTCTCGTATAATCTGAGTATGTGCGTACGTACGCTATTTAGATGGATAACCGACGCTGCCAGACGCGAGAC\n++\n+BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB\n' |
| b |
| diff -r 000000000000 -r b2e3553e1be2 test-data/demultiplexed/PopA_01.rem.1.fa.gz |
| b |
| Binary file test-data/demultiplexed/PopA_01.rem.1.fa.gz has changed |
| b |
| diff -r 000000000000 -r b2e3553e1be2 test-data/demultiplexed/PopA_01.rem.2.fa.gz |
| b |
| Binary file test-data/demultiplexed/PopA_01.rem.2.fa.gz has changed |
| b |
| diff -r 000000000000 -r b2e3553e1be2 test-data/demultiplexed/PopA_02.1.fq --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/demultiplexed/PopA_02.1.fq Mon Jul 01 10:58:28 2019 -0400 |
| b |
| b'@@ -0,0 +1,240 @@\n+@lane1_fakedata0_0 1:N:0:/1\n+AATTCGGCTTGCAACGCAAGTGACGATTCCCACGGACATAACTGATCTAAGTAACTTCCAAATCTGGGAATGGGATTTCATAATTAAGGACTAT\n++\n+BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB\n+@lane1_fakedata0_1 1:N:0:/1\n+AATTCGGCTTGCAACGCAAGTGACGATTCCCACGGACATAACTGATCTAAGTAACTTCCAAATCTGGGAATGGGATTTCATAATTAAGGACTAT\n++\n+BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB\n+@lane1_fakedata0_2 1:N:0:/1\n+AATTCGGCTTGCAACGCAAGTGACGATTCCCACGGACATAACTGATCTAAGTAACTTCCAAATCTGGGAATGGGATTTCATAATTAAGGACTAT\n++\n+BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB\n+@lane1_fakedata0_3 1:N:0:/1\n+AATTCGGCTTGCAACGCAAGTGACGATTCCCACGGACATAACTGATCTAAGTAACTTCCAAATCTGGGAATGGGATTTCATAATTAAGGACTAT\n++\n+BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB\n+@lane1_fakedata0_4 1:N:0:/1\n+AATTCGGCTTGCAACGCAAGTGACGATTCCCACGGACATAACTGATCTAAGTAACTTCCAAATCTGGGAATGGGATTTCATAATTAAGGACTAT\n++\n+BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB\n+@lane1_fakedata0_5 1:N:0:/1\n+AATTCGGCTTGCAACGCAAGTGACGATTCCCACGGACATAACTGATCTAAGTAACTTCCAAATCTGGGAATGGGATTTCATAATTAAGGACTAT\n++\n+BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB\n+@lane1_fakedata0_6 1:N:0:/1\n+AATTCGGCTTGCAACGCAAGTGACGATTCCCACGGACATAACTGATCTAAGTAACTTCCAAATCTGGGAATGGGATTTCATAATTAAGGACTAT\n++\n+BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB\n+@lane1_fakedata0_7 1:N:0:/1\n+AATTCGGCTTGCAACGCAAGTGACGATTCCCACGGACATAACTGATCTAAGTAACTTCCAAATCTGGGAATGGGATTTCATAATTAAGGACTAT\n++\n+BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB\n+@lane1_fakedata0_8 1:N:0:/1\n+AATTCGGCTTGCAACGCAAGTGACGATTCCCACGGACATAACTGATCTAAGTAACTTCCAAATCTGGGAATGGGATTTCATAATTAAGGACTAT\n++\n+BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB\n+@lane1_fakedata0_9 1:N:0:/1\n+AATTCGGCTTGCAACGCAAGTGACGATTCCCACGGACATAACTGATCTAAGTAACTTCCAAATCTGGGAATGGGATTTCATAATTAAGGACTAT\n++\n+BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB\n+@lane1_fakedata0_10 1:N:0:/1\n+AATTCGGCTTGCAACGCAAGTGACGATTCCCACGGACATAACTGATCTAAGTAACTTCCAAATCTGGGAATGGGATTTCATAATTAAGGACTAT\n++\n+BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB\n+@lane1_fakedata0_11 1:N:0:/1\n+AATTCGGCTTGCAACGCAAGTGACGATTCCCACGGACATAACTGATCTAAGTAACTTCCAAATCTGGGAATGGGATTTCATAATTAAGGACTAT\n++\n+BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB\n+@lane1_fakedata0_12 1:N:0:/1\n+AATTCGGCTTGCAACGCAAGTGACGATTCCCACGGACATAACTGATCTAAGTAACTTCCAAATCTGGGAATGGGATTTCATAATTAAGGACTAT\n++\n+BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB\n+@lane1_fakedata0_13 1:N:0:/1\n+AATTCGGCTTGCAACGCAAGTGACGATTCCCACGGACATAACTGATCTAAGTAACTTCCAAATCTGGGAATGGGATTTCATAATTAAGGACTAT\n++\n+BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB\n+@lane1_fakedata0_14 1:N:0:/1\n+AATTCGGCTTGCAACGCAAGTGACGATTCCCACGGACATAACTGATCTAAGTAACTTCCAAATCTGGGAATGGGATTTCATAATTAAGGACTAT\n++\n+BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB\n+@lane1_fakedata0_15 1:N:0:/1\n+AATTCGGCTTGCAACGCAAGTGACGATTCCCACGGACATAACTGATCTAAGTAACTTCCAAATCTGGGAATGGGATTTCATAATTAAGGACTAT\n++\n+BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB\n+@lane1_fakedata0_16 1:N:0:/1\n+AATTCGGCTTGCAACGCAAGTGACGATTCCCACGGACATAACTGATCTAAGTAACTTCCAAATCTGGGAATGGGATTTCATAATTAAGGACTAT\n++\n+BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB\n+@lane1_fakedata0_17 1:N:0:/1\n+AATTCGGCTTGCAACGCAAGTGACGATTCCCACGGACATAACTGATCTAAGTAACTTCCAAATCTGGGAATGGGATTTCATAATTAAGGACTAT\n++\n+BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB'..b'ACCACAGCATCAATTCTAAAAATGACTACCAGAGAGACAACTCCGCAGTTAAACACTCTGACTGCCACGCCAGCTACCTCTAGA\n++\n+BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB\n+@lane1_fakedata2_15 1:N:0:/1\n+AATTCTCTACACCACAGCATCAATTCTAAAAATGACTACCAGAGAGACAACTCCGCAGTTAAACACTCTGACTGCCACGCCAGCTACCTCTAGA\n++\n+BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB\n+@lane1_fakedata2_16 1:N:0:/1\n+AATTCTCTACACCACAGCATCAATTCTAAAAATGACTACCAGAGAGACAACTCCGCAGTTAAACACTCTGACTGCCACGCCAGCTACCTCTAGA\n++\n+BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB\n+@lane1_fakedata2_17 1:N:0:/1\n+AATTCTCTACACCACAGCATCAATTCTAAAAATGACTACCAGAGAGACAACTCCGCAGTTAAACACTCTGACTGCCACGCCAGCTACCTCTAGA\n++\n+BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB\n+@lane1_fakedata2_18 1:N:0:/1\n+AATTCTCTACACCACAGCATCAATTCTAAAAATGACTACCAGAGAGACAACTCCGCAGTTAAACACTCTGACTGCCACGCCAGCTACCTCTAGA\n++\n+BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB\n+@lane1_fakedata2_19 1:N:0:/1\n+AATTCTCTACACCACAGCATCAATTCTAAAAATGACTACCAGAGAGACAACTCCGCAGTTAAACACTCTGACTGCCACGCCAGCTACCTCTAGA\n++\n+BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB\n+@lane1_fakedata7_0 1:N:0:/1\n+AATTCGTTTGCTGCTTCAGGAATCTCTCGTATAATCTGAGTATGTGCGTACGTACGCTATTTAGATGGATAACCGACGCTGCCAGACGCGAGAC\n++\n+BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB\n+@lane1_fakedata7_1 1:N:0:/1\n+AATTCGTTTGCTGCTTCAGGAATCTCTCGTATAATCTGAGTATGTGCGTACGTACGCTATTTAGATGGATAACCGACGCTGCCAGACGCGAGAC\n++\n+BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB\n+@lane1_fakedata7_2 1:N:0:/1\n+AATTCGTTTGCTGCTTCAGGAATCTCTCGTATAATCTGAGTATGTGCGTACGTACGCTATTTAGATGGATAACCGACGCTGCCAGACGCGAGAC\n++\n+BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB\n+@lane1_fakedata7_3 1:N:0:/1\n+AATTCGTTTGCTGCTTCAGGAATCTCTCGTATAATCTGAGTATGTGCGTACGTACGCTATTTAGATGGATAACCGACGCTGCCAGACGCGAGAC\n++\n+BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB\n+@lane1_fakedata7_4 1:N:0:/1\n+AATTCGTTTGCTGCTTCAGGAATCTCTCGTATAATCTGAGTATGTGCGTACGTACGCTATTTAGATGGATAACCGACGCTGCCAGACGCGAGAC\n++\n+BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB\n+@lane1_fakedata7_5 1:N:0:/1\n+AATTCGTTTGCTGCTTCAGGAATCTCTCGTATAATCTGAGTATGTGCGTACGTACGCTATTTAGATGGATAACCGACGCTGCCAGACGCGAGAC\n++\n+BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB\n+@lane1_fakedata7_6 1:N:0:/1\n+AATTCGTTTGCTGCTTCAGGAACCTCTCGTATACTCTGAGTATGTGCGTACGTACGCTATTTAGATGGATAACCGACGCTGCCAGACGAGAGAC\n++\n+BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB\n+@lane1_fakedata7_7 1:N:0:/1\n+AATTCGTTTGCTGCTTCAGGAATCTCTCGTATACTCTGAGTATGTGCGTACGTACGCTATTTAGATGGATAACCGACGCTGCCAGACGAGAGAC\n++\n+BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB\n+@lane1_fakedata7_8 1:N:0:/1\n+AATTCGTTTGCTGCTTCAGGAATCTCTCGTATACTCTGAGTATGTGCGTACGTACGCTATTTAGATGGATAACCGACGCTGCCAGACGAGAGAC\n++\n+BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB\n+@lane1_fakedata7_9 1:N:0:/1\n+AATTCGTTTGCTGCTTCAGGAATCTCTCGTATACTCTGAGTATGTGCGTACGTACGCTATTTAGATGGATAACCGACGCTGCCAGACGAGAGAC\n++\n+BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB\n+@lane1_fakedata7_10 1:N:0:/1\n+AATTCGTTTGCTGCTTCAGGAATCTTTCGTATACTCTGAGTATGTGCGTACGTACGCTATTTAGATGGATAACCGACGCTGCCAGACGAGAGAC\n++\n+BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB\n+@lane1_fakedata7_11 1:N:0:/1\n+AATTCGTTTGCTGCTTCAGGAATCTCTCGTATACTCTGAGTATGTGCGTACGTACGCTATTTAGATGGATAACCGACGCTGCCAGACGAGAGAC\n++\n+BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB\n' |
| b |
| diff -r 000000000000 -r b2e3553e1be2 test-data/demultiplexed/PopA_02.2.fq --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/demultiplexed/PopA_02.2.fq Mon Jul 01 10:58:28 2019 -0400 |
| b |
| b'@@ -0,0 +1,240 @@\n+@lane1_fakedata0_0 1:N:0:/2\n+CCGTATTCTCCCATGCGACAGTAGGACCTCCGCATCCCCCTTTGATGTTATCAATCATAAGACGCTTCGATGGGCCTAGGTCTGTGGATTGCTCGTCGTA\n++\n+BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB\n+@lane1_fakedata0_1 1:N:0:/2\n+CCGTATTCTCCCATGCGACAGTAGGACCTCCGCATCCCCCTTTGATGTTATCAATCATAAGACGCTTCGATGGGCCTAAGTCTGTGGATTGCTCGTCGTA\n++\n+BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB\n+@lane1_fakedata0_2 1:N:0:/2\n+CCGTATTCTCCCATGCGACAGTAGGACCTCCGCATCCCCCTTTGATGTTATCAATCATAAGACGCTTCGATGGGCCTAGGTCTGTGGATTGCTCGTCGTA\n++\n+BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB\n+@lane1_fakedata0_3 1:N:0:/2\n+CCGTATTCTCCCATGCGACAGTAGGACCTCCGCATCCCCCTTTGATGTTATCAATCATAAGACGCTTCGATGGGCCTAGGTCTGTGGATTGCTCGTCGTA\n++\n+BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB\n+@lane1_fakedata0_4 1:N:0:/2\n+CCGTACTCTCCCATGCGACAGTAGGACCTCCGCATCCCCCTTTGATGTTATCAATCATAAGACGCTTCGATGGGCCTAGGTCTGTGGATTGCTCGTCGTA\n++\n+BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB\n+@lane1_fakedata0_5 1:N:0:/2\n+CCGTATTCTCCCATGCGACAGTAGGACCTCCGCATCCCCCTTTGATGTTATCAATCATAAGACGCTTCGATGGGCCTAGGTCTGTGGATTGCTCGTCGTA\n++\n+BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB\n+@lane1_fakedata0_6 1:N:0:/2\n+CCGTATTCTCCCATGCGACAGTAGGACCTCCGCATCCCCCTTTGATGTTATCAATCATAAGACGCTTCGATGGGCCTAGGTCTGTGGATTGCTCGTCGTA\n++\n+BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB\n+@lane1_fakedata0_7 1:N:0:/2\n+CCGTATTCTCCCATGCGACAGTAGGACCTCCGCATCCCCCTTTGATGTTATCAATCATAAGACGCTTCGATGGGCCTAGGTCTGTGGATTGCTCGTCGTA\n++\n+BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB\n+@lane1_fakedata0_8 1:N:0:/2\n+CCGTATTCTCCCATGCGACAGTAGGACCTCCGCATCCCCCTTTGATGTTATCAATCATAAGACGCTTCGATGGGCCTAGGTCTGTGGATTGCTCGTCGTA\n++\n+BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB\n+@lane1_fakedata0_9 1:N:0:/2\n+CCGTATTCTCCCATGCGACAGTAGGACCTCCGCATCCCCCTTTGATGTTATCAATCATAAGACGCTTCGATGGGCCTAGGTCTGTGGATTGCTCGTCGTA\n++\n+BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB\n+@lane1_fakedata0_10 1:N:0:/2\n+CCGTATTCTCCCATGCGACAGTAGGACCTCCGCATCCCCCTTTGATGTTATCAATCATAAGACGCTTCGATGGGCCTAGGTCTGTGGATTGCTCGTCGTA\n++\n+BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB\n+@lane1_fakedata0_11 1:N:0:/2\n+CCGTATTCTCCCATGCGACAGTAGGACCTCCGCATCCCCCTTTGATGTTATCAATCATAAGACGCTTCGATGGGCCTAGGTCTGTGGATTGCTCGTCGTA\n++\n+BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB\n+@lane1_fakedata0_12 1:N:0:/2\n+CCGTATTCTCCCATGCGACAGTAGGACCTCCGCATCCCCCTTTGATGTTATCAATCATAAGACGCTTCGATGGGCCTAGGTCTGTGGATTGCTCGTCGTA\n++\n+BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB\n+@lane1_fakedata0_13 1:N:0:/2\n+CCGTATTCTGCCATGCGACAGTAGGACCTCCGCATCCCCCTTTGATGTTATCAATCATAAGACGCTTCGATGGGCCTAGGTCTGTGGATTGCTCGTCGTA\n++\n+BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB\n+@lane1_fakedata0_14 1:N:0:/2\n+CCGTGTATTCTCCCATGCGACAGCAGGACCTCCCATCCCCCTCTGATGTTATCAATCATAAGACGCTTCGATGGGCCTAGGTCTGTGGATTGCTCGTCGT\n++\n+BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB\n+@lane1_fakedata0_15 1:N:0:/2\n+CCGTGTATTCTCCCATGCGACAGCAGGACCTCCCATCCCCCTCTGATGTTATCAATCATAAGACGCTTCGATGGGCCTAGGTCTGTGGATTGCTCGTCGT\n++\n+BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB\n+@lane1_fakedata0_16 1:N:0:/2\n+CCGTGTATTCTCCCATGCGCCAGCAGGACCTCCCATCCCCCTCTGATGTTATCAATCATAAGACGCTTCGATGGGCCTAGGTCTGTGGATTGCTCGTCGT\n++\n+BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB'..b' 1:N:0:/2\n+CCGGTTCACTAAACTCACTCAACGGTTGGCGATATTGGCCGTGAACTCAGGAATGCTATGTAATCCAGTCAAGGTACCGAGCGAAGGACGTCCAGCAGCC\n++\n+BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB\n+@lane1_fakedata2_16 1:N:0:/2\n+CCGGTTCACTAAACTCACTCAACGGTTGGCGATATTGGCCGTGAACTCAGGAATGCTATGTAATCCAGTCAAGGTACCGAGCGAAGGACGTCCAGCAGCC\n++\n+BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB\n+@lane1_fakedata2_17 1:N:0:/2\n+CCGGTTCACTAAACTCACTCAACGGTTGGCGATATTGGCCGTGAACTCAGGAATGCTATGTAATCCAGTCAAGGTACCGAGCGAAGGACGTCCAGCAGCC\n++\n+BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB\n+@lane1_fakedata2_18 1:N:0:/2\n+CCGGTTCACTAAACTCACTCAACGGTTGGCGATATTGGCCGTGAACTCAGGAATGCTATGTAATCCAGTCAAGGTACCGAGCGAAGGACGTCCAGCAGCC\n++\n+BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB\n+@lane1_fakedata2_19 1:N:0:/2\n+CCGGTTCACTAAACTCACTCAACGGTTGGCGATATTGGCCGTGAACTCAGGAATGCTATGTAATCCAGTCAAGGTACCGAGCGAAGGACGTCCAGCAGCC\n++\n+BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB\n+@lane1_fakedata7_0 1:N:0:/2\n+CCGCATCAGCATCAGTAGTTTTCAACGAGCTGGCCGAAGGTGTATAACTATGTGGTAGAGAGAAACTGCTGCTATCACTCACGATATAAGCCCTCTGACG\n++\n+BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB\n+@lane1_fakedata7_1 1:N:0:/2\n+CCGCATCAGCATCAGTAGTTTTCAACGAGCTGGCCGAAGGTGTATAACTATGTGGTAGAGAGAAACTGCTGCTATCACTCACGATATAAGCCCTCTGACG\n++\n+BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB\n+@lane1_fakedata7_2 1:N:0:/2\n+CCGCATCAGCATCAGTAGTTTTCAACGAGCTGGCCGAAGGTGTATAACTATGTGGTAGAGAGAAACTGCTGCTATCACTCACGATATAAGCCCTCTGACG\n++\n+BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB\n+@lane1_fakedata7_3 1:N:0:/2\n+CCGCATCAGCATCAGTAGTTTTCAACGAGCTGGCCGAAGGTGTATAACTATGTGGTAGAGAGAAACTGCTGCTATCACTCACGATATAAGCCCTCTGACG\n++\n+BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB\n+@lane1_fakedata7_4 1:N:0:/2\n+CCGCATCAGCATCAGTAGTTTTCAACGAGCTGGCCGAAGGTGTATAACTATGTGGTAGAGAGAAACTGCTGCTATCACTCACGATATAAGCCCTCTGACG\n++\n+BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB\n+@lane1_fakedata7_5 1:N:0:/2\n+CCGCATCAGCATCAGTAGTTTTCAACGAGCTGGCCGAAGGTGTATAACTATGTGGTAGAGAGAAACTGCTGCTATCACTCACGATATAAGCCCTCTGACG\n++\n+BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB\n+@lane1_fakedata7_6 1:N:0:/2\n+CCGATCAGCATCAGTAGTTTTCAACGAGCTGGCCCAATGGTGTATAACTATGTGGTAGAGAGAAACTGCTGCTATCACTCACGATATAAGCCCTCTGACG\n++\n+BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB\n+@lane1_fakedata7_7 1:N:0:/2\n+CCGATCAGCATCAGTAGTTTTCAACGAGCTGGCCCAATGGTGTATAACGATGTGGTAGAGAGAAACTGCTGCTATCACTCACGATATAAGCCCTCTGACG\n++\n+BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB\n+@lane1_fakedata7_8 1:N:0:/2\n+CCGATCAGCATCAGTAGTTTTCAACGAGCTGGCCCAATGGTGTATAACTATGTGGTAGAGAGAAACTGCTGCTATCACTCACGATATAAGCCCTCTGACG\n++\n+BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB\n+@lane1_fakedata7_9 1:N:0:/2\n+CCGATCAGCATCAGTAGTTTTCAACGAGCTGGCCCAATGGTGTATAACTATGTGGTAGAGAGAAACTGCTGCTATCACTCACGATATAAGCCCTCTGACG\n++\n+BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB\n+@lane1_fakedata7_10 1:N:0:/2\n+CCGATCAGCATCAGTAGTTTTCAACGAGCTGGCCCAATGGTGTATAACTATGTGGTAGAGAGAAACTGCTGCTATCACTCACGATATAAGCCCTCTGACG\n++\n+BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB\n+@lane1_fakedata7_11 1:N:0:/2\n+CCGATCAGCATCAGTAGTTTTCAACGAGCTGGCCCTATGGTGTATAACTATGTGGTAGAGAGAAACTGCTGCTATCACTCACGATATAAGCCCTCTGACG\n++\n+BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB\n' |
| b |
| diff -r 000000000000 -r b2e3553e1be2 test-data/denovo_map/denovo_map.log --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/denovo_map/denovo_map.log Mon Jul 01 10:58:28 2019 -0400 |
| b |
| b"@@ -0,0 +1,309 @@\n+denovo_map.pl version 2.4 started at 2019-06-18 10:34:45\n+/home/berntm/miniconda3/envs/mulled-v1-2b57e7596f85ebb3b321e6c9681e8fd9250523a80d97945c46ac7743359454e7/bin/denovo_map.pl --samples demultiplexed --popmap denovo_map/popmap_cstacks.tsv -o stacks_outputs --paired\n+\n+ustacks\n+==========\n+\n+Sample 1 of 2 'PopA_01'\n+----------\n+ustacks -t fastq -f demultiplexed/PopA_01.1.fq -o stacks_outputs -i 1 --name PopA_01\n+ustacks parameters selected:\n+ Input file: 'demultiplexed/PopA_01.1.fq'\n+ Sample ID: 1\n+ Min depth of coverage to create a stack (m): 3\n+ Repeat removal algorithm: enabled\n+ Max distance allowed between stacks (M): 2\n+ Max distance allowed to align secondary reads: 4\n+ Max number of stacks allowed per de novo locus: 3\n+ Deleveraging algorithm: disabled\n+ Gapped assembly: enabled\n+ Minimum alignment length: 0.8\n+ Model type: SNP\n+ Alpha significance level for model: 0.05\n+\n+Loading RAD-Tags...\n+\n+Loaded 66 reads; formed:\n+ 4 stacks representing 63 primary reads (95.5%)\n+ 3 secondary stacks representing 3 secondary reads (4.5%)\n+\n+Stack coverage: mean=15.75; stdev=7.46; max=27; n_reads=63(95.5%)\n+Removing repetitive stacks: cov > 39 (mean+3*stdev)...\n+ Blacklisted 0 stacks.\n+Coverage after repeat removal: mean=15.75; stdev=7.46; max=27; n_reads=63(95.5%)\n+\n+Assembling stacks (max. dist. M=2)...\n+ Assembled 4 stacks into 3; blacklisted 0 stacks.\n+Coverage after assembling stacks: mean=21.00; stdev=4.24; max=27; n_reads=63(95.5%)\n+\n+Merging secondary stacks (max. dist. N=4 from consensus)...\n+ Merged 3 out of 3 secondary reads (100.0%), 1 merged with gapped alignments.\n+Coverage after merging secondary stacks: mean=22.00; stdev=4.32; max=28; n_reads=66(100.0%)\n+\n+Assembling stacks, allowing for gaps (min. match length 80.0%)...\n+ Assembled 3 stacks into 3 stacks.\n+Coverage after gapped assembly: mean=22.00; stdev=4.32; max=28; n_reads=66(100.0%)\n+\n+Merging secondary stacks, allowing for gaps (min. match length 80.0%)...\n+ Merged 0 out of 0 secondary reads (-nan%).\n+Coverage after merging gapped secondary stacks: mean=22.00; stdev=4.32; max=28; n_reads=66(100.0%)\n+\n+Final coverage: mean=22.00; stdev=4.32; max=28; n_reads=66(100.0%)\n+Calling consensus sequences and haplotypes for catalog assembly...\n+Writing tags, SNPs, and alleles files...\n+Refetching read IDs...done.\n+ustacks is done.\n+\n+Sample 2 of 2 'PopA_02'\n+----------\n+ustacks -t fastq -f demultiplexed/PopA_02.1.fq -o stacks_outputs -i 2 --name PopA_02\n+ustacks parameters selected:\n+ Input file: 'demultiplexed/PopA_02.1.fq'\n+ Sample ID: 2\n+ Min depth of coverage to create a stack (m): 3\n+ Repeat removal algorithm: enabled\n+ Max distance allowed between stacks (M): 2\n+ Max distance allowed to align secondary reads: 4\n+ Max number of stacks allowed per de novo locus: 3\n+ Deleveraging algorithm: disabled\n+ Gapped assembly: enabled\n+ Minimum alignment length: 0.8\n+ Model type: SNP\n+ Alpha significance level for model: 0.05\n+\n+Loading RAD-Tags...\n+\n+Loaded 60 reads; formed:\n+ 4 stacks representing 55 primary reads (91.7%)\n+ 5 secondary stacks representing 5 secondary reads (8.3%)\n+\n+Stack coverage: mean=13.75; stdev=9.12; max=26; n_reads=55(91.7%)\n+Removing repetitive stacks: cov > 42 (mean+3*stdev)...\n+ Blacklisted 0 stacks.\n+Coverage after repeat removal: mean=13.75; stdev=9.12; max=26; n_reads=55(91.7%)\n+\n+Assembling stacks (max. dist. M=2)...\n+ Assembled 4 stacks into 3; blacklisted 0 stacks.\n+Coverage after assembling stacks: mean=18.33; stdev=6.55; max=26; n_reads=55(91.7%)\n+\n+Merging secondary stacks (max. dist. N=4 from consensus)...\n+ Merged 5 out of 5 secondary reads (100.0%), 0 merged with gapped alignments.\n+Coverage after merging secondary stacks: mean=20.00; stdev=6.53; max=28; n_reads=60(100.0%)\n+\n+Assembling stacks, allowing for gaps (min. match length 80.0%)...\n+ Assembled 3 stacks into 3 stacks.\n+Coverage after gapped assembly: mean=20.00; stdev=6.53; max=28; n_reads=60(100.0%)\n+\n+Merging seconda"..b" 3 catalog loci; found a paired-end read for 66 (100.0%) of the assembled forward reads; wrote 132 records.\n+Sample 'PopA_02': matched 3 sample loci to 3 catalog loci; found a paired-end read for 60 (100.0%) of the assembled forward reads; wrote 120 records.\n+\n+tsv2bam is done.\n+\n+gstacks\n+==========\n+gstacks -P stacks_outputs -M denovo_map/popmap_cstacks.tsv\n+\n+Logging to 'stacks_outputs/gstacks.log'.\n+Locus/sample distributions will be written to 'stacks_outputs/gstacks.log.distribs'.\n+\n+Configuration for this run:\n+ Input mode: denovo\n+ Population map: 'denovo_map/popmap_cstacks.tsv'\n+ Input files: 2, e.g. 'stacks_outputs/PopA_01.matches.bam'\n+ Output to: 'stacks_outputs/'\n+ Model: marukilow (var_alpha: 0.01, gt_alpha: 0.05)\n+\n+Reading BAM headers...\n+Processing all loci...\n+20%...\n+50%...\n+100%\n+\n+Attempted to assemble and align paired-end reads for 3 loci:\n+ 0 loci had no or almost no paired-end reads (0.0%);\n+ 0 loci had paired-end reads that couldn't be assembled into a contig (0.0%);\n+ For the remaining 3 loci (100.0%), a paired-end contig was assembled;\n+ Average contig size was 204.3 bp;\n+ 0 paired-end contigs overlapped the forward region (0.0%)\n+ Mean overlap: -nanbp; mean size of overlapped loci after merging: -nan;\n+ Out of 252 paired-end reads in these loci (mean 84.0 reads per locus),\n+ 252 were successfuly aligned (100.0%);\n+ Mean insert length was -nan, stdev: nan (based on aligned reads in overlapped loci).\n+\n+Genotyped 3 loci:\n+ effective per-sample coverage: mean=31.0x, stdev=1.0x, min=30.0x, max=32.0x\n+ mean number of sites per locus: 194.3\n+ a consistent phasing was found for 5 of out 5 (100.0%) diploid loci needing phasing\n+\n+gstacks is done.\n+\n+populations\n+==========\n+populations -P stacks_outputs -M denovo_map/popmap_cstacks.tsv\n+\n+Logging to 'stacks_outputs/populations.log'.\n+Locus/sample distributions will be written to 'stacks_outputs/populations.log.distribs'.\n+populations parameters selected:\n+ Percent samples limit per population: 0\n+ Locus Population limit: 1\n+ Percent samples overall: 0\n+ Minor allele frequency cutoff: 0\n+ Maximum observed heterozygosity cutoff: 1\n+ Applying Fst correction: none.\n+ Pi/Fis kernel smoothing: off\n+ Fstats kernel smoothing: off\n+ Bootstrap resampling: off\n+\n+Parsing population map...\n+The population map contained 2 samples, 1 population(s), 1 group(s).\n+Working on 2 samples.\n+Working on 1 population(s):\n+ 1: PopA_01, PopA_02\n+Working on 1 group(s) of populations:\n+ defaultgrp: 1\n+\n+Genotyping markers will be written to 'stacks_outputs/populations.markers.tsv'\n+Raw Genotypes/Haplotypes will be written to 'stacks_outputs/populations.haplotypes.tsv'\n+Population-level summary statistics will be written to 'stacks_outputs/populations.sumstats.tsv'\n+Population-level haplotype summary statistics will be written to 'stacks_outputs/populations.hapstats.tsv'\n+\n+Processing data in batches:\n+ * load a batch of catalog loci and apply filters\n+ * compute SNP- and haplotype-wise per-population statistics\n+ * write the above statistics in the output files\n+ * export the genotypes/haplotypes in specified format(s)\n+More details in 'stacks_outputs/populations.log.distribs'.\n+Now processing...\n+Batch 1 \n+\n+Removed 0 loci that did not pass sample/population constraints from 3 loci.\n+Kept 3 loci, composed of 613 sites; 0 of those sites were filtered, 6 variant sites remained.\n+Number of loci with PE contig: 3.00 (100.0%);\n+ Mean length of loci: 194.33bp (stderr 0.33);\n+Number of loci with SE/PE overlap: 0.00 (0.0%);\n+ Mean length of overlapping loci: -nanbp (stderr -0.00); mean overlap: -nanbp (stderr -0.00);\n+Mean genotyped sites per locus: 194.33bp (stderr 0.33).\n+\n+Population summary statistics (more detail in populations.sumstats_summary.tsv):\n+ 1: 2 samples per locus; pi: 0.61111; all/variant/polymorphic sites: 583/6/6; private alleles: 0\n+Populations is done.\n+denovo_map.pl is done.\n+\n+denovo_map.pl completed at 2019-06-18 10:34:45\n" |
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| diff -r 000000000000 -r b2e3553e1be2 test-data/denovo_map/popmap_cstacks.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/denovo_map/popmap_cstacks.tsv Mon Jul 01 10:58:28 2019 -0400 |
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| @@ -0,0 +1,2 @@ +PopA_01 1 +PopA_02 1 |
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| diff -r 000000000000 -r b2e3553e1be2 test-data/gentest.sh --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/gentest.sh Mon Jul 01 10:58:28 2019 -0400 |
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| @@ -0,0 +1,19 @@ +#!/usr/bin/env bash + +mkdir stacks_outputs + +denovo_map.pl --samples demultiplexed --popmap denovo_map/popmap_cstacks.tsv -o stacks_outputs --paired && +gunzip -c stacks_outputs/catalog.calls > stacks_outputs/catalog.calls.vcf +rm stacks_outputs/catalog.calls + +mv stacks_outputs/PopA_0{1,2}.{tags,snps,alleles}.tsv ustacks/ +mv stacks_outputs/catalog.{tags,snps,alleles}.tsv cstacks/ +mv stacks_outputs/PopA_0{1,2}.matches.tsv sstacks/ +mv stacks_outputs/PopA_0{1,2}.matches.bam tsv2bam/ +mv stacks_outputs/tsv2bam.log tsv2bam/ +mv stacks_outputs/catalog.{calls.vcf,fa.gz} gstacks/ +mv stacks_outputs/gstacks.log* gstacks/ +mv stacks_outputs/populations.* populations/ +mv stacks_outputs/denovo_map.log denovo_map/ + +rmdir stacks_outputs |
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| diff -r 000000000000 -r b2e3553e1be2 test-data/gstacks/catalog.calls.vcf --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/gstacks/catalog.calls.vcf Mon Jul 01 10:58:28 2019 -0400 |
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| b'@@ -0,0 +1,597 @@\n+##fileformat=VCFv4.2\n+##fileDate=20190618\n+##source="Stacks v2.4"\n+##INFO=<ID=AD,Number=R,Type=Integer,Description="Total Depth for Each Allele">\n+##INFO=<ID=AF,Number=A,Type=Float,Description="Allele Frequency">\n+##INFO=<ID=DP,Number=1,Type=Integer,Description="Total Depth">\n+##INFO=<ID=NS,Number=1,Type=Integer,Description="Number of Samples With Data">\n+##FORMAT=<ID=AD,Number=R,Type=Integer,Description="Allele Depth">\n+##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read Depth">\n+##FORMAT=<ID=HQ,Number=2,Type=Integer,Description="Haplotype Quality">\n+##FORMAT=<ID=GL,Number=G,Type=Float,Description="Genotype Likelihood">\n+##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality">\n+##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">\n+#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT\tPopA_01\tPopA_02\n+1\t1\t.\tA\t.\t.\t.\tDP=30;AD=30\tDP\t18\t12\n+1\t2\t.\tA\t.\t.\t.\tDP=30;AD=30\tDP\t18\t12\n+1\t3\t.\tT\t.\t.\t.\tDP=30;AD=30\tDP\t18\t12\n+1\t4\t.\tT\t.\t.\t.\tDP=30;AD=30\tDP\t18\t12\n+1\t5\t.\tC\t.\t.\t.\tDP=30;AD=30\tDP\t18\t12\n+1\t6\t.\tG\t.\t.\t.\tDP=30;AD=30\tDP\t18\t12\n+1\t7\t.\tT\t.\t.\t.\tDP=30;AD=30\tDP\t18\t12\n+1\t8\t.\tT\t.\t.\t.\tDP=30;AD=30\tDP\t18\t12\n+1\t9\t.\tT\t.\t.\t.\tDP=30;AD=30\tDP\t18\t12\n+1\t10\t.\tG\t.\t.\t.\tDP=30;AD=30\tDP\t18\t12\n+1\t11\t.\tC\t.\t.\t.\tDP=30;AD=30\tDP\t18\t12\n+1\t12\t.\tT\t.\t.\t.\tDP=30;AD=30\tDP\t18\t12\n+1\t13\t.\tG\t.\t.\t.\tDP=30;AD=30\tDP\t18\t12\n+1\t14\t.\tC\t.\t.\t.\tDP=30;AD=30\tDP\t18\t12\n+1\t15\t.\tT\t.\t.\t.\tDP=30;AD=30\tDP\t18\t12\n+1\t16\t.\tT\t.\t.\t.\tDP=30;AD=30\tDP\t18\t12\n+1\t17\t.\tC\t.\t.\t.\tDP=30;AD=30\tDP\t18\t12\n+1\t18\t.\tA\t.\t.\t.\tDP=30;AD=30\tDP\t18\t12\n+1\t19\t.\tG\t.\t.\t.\tDP=30;AD=30\tDP\t18\t12\n+1\t20\t.\tG\t.\t.\t.\tDP=30;AD=30\tDP\t18\t12\n+1\t21\t.\tA\t.\t.\t.\tDP=30;AD=30\tDP\t18\t12\n+1\t22\t.\tA\t.\t.\t.\tDP=30;AD=30\tDP\t18\t12\n+1\t23\t.\tT\t.\t.\t.\tDP=30;AD=29\tDP\t18\t12\n+1\t24\t.\tC\t.\t.\t.\tDP=30;AD=30\tDP\t18\t12\n+1\t25\t.\tT\t.\t.\t.\tDP=30;AD=30\tDP\t18\t12\n+1\t26\t.\tC\t.\t.\t.\tDP=30;AD=29\tDP\t18\t12\n+1\t27\t.\tT\t.\t.\t.\tDP=30;AD=30\tDP\t18\t12\n+1\t28\t.\tC\t.\t.\t.\tDP=30;AD=30\tDP\t18\t12\n+1\t29\t.\tG\t.\t.\t.\tDP=30;AD=30\tDP\t18\t12\n+1\t30\t.\tT\t.\t.\t.\tDP=30;AD=30\tDP\t18\t12\n+1\t31\t.\tA\t.\t.\t.\tDP=30;AD=30\tDP\t18\t12\n+1\t32\t.\tT\t.\t.\t.\tDP=30;AD=30\tDP\t18\t12\n+1\t33\t.\tA\t.\t.\t.\tDP=30;AD=30\tDP\t18\t12\n+1\t34\t.\tA\tC\t40\t.\tDP=30;AD=15,15;AF=0.5\tGT:PS:FT:GQ:DP:AD:GL\t0|1:34:.:40:18:9,9:-20.07,0.00,-20.07\t0|1:34:.:40:12:6,6:-13.54,-0.00,-13.54\n+1\t35\t.\tT\t.\t.\t.\tDP=30;AD=30\tDP\t18\t12\n+1\t36\t.\tC\t.\t.\t.\tDP=30;AD=30\tDP\t18\t12\n+1\t37\t.\tT\t.\t.\t.\tDP=30;AD=30\tDP\t18\t12\n+1\t38\t.\tG\t.\t.\t.\tDP=30;AD=30\tDP\t18\t12\n+1\t39\t.\tA\t.\t.\t.\tDP=30;AD=30\tDP\t18\t12\n+1\t40\t.\tG\t.\t.\t.\tDP=30;AD=30\tDP\t18\t12\n+1\t41\t.\tT\t.\t.\t.\tDP=30;AD=30\tDP\t18\t12\n+1\t42\t.\tA\t.\t.\t.\tDP=30;AD=30\tDP\t18\t12\n+1\t43\t.\tT\t.\t.\t.\tDP=30;AD=30\tDP\t18\t12\n+1\t44\t.\tG\t.\t.\t.\tDP=30;AD=30\tDP\t18\t12\n+1\t45\t.\tT\t.\t.\t.\tDP=30;AD=30\tDP\t18\t12\n+1\t46\t.\tG\t.\t.\t.\tDP=30;AD=30\tDP\t18\t12\n+1\t47\t.\tC\t.\t.\t.\tDP=30;AD=30\tDP\t18\t12\n+1\t48\t.\tG\t.\t.\t.\tDP=30;AD=30\tDP\t18\t12\n+1\t49\t.\tT\t.\t.\t.\tDP=30;AD=30\tDP\t18\t12\n+1\t50\t.\tA\t.\t.\t.\tDP=30;AD=30\tDP\t18\t12\n+1\t51\t.\tC\t.\t.\t.\tDP=30;AD=30\tDP\t18\t12\n+1\t52\t.\tG\t.\t.\t.\tDP=30;AD=30\tDP\t18\t12\n+1\t53\t.\tT\t.\t.\t.\tDP=30;AD=30\tDP\t18\t12\n+1\t54\t.\tA\t.\t.\t.\tDP=30;AD=30\tDP\t18\t12\n+1\t55\t.\tC\t.\t.\t.\tDP=30;AD=30\tDP\t18\t12\n+1\t56\t.\tG\t.\t.\t.\tDP=30;AD=30\tDP\t18\t12\n+1\t57\t.\tC\t.\t.\t.\tDP=30;AD=30\tDP\t18\t12\n+1\t58\t.\tT\t.\t.\t.\tDP=30;AD=30\tDP\t18\t12\n+1\t59\t.\tA\t.\t.\t.\tDP=30;AD=30\tDP\t18\t12\n+1\t60\t.\tT\t.\t.\t.\tDP=30;AD=30\tDP\t18\t12\n+1\t61\t.\tT\t.\t.\t.\tDP=30;AD=30\tDP\t18\t12\n+1\t62\t.\tT\t.\t.\t.\tDP=30;AD=30\tDP\t18\t12\n+1\t63\t.\tA\t.\t.\t.\tDP=30;AD=30\tDP\t18\t12\n+1\t64\t.\tG\t.\t.\t.\tDP=30;AD=30\tDP\t18\t12\n+1\t65\t.\tA\t.\t.\t.\tDP=30;AD=30\tDP\t18\t12\n+1\t66\t.\tT\t.\t.\t.\tDP=30;AD=30\tDP\t18\t12\n+1\t67\t.\tG\t.\t.\t.\tDP=30;AD=30\tDP\t18\t12\n+1\t68\t.\tG\t.\t.\t.\tDP=30;AD=30\tDP\t18\t12\n+1\t69\t.\tA\t.\t.\t.\tDP=30;AD=30\tDP\t18\t12\n+1\t70\t.\tT\t.\t.\t.\tDP=30;AD=30\tDP\t18\t12\n+1\t71\t.\tA\t.\t.\t.\tDP=30;AD=30\tDP\t18\t12\n+1\t72\t.\tA\t.\t.\t.\tDP=30;AD=30\tDP\t18\t12\n+1\t73\t.\tC\t.\t.\t.\tDP=30;AD=30\tDP\t18\t12\n+1\t74\t.\tC\t.\t.\t.\tDP=30;AD=30\tDP\t18\t12\n+1\t75\t.\tG\t.\t.\t.\tDP=30;AD=30\tDP\t18\t12\n+1\t76\t.\tA\t.\t.\t.\tDP=30;AD=30\tDP\t18\t12\n+1\t77\t.\tC\t.\t.\t.\tDP=30;AD=30\tDP\t18\t12\n+1\t78\t.\tG\t.\t.\t.\tDP=30;AD=30\tDP\t18\t12\n+1\t79\t.\tC\t.\t.\t.\tDP=30;AD=30\tDP\t18\t12\n+1\t80\t.\tT\t.\t.\t.\tDP=30;AD=30\tDP\t18\t12\n+1\t81\t.\tG\t.\t.\t.\tDP=30;AD=30\tDP\t18\t12\n+1\t82\t.\tC\t.\t.\t.\tDP=30;AD=30\tDP\t18\t12\n+1\t83\t.\tC\t.\t.\t.\tDP=30;AD=3'..b'G\t.\t.\t.\tDP=30;AD=30\tDP\t17\t13\n+3\t106\t.\tG\t.\t.\t.\tDP=30;AD=30\tDP\t17\t13\n+3\t107\t.\tC\t.\t.\t.\tDP=30;AD=30\tDP\t17\t13\n+3\t108\t.\tT\t.\t.\t.\tDP=30;AD=30\tDP\t17\t13\n+3\t109\t.\tG\t.\t.\t.\tDP=30;AD=30\tDP\t17\t13\n+3\t110\t.\tC\t.\t.\t.\tDP=30;AD=30\tDP\t17\t13\n+3\t111\t.\tT\t.\t.\t.\tDP=30;AD=30\tDP\t17\t13\n+3\t112\t.\tG\t.\t.\t.\tDP=30;AD=30\tDP\t17\t13\n+3\t113\t.\tG\t.\t.\t.\tDP=30;AD=30\tDP\t17\t13\n+3\t114\t.\tA\t.\t.\t.\tDP=30;AD=30\tDP\t17\t13\n+3\t115\t.\tC\t.\t.\t.\tDP=30;AD=30\tDP\t17\t13\n+3\t116\t.\tG\t.\t.\t.\tDP=30;AD=30\tDP\t17\t13\n+3\t117\t.\tT\t.\t.\t.\tDP=30;AD=30\tDP\t17\t13\n+3\t118\t.\tC\t.\t.\t.\tDP=30;AD=30\tDP\t17\t13\n+3\t119\t.\tC\t.\t.\t.\tDP=30;AD=30\tDP\t17\t13\n+3\t120\t.\tT\t.\t.\t.\tDP=30;AD=30\tDP\t17\t13\n+3\t121\t.\tT\t.\t.\t.\tDP=30;AD=30\tDP\t17\t13\n+3\t122\t.\tC\t.\t.\t.\tDP=30;AD=30\tDP\t17\t13\n+3\t123\t.\tG\t.\t.\t.\tDP=30;AD=30\tDP\t17\t13\n+3\t124\t.\tC\t.\t.\t.\tDP=30;AD=30\tDP\t17\t13\n+3\t125\t.\tT\t.\t.\t.\tDP=30;AD=30\tDP\t17\t13\n+3\t126\t.\tC\t.\t.\t.\tDP=30;AD=30\tDP\t17\t13\n+3\t127\t.\tG\t.\t.\t.\tDP=30;AD=30\tDP\t17\t13\n+3\t128\t.\tG\t.\t.\t.\tDP=30;AD=30\tDP\t17\t13\n+3\t129\t.\tT\t.\t.\t.\tDP=30;AD=30\tDP\t17\t13\n+3\t130\t.\tA\t.\t.\t.\tDP=30;AD=30\tDP\t17\t13\n+3\t131\t.\tC\t.\t.\t.\tDP=30;AD=30\tDP\t17\t13\n+3\t132\t.\tC\t.\t.\t.\tDP=30;AD=29\tDP\t17\t13\n+3\t133\t.\tT\t.\t.\t.\tDP=30;AD=30\tDP\t17\t13\n+3\t134\t.\tT\t.\t.\t.\tDP=30;AD=30\tDP\t17\t13\n+3\t135\t.\tG\t.\t.\t.\tDP=30;AD=30\tDP\t17\t13\n+3\t136\t.\tA\t.\t.\t.\tDP=30;AD=30\tDP\t17\t13\n+3\t137\t.\tC\t.\t.\t.\tDP=30;AD=30\tDP\t17\t13\n+3\t138\t.\tT\t.\t.\t.\tDP=30;AD=30\tDP\t17\t13\n+3\t139\t.\tG\t.\t.\t.\tDP=30;AD=30\tDP\t17\t13\n+3\t140\t.\tG\t.\t.\t.\tDP=30;AD=30\tDP\t17\t13\n+3\t141\t.\tA\t.\t.\t.\tDP=30;AD=30\tDP\t17\t13\n+3\t142\t.\tT\t.\t.\t.\tDP=30;AD=30\tDP\t17\t13\n+3\t143\t.\tT\t.\t.\t.\tDP=30;AD=30\tDP\t17\t13\n+3\t144\t.\tA\t.\t.\t.\tDP=30;AD=30\tDP\t17\t13\n+3\t145\t.\tT\tC\t40\t.\tDP=30;AD=16,14;AF=0.467\tGT:PS:FT:GQ:DP:AD:GL\t1|0:145:.:40:17:8,9:-20.29,0.00,-17.57\t1|0:145:.:40:13:8,5:-10.39,-0.00,-18.77\n+3\t146\t.\tA\t.\t.\t.\tDP=30;AD=30\tDP\t17\t13\n+3\t147\t.\tT\t.\t.\t.\tDP=30;AD=30\tDP\t17\t13\n+3\t148\t.\tA\t.\t.\t.\tDP=30;AD=30\tDP\t17\t13\n+3\t149\t.\tG\t.\t.\t.\tDP=30;AD=30\tDP\t17\t13\n+3\t150\t.\tC\t.\t.\t.\tDP=30;AD=30\tDP\t17\t13\n+3\t151\t.\tA\t.\t.\t.\tDP=30;AD=30\tDP\t17\t13\n+3\t152\t.\tT\t.\t.\t.\tDP=30;AD=30\tDP\t17\t13\n+3\t153\t.\tT\t.\t.\t.\tDP=30;AD=30\tDP\t17\t13\n+3\t154\t.\tC\t.\t.\t.\tDP=30;AD=30\tDP\t17\t13\n+3\t155\t.\tC\t.\t.\t.\tDP=30;AD=30\tDP\t17\t13\n+3\t156\t.\tT\t.\t.\t.\tDP=30;AD=29\tDP\t17\t13\n+3\t157\t.\tT\tG\t40\t.\tDP=30;AD=16,14;AF=0.467\tGT:PS:FT:GQ:DP:AD:GL\t1|0:145:.:40:17:8,9:-20.29,0.00,-17.57\t1|0:145:.:40:13:8,5:-10.39,-0.00,-18.77\n+3\t158\t.\tA\t.\t.\t.\tDP=30;AD=30\tDP\t17\t13\n+3\t159\t.\tG\t.\t.\t.\tDP=30;AD=30\tDP\t17\t13\n+3\t160\t.\tT\t.\t.\t.\tDP=30;AD=30\tDP\t17\t13\n+3\t161\t.\tT\t.\t.\t.\tDP=30;AD=30\tDP\t17\t13\n+3\t162\t.\tC\t.\t.\t.\tDP=30;AD=30\tDP\t17\t13\n+3\t163\t.\tA\t.\t.\t.\tDP=30;AD=30\tDP\t17\t13\n+3\t164\t.\tC\t.\t.\t.\tDP=30;AD=30\tDP\t17\t13\n+3\t165\t.\tG\t.\t.\t.\tDP=30;AD=30\tDP\t17\t13\n+3\t166\t.\tG\t.\t.\t.\tDP=30;AD=30\tDP\t17\t13\n+3\t167\t.\tC\t.\t.\t.\tDP=30;AD=30\tDP\t17\t13\n+3\t168\t.\tC\t.\t.\t.\tDP=30;AD=30\tDP\t17\t13\n+3\t169\t.\tA\t.\t.\t.\tDP=30;AD=30\tDP\t17\t13\n+3\t170\t.\tA\t.\t.\t.\tDP=30;AD=30\tDP\t17\t13\n+3\t171\t.\tT\t.\t.\t.\tDP=30;AD=30\tDP\t17\t13\n+3\t172\t.\tA\t.\t.\t.\tDP=30;AD=30\tDP\t17\t13\n+3\t173\t.\tT\t.\t.\t.\tDP=30;AD=30\tDP\t17\t13\n+3\t174\t.\tC\t.\t.\t.\tDP=30;AD=30\tDP\t17\t13\n+3\t175\t.\tG\t.\t.\t.\tDP=30;AD=30\tDP\t17\t13\n+3\t176\t.\tC\t.\t.\t.\tDP=30;AD=30\tDP\t17\t13\n+3\t177\t.\tC\t.\t.\t.\tDP=30;AD=30\tDP\t17\t13\n+3\t178\t.\tA\t.\t.\t.\tDP=30;AD=30\tDP\t17\t13\n+3\t179\t.\tA\t.\t.\t.\tDP=30;AD=30\tDP\t17\t13\n+3\t180\t.\tC\t.\t.\t.\tDP=30;AD=30\tDP\t17\t13\n+3\t181\t.\tC\t.\t.\t.\tDP=30;AD=30\tDP\t17\t13\n+3\t182\t.\tG\t.\t.\t.\tDP=30;AD=30\tDP\t17\t13\n+3\t183\t.\tT\t.\t.\t.\tDP=30;AD=30\tDP\t17\t13\n+3\t184\t.\tT\t.\t.\t.\tDP=30;AD=30\tDP\t17\t13\n+3\t185\t.\tG\t.\t.\t.\tDP=30;AD=30\tDP\t17\t13\n+3\t186\t.\tA\t.\t.\t.\tDP=30;AD=30\tDP\t17\t13\n+3\t187\t.\tG\t.\t.\t.\tDP=30;AD=30\tDP\t17\t13\n+3\t188\t.\tT\t.\t.\t.\tDP=30;AD=30\tDP\t17\t13\n+3\t189\t.\tG\t.\t.\t.\tDP=30;AD=30\tDP\t17\t13\n+3\t190\t.\tA\t.\t.\t.\tDP=30;AD=30\tDP\t17\t13\n+3\t191\t.\tG\t.\t.\t.\tDP=30;AD=30\tDP\t17\t13\n+3\t192\t.\tT\t.\t.\t.\tDP=30;AD=30\tDP\t17\t13\n+3\t193\t.\tT\t.\t.\t.\tDP=30;AD=30\tDP\t17\t13\n+3\t194\t.\tT\t.\t.\t.\tDP=30;AD=30\tDP\t17\t13\n+3\t195\t.\tA\t.\t.\t.\tDP=30;AD=30\tDP\t17\t13\n+3\t196\t.\tG\t.\t.\t.\tDP=30;AD=30\tDP\t17\t13\n+3\t197\t.\tT\t.\t.\t.\tDP=30;AD=30\tDP\t17\t13\n+3\t198\t.\tG\t.\t.\t.\tDP=30;AD=30\tDP\t17\t13\n+3\t199\t.\tA\t.\t.\t.\tDP=30;AD=30\tDP\t17\t13\n+3\t200\t.\tA\t.\t.\t.\tDP=30;AD=30\tDP\t17\t13\n+3\t201\t.\tC\t.\t.\t.\tDP=30;AD=30\tDP\t17\t13\n+3\t202\t.\tC\t.\t.\t.\tDP=30;AD=30\tDP\t17\t13\n+3\t203\t.\tG\t.\t.\t.\tDP=30;AD=30\tDP\t17\t13\n+3\t204\t.\tG\t.\t.\t.\tDP=30;AD=30\tDP\t17\t13\n' |
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| diff -r 000000000000 -r b2e3553e1be2 test-data/gstacks/catalog.fa.gz |
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| Binary file test-data/gstacks/catalog.fa.gz has changed |
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| diff -r 000000000000 -r b2e3553e1be2 test-data/gstacks/gstacks.log --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/gstacks/gstacks.log Mon Jul 01 10:58:28 2019 -0400 |
| b |
| @@ -0,0 +1,34 @@ +gstacks v2.4, executed 2019-06-18 10:34:45 (zlib-1.2.11) +gstacks -P stacks_outputs -M denovo_map/popmap_cstacks.tsv +Locus/sample distributions will be written to 'stacks_outputs/gstacks.log.distribs'. + +Configuration for this run: + Input mode: denovo + Population map: 'denovo_map/popmap_cstacks.tsv' + Input files: 2, e.g. 'stacks_outputs/PopA_01.matches.bam' + Output to: 'stacks_outputs/' + Model: marukilow (var_alpha: 0.01, gt_alpha: 0.05) + +Reading BAM headers... +Processing all loci... +20%... +50%... +100% + +Attempted to assemble and align paired-end reads for 3 loci: + 0 loci had no or almost no paired-end reads (0.0%); + 0 loci had paired-end reads that couldn't be assembled into a contig (0.0%); + For the remaining 3 loci (100.0%), a paired-end contig was assembled; + Average contig size was 204.3 bp; + 0 paired-end contigs overlapped the forward region (0.0%) + Mean overlap: -nanbp; mean size of overlapped loci after merging: -nan; + Out of 252 paired-end reads in these loci (mean 84.0 reads per locus), + 252 were successfuly aligned (100.0%); + Mean insert length was -nan, stdev: nan (based on aligned reads in overlapped loci). + +Genotyped 3 loci: + effective per-sample coverage: mean=31.0x, stdev=1.0x, min=30.0x, max=32.0x + mean number of sites per locus: 194.3 + a consistent phasing was found for 5 of out 5 (100.0%) diploid loci needing phasing + +gstacks is done. |
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| diff -r 000000000000 -r b2e3553e1be2 test-data/gstacks/gstacks.log.distribs --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/gstacks/gstacks.log.distribs Mon Jul 01 10:58:28 2019 -0400 |
| b |
| @@ -0,0 +1,43 @@ +# Note: Individual distributions can be extracted using the `stacks-dist-extract` utility. +# e.g. `stacks-dist-extract gstacks.log.distribs dist_name` + +BEGIN effective_coverages_per_sample +# For mean_cov_ns, the coverage at each locus is weighted by the number of +# samples present at that locus (i.e. coverage at shared loci counts more). +sample n_loci n_used_fw_reads mean_cov mean_cov_ns +PopA_01 3 96 32.000 32.000 +PopA_02 3 90 30.000 30.000 +END effective_coverages_per_sample + +BEGIN phasing_rates_per_sample +sample n_gts n_multisnp_hets n_phased misphasing_rate +PopA_01 3 2 2 0.000 +PopA_02 3 3 3 0.000 +END phasing_rates_per_sample + +BEGIN clockings +Num. threads: 1 +Parallel time: 0.0 +Average thread time spent: + 0.0 reading (3.1%) + 0.0 processing (95.2%) + 0.0 pre-alignments block (72.2%) + 0.0 reformatting fw-reads (0.1%) + 0.0 assembling (22.2%) + 0.0 initializing alignments (5.4%) + 0.0 aligning (42.9%) + 0.0 merging read pairs (1.5%) + 0.0 post-alignments block (21.2%) + 0.0 filtering reads (0.0%) + 0.0 counting nucleotides (3.5%) + 0.0 genotyping (1.9%) + 0.0 haplotyping (1.0%) + 0.0 computing consensus (0.1%) + 0.0 building_fa (0.1%) + 0.0 building_vcf (14.6%) + 0.0 writing_fa (0.1%) + 0.0 writing_vcf (1.3%) + 0.0 clocking (0.2%) +Total time spent writing vcf: 0.0 (1.3%) +VCFwrite block size: mean=1.0(n=3); max=1 +END clockings |
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| diff -r 000000000000 -r b2e3553e1be2 test-data/kmerfilter/kfreqdist.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/kmerfilter/kfreqdist.tsv Mon Jul 01 10:58:28 2019 -0400 |
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| @@ -0,0 +1,3 @@ +# KmerFrequency Count +1 408 +2 136 |
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| diff -r 000000000000 -r b2e3553e1be2 test-data/kmerfilter/kmerfilter.log --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/kmerfilter/kmerfilter.log Mon Jul 01 10:58:28 2019 -0400 |
| [ |
| @@ -0,0 +1,22 @@ +Using a kmer size of 16 +Filtering out reads by identifying rare kmers: On. + A kmer is considered rare when its coverage is at 15% or below the median kmer coverage for the read. + A read is dropped when it contains 13 or more rare kmers in a row. +Filtering out reads by identifying abundant kmers: On. + Kmer is considered abundant when it occurs 20000 or more times. + A read is dropped when it contains 80% or more abundant kmers. +Normalizing read depth: Off. +Found 1 input file(s). +Found 0 paired input file(s). +Generating kmer distribution... +Generating kmers from file 1 of 1 [R1_0001.fastq] +540 unique k-mers recorded. +Filtering reads by kmer frequency... +Processing file 1 of 1 [R1_0001.fastq] + 5 total reads; -0 rare k-mer reads; -0 abundant k-mer reads; 5 retained reads. +Outputing details to log: 'stacks_outputs/kmer_filter.log' + +5 total sequences; + 0 rare k-mer reads; + 0 abundant k-mer reads; +5 retained reads. |
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| diff -r 000000000000 -r b2e3553e1be2 test-data/populations/blacklist.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/populations/blacklist.tsv Mon Jul 01 10:58:28 2019 -0400 |
| b |
| @@ -0,0 +1,1 @@ +666 |
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| diff -r 000000000000 -r b2e3553e1be2 test-data/populations/populations.fixed.phylip --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/populations/populations.fixed.phylip Mon Jul 01 10:58:28 2019 -0400 |
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| @@ -0,0 +1,3 @@ +1 0 +1 +# Stacks v2.4; Phylip sequential; June 17, 2019 |
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| diff -r 000000000000 -r b2e3553e1be2 test-data/populations/populations.fixed.phylip.log --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/populations/populations.fixed.phylip.log Mon Jul 01 10:58:28 2019 -0400 |
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| @@ -0,0 +1,2 @@ +# Stacks v2.4; Phylip sequential; June 17, 2019 +# Seq Pos Locus ID Column Population |
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| diff -r 000000000000 -r b2e3553e1be2 test-data/populations/populations.fst_summary.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/populations/populations.fst_summary.tsv Mon Jul 01 10:58:28 2019 -0400 |
| b |
| @@ -0,0 +1,1 @@ + 1 |
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| diff -r 000000000000 -r b2e3553e1be2 test-data/populations/populations.haplotypes.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/populations/populations.haplotypes.tsv Mon Jul 01 10:58:28 2019 -0400 |
| b |
| @@ -0,0 +1,4 @@ +# Catalog Locus ID Cnt PopA_01 PopA_02 +1 2 AC/CA AC/CA +2 2 GG/GG AA/GG +3 2 CG/TT CG/TT |
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| diff -r 000000000000 -r b2e3553e1be2 test-data/populations/populations.haps.genepop --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/populations/populations.haps.genepop Mon Jul 01 10:58:28 2019 -0400 |
| b |
| @@ -0,0 +1,5 @@ +Stacks v2.4; GenePop v4.1.3; June 17, 2019 +1,2,3 +pop +PopA_01, 0102 0102 0101 +PopA_02, 0102 0102 0102 |
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| diff -r 000000000000 -r b2e3553e1be2 test-data/populations/populations.haps.radpainter --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/populations/populations.haps.radpainter Mon Jul 01 10:58:28 2019 -0400 |
| b |
| @@ -0,0 +1,4 @@ +PopA_01 PopA_02 +AC/CA AC/CA +CG/TT CG/TT +GG AA/GG |
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| diff -r 000000000000 -r b2e3553e1be2 test-data/populations/populations.haps.vcf --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/populations/populations.haps.vcf Mon Jul 01 10:58:28 2019 -0400 |
| b |
| @@ -0,0 +1,18 @@ +##fileformat=VCFv4.2 +##fileDate=20190617 +##source="Stacks v2.4" +##INFO=<ID=AD,Number=R,Type=Integer,Description="Total Depth for Each Allele"> +##INFO=<ID=AF,Number=A,Type=Float,Description="Allele Frequency"> +##INFO=<ID=DP,Number=1,Type=Integer,Description="Total Depth"> +##INFO=<ID=NS,Number=1,Type=Integer,Description="Number of Samples With Data"> +##FORMAT=<ID=AD,Number=R,Type=Integer,Description="Allele Depth"> +##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read Depth"> +##FORMAT=<ID=HQ,Number=2,Type=Integer,Description="Haplotype Quality"> +##FORMAT=<ID=GL,Number=G,Type=Float,Description="Genotype Likelihood"> +##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality"> +##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype"> +##INFO=<ID=loc_strand,Number=1,Type=Character,Description="Genomic strand the corresponding Stacks locus aligns on"> +#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT PopA_01 PopA_02 +1 1 . AC CA . PASS snp_columns=34,89 GT 0/1 0/1 +2 1 . CG TT . PASS snp_columns=145,157 GT 0/1 0/1 +3 1 . GG AA . PASS snp_columns=163,182 GT 0/0 0/1 |
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| diff -r 000000000000 -r b2e3553e1be2 test-data/populations/populations.hapstats.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/populations/populations.hapstats.tsv Mon Jul 01 10:58:28 2019 -0400 |
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| @@ -0,0 +1,5 @@ +# 1 PopA_01,PopA_02 +# Locus ID Chr BP Pop ID N Haplotype Cnt Gene Diversity Smoothed Gene Diversity Smoothed Gene Diversity P-value Haplotype Diversity Smoothed Haplotype Diversity Smoothed Haplotype Diversity P-value HWE P-value HWE P-value SE Haplotypes +1 un 1 1 4 2 0.66667 0.00000 0.00000 1.33333 0.00000 0.00000 0.00000 0.00000 AC:2;CA:2 +2 un 205 1 4 2 0.50000 0.00000 0.00000 1.00000 0.00000 0.00000 0.00000 0.00000 AA:1;GG:3 +3 un 410 1 4 2 0.66667 0.00000 0.00000 1.33333 0.00000 0.00000 0.00000 0.00000 CG:2;TT:2 |
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| diff -r 000000000000 -r b2e3553e1be2 test-data/populations/populations.hzar.csv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/populations/populations.hzar.csv Mon Jul 01 10:58:28 2019 -0400 |
| b |
| @@ -0,0 +1,3 @@ +# Stacks v2.4; HZAR v0.2-5; June 18, 2019 +Population,Distance,1_33.A,1_33.B,1_33.N,1_88.A,1_88.B,1_88.N,2_162.A,2_162.B,2_162.N,2_181.A,2_181.B,2_181.N,3_144.A,3_144.B,3_144.N,3_156.A,3_156.B,3_156.N +1,0,0.5,0.5,4,0.5,0.5,4,0.75,0.25,4,0.75,0.25,4,0.5,0.5,4,0.5,0.5,4 |
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| diff -r 000000000000 -r b2e3553e1be2 test-data/populations/populations.loci.fa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/populations/populations.loci.fa Mon Jul 01 10:58:28 2019 -0400 |
| b |
| @@ -0,0 +1,7 @@ +# Stacks version 2.4; June 17, 2019 +>CLocus_1 +AATTCGTTTGCTGCTTCAGGAATCTCTCGTATAATCTGAGTATGTGCGTACGTACGCTATTTAGATGGATAACCGACGCTGCCAGACGAGAGACNNNNNNNNNNCGTCAGAGGGCTTATATCGTGAGTGATAGCAGCAGTTTCTCTCTACCACATAGTTATACACCATTGGGCCAGCTCGTTGAAAACTACTGATGCTGATCGG +>CLocus_2 +AATTCTCTACACCACAGCATCAATTCTAAAAATGACTACCAGAGAGACAACTCCGCAGTTAAACACTCTGACTGCCACGCCAGCTACCTCTAGANNNNNNNNNNGGCTGCTGGACGTCCTTCGCTCGGTACCTTGACTGGATTATATAGCATTCCTTAGTTCACGGCCAATATCGCCAACCGTTGAGTGAGTTTAGTGAACCGG +>CLocus_3 +AATTCGGCTTGCAACGCAAGTGACGATTCCCACGGACATAACTGATCTAAGTAACTTCCAAATCTGGGAATGGGATTTCATAATTAAGGACTATNNNNNNNNNNTACGACGAGCAATCCACAGACCTAGGCCCATCGAAGCGTCTTATGATTGATAACATCAGAGGGGGATGGGAGGTCCTGCTGTCGCATGGGAGAATACACGG |
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| diff -r 000000000000 -r b2e3553e1be2 test-data/populations/populations.log --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/populations/populations.log Mon Jul 01 10:58:28 2019 -0400 |
| b |
| @@ -0,0 +1,47 @@ +populations v2.4, executed 2019-06-18 10:34:45 (zlib-1.2.11) +populations -P stacks_outputs -M denovo_map/popmap_cstacks.tsv +Locus/sample distributions will be written to 'stacks_outputs/populations.log.distribs'. +populations parameters selected: + Percent samples limit per population: 0 + Locus Population limit: 1 + Percent samples overall: 0 + Minor allele frequency cutoff: 0 + Maximum observed heterozygosity cutoff: 1 + Applying Fst correction: none. + Pi/Fis kernel smoothing: off + Fstats kernel smoothing: off + Bootstrap resampling: off + +Parsing population map... +The population map contained 2 samples, 1 population(s), 1 group(s). +Working on 2 samples. +Working on 1 population(s): + 1: PopA_01, PopA_02 +Working on 1 group(s) of populations: + defaultgrp: 1 + +Genotyping markers will be written to 'stacks_outputs/populations.markers.tsv' +Raw Genotypes/Haplotypes will be written to 'stacks_outputs/populations.haplotypes.tsv' +Population-level summary statistics will be written to 'stacks_outputs/populations.sumstats.tsv' +Population-level haplotype summary statistics will be written to 'stacks_outputs/populations.hapstats.tsv' + +Processing data in batches: + * load a batch of catalog loci and apply filters + * compute SNP- and haplotype-wise per-population statistics + * write the above statistics in the output files + * export the genotypes/haplotypes in specified format(s) +More details in 'stacks_outputs/populations.log.distribs'. +Now processing... +Batch 1 + +Removed 0 loci that did not pass sample/population constraints from 3 loci. +Kept 3 loci, composed of 613 sites; 0 of those sites were filtered, 6 variant sites remained. +Number of loci with PE contig: 3.00 (100.0%); + Mean length of loci: 194.33bp (stderr 0.33); +Number of loci with SE/PE overlap: 0.00 (0.0%); + Mean length of overlapping loci: -nanbp (stderr -0.00); mean overlap: -nanbp (stderr -0.00); +Mean genotyped sites per locus: 194.33bp (stderr 0.33). + +Population summary statistics (more detail in populations.sumstats_summary.tsv): + 1: 2 samples per locus; pi: 0.61111; all/variant/polymorphic sites: 583/6/6; private alleles: 0 +Populations is done. |
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| diff -r 000000000000 -r b2e3553e1be2 test-data/populations/populations.log.distribs --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/populations/populations.log.distribs Mon Jul 01 10:58:28 2019 -0400 |
| b |
| @@ -0,0 +1,42 @@ +# Note: Individual distributions can be extracted using the `stacks-dist-extract` utility. +# e.g. `stacks-dist-extract populations.log.distribs dist_name` + +BEGIN batch_progress +Batch 1: analyzed 3 loci; filtered 0 loci; 3 loci seen. +END batch_progress + +BEGIN samples_per_loc_prefilters +# Distribution of valid samples matched to a catalog locus prior to filtering. +n_samples n_loci +2 3 +END samples_per_loc_prefilters + +BEGIN missing_samples_per_loc_prefilters +# Distribution of missing samples for each catalog locus prior to filtering. +# Absent samples at locus Count +0 3 +END missing_samples_per_loc_prefilters + +BEGIN snps_per_loc_prefilters +# Distribution of the number of SNPs per catalog locus prior to filtering. +n_snps n_loci +2 3 +END snps_per_loc_prefilters + +BEGIN samples_per_loc_postfilters +# Distribution of valid samples matched to a catalog locus after filtering. +n_samples n_loci +2 3 +END samples_per_loc_postfilters + +BEGIN missing_samples_per_loc_postfilters +# Distribution of missing samples for each catalog locus after filtering. +# Absent samples at locus Count +0 3 +END missing_samples_per_loc_postfilters + +BEGIN snps_per_loc_postfilters +# Distribution of the number of SNPs per catalog locus (after filtering). +n_snps n_loci +2 3 +END snps_per_loc_postfilters |
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| diff -r 000000000000 -r b2e3553e1be2 test-data/populations/populations.markers.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/populations/populations.markers.tsv Mon Jul 01 10:58:28 2019 -0400 |
| b |
| @@ -0,0 +1,4 @@ +# Catalog Locus ID Total Genotypes Max Genotype Freqs F Mean Log Likelihood Genotype Map +1 2 100.00000 ab:2(100.0%); 0.00000 1.00000 AC:a;CA:b; +2 2 50.00000 aa:1(50.0%);ab:1(50.0%); 0.00000 1.00000 AA:b;GG:a; +3 2 100.00000 ab:2(100.0%); 0.00000 1.00000 CG:a;TT:b; |
| b |
| diff -r 000000000000 -r b2e3553e1be2 test-data/populations/populations.phistats_summary.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/populations/populations.phistats_summary.tsv Mon Jul 01 10:58:28 2019 -0400 |
| b |
| @@ -0,0 +1,5 @@ +# Phi_st Means + 1 + +# Fst' Means + 1 |
| b |
| diff -r 000000000000 -r b2e3553e1be2 test-data/populations/populations.plink.map --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/populations/populations.plink.map Mon Jul 01 10:58:28 2019 -0400 |
| b |
| @@ -0,0 +1,7 @@ +# Stacks v2.4; PLINK v1.07; June 17, 2019 +un 1_33 0 34 +un 1_88 0 89 +un 2_144 0 349 +un 2_156 0 361 +un 3_162 0 571 +un 3_181 0 590 |
| b |
| diff -r 000000000000 -r b2e3553e1be2 test-data/populations/populations.plink.ped --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/populations/populations.plink.ped Mon Jul 01 10:58:28 2019 -0400 |
| b |
| @@ -0,0 +1,3 @@ +# Stacks v2.4; PLINK v1.07; June 17, 2019 +1 PopA_01 0 0 0 0 A C A C C T G T G G G G +1 PopA_02 0 0 0 0 A C A C C T G T A G A G |
| b |
| diff -r 000000000000 -r b2e3553e1be2 test-data/populations/populations.samples-raw.fa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/populations/populations.samples-raw.fa Mon Jul 01 10:58:28 2019 -0400 |
| [ |
| @@ -0,0 +1,25 @@ +# Stacks version 2.4; June 17, 2019 +>CLocus_1_Sample_1_Locus_1_Allele_0 [PopA_01] +AATTCGTTTGCTGCTTCAGGAATCTCTCGTATAATCTGAGTATGTGCGTACGTACGCTATTTAGATGGATAACCGACGCTGCCAGACGCGAGACNNNNNNNNNNCGTCAGAGGGCTTATATCGTGAGTGATAGCAGCAGTTTCTCTCTACCACATAGTTATACACCATTGGGCCAGCTCGTTGAAAACTACTGATGCTGATCGG +>CLocus_1_Sample_1_Locus_1_Allele_1 [PopA_01] +AATTCGTTTGCTGCTTCAGGAATCTCTCGTATACTCTGAGTATGTGCGTACGTACGCTATTTAGATGGATAACCGACGCTGCCAGACGAGAGACNNNNNNNNNNCGTCAGAGGGCTTATATCGTGAGTGATAGCAGCAGTTTCTCTCTACCACATAGTTATACACCATTGGGCCAGCTCGTTGAAAACTACTGATGCTGATCGG +>CLocus_1_Sample_2_Locus_1_Allele_0 [PopA_02] +AATTCGTTTGCTGCTTCAGGAATCTCTCGTATAATCTGAGTATGTGCGTACGTACGCTATTTAGATGGATAACCGACGCTGCCAGACGCGAGACNNNNNNNNNNCGTCAGAGGGCTTATATCGTGAGTGATAGCAGCAGTTTCTCTCTACCACATAGTTATACACCATTGGGCCAGCTCGTTGAAAACTACTGATGCTGATCGG +>CLocus_1_Sample_2_Locus_1_Allele_1 [PopA_02] +AATTCGTTTGCTGCTTCAGGAATCTCTCGTATACTCTGAGTATGTGCGTACGTACGCTATTTAGATGGATAACCGACGCTGCCAGACGAGAGACNNNNNNNNNNCGTCAGAGGGCTTATATCGTGAGTGATAGCAGCAGTTTCTCTCTACCACATAGTTATACACCATTGGGCCAGCTCGTTGAAAACTACTGATGCTGATCGG +>CLocus_2_Sample_1_Locus_2_Allele_0 [PopA_01] +AATTCTCTACACCACAGCATCAATTCTAAAAATGACTACCAGAGAGACAACTCCGCAGTTAAACACTCTGACTGCCACGCCAGCTACCTCTAGANNNNNNNNNNGGCTGCTGGACGTCCTTCGCTCGGTACCTTGACTGGATTACATAGCATTCCTGAGTTCACGGCCAATATCGCCAACCGTTGAGTGAGTTTAGTGAACCGG +>CLocus_2_Sample_1_Locus_2_Allele_1 [PopA_01] +AATTCTCTACACCACAGCATCAATTCTAAAAATGACTACCAGAGAGACAACTCCGCAGTTAAACACTCTGACTGCCACGCCAGCTACCTCTAGANNNNNNNNNNGGCTGCTGGACGTCCTTCGCTCGGTACCTTGACTGGATTATATAGCATTCCTTAGTTCACGGCCAATATCGCCAACCGTTGAGTGAGTTTAGTGAACCGG +>CLocus_2_Sample_2_Locus_2_Allele_0 [PopA_02] +AATTCTCTACACCACAGCATCAATTCTAAAAATGACTACCAGAGAGACAACTCCGCAGTTAAACACTCTGACTGCCACGCCAGCTACCTCTAGANNNNNNNNNNGGCTGCTGGACGTCCTTCGCTCGGTACCTTGACTGGATTACATAGCATTCCTGAGTTCACGGCCAATATCGCCAACCGTTGAGTGAGTTTAGTGAACCGG +>CLocus_2_Sample_2_Locus_2_Allele_1 [PopA_02] +AATTCTCTACACCACAGCATCAATTCTAAAAATGACTACCAGAGAGACAACTCCGCAGTTAAACACTCTGACTGCCACGCCAGCTACCTCTAGANNNNNNNNNNGGCTGCTGGACGTCCTTCGCTCGGTACCTTGACTGGATTATATAGCATTCCTTAGTTCACGGCCAATATCGCCAACCGTTGAGTGAGTTTAGTGAACCGG +>CLocus_3_Sample_1_Locus_3_Allele_0 [PopA_01] +AATTCGGCTTGCAACGCAAGTGACGATTCCCACGGACATAACTGATCTAAGTAACTTCCAAATCTGGGAATGGGATTTCATAATTAAGGACTATNNNNNNNNNNTACGACGAGCAATCCACAGACCTAGGCCCATCGAAGCGTCTTATGATTGATAACATCAGAGGGGGATGGGAGGTCCTGCTGTCGCATGGGAGAATACACGG +>CLocus_3_Sample_1_Locus_3_Allele_1 [PopA_01] +AATTCGGCTTGCAACGCAAGTGACGATTCCCACGGACATAACTGATCTAAGTAACTTCCAAATCTGGGAATGGGATTTCATAATTAAGGACTATNNNNNNNNNNTACGACGAGCAATCCACAGACCTAGGCCCATCGAAGCGTCTTATGATTGATAACATCAGAGGGGGATGGGAGGTCCTGCTGTCGCATGGGAGAATACACGG +>CLocus_3_Sample_2_Locus_3_Allele_0 [PopA_02] +AATTCGGCTTGCAACGCAAGTGACGATTCCCACGGACATAACTGATCTAAGTAACTTCCAAATCTGGGAATGGGATTTCATAATTAAGGACTATNNNNNNNNNNTACGACGAGCAATCCACAGACCTAGGCCCATCGAAGCGTCTTATGATTGATAACATCAAAGGGGGATGGGAGGTCCTACTGTCGCATGGGAGAATACACGG +>CLocus_3_Sample_2_Locus_3_Allele_1 [PopA_02] +AATTCGGCTTGCAACGCAAGTGACGATTCCCACGGACATAACTGATCTAAGTAACTTCCAAATCTGGGAATGGGATTTCATAATTAAGGACTATNNNNNNNNNNTACGACGAGCAATCCACAGACCTAGGCCCATCGAAGCGTCTTATGATTGATAACATCAGAGGGGGATGGGAGGTCCTGCTGTCGCATGGGAGAATACACGG |
| b |
| diff -r 000000000000 -r b2e3553e1be2 test-data/populations/populations.samples.fa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/populations/populations.samples.fa Mon Jul 01 10:58:28 2019 -0400 |
| [ |
| @@ -0,0 +1,25 @@ +# Stacks version 2.4; June 17, 2019 +>CLocus_1_Sample_1_Locus_1_Allele_0 [PopA_01] +AATTCGTTTGCTGCTTCAGGAATCTCTCGTATAATCTGAGTATGTGCGTACGTACGCTATTTAGATGGATAACCGACGCTGCCAGACGCGAGACNNNNNNNNNNCGTCAGAGGGCTTATATCGTGAGTGATAGCAGCAGTTTCTCTCTACCACATAGTTATACACCATTGGGCCAGCTCGTTGAAAACTACTGATGCTGATCGG +>CLocus_1_Sample_1_Locus_1_Allele_1 [PopA_01] +AATTCGTTTGCTGCTTCAGGAATCTCTCGTATACTCTGAGTATGTGCGTACGTACGCTATTTAGATGGATAACCGACGCTGCCAGACGAGAGACNNNNNNNNNNCGTCAGAGGGCTTATATCGTGAGTGATAGCAGCAGTTTCTCTCTACCACATAGTTATACACCATTGGGCCAGCTCGTTGAAAACTACTGATGCTGATCGG +>CLocus_1_Sample_2_Locus_1_Allele_0 [PopA_02] +AATTCGTTTGCTGCTTCAGGAATCTCTCGTATAATCTGAGTATGTGCGTACGTACGCTATTTAGATGGATAACCGACGCTGCCAGACGCGAGACNNNNNNNNNNCGTCAGAGGGCTTATATCGTGAGTGATAGCAGCAGTTTCTCTCTACCACATAGTTATACACCATTGGGCCAGCTCGTTGAAAACTACTGATGCTGATCGG +>CLocus_1_Sample_2_Locus_1_Allele_1 [PopA_02] +AATTCGTTTGCTGCTTCAGGAATCTCTCGTATACTCTGAGTATGTGCGTACGTACGCTATTTAGATGGATAACCGACGCTGCCAGACGAGAGACNNNNNNNNNNCGTCAGAGGGCTTATATCGTGAGTGATAGCAGCAGTTTCTCTCTACCACATAGTTATACACCATTGGGCCAGCTCGTTGAAAACTACTGATGCTGATCGG +>CLocus_2_Sample_1_Locus_2_Allele_0 [PopA_01] +AATTCTCTACACCACAGCATCAATTCTAAAAATGACTACCAGAGAGACAACTCCGCAGTTAAACACTCTGACTGCCACGCCAGCTACCTCTAGANNNNNNNNNNGGCTGCTGGACGTCCTTCGCTCGGTACCTTGACTGGATTACATAGCATTCCTGAGTTCACGGCCAATATCGCCAACCGTTGAGTGAGTTTAGTGAACCGG +>CLocus_2_Sample_1_Locus_2_Allele_1 [PopA_01] +AATTCTCTACACCACAGCATCAATTCTAAAAATGACTACCAGAGAGACAACTCCGCAGTTAAACACTCTGACTGCCACGCCAGCTACCTCTAGANNNNNNNNNNGGCTGCTGGACGTCCTTCGCTCGGTACCTTGACTGGATTATATAGCATTCCTTAGTTCACGGCCAATATCGCCAACCGTTGAGTGAGTTTAGTGAACCGG +>CLocus_2_Sample_2_Locus_2_Allele_0 [PopA_02] +AATTCTCTACACCACAGCATCAATTCTAAAAATGACTACCAGAGAGACAACTCCGCAGTTAAACACTCTGACTGCCACGCCAGCTACCTCTAGANNNNNNNNNNGGCTGCTGGACGTCCTTCGCTCGGTACCTTGACTGGATTACATAGCATTCCTGAGTTCACGGCCAATATCGCCAACCGTTGAGTGAGTTTAGTGAACCGG +>CLocus_2_Sample_2_Locus_2_Allele_1 [PopA_02] +AATTCTCTACACCACAGCATCAATTCTAAAAATGACTACCAGAGAGACAACTCCGCAGTTAAACACTCTGACTGCCACGCCAGCTACCTCTAGANNNNNNNNNNGGCTGCTGGACGTCCTTCGCTCGGTACCTTGACTGGATTATATAGCATTCCTTAGTTCACGGCCAATATCGCCAACCGTTGAGTGAGTTTAGTGAACCGG +>CLocus_3_Sample_1_Locus_3_Allele_0 [PopA_01] +AATTCGGCTTGCAACGCAAGTGACGATTCCCACGGACATAACTGATCTAAGTAACTTCCAAATCTGGGAATGGGATTTCATAATTAAGGACTATNNNNNNNNNNTACGACGAGCAATCCACAGACCTAGGCCCATCGAAGCGTCTTATGATTGATAACATCAGAGGGGGATGGGAGGTCCTGCTGTCGCATGGGAGAATACACGG +>CLocus_3_Sample_1_Locus_3_Allele_1 [PopA_01] +AATTCGGCTTGCAACGCAAGTGACGATTCCCACGGACATAACTGATCTAAGTAACTTCCAAATCTGGGAATGGGATTTCATAATTAAGGACTATNNNNNNNNNNTACGACGAGCAATCCACAGACCTAGGCCCATCGAAGCGTCTTATGATTGATAACATCAGAGGGGGATGGGAGGTCCTGCTGTCGCATGGGAGAATACACGG +>CLocus_3_Sample_2_Locus_3_Allele_0 [PopA_02] +AATTCGGCTTGCAACGCAAGTGACGATTCCCACGGACATAACTGATCTAAGTAACTTCCAAATCTGGGAATGGGATTTCATAATTAAGGACTATNNNNNNNNNNTACGACGAGCAATCCACAGACCTAGGCCCATCGAAGCGTCTTATGATTGATAACATCAAAGGGGGATGGGAGGTCCTACTGTCGCATGGGAGAATACACGG +>CLocus_3_Sample_2_Locus_3_Allele_1 [PopA_02] +AATTCGGCTTGCAACGCAAGTGACGATTCCCACGGACATAACTGATCTAAGTAACTTCCAAATCTGGGAATGGGATTTCATAATTAAGGACTATNNNNNNNNNNTACGACGAGCAATCCACAGACCTAGGCCCATCGAAGCGTCTTATGATTGATAACATCAGAGGGGGATGGGAGGTCCTGCTGTCGCATGGGAGAATACACGG |
| b |
| diff -r 000000000000 -r b2e3553e1be2 test-data/populations/populations.snps.genepop --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/populations/populations.snps.genepop Mon Jul 01 10:58:28 2019 -0400 |
| b |
| @@ -0,0 +1,5 @@ +# Stacks v2.4; GenePop v4.1.3; June 17, 2019 +1_33,1_88,2_144,2_156,3_162,3_181 +pop +PopA_01, 0102 0102 0204 0304 0303 0303 +PopA_02, 0102 0102 0204 0304 0103 0103 |
| b |
| diff -r 000000000000 -r b2e3553e1be2 test-data/populations/populations.snps.vcf --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/populations/populations.snps.vcf Mon Jul 01 10:58:28 2019 -0400 |
| b |
| @@ -0,0 +1,21 @@ +##fileformat=VCFv4.2 +##fileDate=20190617 +##source="Stacks v2.4" +##INFO=<ID=AD,Number=R,Type=Integer,Description="Total Depth for Each Allele"> +##INFO=<ID=AF,Number=A,Type=Float,Description="Allele Frequency"> +##INFO=<ID=DP,Number=1,Type=Integer,Description="Total Depth"> +##INFO=<ID=NS,Number=1,Type=Integer,Description="Number of Samples With Data"> +##FORMAT=<ID=AD,Number=R,Type=Integer,Description="Allele Depth"> +##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read Depth"> +##FORMAT=<ID=HQ,Number=2,Type=Integer,Description="Haplotype Quality"> +##FORMAT=<ID=GL,Number=G,Type=Float,Description="Genotype Likelihood"> +##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality"> +##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype"> +##INFO=<ID=loc_strand,Number=1,Type=Character,Description="Genomic strand the corresponding Stacks locus aligns on"> +#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT PopA_01 PopA_02 +1 34 . A C . PASS NS=2;AF=0.500 GT:DP:AD:GQ:GL 0/1:18:9,9:40:-20.07,0.00,-20.07 0/1:12:6,6:40:-13.54,-0.00,-13.54 +1 89 . A C . PASS NS=2;AF=0.500 GT:DP:AD:GQ:GL 0/1:18:9,9:40:-20.07,0.00,-20.07 0/1:12:6,6:40:-13.54,-0.00,-13.54 +2 145 . C T . PASS NS=2;AF=0.500 GT:DP:AD:GQ:GL 0/1:17:9,8:40:-17.57,0.00,-20.29 0/1:13:5,8:40:-18.77,-0.00,-10.39 +2 157 . G T . PASS NS=2;AF=0.500 GT:DP:AD:GQ:GL 0/1:17:9,8:40:-17.57,0.00,-20.29 0/1:13:5,8:40:-18.77,-0.00,-10.39 +3 163 . G A . PASS NS=2;AF=0.250 GT:DP:AD:GQ:GL 0/0:23:23,0:40:-0.00,-6.89,-68.45 0/1:23:11,12:40:-28.67,0.00,-25.99 +3 182 . G A . PASS NS=2;AF=0.250 GT:DP:AD:GQ:GL 0/0:23:23,0:40:-0.00,-6.89,-68.45 0/1:23:11,12:40:-28.67,0.00,-25.99 |
| b |
| diff -r 000000000000 -r b2e3553e1be2 test-data/populations/populations.structure --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/populations/populations.structure Mon Jul 01 10:58:28 2019 -0400 |
| b |
| @@ -0,0 +1,6 @@ +# Stacks v2.4; Structure v2.3; June 17, 2019 + 1_33 1_88 2_144 2_156 3_162 3_181 +PopA_01 1 1 1 2 3 3 3 +PopA_01 1 2 2 4 4 3 3 +PopA_02 1 1 1 2 3 1 1 +PopA_02 1 2 2 4 4 3 3 |
| b |
| diff -r 000000000000 -r b2e3553e1be2 test-data/populations/populations.sumstats.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/populations/populations.sumstats.tsv Mon Jul 01 10:58:28 2019 -0400 |
| b |
| @@ -0,0 +1,8 @@ +# 1 PopA_01,PopA_02 +# Locus ID Chr BP Col Pop ID P Nuc Q Nuc N P Obs Het Obs Hom Exp Het Exp Hom Pi Smoothed Pi Smoothed Pi P-value Fis Smoothed Fis Smoothed Fis P-value HWE P-value Private +1 un 34 33 1 A C 2 0.50000000 1.00000 0.00000 0.50000 0.50000 0.66667 0.00000 0.00000 -0.50000 0.00000 0.00000 0.00000 0 +1 un 89 88 1 A C 2 0.50000000 1.00000 0.00000 0.50000 0.50000 0.66667 0.00000 0.00000 -0.50000 0.00000 0.00000 0.00000 0 +2 un 367 162 1 G A 2 0.75000000 0.50000 0.50000 0.37500 0.62500 0.50000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0 +2 un 386 181 1 G A 2 0.75000000 0.50000 0.50000 0.37500 0.62500 0.50000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0 +3 un 554 144 1 C T 2 0.50000000 1.00000 0.00000 0.50000 0.50000 0.66667 0.00000 0.00000 -0.50000 0.00000 0.00000 0.00000 0 +3 un 566 156 1 G T 2 0.50000000 1.00000 0.00000 0.50000 0.50000 0.66667 0.00000 0.00000 -0.50000 0.00000 0.00000 0.00000 0 |
| b |
| diff -r 000000000000 -r b2e3553e1be2 test-data/populations/populations.sumstats_summary.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/populations/populations.sumstats_summary.tsv Mon Jul 01 10:58:28 2019 -0400 |
| b |
| @@ -0,0 +1,6 @@ +# Variant positions +# Pop ID Private Num_Indv Var StdErr P Var StdErr Obs_Het Var StdErr Obs_Hom Var StdErr Exp_Het Var StdErr Exp_Hom Var StdErr Pi Var StdErr Fis Var StdErr +1 0 2.00000 0.00000 0.00000 0.58333 0.01667 0.05270 0.83333 0.06667 0.10541 0.16667 0.06667 0.10541 0.45833 0.00417 0.02635 0.54167 0.00417 0.02635 0.61111 0.00741 0.03514 -0.33333 0.06667 0.00000 +# All positions (variant and fixed) +# Pop ID Private Sites Variant_Sites Polymorphic_Sites %Polymorphic_Loci Num_Indv Var StdErr P Var StdErr Obs_Het Var StdErr Obs_Hom Var StdErr Exp_Het Var StdErr Exp_Hom Var StdErr Pi Var StdErr Fis Var StdErr +1 0 583 6 6 1.02916 2.00000 0.00000 0.00000 0.99571 0.00191 0.00181 0.00858 0.00766 0.00362 0.99142 0.00766 0.00362 0.00472 0.00218 0.00193 0.99528 0.00218 0.00193 0.00629 0.00387 0.00258 -0.00343 0.00171 0.00000 |
| b |
| diff -r 000000000000 -r b2e3553e1be2 test-data/populations/populations.treemix --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/populations/populations.treemix Mon Jul 01 10:58:28 2019 -0400 |
| b |
| @@ -0,0 +1,8 @@ +# Stacks v2.4; TreeMix v1.1; June 17, 2019 +1 +2,2 +2,2 +2,2 +2,2 +3,1 +3,1 |
| b |
| diff -r 000000000000 -r b2e3553e1be2 test-data/populations/populations.var.phylip --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/populations/populations.var.phylip Mon Jul 01 10:58:28 2019 -0400 |
| b |
| @@ -0,0 +1,3 @@ +1 6 +1 MMYKRR +# Stacks v2.4; Phylip sequential; June 17, 2019 |
| b |
| diff -r 000000000000 -r b2e3553e1be2 test-data/populations/populations.var.phylip.log --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/populations/populations.var.phylip.log Mon Jul 01 10:58:28 2019 -0400 |
| b |
| @@ -0,0 +1,8 @@ +# Stacks v2.4; Phylip sequential; June 17, 2019 +# Seq Pos Locus ID Column Population +0 1 33 1:M, +1 1 88 1:M, +2 2 144 1:Y, +3 2 156 1:K, +4 3 162 1:R, +5 3 181 1:R, |
| b |
| diff -r 000000000000 -r b2e3553e1be2 test-data/procrad/R1.fa.discards --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/procrad/R1.fa.discards Mon Jul 01 10:58:28 2019 -0400 |
| b |
| b'@@ -0,0 +1,9556 @@\n+>lane1_fakedata0_11 1:N:0:\n+GGTTGTAATTTGGCTTGCAACGCAAGTGACGATTCCCACGGACATAACTGATCTAAGTAACTTCCAAATCTGGGAATGGGATTTCATAATTAAGGACTAT\n+>lane1_fakedata1_0 1:N:0:\n+GGTGTGAATTACGTCCGCGTTTGGATTTTGGACTCGGGTCCTGTGTCCGCTGCCAGGACAAGTAAGCTGAAAGTATTCCCTTCTCCTTTTTAGGGTAGCT\n+>lane1_fakedata1_1 1:N:0:\n+GGTGTGAATTACGTCCGCGTTTGGATTTTGGACTCGGGTCCTGTGTCCGTTGCCAGGACAAGTAAGCTGAAAGTATTCCCTTCTCCTTTTTAGGGTAGCT\n+>lane1_fakedata1_2 1:N:0:\n+GGTGTGAATTACGTCCGCGTTTGGATTTTGGACTCGGGTCCTGTGTCCGTTGCCAGGACAAGTAAGCTGAAAGTATTCCCTTCTCCTTTTTAGGGTAGCT\n+>lane1_fakedata1_3 1:N:0:\n+GGTGTGAATTACGTCCGCGTTTGGATTTTGGACTCGGGTCCTGTGTCCGTTGCCAGGACAAGTAAGCTGAAAGTATTCCCTTCTCCTTTTTAGGGTAGCT\n+>lane1_fakedata1_4 1:N:0:\n+GGTGTGAATTACGTCCGCGTTTGGATTTTGGACTCGGGTCCTGTGTCCGTTGCCAGGACAAGTAAGCTGAAAGTATTCCCTTCTCCTTTTTAGGGTAGCT\n+>lane1_fakedata1_5 1:N:0:\n+GGTGTGAATTACGTCCGCGTTTGGATTTTGGACTCGGGTCCTGTGTCCGTTGCCAGGACAAGTAAGCTGAAAGTATTCCCTTCTCCTTTTTAGGGTAGCT\n+>lane1_fakedata1_6 1:N:0:\n+GGTGTGAATTACGTCCGCGGTTGGATTTTGGACTCGGGTCCTGTGTCCGTTGCCAGGACAAGTAAGCTGAAAGTATTCCCTTCTCCTTTTTAGGGTAGCT\n+>lane1_fakedata1_7 1:N:0:\n+GGTGTGAATTACGTCCGCGTTTGGATTTTGGACTCGGGTCCTGTGTCCGTTGCCAGGACAAGTAAGCTGAAAGTATTCCCTTCTCCTTTTTAGGGTAGCT\n+>lane1_fakedata1_8 1:N:0:\n+GGTGTGAATTACGTCCGCGTTTGGATTTTGGACTCGGGTCCTGTGTCCGTTGCCAGGACAAGTAAGCTGAAAGTATTCCCTTCTCCTTTTTAGGGTAGCT\n+>lane1_fakedata1_9 1:N:0:\n+GGTGTGAATTACGTCCGCGTTTGGATTTTGGACTCGGGTCCTGTGTCCGTTGCCAGGACAAGTAAGCTGAAAGTATTCCCTTCTCCTTTTTAGGGTAGCT\n+>lane1_fakedata1_0 1:N:0:\n+TTTAAGAATTACGTCCGCGTTTAGATTTTGGACTCGGGTCCTGTGTCCGTTGCCAGGACAAGTAAGCTGAAAGTATTCCCTTCTCTTTTTTAGGGTAGCT\n+>lane1_fakedata1_1 1:N:0:\n+TTTAAGAATTACGTCCGCGTTTAGATTTTGGACTCGGGTCCTGTGTCCGTTGCCAGGACAAGTAAGCTGAAAGTATTCCCTTCTCTTTTTTAGGGTAGCT\n+>lane1_fakedata1_2 1:N:0:\n+TTTAAGAATTACGTCCGCGTTTAGATTTTGGACTCGGGTCCTGTGTCCGTTGCCAGGACAAGTAAGCTGAAAGTATTCCCTTCTCTTTTTTAGGGTAGCT\n+>lane1_fakedata1_3 1:N:0:\n+TTTAAGAATTACGTCCGCGTTTAGATTTTGGACTCGGGTCCTGTGTCCGTTGCCAGGACAAGTAAGCTGAAAGTATTCCCTTCTCTTTTTTAGGGTAGCT\n+>lane1_fakedata1_4 1:N:0:\n+TTTAAGAATTACGTCCGCGTTTAGATTTTGGACTCGGGTCCTGTGTCCGTTGCCAGGACAAGTAAGCTGAAAGTATTCCCTTCTCTTTTTTAGGGTAGCT\n+>lane1_fakedata1_5 1:N:0:\n+TTTAAGAATTACGTCCGCGTTTAGATTTGGGACTCGGGTCCTGTGTCCGTTGCCAGGACAAGTAAGCTGAAAGTATTCCCTTCTCTTTTTTAGGGTAGCT\n+>lane1_fakedata1_6 1:N:0:\n+TTTAAGAATTACGTCCGCGTTTAGATTTTGGACTCGGGTCCTGTGTCCGTTGCCAGGACAAGTAAGCTGAAAGTATTCCCTTCTCTTTTTTAGGGTAGCT\n+>lane1_fakedata1_7 1:N:0:\n+TTTAAGAATTACGTCCGCGTTTAGATTTTGGACTCGGGTCCTGTGTCCGTTGCCAGGACAAGTAAGCTGAAAGTATTCCCTTCTCTTTTTTAGGGTAGCT\n+>lane1_fakedata1_8 1:N:0:\n+TTTAAGAATTACGTCCGCGTTTAGATTTTGGACTCGGGTCCTGTGTCCGTTGCCAGGACAAGTAAGCTGAAAGTATTCCCTTCTCTTTTTTAGGGTAGCT\n+>lane1_fakedata1_9 1:N:0:\n+TTTAAGAATTACGTCCGCGTTGAGATTTTGGACTCGGGTCCTGTGTCCGTTGCCAGGACAAGTAAGCTGAAAGTATTCCCTTCTCTTTTTTAGGGTAGCT\n+>lane1_fakedata1_10 1:N:0:\n+TTTAAGAATTACGTCCGCGTTTAGATTTTGGACTCGGGTCCTGTGTCCGTTGCCAGGACAAGTAAGCTGAAAGTATTCCCTTCTCTTTTTTAGGGTAGCT\n+>lane1_fakedata1_11 1:N:0:\n+TTTAAGAATTACGTCCGCGTTTAGATTTTGGACTCGGGTCCTGTGTCCGTTGCCAGGACAAGTAAGCTGAAAGTATTCCCTTCTCTTTTTTAGGGTAGCT\n+>lane1_fakedata1_12 1:N:0:\n+TTTAAGAATTACGTCCGCGTTTAGATTTTGGACTCGGGGCCTGTGTCCGTTGCCAGGACAAGTAAGCTGAAAGTATTCCCTTCTCCTTTTTAGGGTAGCT\n+>lane1_fakedata1_13 1:N:0:\n+TTTAAGAATTACGTCCGCGTTTAGATTTTGGACTCGGGGCCTGTGTCCGTTGCCAGGACAAGTAAGCTGAAAGTATTCCCTTCTCCTTTTTAGGGTAGCT\n+>lane1_fakedata1_14 1:N:0:\n+TTTAAGAATTACGTCCGCGTTTAGATTTTGGACTCGGGGCCTGTGTCCGTTGCCAGGACAAGTAAGCTGAAAGTATTCCCTTCTCCTTTTTAGGGTAGCT\n+>lane1_fakedata1_15 1:N:0:\n+TTTAAGAATTACGTCCGCGTTTAGATTTTGGACTCGGGGCCTGTGTCCGTTGCCAGGACAAGTAAGCTGAAAGTATTCCCTTCTCTTTTTTAGGGTAGCT\n+>lane1_fakedata1_16 1:N:0:\n+TTTAAGAATTACGTCCGCGTTTAGATTTTGGACTCGGGGCCTGTGTCCGTTGCCAGGACAAGTAAGCTGAAAGTATTCCCTTCTCCTTTTTAGGGTAGCT\n+>lane1_fakedata1_17 1:N:0:\n+TTTAAGAATTACGTCCGCGTTTAGATTTTGGACTCGGGGCCTGTGTCCGTTGCCAGGACAAGTAAGCTGAAAGTATTCCCTTCTCCTTTTTAGGGTAGCT\n+>lane1_fakedata1_18 1:N:0:\n+TTTAAGAATTACGTCCGCGTTTAGATTTTGGACTCGGGGCCTGTGTCCGTTGCCAGGACAAGTAAGCTGAAAGTATTCCCTTCTCCTTTTTAGGGTAGCT\n+>lane1_fakedata1_19 1:N:0:\n+TTTAAGAATTACGTCCGCGTTTAGATTTTGGACTCGGGGCCTGTGTCCGTTGCCAGGACAAGTAAGCTGAA'..b'_11 1:N:0:\n+AGGAAAAATTATAACAAAGGTCGACCTGACTCAGCCATTGTTGATAGACGCGAAAATAACGAAGCAGGATGACCGCAAGTGCAAACCATTACCAATGACC\n+>lane1_fakedata9_12 1:N:0:\n+AGGAAAAATTATAACAAAGGTCGACCTGACTCAGCCATTGTTGATAGACGCGAAAATAACGAAGCAGGATGACCGCAAGTGCAAACCATTACCAATGACC\n+>lane1_fakedata9_13 1:N:0:\n+AGGAAAAATTATAACAAAGGTCGACCTGACTCAGCCATTGTTGATAGACGCGAAAATAACGAAGCAGGATGACCGCAAGTGCAAACCATTACCAATGACC\n+>lane1_fakedata9_0 1:N:0:\n+GGGTAAAATTATAACAAAGGTCGACCTGACTCAGCCATTGTTGATAGACGCGAAAATAACGAAGCAGGATGACCGCAAGTGCAAACCATTACCAATGACC\n+>lane1_fakedata9_1 1:N:0:\n+GGGTAAAATTATAACAAAGGTCGACCTGACTCAGCCATTGTTGATAGACGCGAAAATAACGAAGCAGGATGACCGCAAGTGCAAACCATTACCAATGACC\n+>lane1_fakedata9_2 1:N:0:\n+GGGTAAAATTATAACAAAGGTCGACCTGACTCAGCCATTGTTGATAGACGCGAAAATAACGAAGCAGGATGACCGCAAGTGCAAACCATTACCAATGACC\n+>lane1_fakedata9_3 1:N:0:\n+GGGTAAAATTATAACAAAGGTCGACCTGACTCAGCCATTGTTGATAGACGCGAAAATAACGAAGCAGGATTACCGCAAGTGCAAACCATTACCAATGACC\n+>lane1_fakedata9_4 1:N:0:\n+GGGTAAAATTATAACAAAGGTCGACCTGACTCAGCCATTGTTGATAGACGCGAAAATAACGAAGCAGGATGACCGCAAGTGCAAACCATTACCAATGACC\n+>lane1_fakedata9_5 1:N:0:\n+GGGTAAAATTATAACAAAGGTCGACCTGACTCAGCCATTGTTGATAGACGCGAAAATAACGAAGCAGGATGACCGCAAGTGCAAACCATTACCAATGACC\n+>lane1_fakedata9_6 1:N:0:\n+GGGTAAAATTATAACAAAGGTCGACCTGACTCAGCCATTGTTGATAGACGCGAAAATAACGAAGCAGGATGACCGCAAGTGCAAACCATTACCAATGACC\n+>lane1_fakedata9_7 1:N:0:\n+GGGTAAAATTATAACAAAGGTCGACCTGACTCAGCCATTGTTGATAGACGCGAAAATAACGAAGCAGGATGACCGCAAGTGCAAACCATTACCAATGACC\n+>lane1_fakedata9_8 1:N:0:\n+GGGTAAAATTATAACAAAGGTCGACCTGACTCAGCCATTGTTGATAGACGCGAAAATAACGAAGCAGGATGACCGCAAGTGCAAACCATTACCAATGACC\n+>lane1_fakedata9_9 1:N:0:\n+GGGTAAAATTATAACAAAGGTCGACCTGACTCAGCCATTGTTGATAGACGCGAAAATAACGAAGCAGGATGACCGCAAGTGCAAACCATTGCCAATGACC\n+>lane1_fakedata9_10 1:N:0:\n+GGGTAAAATTATAACAAAGGTCGACCTGACTCAGCCATTGTTGATAGACGCGAAAATAACGAAGCAGGATGACCGCAAGTGCAAACCATAACCAATGACC\n+>lane1_fakedata9_11 1:N:0:\n+GGGTAAAATTATAACAAAGGTCGACCTGACTCAGCCATTGTTGATAGACGCGAAAATAACGAAGCAGGATGACCGCAAGTGCAAACCATTACCAATGACC\n+>lane1_fakedata9_12 1:N:0:\n+GGGTAAAATTATAACAAAGGTCGACCTGACTCAGCCATTGTTGATAGACGCGAAAATAACGAAGCAGGATGACCGCAAGTGCAAACCATTACCAATGACC\n+>lane1_fakedata9_13 1:N:0:\n+GGGTAAAATTATAACAAAGGTCGACCTGACTCAGCCATTGTTGATAGACGCGAAAATAACGAAGCAGGATGACCGCAAGTGCAAACCATTACCAATGACC\n+>lane1_fakedata9_14 1:N:0:\n+GGGTAAAATTATAACAAAGGTCGACCTGACTCAGCCATTGTTGATAGACGCGAAAATAACGAAGCAGGATGACCGCAAGTGCAAACCATTACCAATGACC\n+>lane1_fakedata9_15 1:N:0:\n+GGGTAAAATTATAACAAAGGTCGACCTGACTCAGCCATTGTTGATAGACGCGAAAATAACGAAGCAGGATGACCGCAAGTGCAAACCATTACCAATGACC\n+>lane1_fakedata9_16 1:N:0:\n+GGGTAAAATTATAACAAAGGTCGACCTGACTCAGCCATTGTTGATAGACGCGAAAATAACGAAGCAGGATGACCGCAAGTGCAAACCATTACCAATGACC\n+>lane1_fakedata9_17 1:N:0:\n+GGGTAAAATTATAACAAAGGTCGACCTGACTCAGCCATTGTTGATAGACGCGAAAATAACGAAGCAGGATGACCGCAAGTGCAAACCATTACCAATGACC\n+>lane1_fakedata9_18 1:N:0:\n+GGGTAAAATTATAACAAAGGTCGACCTGACTCAGCCATTGTTGATAGACGCGAAAATAACGAAGCAGGATGACCGCAAGTGCAAACCATTACCAATGACC\n+>lane1_fakedata9_19 1:N:0:\n+GGGTAAAATTATAACAAAGGTCGACCTGACTCAGCCATTGTTGATAGACGCGAAAATAACGAAGCAGGATGACCGCAAGTGCAAACCATTACCAATGACC\n+>lane1_fakedata9_20 1:N:0:\n+GGGTAAAATTATAACAAAGGTCGACCTGACTCAGCCATTGTTGATAGACGCGAAAATAACGAAGCAGGATGACCGCAAGTGCAAACCATTACCAATGACC\n+>lane1_fakedata9_21 1:N:0:\n+GGGTAAAATTATAACAAAGGTCGACCTGACTCAGCCATTGTTGATAGACGCGAAAATAACGAAGCAGGATGACCGCAAGTGCAAACCATTACCAATGACC\n+>lane1_fakedata9_22 1:N:0:\n+GGGTAAAATTATAACAAAGGTCGACCTGACTCAGCCATTGTTGATAGACGCGAAAATAACGAAGCAGGATGACCGCAAGTGCAAACCATTACCAATGACC\n+>lane1_fakedata9_23 1:N:0:\n+GGGTAAAATTATAACAAAGGTCGACCTGACTCAGCCATTGTTGATAGACGCGAAAATAACGAAGCAGGATGACCGCAAGTGCAAACCATTACCAATGACC\n+>lane1_fakedata9_0 1:N:0:\n+AAGATAAATTATAACAAAGGTCGACCTGACTCAGCCATTGTTGATAGACGCGAAAATAACGAAGCAGGATGACCGCAAGTGCAAACCATTACCAATGACC\n+>lane1_fakedata9_1 1:N:0:\n+AAGATAAATTATAACAAAGGTCGACCTGACTCAGCCATTGTTGATAGACGCGAAAATAACGAAGCAGGATGACCGCAAGTGCAAACCATTACCAATGACC\n+>lane1_fakedata9_2 1:N:0:\n+AAGATAAATTATAACAAAGGTCGACCTGACTCAGCCATTGTTGATAGACGCGAAAATAACGAAGCAGGATGACCGCAAGTGCAAACCATTACCAATGACC\n+>lane1_fakedata9_3 1:N:0:\n+AAGATAAATTATAACAAAGGTCGACCTGACTCAGCCATTGTTGATAGACGCGAAAATAACGAAGCAGGATGACCGCAAGTGCAAACCATTACCAATGACC\n' |
| b |
| diff -r 000000000000 -r b2e3553e1be2 test-data/procrad/R1.fq --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/procrad/R1.fq Mon Jul 01 10:58:28 2019 -0400 |
| b |
| b'@@ -0,0 +1,28000 @@\n+@lane1_fakedata0_0 1:N:0:\n+GGTGTGAATTCGGCTTGCAACGCAAGTGACGATTCCCACGGACATAACTGATCTAAGTAACTTCCAAATCTGGGAATGGGATTTCATAATTAAGGACTAT\n++\n+BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB\n+@lane1_fakedata0_1 1:N:0:\n+GGTGTGAATTCGGCTTGCAACGCAAGTGACGATTCCCACGGACATAACTGATCTAAGTAACTTCCAAATCTGGGAATGGGATTTCATAATTAAGGACTAT\n++\n+BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB\n+@lane1_fakedata0_2 1:N:0:\n+GGTGTGAATTCGGCTTGCAACGCAAGTGACGATTCCCACGGACATAACTGATCTAAGTAACTTCCAAATCTGGGAATGGGATTTCATAATTAAGGACTAT\n++\n+BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB\n+@lane1_fakedata0_3 1:N:0:\n+GGTGTGAATTCGGCTTGCAACGCAAGTGACGATTCCCACGGACATAACTGATCTAAGTAACTTCCAAATCTGGGAATGGGATTTCATAATTAAGGACTAT\n++\n+BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB\n+@lane1_fakedata0_4 1:N:0:\n+GGTGTGAATTCGGCTTGCAACGCAAGTGACGATTCCCACGGACATAACTGATCTAAGTAACTTCCAAATCTGGGAATGGGATTTCATAATTAAGGACTAT\n++\n+BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB\n+@lane1_fakedata0_5 1:N:0:\n+GGTGTGAATTCGGCTTGCAACGCAAGTGACGATTCCCACGGACATAACTGATCTAAGTAACTTCCAAATCTGGGAATGGGATTTCATAATTAAGGACTAT\n++\n+BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB\n+@lane1_fakedata0_6 1:N:0:\n+GGTGTGAATTCGGCTTGCAACGCAAGTGACGATTCCCACGGACATAACTGATCTAAGTAACTTCCAAATCTGGGAATGGGATTTCATAATTAAGGACTAT\n++\n+BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB\n+@lane1_fakedata0_7 1:N:0:\n+GGTGTGAATTCGGCTTGCAACGCAAGTGACGATTCCCACGGACATAACTGATCTAAGTAACTTCCAAATCTGGGAATGGGATTTCATAATTAAGGACTAT\n++\n+BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB\n+@lane1_fakedata0_8 1:N:0:\n+GGTGTGAATTCGGCTTGCAACGCAAGTGACGATTCCCACGGACATAACTGATCTAAGTAACTTCCAAATCTGGGAATGGGATTTCATAATTAAGGACTAT\n++\n+BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB\n+@lane1_fakedata0_9 1:N:0:\n+GGTGTGAATTCGGCTTGCAACGCAAGTGACGATTCCCACGGACATAACTGATCTAAGTAACTTCCAAATCTGGGAATGGGATTTCATAATTAAGGACTAT\n++\n+BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB\n+@lane1_fakedata0_10 1:N:0:\n+GGTGTGAATTCGGCTTGCAACGCAAGTGACGATTCCCACGGACATAACTGATCTAAGTAACTTCCAAATCTGGGAATGGGATTTCATAATTAAGGACTAT\n++\n+BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB\n+@lane1_fakedata0_11 1:N:0:\n+GGTGTGAATTCGGCTTGCAACGCAAGTGACGATTCCCACGGACATAACTGATCTAAGTAACTTCCAAATCTGGGAATGGGATTTCATAATTAAGGACTAT\n++\n+BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB\n+@lane1_fakedata0_12 1:N:0:\n+GGTGTGAATTCGGCTTGCAACGCAAGTGACGATTCCCACGGACATAACTGATCTAAGTAACTTCCAAATCTGGGAATGGGATTTCATAATTAAGGACTAT\n++\n+BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB\n+@lane1_fakedata0_13 1:N:0:\n+GGTGTGAATTCGGCTTGCAACGCAAGTGACGATTCCCACGGACATAACTGATCTAAGTAACTTCCAAATCTGGGAATGGGATTTCATAATTAAGGACTAT\n++\n+BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB\n+@lane1_fakedata0_14 1:N:0:\n+GGTGTGAATTCGGCTTGCAACGCAAGTGACGATTCCCACGGACATAACTGATCTAAGTAACTTCCAAATCTGGGAATGGGATTTCATAATTAAGGACTAT\n++\n+BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB\n+@lane1_fakedata0_15 1:N:0:\n+GGTGTGAATTCGGCTTGCAACGCAAGTGACGATTCCCACGGACATAACTGATCTAAGTAACTTCCAAATCTGGGAATGGGATTTCATAATTAAGGACTAT\n++\n+BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB\n+@lane1_fakedata0_16 1:N:0:\n+GGTGTGAATTCGGCTTGCAACGCAAGTGACGATTCCCACGGACATAACTGATCTAAGTAACTTCCAAATCTGGGAATGGGATTTCATAATTAAGGACTAT\n++\n+BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB'..b'BBBBBBB\n+@lane1_fakedata9_11 1:N:0:\n+GGGTAAAATTATAACAAAGGTCGACCTGACTCAGCCATTGTTGATAGACGCGAAAATAACGAAGCAGGATGACCGCAAGTGCAAACCATTACCAATGACC\n++\n+BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB\n+@lane1_fakedata9_12 1:N:0:\n+GGGTAAAATTATAACAAAGGTCGACCTGACTCAGCCATTGTTGATAGACGCGAAAATAACGAAGCAGGATGACCGCAAGTGCAAACCATTACCAATGACC\n++\n+BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB\n+@lane1_fakedata9_13 1:N:0:\n+GGGTAAAATTATAACAAAGGTCGACCTGACTCAGCCATTGTTGATAGACGCGAAAATAACGAAGCAGGATGACCGCAAGTGCAAACCATTACCAATGACC\n++\n+BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB\n+@lane1_fakedata9_14 1:N:0:\n+GGGTAAAATTATAACAAAGGTCGACCTGACTCAGCCATTGTTGATAGACGCGAAAATAACGAAGCAGGATGACCGCAAGTGCAAACCATTACCAATGACC\n++\n+BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB\n+@lane1_fakedata9_15 1:N:0:\n+GGGTAAAATTATAACAAAGGTCGACCTGACTCAGCCATTGTTGATAGACGCGAAAATAACGAAGCAGGATGACCGCAAGTGCAAACCATTACCAATGACC\n++\n+BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB\n+@lane1_fakedata9_16 1:N:0:\n+GGGTAAAATTATAACAAAGGTCGACCTGACTCAGCCATTGTTGATAGACGCGAAAATAACGAAGCAGGATGACCGCAAGTGCAAACCATTACCAATGACC\n++\n+BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB\n+@lane1_fakedata9_17 1:N:0:\n+GGGTAAAATTATAACAAAGGTCGACCTGACTCAGCCATTGTTGATAGACGCGAAAATAACGAAGCAGGATGACCGCAAGTGCAAACCATTACCAATGACC\n++\n+BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB\n+@lane1_fakedata9_18 1:N:0:\n+GGGTAAAATTATAACAAAGGTCGACCTGACTCAGCCATTGTTGATAGACGCGAAAATAACGAAGCAGGATGACCGCAAGTGCAAACCATTACCAATGACC\n++\n+BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB\n+@lane1_fakedata9_19 1:N:0:\n+GGGTAAAATTATAACAAAGGTCGACCTGACTCAGCCATTGTTGATAGACGCGAAAATAACGAAGCAGGATGACCGCAAGTGCAAACCATTACCAATGACC\n++\n+BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB\n+@lane1_fakedata9_20 1:N:0:\n+GGGTAAAATTATAACAAAGGTCGACCTGACTCAGCCATTGTTGATAGACGCGAAAATAACGAAGCAGGATGACCGCAAGTGCAAACCATTACCAATGACC\n++\n+BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB\n+@lane1_fakedata9_21 1:N:0:\n+GGGTAAAATTATAACAAAGGTCGACCTGACTCAGCCATTGTTGATAGACGCGAAAATAACGAAGCAGGATGACCGCAAGTGCAAACCATTACCAATGACC\n++\n+BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB\n+@lane1_fakedata9_22 1:N:0:\n+GGGTAAAATTATAACAAAGGTCGACCTGACTCAGCCATTGTTGATAGACGCGAAAATAACGAAGCAGGATGACCGCAAGTGCAAACCATTACCAATGACC\n++\n+BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB\n+@lane1_fakedata9_23 1:N:0:\n+GGGTAAAATTATAACAAAGGTCGACCTGACTCAGCCATTGTTGATAGACGCGAAAATAACGAAGCAGGATGACCGCAAGTGCAAACCATTACCAATGACC\n++\n+BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB\n+@lane1_fakedata9_0 1:N:0:\n+AAGATAAATTATAACAAAGGTCGACCTGACTCAGCCATTGTTGATAGACGCGAAAATAACGAAGCAGGATGACCGCAAGTGCAAACCATTACCAATGACC\n++\n+BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB\n+@lane1_fakedata9_1 1:N:0:\n+AAGATAAATTATAACAAAGGTCGACCTGACTCAGCCATTGTTGATAGACGCGAAAATAACGAAGCAGGATGACCGCAAGTGCAAACCATTACCAATGACC\n++\n+BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB\n+@lane1_fakedata9_2 1:N:0:\n+AAGATAAATTATAACAAAGGTCGACCTGACTCAGCCATTGTTGATAGACGCGAAAATAACGAAGCAGGATGACCGCAAGTGCAAACCATTACCAATGACC\n++\n+BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB\n+@lane1_fakedata9_3 1:N:0:\n+AAGATAAATTATAACAAAGGTCGACCTGACTCAGCCATTGTTGATAGACGCGAAAATAACGAAGCAGGATGACCGCAAGTGCAAACCATTACCAATGACC\n++\n+BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB\n' |
| b |
| diff -r 000000000000 -r b2e3553e1be2 test-data/procrad/R1.fq.discards --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/procrad/R1.fq.discards Mon Jul 01 10:58:28 2019 -0400 |
| b |
| b'@@ -0,0 +1,19112 @@\n+@lane1_fakedata0_11 1:N:0:\n+GGTTGTAATTTGGCTTGCAACGCAAGTGACGATTCCCACGGACATAACTGATCTAAGTAACTTCCAAATCTGGGAATGGGATTTCATAATTAAGGACTAT\n++\n+BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB\n+@lane1_fakedata1_0 1:N:0:\n+GGTGTGAATTACGTCCGCGTTTGGATTTTGGACTCGGGTCCTGTGTCCGCTGCCAGGACAAGTAAGCTGAAAGTATTCCCTTCTCCTTTTTAGGGTAGCT\n++\n+BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB\n+@lane1_fakedata1_1 1:N:0:\n+GGTGTGAATTACGTCCGCGTTTGGATTTTGGACTCGGGTCCTGTGTCCGTTGCCAGGACAAGTAAGCTGAAAGTATTCCCTTCTCCTTTTTAGGGTAGCT\n++\n+BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB\n+@lane1_fakedata1_2 1:N:0:\n+GGTGTGAATTACGTCCGCGTTTGGATTTTGGACTCGGGTCCTGTGTCCGTTGCCAGGACAAGTAAGCTGAAAGTATTCCCTTCTCCTTTTTAGGGTAGCT\n++\n+BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB\n+@lane1_fakedata1_3 1:N:0:\n+GGTGTGAATTACGTCCGCGTTTGGATTTTGGACTCGGGTCCTGTGTCCGTTGCCAGGACAAGTAAGCTGAAAGTATTCCCTTCTCCTTTTTAGGGTAGCT\n++\n+BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB\n+@lane1_fakedata1_4 1:N:0:\n+GGTGTGAATTACGTCCGCGTTTGGATTTTGGACTCGGGTCCTGTGTCCGTTGCCAGGACAAGTAAGCTGAAAGTATTCCCTTCTCCTTTTTAGGGTAGCT\n++\n+BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB\n+@lane1_fakedata1_5 1:N:0:\n+GGTGTGAATTACGTCCGCGTTTGGATTTTGGACTCGGGTCCTGTGTCCGTTGCCAGGACAAGTAAGCTGAAAGTATTCCCTTCTCCTTTTTAGGGTAGCT\n++\n+BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB\n+@lane1_fakedata1_6 1:N:0:\n+GGTGTGAATTACGTCCGCGGTTGGATTTTGGACTCGGGTCCTGTGTCCGTTGCCAGGACAAGTAAGCTGAAAGTATTCCCTTCTCCTTTTTAGGGTAGCT\n++\n+BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB\n+@lane1_fakedata1_7 1:N:0:\n+GGTGTGAATTACGTCCGCGTTTGGATTTTGGACTCGGGTCCTGTGTCCGTTGCCAGGACAAGTAAGCTGAAAGTATTCCCTTCTCCTTTTTAGGGTAGCT\n++\n+BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB\n+@lane1_fakedata1_8 1:N:0:\n+GGTGTGAATTACGTCCGCGTTTGGATTTTGGACTCGGGTCCTGTGTCCGTTGCCAGGACAAGTAAGCTGAAAGTATTCCCTTCTCCTTTTTAGGGTAGCT\n++\n+BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB\n+@lane1_fakedata1_9 1:N:0:\n+GGTGTGAATTACGTCCGCGTTTGGATTTTGGACTCGGGTCCTGTGTCCGTTGCCAGGACAAGTAAGCTGAAAGTATTCCCTTCTCCTTTTTAGGGTAGCT\n++\n+BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB\n+@lane1_fakedata1_0 1:N:0:\n+TTTAAGAATTACGTCCGCGTTTAGATTTTGGACTCGGGTCCTGTGTCCGTTGCCAGGACAAGTAAGCTGAAAGTATTCCCTTCTCTTTTTTAGGGTAGCT\n++\n+BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB\n+@lane1_fakedata1_1 1:N:0:\n+TTTAAGAATTACGTCCGCGTTTAGATTTTGGACTCGGGTCCTGTGTCCGTTGCCAGGACAAGTAAGCTGAAAGTATTCCCTTCTCTTTTTTAGGGTAGCT\n++\n+BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB\n+@lane1_fakedata1_2 1:N:0:\n+TTTAAGAATTACGTCCGCGTTTAGATTTTGGACTCGGGTCCTGTGTCCGTTGCCAGGACAAGTAAGCTGAAAGTATTCCCTTCTCTTTTTTAGGGTAGCT\n++\n+BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB\n+@lane1_fakedata1_3 1:N:0:\n+TTTAAGAATTACGTCCGCGTTTAGATTTTGGACTCGGGTCCTGTGTCCGTTGCCAGGACAAGTAAGCTGAAAGTATTCCCTTCTCTTTTTTAGGGTAGCT\n++\n+BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB\n+@lane1_fakedata1_4 1:N:0:\n+TTTAAGAATTACGTCCGCGTTTAGATTTTGGACTCGGGTCCTGTGTCCGTTGCCAGGACAAGTAAGCTGAAAGTATTCCCTTCTCTTTTTTAGGGTAGCT\n++\n+BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB\n+@lane1_fakedata1_5 1:N:0:\n+TTTAAGAATTACGTCCGCGTTTAGATTTGGGACTCGGGTCCTGTGTCCGTTGCCAGGACAAGTAAGCTGAAAGTATTCCCTTCTCTTTTTTAGGGTAGCT\n++\n+BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB\n'..b'BBBBBBB\n+@lane1_fakedata9_11 1:N:0:\n+GGGTAAAATTATAACAAAGGTCGACCTGACTCAGCCATTGTTGATAGACGCGAAAATAACGAAGCAGGATGACCGCAAGTGCAAACCATTACCAATGACC\n++\n+BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB\n+@lane1_fakedata9_12 1:N:0:\n+GGGTAAAATTATAACAAAGGTCGACCTGACTCAGCCATTGTTGATAGACGCGAAAATAACGAAGCAGGATGACCGCAAGTGCAAACCATTACCAATGACC\n++\n+BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB\n+@lane1_fakedata9_13 1:N:0:\n+GGGTAAAATTATAACAAAGGTCGACCTGACTCAGCCATTGTTGATAGACGCGAAAATAACGAAGCAGGATGACCGCAAGTGCAAACCATTACCAATGACC\n++\n+BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB\n+@lane1_fakedata9_14 1:N:0:\n+GGGTAAAATTATAACAAAGGTCGACCTGACTCAGCCATTGTTGATAGACGCGAAAATAACGAAGCAGGATGACCGCAAGTGCAAACCATTACCAATGACC\n++\n+BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB\n+@lane1_fakedata9_15 1:N:0:\n+GGGTAAAATTATAACAAAGGTCGACCTGACTCAGCCATTGTTGATAGACGCGAAAATAACGAAGCAGGATGACCGCAAGTGCAAACCATTACCAATGACC\n++\n+BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB\n+@lane1_fakedata9_16 1:N:0:\n+GGGTAAAATTATAACAAAGGTCGACCTGACTCAGCCATTGTTGATAGACGCGAAAATAACGAAGCAGGATGACCGCAAGTGCAAACCATTACCAATGACC\n++\n+BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB\n+@lane1_fakedata9_17 1:N:0:\n+GGGTAAAATTATAACAAAGGTCGACCTGACTCAGCCATTGTTGATAGACGCGAAAATAACGAAGCAGGATGACCGCAAGTGCAAACCATTACCAATGACC\n++\n+BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB\n+@lane1_fakedata9_18 1:N:0:\n+GGGTAAAATTATAACAAAGGTCGACCTGACTCAGCCATTGTTGATAGACGCGAAAATAACGAAGCAGGATGACCGCAAGTGCAAACCATTACCAATGACC\n++\n+BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB\n+@lane1_fakedata9_19 1:N:0:\n+GGGTAAAATTATAACAAAGGTCGACCTGACTCAGCCATTGTTGATAGACGCGAAAATAACGAAGCAGGATGACCGCAAGTGCAAACCATTACCAATGACC\n++\n+BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB\n+@lane1_fakedata9_20 1:N:0:\n+GGGTAAAATTATAACAAAGGTCGACCTGACTCAGCCATTGTTGATAGACGCGAAAATAACGAAGCAGGATGACCGCAAGTGCAAACCATTACCAATGACC\n++\n+BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB\n+@lane1_fakedata9_21 1:N:0:\n+GGGTAAAATTATAACAAAGGTCGACCTGACTCAGCCATTGTTGATAGACGCGAAAATAACGAAGCAGGATGACCGCAAGTGCAAACCATTACCAATGACC\n++\n+BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB\n+@lane1_fakedata9_22 1:N:0:\n+GGGTAAAATTATAACAAAGGTCGACCTGACTCAGCCATTGTTGATAGACGCGAAAATAACGAAGCAGGATGACCGCAAGTGCAAACCATTACCAATGACC\n++\n+BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB\n+@lane1_fakedata9_23 1:N:0:\n+GGGTAAAATTATAACAAAGGTCGACCTGACTCAGCCATTGTTGATAGACGCGAAAATAACGAAGCAGGATGACCGCAAGTGCAAACCATTACCAATGACC\n++\n+BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB\n+@lane1_fakedata9_0 1:N:0:\n+AAGATAAATTATAACAAAGGTCGACCTGACTCAGCCATTGTTGATAGACGCGAAAATAACGAAGCAGGATGACCGCAAGTGCAAACCATTACCAATGACC\n++\n+BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB\n+@lane1_fakedata9_1 1:N:0:\n+AAGATAAATTATAACAAAGGTCGACCTGACTCAGCCATTGTTGATAGACGCGAAAATAACGAAGCAGGATGACCGCAAGTGCAAACCATTACCAATGACC\n++\n+BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB\n+@lane1_fakedata9_2 1:N:0:\n+AAGATAAATTATAACAAAGGTCGACCTGACTCAGCCATTGTTGATAGACGCGAAAATAACGAAGCAGGATGACCGCAAGTGCAAACCATTACCAATGACC\n++\n+BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB\n+@lane1_fakedata9_3 1:N:0:\n+AAGATAAATTATAACAAAGGTCGACCTGACTCAGCCATTGTTGATAGACGCGAAAATAACGAAGCAGGATGACCGCAAGTGCAAACCATTACCAATGACC\n++\n+BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB\n' |
| b |
| diff -r 000000000000 -r b2e3553e1be2 test-data/procrad/R1.fq.gzip |
| b |
| Binary file test-data/procrad/R1.fq.gzip has changed |
| b |
| diff -r 000000000000 -r b2e3553e1be2 test-data/procrad/R2.fq --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/procrad/R2.fq Mon Jul 01 10:58:28 2019 -0400 |
| b |
| b'@@ -0,0 +1,28000 @@\n+@lane1_fakedata0_0 1:N:0:\n+CCGTGTATTCTCCCATGCGACAGCAGGACCTCCCATCCCCCTCTGATGTTATCAATCATATGACGCTTCGATGGGCCTAGGTCTGTGGATTGCTCGTCGT\n++\n+BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB\n+@lane1_fakedata0_1 1:N:0:\n+CCGTGTATTCTCCCATGCGACAGCAGGACCTCCCATCCCCCTCTGATGTTATCAATCATAAGACGCTTCGATGGGCCTAGGTCTGTGGATTGCTCGTCGT\n++\n+BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB\n+@lane1_fakedata0_2 1:N:0:\n+CCGTGTATTCTCCCATGCGACAGCAGGACCTCCCATCCCCCTCTGATGTTATCAATCATAAGACGCTTCGATGGGCCTAGGTCTGTGGATTGCTCGTCGT\n++\n+BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB\n+@lane1_fakedata0_3 1:N:0:\n+CCGTGTATTCTCCCATGCGACAGCAGGACCTCCCATCCCCCTCTGATGTTATCAATCATAAGACGCTTCGATGGGCCTGGGTCTGTGGATTGCTCGTCGT\n++\n+BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB\n+@lane1_fakedata0_4 1:N:0:\n+CCGTGTATTCTCCCATGCGACAGCAGGACCTCCCATCCCCCTCTGATGTTATCAATCATAAGACGCTTCGATGGGCCTAGGTCTGTGGATTGCTCGTCGT\n++\n+BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB\n+@lane1_fakedata0_5 1:N:0:\n+CCGTGTATTCTCCCATGCGACAGCAGGACCTCCCATCCCCCTCTGATGTTATCAATCATAAGACGCTTCGATGGGCCTAGGTCTGTGGATTGCTCGTCGT\n++\n+BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB\n+@lane1_fakedata0_6 1:N:0:\n+CCGTGTATTCTTCCATGCGACAGCAGGACCTCCCATCCCCCTCTGATGTTATCAATCATAAGACGCTTCGATGGGCCTAGGTCTGTGGATTGCTCGTCGT\n++\n+BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB\n+@lane1_fakedata0_7 1:N:0:\n+CCGTGTATTCTCCCATGCGACAGCAGGACCTCCCATCCCCCTCTGATGTTATCAATCATAAGACGCTTCGATGGGCCTAGGTCTGTGGATTGCTCGTCGT\n++\n+BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB\n+@lane1_fakedata0_8 1:N:0:\n+CCGTGTATTCTCCCATGCGACAGCAGGACCTCCCATCCCCCTCTGATGTTATCAATCATAAGACGCTTCGATGGGCCTAGGTCTGTGGATTGCTCGTCGT\n++\n+BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB\n+@lane1_fakedata0_9 1:N:0:\n+CCGTGTATTCTCCCATGCGACAGCAGGACCTCCCATCCCCCTCTGATGTTATCAATCATAAGACGCTTCGATGGGCCTAGGTCTGTGGATTGCTCGTCGT\n++\n+BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB\n+@lane1_fakedata0_10 1:N:0:\n+CCGTGTATTCTCCCATGCGACAGCAGGACCTCCCATCCCCCTCTGATGTTATCAATCATAAGACGCTTCGATGGGCCTAGGTCTGTGGATTGCTCGTCGT\n++\n+BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB\n+@lane1_fakedata0_11 1:N:0:\n+CCGTATTCTCCCATGCGACAGTAGGACCTCCGGATCCCCCTTTGATGTTATCAATCATAAGACGCTTCGATGGGCCTAGGTCTGTGGATTGCTCGTCGTA\n++\n+BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB\n+@lane1_fakedata0_12 1:N:0:\n+CCGTATTCTCCCATGCGACAGTAGGACCTCCGGATCCCCCTTTGATGTTATCAATCATAAGACGCTTCGATGGGCCTAGGTCTGTGGATTGCTCGTCGTA\n++\n+BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB\n+@lane1_fakedata0_13 1:N:0:\n+CCGTATTCTCCCATGCGACAGTAGGACCTCCGGATCCCCCTTTGATGTTATCAATCATAAGACGCTTCGATGGGCCTAGGTCTGTGGATTGCTCGTCGTA\n++\n+BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB\n+@lane1_fakedata0_14 1:N:0:\n+CCGTATTCTCCCATGCGACAGTAGGACCTCCGGATCCCCCTTTGATGTTATCAATCATAAGACGCTTCGATGGGCCTAGGTCTGTGGATTGCTCGTCGTA\n++\n+BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB\n+@lane1_fakedata0_15 1:N:0:\n+CCGTATTCTCCCATGCGACAGTAGGACCTCCGGATCCCCCTTTGATGTTATCAATCATAAGACGCTTCGATGGGCCTAGGTCTGTGGATTGCTCGTCGTA\n++\n+BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB\n+@lane1_fakedata0_16 1:N:0:\n+CCGTATTCTCCCATGCGACAGTAGGACCTCCGGATCCCCCTTTGATGTTATCAATCATAAGACGCTTCGATGGGCCTAGGTCTGTGGATTGCTCGTCGTA\n++\n+BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB'..b'BBBBBBB\n+@lane1_fakedata9_11 1:N:0:\n+CCGCGGTTAAAATTGCTCAGTTCCGTCCAAGCAGGTTCTTTCCTCAACCGATGCGATTGGGTTCGCAACAGCGAGCAAGGTTGCATGCTTGGTAGCCGAA\n++\n+BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB\n+@lane1_fakedata9_12 1:N:0:\n+CCGCGGTTAAAATTGCTCAGTTCCGTCCAAGCAGGTTCTTTCCTCAACCGATGCGATTGGGTTCGCAACAGCGAGCAAGGTTGCATGCTTGGTAGCCGAA\n++\n+BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB\n+@lane1_fakedata9_13 1:N:0:\n+CCGCGGTTAAAATTGCTCAGTTCCGTCCAAGCAGGTTCTTTCCTCAACCGATGCGATTGGGTTCGCAACAGCGAGCAAGGTTGCATGCTTGGTAGCCGAA\n++\n+BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB\n+@lane1_fakedata9_14 1:N:0:\n+CCGCGGTTAAAATTGCTCAGTTCCGTCCAAGCAGGTTCTTTCCTCAACCGATGCGATTGGGTTCGCAACAGCGAGCAAGGTTGCATGCTTGGTAGCCGAA\n++\n+BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB\n+@lane1_fakedata9_15 1:N:0:\n+CCGCGGTTAAAATTGCTCAGTTCCGTCCAAGCAGGTTCTTTCCTCAACCGATGCGATTGGGTTCGCAACAGCGAGCAAGGTTGCGTGCTTGGTAGCCGAA\n++\n+BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB\n+@lane1_fakedata9_16 1:N:0:\n+CCGCGGTTAAAATTGCTCAGTTCCGTCCAAGCAGGTTCTTTCCTCAACCGATGCGATTGGGTTCGCAACAGCGAGCAAGGTGGCATGCTTGGTAGCCGAA\n++\n+BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB\n+@lane1_fakedata9_17 1:N:0:\n+CCGCGGTTAAAATTGCTCAGTTCCGTCCAAGCAGGTTCTTTCCTCAACCGATGCGATTGGGTTCGCAACAGCGAGCAAGGTTGCATGCTTGGTAGCCGAA\n++\n+BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB\n+@lane1_fakedata9_18 1:N:0:\n+CCGCGGTTAAAATTGCTCAGTTCCGTCCAAGCAGGTTCTTTCCTCAACCGATGCGATTGGGTTCGCAACAGCGAGCAAGGTTGCATGCTTGGTAGCCGAA\n++\n+BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB\n+@lane1_fakedata9_19 1:N:0:\n+CCGCGGTTAAAATTGCTCAGTTCCGTCCAAGCAGGTTCTTTCCTCAACCGATGCGATTGGGTTCGCAACAGCGAGCAAGGTTGCATGCTTGGTAGCCGAA\n++\n+BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB\n+@lane1_fakedata9_20 1:N:0:\n+CCGCGGTTAAAATTGCTCAGTTCCGTCCAAGCAGGTTCTTTCCTCAACCGATGCGATTGGGTTCGCAACAGCGAGCAAGGTTGCATGCTTGGTAGCCGAA\n++\n+BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB\n+@lane1_fakedata9_21 1:N:0:\n+CCGCGGTTAAAATTGCTCAGTTCCGTCCAAGCAGGTTCTTTCCTCAACCGATGCGATTGGGTTCGCAACAGCGAGCAAGGTTGCATGCTTGGTAGCCGAA\n++\n+BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB\n+@lane1_fakedata9_22 1:N:0:\n+CCGCGGTTAAAATTGCTCAGTTCCGTCCAAGCAGGTTCTTTCCTCAACCGATGCGATTGGGTTCGCAACAGCGAGCAAGGTTGCATGCTTGGTAGCCGAA\n++\n+BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB\n+@lane1_fakedata9_23 1:N:0:\n+CCGCGGTTAAAATTGCTCAGTTCCGTCCAAGCAGGTTCTTTCCTCAACCGATGCGATTGGGTTAGCAACAGCGAGCAAGGTTGCATGCTTGGTAGCCGAA\n++\n+BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB\n+@lane1_fakedata9_0 1:N:0:\n+CCGCGGTTAAAATTGCTCAGTTCCGTCCAAGCAGGTTCTTTCCTCAACCGATGCGATTGGGTTCGCAACAGCGAGCAAGGTTGCATGCTTGGTAGCCGAA\n++\n+BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB\n+@lane1_fakedata9_1 1:N:0:\n+CCGCGGTTAAAATTGCTCAGTTCCGTCCAAGCAGGTTCTTTCCTCAACCGATGCGATTGGGTTCGCAACAGCGAGCAAGGTTGCATGCTTGGTAGCCGAA\n++\n+BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB\n+@lane1_fakedata9_2 1:N:0:\n+CCGCGGTTAAAATTGCTCAGTTCCGTCCAAGCAGGTTCTTTCCTCAACCGATGCGATTGGGTTCGCAACAGCGAGCAAGGTTGCATGCTTGGTAGCCGAA\n++\n+BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB\n+@lane1_fakedata9_3 1:N:0:\n+CCGCGGTTAAAATTGCTCAGTTCCGTCCAAGCAGGTTCTTTCCTCAACCGATGCGATTGGGTTCGCAACAGCGAGCAAGGTTGCATGCTTGGTAGCCGAA\n++\n+BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB\n' |
| b |
| diff -r 000000000000 -r b2e3553e1be2 test-data/procrad/R2.fq.discards --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/procrad/R2.fq.discards Mon Jul 01 10:58:28 2019 -0400 |
| b |
| b'@@ -0,0 +1,28000 @@\n+@lane1_fakedata0_0 1:N:0:\n+CCGTGTATTCTCCCATGCGACAGCAGGACCTCCCATCCCCCTCTGATGTTATCAATCATATGACGCTTCGATGGGCCTAGGTCTGTGGATTGCTCGTCGT\n++\n+BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB\n+@lane1_fakedata0_1 1:N:0:\n+CCGTGTATTCTCCCATGCGACAGCAGGACCTCCCATCCCCCTCTGATGTTATCAATCATAAGACGCTTCGATGGGCCTAGGTCTGTGGATTGCTCGTCGT\n++\n+BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB\n+@lane1_fakedata0_2 1:N:0:\n+CCGTGTATTCTCCCATGCGACAGCAGGACCTCCCATCCCCCTCTGATGTTATCAATCATAAGACGCTTCGATGGGCCTAGGTCTGTGGATTGCTCGTCGT\n++\n+BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB\n+@lane1_fakedata0_3 1:N:0:\n+CCGTGTATTCTCCCATGCGACAGCAGGACCTCCCATCCCCCTCTGATGTTATCAATCATAAGACGCTTCGATGGGCCTGGGTCTGTGGATTGCTCGTCGT\n++\n+BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB\n+@lane1_fakedata0_4 1:N:0:\n+CCGTGTATTCTCCCATGCGACAGCAGGACCTCCCATCCCCCTCTGATGTTATCAATCATAAGACGCTTCGATGGGCCTAGGTCTGTGGATTGCTCGTCGT\n++\n+BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB\n+@lane1_fakedata0_5 1:N:0:\n+CCGTGTATTCTCCCATGCGACAGCAGGACCTCCCATCCCCCTCTGATGTTATCAATCATAAGACGCTTCGATGGGCCTAGGTCTGTGGATTGCTCGTCGT\n++\n+BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB\n+@lane1_fakedata0_6 1:N:0:\n+CCGTGTATTCTTCCATGCGACAGCAGGACCTCCCATCCCCCTCTGATGTTATCAATCATAAGACGCTTCGATGGGCCTAGGTCTGTGGATTGCTCGTCGT\n++\n+BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB\n+@lane1_fakedata0_7 1:N:0:\n+CCGTGTATTCTCCCATGCGACAGCAGGACCTCCCATCCCCCTCTGATGTTATCAATCATAAGACGCTTCGATGGGCCTAGGTCTGTGGATTGCTCGTCGT\n++\n+BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB\n+@lane1_fakedata0_8 1:N:0:\n+CCGTGTATTCTCCCATGCGACAGCAGGACCTCCCATCCCCCTCTGATGTTATCAATCATAAGACGCTTCGATGGGCCTAGGTCTGTGGATTGCTCGTCGT\n++\n+BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB\n+@lane1_fakedata0_9 1:N:0:\n+CCGTGTATTCTCCCATGCGACAGCAGGACCTCCCATCCCCCTCTGATGTTATCAATCATAAGACGCTTCGATGGGCCTAGGTCTGTGGATTGCTCGTCGT\n++\n+BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB\n+@lane1_fakedata0_10 1:N:0:\n+CCGTGTATTCTCCCATGCGACAGCAGGACCTCCCATCCCCCTCTGATGTTATCAATCATAAGACGCTTCGATGGGCCTAGGTCTGTGGATTGCTCGTCGT\n++\n+BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB\n+@lane1_fakedata0_11 1:N:0:\n+CCGTATTCTCCCATGCGACAGTAGGACCTCCGGATCCCCCTTTGATGTTATCAATCATAAGACGCTTCGATGGGCCTAGGTCTGTGGATTGCTCGTCGTA\n++\n+BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB\n+@lane1_fakedata0_12 1:N:0:\n+CCGTATTCTCCCATGCGACAGTAGGACCTCCGGATCCCCCTTTGATGTTATCAATCATAAGACGCTTCGATGGGCCTAGGTCTGTGGATTGCTCGTCGTA\n++\n+BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB\n+@lane1_fakedata0_13 1:N:0:\n+CCGTATTCTCCCATGCGACAGTAGGACCTCCGGATCCCCCTTTGATGTTATCAATCATAAGACGCTTCGATGGGCCTAGGTCTGTGGATTGCTCGTCGTA\n++\n+BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB\n+@lane1_fakedata0_14 1:N:0:\n+CCGTATTCTCCCATGCGACAGTAGGACCTCCGGATCCCCCTTTGATGTTATCAATCATAAGACGCTTCGATGGGCCTAGGTCTGTGGATTGCTCGTCGTA\n++\n+BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB\n+@lane1_fakedata0_15 1:N:0:\n+CCGTATTCTCCCATGCGACAGTAGGACCTCCGGATCCCCCTTTGATGTTATCAATCATAAGACGCTTCGATGGGCCTAGGTCTGTGGATTGCTCGTCGTA\n++\n+BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB\n+@lane1_fakedata0_16 1:N:0:\n+CCGTATTCTCCCATGCGACAGTAGGACCTCCGGATCCCCCTTTGATGTTATCAATCATAAGACGCTTCGATGGGCCTAGGTCTGTGGATTGCTCGTCGTA\n++\n+BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB'..b'BBBBBBB\n+@lane1_fakedata9_11 1:N:0:\n+CCGCGGTTAAAATTGCTCAGTTCCGTCCAAGCAGGTTCTTTCCTCAACCGATGCGATTGGGTTCGCAACAGCGAGCAAGGTTGCATGCTTGGTAGCCGAA\n++\n+BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB\n+@lane1_fakedata9_12 1:N:0:\n+CCGCGGTTAAAATTGCTCAGTTCCGTCCAAGCAGGTTCTTTCCTCAACCGATGCGATTGGGTTCGCAACAGCGAGCAAGGTTGCATGCTTGGTAGCCGAA\n++\n+BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB\n+@lane1_fakedata9_13 1:N:0:\n+CCGCGGTTAAAATTGCTCAGTTCCGTCCAAGCAGGTTCTTTCCTCAACCGATGCGATTGGGTTCGCAACAGCGAGCAAGGTTGCATGCTTGGTAGCCGAA\n++\n+BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB\n+@lane1_fakedata9_14 1:N:0:\n+CCGCGGTTAAAATTGCTCAGTTCCGTCCAAGCAGGTTCTTTCCTCAACCGATGCGATTGGGTTCGCAACAGCGAGCAAGGTTGCATGCTTGGTAGCCGAA\n++\n+BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB\n+@lane1_fakedata9_15 1:N:0:\n+CCGCGGTTAAAATTGCTCAGTTCCGTCCAAGCAGGTTCTTTCCTCAACCGATGCGATTGGGTTCGCAACAGCGAGCAAGGTTGCGTGCTTGGTAGCCGAA\n++\n+BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB\n+@lane1_fakedata9_16 1:N:0:\n+CCGCGGTTAAAATTGCTCAGTTCCGTCCAAGCAGGTTCTTTCCTCAACCGATGCGATTGGGTTCGCAACAGCGAGCAAGGTGGCATGCTTGGTAGCCGAA\n++\n+BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB\n+@lane1_fakedata9_17 1:N:0:\n+CCGCGGTTAAAATTGCTCAGTTCCGTCCAAGCAGGTTCTTTCCTCAACCGATGCGATTGGGTTCGCAACAGCGAGCAAGGTTGCATGCTTGGTAGCCGAA\n++\n+BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB\n+@lane1_fakedata9_18 1:N:0:\n+CCGCGGTTAAAATTGCTCAGTTCCGTCCAAGCAGGTTCTTTCCTCAACCGATGCGATTGGGTTCGCAACAGCGAGCAAGGTTGCATGCTTGGTAGCCGAA\n++\n+BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB\n+@lane1_fakedata9_19 1:N:0:\n+CCGCGGTTAAAATTGCTCAGTTCCGTCCAAGCAGGTTCTTTCCTCAACCGATGCGATTGGGTTCGCAACAGCGAGCAAGGTTGCATGCTTGGTAGCCGAA\n++\n+BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB\n+@lane1_fakedata9_20 1:N:0:\n+CCGCGGTTAAAATTGCTCAGTTCCGTCCAAGCAGGTTCTTTCCTCAACCGATGCGATTGGGTTCGCAACAGCGAGCAAGGTTGCATGCTTGGTAGCCGAA\n++\n+BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB\n+@lane1_fakedata9_21 1:N:0:\n+CCGCGGTTAAAATTGCTCAGTTCCGTCCAAGCAGGTTCTTTCCTCAACCGATGCGATTGGGTTCGCAACAGCGAGCAAGGTTGCATGCTTGGTAGCCGAA\n++\n+BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB\n+@lane1_fakedata9_22 1:N:0:\n+CCGCGGTTAAAATTGCTCAGTTCCGTCCAAGCAGGTTCTTTCCTCAACCGATGCGATTGGGTTCGCAACAGCGAGCAAGGTTGCATGCTTGGTAGCCGAA\n++\n+BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB\n+@lane1_fakedata9_23 1:N:0:\n+CCGCGGTTAAAATTGCTCAGTTCCGTCCAAGCAGGTTCTTTCCTCAACCGATGCGATTGGGTTAGCAACAGCGAGCAAGGTTGCATGCTTGGTAGCCGAA\n++\n+BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB\n+@lane1_fakedata9_0 1:N:0:\n+CCGCGGTTAAAATTGCTCAGTTCCGTCCAAGCAGGTTCTTTCCTCAACCGATGCGATTGGGTTCGCAACAGCGAGCAAGGTTGCATGCTTGGTAGCCGAA\n++\n+BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB\n+@lane1_fakedata9_1 1:N:0:\n+CCGCGGTTAAAATTGCTCAGTTCCGTCCAAGCAGGTTCTTTCCTCAACCGATGCGATTGGGTTCGCAACAGCGAGCAAGGTTGCATGCTTGGTAGCCGAA\n++\n+BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB\n+@lane1_fakedata9_2 1:N:0:\n+CCGCGGTTAAAATTGCTCAGTTCCGTCCAAGCAGGTTCTTTCCTCAACCGATGCGATTGGGTTCGCAACAGCGAGCAAGGTTGCATGCTTGGTAGCCGAA\n++\n+BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB\n+@lane1_fakedata9_3 1:N:0:\n+CCGCGGTTAAAATTGCTCAGTTCCGTCCAAGCAGGTTCTTTCCTCAACCGATGCGATTGGGTTCGCAACAGCGAGCAAGGTTGCATGCTTGGTAGCCGAA\n++\n+BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB\n' |
| b |
| diff -r 000000000000 -r b2e3553e1be2 test-data/procrad/R2.fq.gzip |
| b |
| Binary file test-data/procrad/R2.fq.gzip has changed |
| b |
| diff -r 000000000000 -r b2e3553e1be2 test-data/procrad/barcodes --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/procrad/barcodes Mon Jul 01 10:58:28 2019 -0400 |
| b |
| @@ -0,0 +1,40 @@ +ATGGGG PopA_01 +GGGTAA PopA_02 +AGGAAA PopA_03 +TTTAAG PopA_04 +GGTGTG PopA_05 +TGATGT PopA_06 +GGTTGT PopA_07 +ATAAGT PopA_08 +AAGATA PopA_09 +TGTGAG PopA_10 +ATAGTT PopA_11 +GGAAGG PopA_12 +TTTGTG PopA_13 +TTAAAT PopA_14 +AATAAG PopA_15 +AAGAGG PopA_16 +TAGTGT PopA_17 +TGGAAG PopA_18 +GGGTTG PopA_19 +CATCAT PopA_20 +GGAGAG PopB_20 +GTTTTA PopB_01 +TGATAA PopB_02 +GTTGAT PopB_03 +AGATTA PopB_04 +GTATAG PopB_05 +TTGGGA PopB_06 +ATATAT PopB_07 +GATGAG PopB_08 +GGGAAT PopB_09 +AGTAAT PopB_10 +GGGATA PopB_11 +GAGAAG PopB_12 +AGTAGA PopB_13 +AAGGAT PopB_14 +AGGGTA PopB_15 +TGTTTT PopB_16 +ATGATG PopB_17 +GAGTTA PopB_18 +ATGTAG PopB_19 |
| b |
| diff -r 000000000000 -r b2e3553e1be2 test-data/procrad/process_radtags.out --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/procrad/process_radtags.out Mon Jul 01 10:58:28 2019 -0400 |
| b |
| @@ -0,0 +1,55 @@ +process_radtags v2.2, executed 2018-11-23 13:34:27 +process_radtags -p stacks_inputs/ -i fastq -b /tmp/tmp2_xu5h/files/000/dataset_2.dat --inline_null -e ecoRI -o stacks_outputs +File Retained Reads Low Quality Barcode Not Found RAD cutsite Not Found Total +R1.fastq 2222 0 0 4778 7000 + +Total Sequences 7000 +Barcode Not Found 0 +Low Quality 0 +RAD Cutsite Not Found 4778 +Retained Reads 2222 + +Barcode Filename Total NoRadTag LowQuality Retained +ATGGGG PopA_01 160 94 0 66 +GGGTAA PopA_02 146 86 0 60 +AGGAAA PopA_03 224 132 0 92 +TTTAAG PopA_04 168 146 0 22 +GGTGTG PopA_05 220 154 0 66 +TGATGT PopA_06 214 147 0 67 +GGTTGT PopA_07 182 137 0 45 +ATAAGT PopA_08 232 164 0 68 +AAGATA PopA_09 182 134 0 48 +TGTGAG PopA_10 168 128 0 40 +ATAGTT PopA_11 200 132 0 68 +GGAAGG PopA_12 178 136 0 42 +TTTGTG PopA_13 190 152 0 38 +TTAAAT PopA_14 166 96 0 70 +AATAAG PopA_15 152 74 0 78 +AAGAGG PopA_16 174 112 0 62 +TAGTGT PopA_17 242 146 0 96 +TGGAAG PopA_18 148 98 0 50 +GGGTTG PopA_19 110 64 0 46 +CATCAT PopA_20 178 144 0 34 +GGAGAG PopB_20 210 142 0 68 +GTTTTA PopB_01 136 90 0 46 +TGATAA PopB_02 166 108 0 58 +GTTGAT PopB_03 148 74 0 74 +AGATTA PopB_04 180 156 0 24 +GTATAG PopB_05 136 106 0 30 +TTGGGA PopB_06 166 112 0 54 +ATATAT PopB_07 242 156 0 86 +GATGAG PopB_08 208 152 0 56 +GGGAAT PopB_09 198 126 0 72 +AGTAAT PopB_10 164 120 0 44 +GGGATA PopB_11 146 90 0 56 +GAGAAG PopB_12 162 110 0 52 +AGTAGA PopB_13 204 146 0 58 +AAGGAT PopB_14 180 128 0 52 +AGGGTA PopB_15 134 72 0 62 +TGTTTT PopB_16 138 98 0 40 +ATGATG PopB_17 142 100 0 42 +GAGTTA PopB_18 160 112 0 48 +ATGTAG PopB_19 146 104 0 42 + +Sequences not recorded +Barcode Total |
| b |
| diff -r 000000000000 -r b2e3553e1be2 test-data/procrad/process_radtags_paired.out --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/procrad/process_radtags_paired.out Mon Jul 01 10:58:28 2019 -0400 |
| b |
| @@ -0,0 +1,55 @@ +process_radtags v2.2, executed 2018-11-23 13:35:34 +process_radtags -p stacks_inputs/ --paired -i fastq -b /tmp/tmp2_xu5h/files/000/dataset_91.dat --len_limit 50 -D -y gzfasta --inline_null -e ecoRI -o stacks_outputs +File Retained Reads Low Quality Barcode Not Found RAD cutsite Not Found Total +reads_R1_0.fastq 9222 0 0 4778 14000 + +Total Sequences 14000 +Barcode Not Found 0 +Low Quality 0 +RAD Cutsite Not Found 4778 +Retained Reads 9222 + +Barcode Filename Total NoRadTag LowQuality Retained +ATGGGG PopA_01 320 94 0 226 +GGGTAA PopA_02 292 86 0 206 +AGGAAA PopA_03 448 132 0 316 +TTTAAG PopA_04 336 146 0 190 +GGTGTG PopA_05 440 154 0 286 +TGATGT PopA_06 428 147 0 281 +GGTTGT PopA_07 364 137 0 227 +ATAAGT PopA_08 464 164 0 300 +AAGATA PopA_09 364 134 0 230 +TGTGAG PopA_10 336 128 0 208 +ATAGTT PopA_11 400 132 0 268 +GGAAGG PopA_12 356 136 0 220 +TTTGTG PopA_13 380 152 0 228 +TTAAAT PopA_14 332 96 0 236 +AATAAG PopA_15 304 74 0 230 +AAGAGG PopA_16 348 112 0 236 +TAGTGT PopA_17 484 146 0 338 +TGGAAG PopA_18 296 98 0 198 +GGGTTG PopA_19 220 64 0 156 +CATCAT PopA_20 356 144 0 212 +GGAGAG PopB_20 420 142 0 278 +GTTTTA PopB_01 272 90 0 182 +TGATAA PopB_02 332 108 0 224 +GTTGAT PopB_03 296 74 0 222 +AGATTA PopB_04 360 156 0 204 +GTATAG PopB_05 272 106 0 166 +TTGGGA PopB_06 332 112 0 220 +ATATAT PopB_07 484 156 0 328 +GATGAG PopB_08 416 152 0 264 +GGGAAT PopB_09 396 126 0 270 +AGTAAT PopB_10 328 120 0 208 +GGGATA PopB_11 292 90 0 202 +GAGAAG PopB_12 324 110 0 214 +AGTAGA PopB_13 408 146 0 262 +AAGGAT PopB_14 360 128 0 232 +AGGGTA PopB_15 268 72 0 196 +TGTTTT PopB_16 276 98 0 178 +ATGATG PopB_17 284 100 0 184 +GAGTTA PopB_18 320 112 0 208 +ATGTAG PopB_19 292 104 0 188 + +Sequences not recorded +Barcode Total |
| b |
| diff -r 000000000000 -r b2e3553e1be2 test-data/refmap/PopA_01.bam |
| b |
| Binary file test-data/refmap/PopA_01.bam has changed |
| b |
| diff -r 000000000000 -r b2e3553e1be2 test-data/refmap/PopA_02.bam |
| b |
| Binary file test-data/refmap/PopA_02.bam has changed |
| b |
| diff -r 000000000000 -r b2e3553e1be2 test-data/refmap/catalog.calls.vcf --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/refmap/catalog.calls.vcf Mon Jul 01 10:58:28 2019 -0400 |
| b |
| b'@@ -0,0 +1,1236 @@\n+##fileformat=VCFv4.2\n+##fileDate=20190617\n+##source="Stacks v2.4"\n+##INFO=<ID=AD,Number=R,Type=Integer,Description="Total Depth for Each Allele">\n+##INFO=<ID=AF,Number=A,Type=Float,Description="Allele Frequency">\n+##INFO=<ID=DP,Number=1,Type=Integer,Description="Total Depth">\n+##INFO=<ID=NS,Number=1,Type=Integer,Description="Number of Samples With Data">\n+##FORMAT=<ID=AD,Number=R,Type=Integer,Description="Allele Depth">\n+##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read Depth">\n+##FORMAT=<ID=HQ,Number=2,Type=Integer,Description="Haplotype Quality">\n+##FORMAT=<ID=GL,Number=G,Type=Float,Description="Genotype Likelihood">\n+##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype 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28\tDP\t18\t10\n+13\t11\t.\tC\t.\t.\t.\tDP=28;AD=28\tDP\t18\t10\n+13\t12\t.\tT\t.\t.\t.\tDP=28;AD=28\tDP\t18\t10\n+13\t13\t.\tG\t.\t.\t.\tDP=28;AD=28\tDP\t18\t10\n+13\t14\t.\tC\t.\t.\t.\tDP=28;AD=28\tDP\t18\t10\n+13\t15\t.\tT\t.\t.\t.\tDP=28;AD=28\tDP\t18\t10\n+13\t16\t.\tT\t.\t.\t.\tDP=28;AD=28\tDP\t18\t10\n+13\t17\t.\tC\t.\t.\t.\tDP=28;AD=28\tDP\t18\t10\n+13\t18\t.\tA\t.\t.\t.\tDP=28;AD=28\tDP\t18\t10\n+13\t19\t.\tG\t.\t.\t.\tDP=28;AD=28\tDP\t18\t10\n+13\t20\t.\tG\t.\t.\t.\tDP=28;AD=28\tDP\t18\t10\n+13\t21\t.\tA\t.\t.\t.\tDP=28;AD=28\tDP\t18\t10\n+13\t22\t.\tA\t.\t.\t.\tDP=28;AD=28\tDP\t18\t10\n+13\t23\t.\tT\t.\t.\t.\tDP=28;AD=28\tDP\t18\t10\n+13\t24\t.\tC\t.\t.\t.\tDP=28;AD=28\tDP\t18\t10\n+13\t25\t.\tT\t.\t.\t.\tDP=28;AD=28\tDP\t18\t10\n+13\t26\t.\tC\t.\t.\t.\tDP=28;AD=28\tDP\t18\t10\n+13\t27\t.\tT\t.\t.\t.\tDP=28;AD=28\tDP\t18\t10\n+13\t28\t.\tC\t.\t.\t.\tDP=28;AD=28\tDP\t18\t10\n+13\t29\t.\tG\t.\t.\t.\tDP=28;AD=28\tDP\t18\t10\n+13\t30\t.\tT\t.\t.\t.\tDP=28;AD=28\tDP\t18\t10\n+13\t31\t.\tA\t.\t.\t.\tDP=28;AD=28\tDP\t18\t10\n+13\t32\t.\tT\t.\t.\t.\tDP=28;AD=28\tDP\t18\t10\n+13\t33\t.\tA\t.\t.\t.\tDP=28;AD=28\tDP\t18\t10\n+13\t34\t.\tA\tC\t40\t.\tDP=28;AD=15,13;AF=0.464\tGT:PS:FT:GQ:DP:AD:GL\t0|1:34:.:40:18:9,9:-19.72,0.00,-19.78\t0|1:34:.:40:10:6,4:-8.39,-0.00,-13.94\n+13\t35\t.\tT\t.\t.\t.\tDP=28;AD=28\tDP\t18\t10\n+13\t36\t.\tC\t.\t.\t.\tDP=28;AD=28\tDP\t18\t10\n+13\t37\t.\tT\t.\t.\t.\tDP=28;AD=28\tDP\t18\t10\n+13\t38\t.\tG\t.\t.\t.\tDP=28;AD=28\tDP\t18\t10\n+13\t39\t.\tA\t.\t.\t.\tDP=28;AD=28\tDP\t18\t10\n+13\t40\t.\tG\t.\t.\t.\tDP=28;AD=28\tDP\t18\t10\n+13\t41\t.\tT\t.\t.\t.\tDP=28;AD=28\tDP\t18\t10\n+13\t42\t.\tA\t.\t.\t.\tDP=28;AD=28\tDP\t18\t10\n+13\t43\t.\tT\t.\t.\t.\tDP=28;AD=28\tDP\t18\t10\n+13\t44\t.\tG\t.\t.\t.\tDP=28;AD=28\tDP\t18\t10\n+13\t45\t.\tT\t.\t.\t.\tDP=28;AD=28\tDP\t18\t10\n+13\t46\t.\tG\t.\t.\t.\tDP=28;AD=28\tDP\t18\t10\n+13\t47\t.\tC\t.\t.\t.\tDP=28;AD=28\tDP\t18\t10\n+13\t48\t.\tG\t.\t.\t.\tDP=28;AD=28\tDP\t18\t10\n+13\t49\t.\tT\t.\t.\t.\tDP=28;AD=28\tDP\t18\t10\n+13\t50\t.\tA\t.\t.\t.\tDP=28;AD=28\tDP\t18\t10\n+13\t51\t.\tC\t.\t.\t.\tDP=28;AD=28\tDP\t18\t10\n+13\t52\t.\tG\t.\t.\t.\tDP=28;AD=28\tDP\t18\t10\n+13\t53\t.\tT\t.\t.\t.\tDP=28;AD=28\tDP\t18\t10\n+13\t54\t.\tA\t.\t.\t.\tDP=28;AD=28\tDP\t18\t10\n+13\t55\t.\tC\t.\t.\t.\tDP=28;AD=28\tDP\t18\t10\n+13\t56\t.\tG\t.\t.\t.\tDP=28;AD=28\tDP\t18\t10\n+13\t57\t.\tC\t.\t.\t.\tDP=28;AD=28\tDP\t18\t10\n+13\t58\t.\tT\t.\t.\t.\tDP=28;AD=28\tDP\t18\t10\n+13\t59\t.\tA\t.\t.\t.\tDP=28;AD=28\tDP\t18\t10\n+13\t60\t.\tT\t.\t.\t.\tDP=28;AD=28\tDP\t18\t10\n+13\t61\t.\tT\t.\t.\t.\tDP=28;AD=28\tDP\t18\t10\n+13\t62\t.\tT\t.\t.\t.\tDP=28;AD=28\tDP\t18\t10\n+13\t63\t.\tA\t.\t.\t.\tDP=28;AD=28\tDP\t18\t10\n+13\t64\t.\tG\t.\t.\t.\tDP=28;AD=28\tDP\t18\t10\n+13\t65\t.\tA\t.\t.\t.\tDP=28;AD=28\tDP\t18\t10\n+13\t66\t.\tT\t.\t.\t.\tDP=28;AD=28\tDP\t18\t10\n+13\t67\t.\tG\t.\t.\t.\tDP=28;AD=28\tDP\t18\t10\n+13\t68\t.\tG\t.\t.\t.\tDP=28;AD=28\tDP\t18\t10\n+13\t69\t.\tA\t.\t.\t.\tDP=28;AD=28\tDP\t18\t10\n+13\t70\t.\tT\t.\t.\t.\tDP=28;AD=28\tDP\t18\t10\n+13\t71\t.\tA\t.\t.\t.\tDP=28;AD=28\tDP\t18\t10\n+13\t72\t.\tA\t.\t.\t.\tDP=28;AD=28\tDP\t18\t10\n+13\t73\t.\tC\t.\t.\t.\tDP=28;AD=28\tDP\t18\t10\n+13\t74\t.\tC\t.\t.\t.\tDP=28;AD=28\tDP\t18\t10\n+13\t75\t.\tG\t.\t.\t.\tDP=28;AD=28\tDP\t18\t10\n+13\t76\t.\tA\t.\t.\t.\tDP=28;AD=28\tDP\t18\t10\n+13\t77\t.\tC\t.\t.\t.\tDP=28;AD=28\tDP\t18\t10\n+13\t78\t.\tG\t.\t.\t.\tDP=28;AD=28\tDP\t18\t10\n+13\t79\t.\tC\t.\t.\t.\tDP=28;AD=28\tDP\t18\t10\n+13\t80\t.\tT\t.\t.\t.\tDP=28;AD=28\tDP\t18\t10\n+13\t81\t.\tG\t.\t.\t.\tDP=28;AD=28\tDP\t18\t10\n+13\t82\t.\tC\t.\t.\t.\tDP=28;AD=28\tDP\t18\t10\n+13\t83\t.\tC\t.\t.\t.\tDP=28;AD=28\tDP\t18\t10\n+13\t84\t.\tA\t.\t.\t.\tDP=28;AD=28\tDP\t18\t10\n+13\t85\t.\tG\t.\t.\t.\tDP=28;AD=28\tDP\t18\t10\n+13\t86\t.\tA\t.\t.\t.\tDP=28;AD=28\tDP\t18\t10\n+13\t87\t.\tC\t.\t.\t.\tDP=28;AD=28\tDP\t18\t10\n+13\t88\t.\tG\t.\t.\t.\tDP=28;AD=28\tDP\t18\t10\n+13\t89\t.\tC\tA\t40\t.\tDP=28;AD=15,13;AF=0.464\tGT:PS:FT:GQ:DP:AD:GL\t0|1:34:.:40:18:9,9:-19.72,0.00,-19.78\t0|1:34:.:40:10:6,4:-8.39,-0.00,-13.94\n+13\t90\t.\tG\t.\t.\t.\tDP=28;AD=28\tDP\t18\t10\n+13\t91\t.\tA\t.\t.\t.\tDP=28;AD=28\tDP\t18\t10\n+13\t92\t.\tG\t.\t.\t.\tDP=28;AD=28\tDP\t18\t10\n+13\t93\t.\tA\t.\t.\t.\tDP=28;AD=28\tDP\t18\t10\n+13\t94\t.\tC\t.\t.\t.\tDP=28;AD=28\tDP\t18\t10\n' 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| diff -r 000000000000 -r b2e3553e1be2 test-data/refmap/catalog.fa.gz |
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| Binary file test-data/refmap/catalog.fa.gz has changed |
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| diff -r 000000000000 -r b2e3553e1be2 test-data/refmap/populations.haplotypes.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/refmap/populations.haplotypes.tsv Mon Jul 01 10:58:28 2019 -0400 |
| b |
| @@ -0,0 +1,14 @@ +# Catalog Locus ID Cnt PopA_01 PopA_02 +1 2 consensus consensus +2 2 consensus consensus +3 2 consensus consensus +4 2 consensus consensus +5 2 consensus consensus +6 2 consensus consensus +7 2 consensus consensus +8 2 consensus consensus +9 2 consensus consensus +10 2 AC/CA AC/CA +11 2 consensus consensus +12 2 AC/CA AC/CA +13 2 AC/CA AC/CA |
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| diff -r 000000000000 -r b2e3553e1be2 test-data/refmap/populations.hapstats.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/refmap/populations.hapstats.tsv Mon Jul 01 10:58:28 2019 -0400 |
| b |
| @@ -0,0 +1,5 @@ +# 1 PopA_01,PopA_02 +# Locus ID Chr BP Pop ID N Haplotype Cnt Gene Diversity Smoothed Gene Diversity Smoothed Gene Diversity P-value Haplotype Diversity Smoothed Haplotype Diversity Smoothed Haplotype Diversity P-value HWE P-value HWE P-value SE Haplotypes +10 Contig_3091 1 1 4 2 0.66667 0.00000 0.00000 1.33333 0.00000 0.00000 0.00000 0.00000 AC:2;CA:2 +12 Contig_3358 1 1 4 2 0.66667 0.00000 0.00000 1.33333 0.00000 0.00000 0.00000 0.00000 AC:2;CA:2 +13 Contig_3569 1 1 4 2 0.66667 0.00000 0.00000 1.33333 0.00000 0.00000 0.00000 0.00000 AC:2;CA:2 |
| b |
| diff -r 000000000000 -r b2e3553e1be2 test-data/refmap/populations.log.distribs --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/refmap/populations.log.distribs Mon Jul 01 10:58:28 2019 -0400 |
| b |
| @@ -0,0 +1,57 @@ +# Note: Individual distributions can be extracted using the `stacks-dist-extract` utility. +# e.g. `stacks-dist-extract populations.log.distribs dist_name` + +BEGIN batch_progress +Contig_95: analyzed 1 loci; filtered 0 loci; 1 loci seen. + 94 genomic sites, of which 0 were covered by multiple loci (0.0%). +Contig_1381: analyzed 2 loci; filtered 0 loci; 2 loci seen. + 94 genomic sites, of which 94 were covered by multiple loci (100.0%). +Contig_2103: analyzed 2 loci; filtered 0 loci; 2 loci seen. + 94 genomic sites, of which 94 were covered by multiple loci (100.0%). +Contig_2644: analyzed 2 loci; filtered 0 loci; 2 loci seen. + 94 genomic sites, of which 94 were covered by multiple loci (100.0%). +Contig_3015: analyzed 2 loci; filtered 0 loci; 2 loci seen. + 94 genomic sites, of which 94 were covered by multiple loci (100.0%). +Contig_3253: analyzed 2 loci; filtered 0 loci; 2 loci seen. + 94 genomic sites, of which 94 were covered by multiple loci (100.0%). +Contig_3569: analyzed 2 loci; filtered 0 loci; 2 loci seen. + 94 genomic sites, of which 94 were covered by multiple loci (100.0%). +END batch_progress + +BEGIN samples_per_loc_prefilters +# Distribution of valid samples matched to a catalog locus prior to filtering. +n_samples n_loci +2 13 +END samples_per_loc_prefilters + +BEGIN missing_samples_per_loc_prefilters +# Distribution of missing samples for each catalog locus prior to filtering. +# Absent samples at locus Count +0 13 +END missing_samples_per_loc_prefilters + +BEGIN snps_per_loc_prefilters +# Distribution of the number of SNPs per catalog locus prior to filtering. +n_snps n_loci +0 10 +2 3 +END snps_per_loc_prefilters + +BEGIN samples_per_loc_postfilters +# Distribution of valid samples matched to a catalog locus after filtering. +n_samples n_loci +2 13 +END samples_per_loc_postfilters + +BEGIN missing_samples_per_loc_postfilters +# Distribution of missing samples for each catalog locus after filtering. +# Absent samples at locus Count +0 13 +END missing_samples_per_loc_postfilters + +BEGIN snps_per_loc_postfilters +# Distribution of the number of SNPs per catalog locus (after filtering). +n_snps n_loci +0 10 +2 3 +END snps_per_loc_postfilters |
| b |
| diff -r 000000000000 -r b2e3553e1be2 test-data/refmap/populations.markers.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/refmap/populations.markers.tsv Mon Jul 01 10:58:28 2019 -0400 |
| b |
| @@ -0,0 +1,14 @@ +# Catalog Locus ID Total Genotypes Max Genotype Freqs F Mean Log Likelihood Genotype Map +1 0 0.00000 0.00000 1.00000 +2 0 0.00000 0.00000 1.00000 +3 0 0.00000 0.00000 1.00000 +4 0 0.00000 0.00000 1.00000 +5 0 0.00000 0.00000 1.00000 +6 0 0.00000 0.00000 1.00000 +7 0 0.00000 0.00000 1.00000 +8 0 0.00000 0.00000 1.00000 +9 0 0.00000 0.00000 1.00000 +10 2 100.00000 ab:2(100.0%); 0.00000 1.00000 AC:a;CA:b; +11 0 0.00000 0.00000 1.00000 +12 2 100.00000 ab:2(100.0%); 0.00000 1.00000 AC:a;CA:b; +13 2 100.00000 ab:2(100.0%); 0.00000 1.00000 AC:a;CA:b; |
| b |
| diff -r 000000000000 -r b2e3553e1be2 test-data/refmap/populations.sumstats.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/refmap/populations.sumstats.tsv Mon Jul 01 10:58:28 2019 -0400 |
| b |
| @@ -0,0 +1,8 @@ +# 1 PopA_01,PopA_02 +# Locus ID Chr BP Col Pop ID P Nuc Q Nuc N P Obs Het Obs Hom Exp Het Exp Hom Pi Smoothed Pi Smoothed Pi P-value Fis Smoothed Fis Smoothed Fis P-value HWE P-value Private +10 Contig_3091 34 33 1 A C 2 0.50000000 1.00000 0.00000 0.50000 0.50000 0.66667 0.00000 0.00000 -0.50000 0.00000 0.00000 0.00000 0 +10 Contig_3091 89 88 1 A C 2 0.50000000 1.00000 0.00000 0.50000 0.50000 0.66667 0.00000 0.00000 -0.50000 0.00000 0.00000 0.00000 0 +12 Contig_3358 34 33 1 A C 2 0.50000000 1.00000 0.00000 0.50000 0.50000 0.66667 0.00000 0.00000 -0.50000 0.00000 0.00000 0.00000 0 +12 Contig_3358 89 88 1 A C 2 0.50000000 1.00000 0.00000 0.50000 0.50000 0.66667 0.00000 0.00000 -0.50000 0.00000 0.00000 0.00000 0 +13 Contig_3569 34 33 1 A C 2 0.50000000 1.00000 0.00000 0.50000 0.50000 0.66667 0.00000 0.00000 -0.50000 0.00000 0.00000 0.00000 0 +13 Contig_3569 89 88 1 A C 2 0.50000000 1.00000 0.00000 0.50000 0.50000 0.66667 0.00000 0.00000 -0.50000 0.00000 0.00000 0.00000 0 |
| b |
| diff -r 000000000000 -r b2e3553e1be2 test-data/refmap/populations.sumstats_summary.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/refmap/populations.sumstats_summary.tsv Mon Jul 01 10:58:28 2019 -0400 |
| b |
| @@ -0,0 +1,6 @@ +# Variant positions +# Pop ID Private Num_Indv Var StdErr P Var StdErr Obs_Het Var StdErr Obs_Hom Var StdErr Exp_Het Var StdErr Exp_Hom Var StdErr Pi Var StdErr Fis Var StdErr +1 0 2.00000 0.00000 0.00000 0.50000 0.00000 0.00000 1.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.50000 0.00000 0.00000 0.50000 0.00000 0.00000 0.66667 0.00000 0.00000 -0.50000 0.00000 0.00000 +# All positions (variant and fixed) +# Pop ID Private Sites Variant_Sites Polymorphic_Sites %Polymorphic_Loci Num_Indv Var StdErr P Var StdErr Obs_Het Var StdErr Obs_Hom Var StdErr Exp_Het Var StdErr Exp_Hom Var StdErr Pi Var StdErr Fis Var StdErr +1 0 1222 6 6 0.49100 2.00000 0.00000 0.00000 0.99755 0.00122 0.00100 0.00491 0.00489 0.00200 0.99509 0.00489 0.00200 0.00245 0.00122 0.00100 0.99755 0.00122 0.00100 0.00327 0.00217 0.00133 -0.00245 0.00122 0.00000 |
| b |
| diff -r 000000000000 -r b2e3553e1be2 test-data/shortreads/PopA_01.forward.fq.gz |
| b |
| Binary file test-data/shortreads/PopA_01.forward.fq.gz has changed |
| b |
| diff -r 000000000000 -r b2e3553e1be2 test-data/shortreads/PopA_01.fq --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/shortreads/PopA_01.fq Mon Jul 01 10:58:28 2019 -0400 |
| b |
| b'@@ -0,0 +1,640 @@\n+@lane1_fakedata0_0 1:N:0:/1\n+ATTCGGCTTGCAACGCAAGTGACGATTCCCACGGACATAACTGATCTAAGTAACTTCCAAATCTGGGAATGGGATTTCATAATTAAGGACTAT\n++\n+BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB\n+@lane1_fakedata0_1 1:N:0:/1\n+ATTCGGCTTGCAACGCAAGTGACGATTCCCACGGACATAACTGATCTAAGTAACTTCCAAATCTGGGAATGGGATTTCATAATTAAGGACTAT\n++\n+BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB\n+@lane1_fakedata0_2 1:N:0:/1\n+ATTCGGCTTGCAACGCAAGTGACGATTCCCACGGACATAACTGATCTAAGTAACTTCCAAATCTGGGAATGGGATTTCATAATTAAGGACTAT\n++\n+BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB\n+@lane1_fakedata0_3 1:N:0:/1\n+ATTCGGCTTGCAACGCAAGTGACGATTCCCACGGACATAACTGATCTAAGTAACTTCCAAATCTGGGAATGGGATTTCATAATTAAGGACTAT\n++\n+BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB\n+@lane1_fakedata0_4 1:N:0:/1\n+ATTCGGCTTGCAACGCAAGTGACGATTCCCACGGACATAACTGATCTAAGTAACTTCCAAATCTGGGAATGGGATTTCATAATTAAGGACTAT\n++\n+BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB\n+@lane1_fakedata0_5 1:N:0:/1\n+ATTCGGCTTGCAACGCAAGTGACGATTCCCACGGACATAACTGATCTAAGTAACTTCCAAATCTGGGAATGGGATTTCATAATTAAGGACTAT\n++\n+BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB\n+@lane1_fakedata0_6 1:N:0:/1\n+ATTCGGCTTGCAACGCAAGTGACGATTCCCACGGACATAACTGATCTAAGTAACTTCCAAATCTGGGAATGGGATTTCATAATTAAGGACTAT\n++\n+BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB\n+@lane1_fakedata0_7 1:N:0:/1\n+ATTCGGCTTGCAACGCAAGTGACGATTCCCACGGACATAACTGATCTAAGTAACTTCCAAATCTGGGAATGGGATTTCATAATTAAGGACTAT\n++\n+BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB\n+@lane1_fakedata0_8 1:N:0:/1\n+ATTCGGCTTGCAACGCAAGTGACGATTCCCACGGACATAACTGATCTAAGTAACTTCCAAATCTGGGAATGGGATTTCATAATTAAGGACTAT\n++\n+BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB\n+@lane1_fakedata0_9 1:N:0:/1\n+ATTCGGCTTGCAACGCAAGTGACGATTCCCACGGACATAACTGATCTAAGTAACTTCCAAATCTGGGAATGGGATTTCATAATTAAGGACTAT\n++\n+BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB\n+@lane1_fakedata0_10 1:N:0:/1\n+ATTCGGCTTGCAACGCAAGTGACGATTCCCACGGACATAACTGATCTAAGTAACTTCCAAATCTGGGAATGGGATTTCATAATTAAGGACTAT\n++\n+BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB\n+@lane1_fakedata0_11 1:N:0:/1\n+ATTCGGCTTGCAACGCAAGTGACGATTCCCACGGACATAACTGATCTAAGTAACTTCCAAATCTGGGAATGGGATTTCATAATTAAGGACTAT\n++\n+BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB\n+@lane1_fakedata0_12 1:N:0:/1\n+ATTCGGCTTGCAACGCAAGTGACGATTCCCACGGACATAACTGATCTAAGTAACTTCCAAATCTGGGAATGGGATTTCATAATTAAGGACTAT\n++\n+BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB\n+@lane1_fakedata0_13 1:N:0:/1\n+ATTCGGCTTGCAACGCAAGTGACGATTCCCACGGACATAACTGATCTAAGTAACTTCCAAATCTGGGAATGGGATTTCATAATTAAGGACTAT\n++\n+BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB\n+@lane1_fakedata0_14 1:N:0:/1\n+ATTCGGCTTGCAACGCAAGTGACGATTCCCACGGACATAACTGATCTAAGTAACTTCCAAATCTGGGAATGGGATTTCATAATTAAGGACTAT\n++\n+BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB\n+@lane1_fakedata0_15 1:N:0:/1\n+ATTCGGCTTGCAACGCAAGTGACGATTCCCACGGACATAACTGATCTAAGTAACTTCCAAGTCTGGGAATGGGATTTCATAATTAAGGACTAT\n++\n+BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB\n+@lane1_fakedata0_16 1:N:0:/1\n+ATTCGGCTTGCAACGCAAGTGACGATTCCCACGGACATAACTGATCTAAGTAACTTCCAAATCTGGGAATGGGATTTCATAATTAAGGACTAT\n++\n+BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB\n+@lane1_fakedata0_17 1:N:0:/1\n+ATTCGGCTTGCAACGCAAGTGACGATTCCCACGGACATAACTGATCTAAGTAACTTCCAAATCTGGGAATGGGATTTCATAATTAAGGACTAT\n++\n+BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB'..b'_fakedata9_2 1:N:0:/1\n+ATTATAACAAAGGTCGACCTGACTCAGCCATTGTTGATAGACGCGAAAATAACGAAGCAGGATGACCGCAAGTGCAAACCATTACCAATGACC\n++\n+BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB\n+@lane1_fakedata9_3 1:N:0:/1\n+ATTATAACAAAGGTCGACCTGACTCAGCCATTGTTGATAGACGCGAAAATAACGAAGCAGGATGACCGCAAGTGCAAACCATTACCAATGACC\n++\n+BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB\n+@lane1_fakedata9_4 1:N:0:/1\n+ATTATAACAAAGGTCGACCTGACTCAGCCATTGTTGATAGACGCGAAAATAACGAAGCAGGATGACCGCAAGTGCAAACCATTACCAATGACC\n++\n+BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB\n+@lane1_fakedata9_5 1:N:0:/1\n+ATTATAACAAAGGTCGACCTGACTCAGCCATTGTTGATAGACGCGAAAATAACGAAGCAGGATGACCGCAAGTGCAAACCATTACCAATGACC\n++\n+BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB\n+@lane1_fakedata9_6 1:N:0:/1\n+ATTATAACAAAGGTCGACCTGACTCAGCCATTGTTGATAGACGCGAAAATAACGAAGCAGGATGACCGCAAGTGCAAACCATTACCAATGACC\n++\n+BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB\n+@lane1_fakedata9_7 1:N:0:/1\n+ATTATAACAAAGGTCGACCTGACTCAGCCATTGTTGATAGACGCGAAAATAACGAAGCAGGATGACCGCAAGTGCAAACCATTACCAATGACC\n++\n+BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB\n+@lane1_fakedata9_8 1:N:0:/1\n+ATTATAACAAAGGTCGACCTGACTCAGCCATTGTTGATAGACGCGAAAATAACGAAGCAGGATGACCGCAAGTGCAAACCATTACCAATGACC\n++\n+BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB\n+@lane1_fakedata9_9 1:N:0:/1\n+ATTATAACAAAGGTCGACCTGACTCAGCCATTGTTGATAGACGCGAAAATAACGAAGCAGGATGACCGCAAGTGCAAACCATTACCAATGACC\n++\n+BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB\n+@lane1_fakedata9_10 1:N:0:/1\n+ATTATAACAAAGGTCGACCTGACTCAGCCATTGTTGATAGACGCGAAAATAACGAAGCAGGATGACCGCAAGTGCAAACCATTACCAATGACC\n++\n+BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB\n+@lane1_fakedata9_11 1:N:0:/1\n+ATTATAACAAAGGTCGACCTGACTCAGCCATTGTTGATAGACGCGAAAATAACGAAGCAGGATGACCGCAAGTGCAAACCATTACCAATGACC\n++\n+BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB\n+@lane1_fakedata9_12 1:N:0:/1\n+ATTATAACAAAGGTCGACCTGACTCAGCCATTGTTGATAGACGCGAAAATAACGAAGCAGGATGACCGCAAGTGCAAACCATTACCGATGACC\n++\n+BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB\n+@lane1_fakedata9_13 1:N:0:/1\n+ATTATAACAAAGGTCGACCTGACTCAGCCATTGTTGATAGACGCGAAAATAACGAAGCAGGATGACCGCAAGTGCAAACCATTACCAATGACC\n++\n+BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB\n+@lane1_fakedata9_14 1:N:0:/1\n+ATTATAACAAAGGTCGACCTGACTCAGCCATTGTTGATAGACGCGAAAATAACGAAGCAGGATGACCGCAAGTGCAAACCATTACCAATGACC\n++\n+BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB\n+@lane1_fakedata9_15 1:N:0:/1\n+ATTATAACAAAGGTCGACCTGACTCAGCCATTGTTGATAGACGCGAAAATAACGAAGCAGGATGACCGCAAGTGCAAACCATTACCAATGACC\n++\n+BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB\n+@lane1_fakedata9_16 1:N:0:/1\n+ATTATAACAAAGGTCGACCTGACTCAGCCATTGTTGATAGACGCGAAAATAACGAAGCAGGATGACCGCAAGTGCAAACCATTACCAATGACC\n++\n+BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB\n+@lane1_fakedata9_17 1:N:0:/1\n+ATTATAACAAAGGTCGACCTGACTCAGCCATTGTTGATAGACGCGAAAATAACGAAGCAGGATGACCGCAAGTGCAAACCATTACCAATGACC\n++\n+BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB\n+@lane1_fakedata9_18 1:N:0:/1\n+ATTATAACAAAGGTCGACCTGACTCAGCCATTGTTGATAGACGCGAAAATAACGAAGCAGGATGACCGCAAGTGCAAACCATTACCAATGACC\n++\n+BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB\n+@lane1_fakedata9_19 1:N:0:/1\n+ATTATAACAAAGGTCGACCTGACTCAGCCATTGTTGATAGACGCGAAAATAACGAAGCAGGATGACCGCAAGTGCAAACCATTACCAATGACC\n++\n+BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB\n' |
| b |
| diff -r 000000000000 -r b2e3553e1be2 test-data/shortreads/PopA_01.rem.forward.fq.gz |
| b |
| Binary file test-data/shortreads/PopA_01.rem.forward.fq.gz has changed |
| b |
| diff -r 000000000000 -r b2e3553e1be2 test-data/shortreads/PopA_01.rem.reverse.fq.gz |
| b |
| Binary file test-data/shortreads/PopA_01.rem.reverse.fq.gz has changed |
| b |
| diff -r 000000000000 -r b2e3553e1be2 test-data/shortreads/PopA_01.reverse.fq.gz |
| b |
| Binary file test-data/shortreads/PopA_01.reverse.fq.gz has changed |
| b |
| diff -r 000000000000 -r b2e3553e1be2 test-data/shortreads/process_shortreads.out --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/shortreads/process_shortreads.out Mon Jul 01 10:58:28 2019 -0400 |
| b |
| @@ -0,0 +1,56 @@ +process_shortreads v2.2, executed 2018-12-03 21:27:19 +process_shortreads -p stacks_inputs/ -i fastq -b /tmp/tmpiZT6X4/files/000/dataset_2.dat --inline_null -o stacks_outputs +File Retained Reads Low Quality Ambiguous Barcodes Trimmed Reads Orphaned paired-end reads Total +R1.fastq 7000 0 0 0 0 7000 + +Total Sequences 7000 +Ambiguous Barcodes 0 +Low Quality 0 +Trimmed Reads 0 +Orphaned Paired-ends 0 +Retained Reads 7000 + +Barcode Filename Total Retained +ATGGGG PopA_01 160 160 +GGGTAA PopA_02 146 146 +AGGAAA PopA_03 224 224 +TTTAAG PopA_04 168 168 +GGTGTG PopA_05 220 220 +TGATGT PopA_06 214 214 +GGTTGT PopA_07 182 182 +ATAAGT PopA_08 232 232 +AAGATA PopA_09 182 182 +TGTGAG PopA_10 168 168 +ATAGTT PopA_11 200 200 +GGAAGG PopA_12 178 178 +TTTGTG PopA_13 190 190 +TTAAAT PopA_14 166 166 +AATAAG PopA_15 152 152 +AAGAGG PopA_16 174 174 +TAGTGT PopA_17 242 242 +TGGAAG PopA_18 148 148 +GGGTTG PopA_19 110 110 +CATCAT PopA_20 178 178 +GGAGAG PopB_20 210 210 +GTTTTA PopB_01 136 136 +TGATAA PopB_02 166 166 +GTTGAT PopB_03 148 148 +AGATTA PopB_04 180 180 +GTATAG PopB_05 136 136 +TTGGGA PopB_06 166 166 +ATATAT PopB_07 242 242 +GATGAG PopB_08 208 208 +GGGAAT PopB_09 198 198 +AGTAAT PopB_10 164 164 +GGGATA PopB_11 146 146 +GAGAAG PopB_12 162 162 +AGTAGA PopB_13 204 204 +AAGGAT PopB_14 180 180 +AGGGTA PopB_15 134 134 +TGTTTT PopB_16 138 138 +ATGATG PopB_17 142 142 +GAGTTA PopB_18 160 160 +ATGTAG PopB_19 146 146 + +Sequences not recorded +Barcode Total |
| b |
| diff -r 000000000000 -r b2e3553e1be2 test-data/sstacks/PopA_01.matches.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/sstacks/PopA_01.matches.tsv Mon Jul 01 10:58:28 2019 -0400 |
| b |
| @@ -0,0 +1,5 @@ +# sstacks version 2.4; generated on 2019-06-18 10:34:45 +1 1 1 AC 9 94M +1 1 1 CA 9 94M +2 1 2 consensus 28 94M +3 1 3 consensus 20 94M |
| b |
| diff -r 000000000000 -r b2e3553e1be2 test-data/sstacks/PopA_02.matches.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/sstacks/PopA_02.matches.tsv Mon Jul 01 10:58:28 2019 -0400 |
| b |
| @@ -0,0 +1,5 @@ +# sstacks version 2.4; generated on 2019-06-18 10:34:45 +1 2 1 AC 6 94M +1 2 1 CA 6 94M +2 2 2 consensus 28 94M +3 2 3 consensus 20 94M |
| b |
| diff -r 000000000000 -r b2e3553e1be2 test-data/sstacks/sstacks.log --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/sstacks/sstacks.log Mon Jul 01 10:58:28 2019 -0400 |
| [ |
| @@ -0,0 +1,48 @@ +Searching for matches by sequence identity... + Parsing stacks_inputs/catalog.tags.tsv + Parsing stacks_inputs/catalog.snps.tsv + Parsing stacks_inputs/catalog.alleles.tsv +Populating kmer dictionary for exact matches...done. +Populating kmer dictionary for gapped alignments...done. + +Processing sample 'stacks_inputs/PopA_01' [1 of 2] + Parsing stacks_inputs/PopA_01.tags.tsv + Parsing stacks_inputs/PopA_01.snps.tsv + Parsing stacks_inputs/PopA_01.alleles.tsv +Searching for sequence matches... +3 sample loci compared against the catalog containing 3 loci. + 3 matching loci, 0 contained no verified haplotypes. + 0 loci matched more than one catalog locus and were excluded. + 0 loci contained SNPs unaccounted for in the catalog and were excluded. + 4 total haplotypes examined from matching loci, 4 verified. +Searching for gapped alignments... +Out of 3 query loci, 0 gapped alignments attempted. + 0 loci matched one catalog locus; 0 total haplotypes examined, 0 verified. + 0 loci matched no catalog locus; + 0 loci matched more than one catalog locus and were excluded. + 0 loci contained SNPs unaccounted for in the catalog and were excluded. + 0 loci had no verified haplotypes. + 0 loci had inconsistent alignments to a catalog locus and were excluded. +Outputing to file stacks_inputs/PopA_01.matches.tsv + +Processing sample 'stacks_inputs/PopA_02' [2 of 2] + Parsing stacks_inputs/PopA_02.tags.tsv + Parsing stacks_inputs/PopA_02.snps.tsv + Parsing stacks_inputs/PopA_02.alleles.tsv +Searching for sequence matches... +3 sample loci compared against the catalog containing 3 loci. + 3 matching loci, 0 contained no verified haplotypes. + 0 loci matched more than one catalog locus and were excluded. + 0 loci contained SNPs unaccounted for in the catalog and were excluded. + 4 total haplotypes examined from matching loci, 4 verified. +Searching for gapped alignments... +Out of 3 query loci, 0 gapped alignments attempted. + 0 loci matched one catalog locus; 0 total haplotypes examined, 0 verified. + 0 loci matched no catalog locus; + 0 loci matched more than one catalog locus and were excluded. + 0 loci contained SNPs unaccounted for in the catalog and were excluded. + 0 loci had no verified haplotypes. + 0 loci had inconsistent alignments to a catalog locus and were excluded. +Outputing to file stacks_inputs/PopA_02.matches.tsv + +sstacks is done. |
| b |
| diff -r 000000000000 -r b2e3553e1be2 test-data/stacks_outputs/catalog.calls |
| b |
| Binary file test-data/stacks_outputs/catalog.calls has changed |
| b |
| diff -r 000000000000 -r b2e3553e1be2 test-data/stacks_outputs/tsv2bam.log --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/stacks_outputs/tsv2bam.log Mon Jul 01 10:58:28 2019 -0400 |
| b |
| @@ -0,0 +1,17 @@ +tsv2bam v2.4, executed 2019-06-18 10:34:45 (zlib-1.2.11) +tsv2bam -P stacks_outputs -M denovo_map/popmap_cstacks.tsv -R demultiplexed/ +Configuration for this run: + Stacks directory: 'stacks_outputs/' + Population map: 'denovo_map/popmap_cstacks.tsv' + Num. samples: 2 + Paired-end reads directory: 'demultiplexed/' + +Paired-end reads files found, e.g. 'demultiplexed/PopA_01.2.fq'. +Loading the catalog... +Processing sample 'PopA_01'... +Processing sample 'PopA_02'... + +Sample 'PopA_01': matched 3 sample loci to 3 catalog loci; found a paired-end read for 66 (100.0%) of the assembled forward reads; wrote 132 records. +Sample 'PopA_02': matched 3 sample loci to 3 catalog loci; found a paired-end read for 60 (100.0%) of the assembled forward reads; wrote 120 records. + +tsv2bam is done. |
| b |
| diff -r 000000000000 -r b2e3553e1be2 test-data/tsv2bam/PopA_01.bam |
| b |
| Binary file test-data/tsv2bam/PopA_01.bam has changed |
| b |
| diff -r 000000000000 -r b2e3553e1be2 test-data/tsv2bam/PopA_01.matches.bam |
| b |
| Binary file test-data/tsv2bam/PopA_01.matches.bam has changed |
| b |
| diff -r 000000000000 -r b2e3553e1be2 test-data/tsv2bam/PopA_02.bam |
| b |
| Binary file test-data/tsv2bam/PopA_02.bam has changed |
| b |
| diff -r 000000000000 -r b2e3553e1be2 test-data/tsv2bam/PopA_02.matches.bam |
| b |
| Binary file test-data/tsv2bam/PopA_02.matches.bam has changed |
| b |
| diff -r 000000000000 -r b2e3553e1be2 test-data/tsv2bam/tsv2bam.log --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/tsv2bam/tsv2bam.log Mon Jul 01 10:58:28 2019 -0400 |
| b |
| @@ -0,0 +1,17 @@ +tsv2bam v2.4, executed 2019-06-17 21:22:16 (zlib-1.2.11) +tsv2bam -P stacks_outputs -M denovo_map/popmap_cstacks.tsv -R demultiplexed/ +Configuration for this run: + Stacks directory: 'stacks_outputs/' + Population map: 'denovo_map/popmap_cstacks.tsv' + Num. samples: 2 + Paired-end reads directory: 'demultiplexed/' + +Paired-end reads files found, e.g. 'demultiplexed/PopA_01.2.fq'. +Loading the catalog... +Processing sample 'PopA_01'... +Processing sample 'PopA_02'... + +Sample 'PopA_01': matched 3 sample loci to 3 catalog loci; found a paired-end read for 66 (100.0%) of the assembled forward reads; wrote 132 records. +Sample 'PopA_02': matched 3 sample loci to 3 catalog loci; found a paired-end read for 60 (100.0%) of the assembled forward reads; wrote 120 records. + +tsv2bam is done. |
| b |
| diff -r 000000000000 -r b2e3553e1be2 test-data/ustacks/PopA_01.alleles.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/ustacks/PopA_01.alleles.tsv Mon Jul 01 10:58:28 2019 -0400 |
| b |
| @@ -0,0 +1,3 @@ +# ustacks version 2.4; generated on 2019-06-18 10:34:45 +1 1 AC 50.00 9 +1 1 CA 50.00 9 |
| b |
| diff -r 000000000000 -r b2e3553e1be2 test-data/ustacks/PopA_01.snps.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/ustacks/PopA_01.snps.tsv Mon Jul 01 10:58:28 2019 -0400 |
| b |
| @@ -0,0 +1,283 @@ +# ustacks version 2.4; generated on 2019-06-18 10:34:45 +1 1 0 O 24.95 A - +1 1 1 O 24.95 A - +1 1 2 O 24.95 T - +1 1 3 O 24.95 T - +1 1 4 O 24.95 C - +1 1 5 O 24.95 G - +1 1 6 O 24.95 T - +1 1 7 O 24.95 T - +1 1 8 O 24.95 T - +1 1 9 O 24.95 G - +1 1 10 O 24.95 C - +1 1 11 O 24.95 T - +1 1 12 O 24.95 G - +1 1 13 O 24.95 C - +1 1 14 O 24.95 T - +1 1 15 O 24.95 T - +1 1 16 O 24.95 C - +1 1 17 O 24.95 A - +1 1 18 O 24.95 G - +1 1 19 O 24.95 G - +1 1 20 O 24.95 A - +1 1 21 O 24.95 A - +1 1 22 O 24.95 T - +1 1 23 O 24.95 C - +1 1 24 O 24.95 T - +1 1 25 O 24.95 C - +1 1 26 O 24.95 T - +1 1 27 O 24.95 C - +1 1 28 O 24.95 G - +1 1 29 O 24.95 T - +1 1 30 O 24.95 A - +1 1 31 O 24.95 T - +1 1 32 O 24.95 A - +1 1 33 E -19.78 A C +1 1 34 O 24.95 T - +1 1 35 O 24.95 C - +1 1 36 O 24.95 T - +1 1 37 O 24.95 G - +1 1 38 O 24.95 A - +1 1 39 O 24.95 G - +1 1 40 O 24.95 T - +1 1 41 O 24.95 A - +1 1 42 O 24.95 T - +1 1 43 O 24.95 G - +1 1 44 O 24.95 T - +1 1 45 O 24.95 G - +1 1 46 O 24.95 C - 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+1 2 4 O 38.82 C - +1 2 5 O 38.82 G - +1 2 6 O 38.82 G - +1 2 7 O 38.82 C - +1 2 8 O 38.82 T - +1 2 9 O 38.82 T - +1 2 10 O 38.82 G - +1 2 11 O 38.82 C - +1 2 12 O 38.82 A - +1 2 13 O 38.82 A - +1 2 14 O 38.82 C - +1 2 15 O 38.82 G - +1 2 16 O 38.82 C - +1 2 17 O 38.82 A - +1 2 18 O 38.82 A - +1 2 19 O 38.82 G - +1 2 20 O 38.82 T - +1 2 21 O 38.82 G - +1 2 22 O 38.82 A - +1 2 23 O 38.82 C - +1 2 24 O 38.82 G - +1 2 25 O 38.82 A - +1 2 26 O 38.82 T - +1 2 27 O 38.82 T - +1 2 28 O 38.82 C - +1 2 29 O 38.82 C - +1 2 30 O 38.82 C - +1 2 31 O 38.82 A - +1 2 32 O 38.82 C - +1 2 33 O 38.82 G - +1 2 34 O 38.82 G - +1 2 35 O 38.82 A - +1 2 36 O 38.82 C - +1 2 37 O 38.82 A - +1 2 38 O 38.82 T - +1 2 39 O 38.82 A - +1 2 40 O 38.82 A - +1 2 41 O 38.82 C - +1 2 42 O 38.82 T - +1 2 43 O 38.82 G - +1 2 44 O 38.82 A - +1 2 45 O 38.82 T - +1 2 46 O 38.82 C - +1 2 47 O 38.82 T - +1 2 48 O 38.82 A - +1 2 49 O 38.82 A - +1 2 50 O 38.82 G - +1 2 51 O 38.82 T - +1 2 52 O 38.82 A - +1 2 53 O 38.82 A - +1 2 54 O 38.82 C - +1 2 55 O 38.82 T - +1 2 56 O 38.82 T - +1 2 57 O 38.82 C - +1 2 58 O 38.82 C - +1 2 59 O 38.82 A - +1 2 60 O 38.82 A - +1 2 61 O 27.99 A - +1 2 62 O 38.82 T - +1 2 63 O 38.82 C - +1 2 64 O 38.82 T - +1 2 65 O 38.82 G - +1 2 66 O 38.82 G - +1 2 67 O 38.82 G - +1 2 68 O 38.82 A - +1 2 69 O 38.82 A - +1 2 70 O 38.82 T - +1 2 71 O 38.82 G - +1 2 72 O 38.82 G - +1 2 73 O 38.82 G - +1 2 74 O 38.82 A - +1 2 75 O 38.82 T - +1 2 76 O 38.82 T - +1 2 77 O 38.82 T - +1 2 78 O 38.82 C - +1 2 79 O 38.82 A - +1 2 80 O 38.82 T - +1 2 81 O 38.82 A - +1 2 82 O 38.82 A - +1 2 83 O 38.82 T - +1 2 84 O 38.82 T - +1 2 85 O 38.82 A - +1 2 86 O 38.82 A - +1 2 87 O 38.82 G - +1 2 88 O 38.82 G - +1 2 89 O 38.82 A - +1 2 90 O 38.82 C - +1 2 91 O 38.82 T - +1 2 92 O 38.82 A - +1 2 93 O 38.82 T - +1 3 0 O 27.73 A - +1 3 1 O 27.73 A - +1 3 2 O 27.73 T - +1 3 3 O 27.73 T - +1 3 4 O 27.73 C - +1 3 5 O 27.73 T - +1 3 6 O 27.73 C - +1 3 7 O 27.73 T - +1 3 8 O 27.73 A - +1 3 9 O 27.73 C - +1 3 10 O 27.73 A - +1 3 11 O 27.73 C - +1 3 12 O 27.73 C - +1 3 13 O 27.73 A - +1 3 14 O 27.73 C - +1 3 15 O 27.73 A - +1 3 16 O 27.73 G - +1 3 17 O 27.73 C - +1 3 18 O 27.73 A - +1 3 19 O 27.73 T - +1 3 20 O 27.73 C - +1 3 21 O 27.73 A - +1 3 22 O 27.73 A - +1 3 23 O 27.73 T - +1 3 24 O 27.73 T - +1 3 25 O 27.73 C - +1 3 26 O 27.73 T - +1 3 27 O 27.73 A - +1 3 28 O 27.73 A - +1 3 29 O 27.73 A - +1 3 30 O 27.73 A - +1 3 31 O 27.73 A - +1 3 32 O 27.73 T - +1 3 33 O 27.73 G - +1 3 34 O 27.73 A - +1 3 35 O 27.73 C - +1 3 36 O 27.73 T - +1 3 37 O 27.73 A - +1 3 38 O 27.73 C - +1 3 39 O 27.73 C - +1 3 40 O 27.73 A - +1 3 41 O 27.73 G - +1 3 42 O 27.73 A - +1 3 43 O 27.73 G - +1 3 44 O 27.73 A - +1 3 45 O 27.73 G - +1 3 46 O 27.73 A - +1 3 47 O 27.73 C - +1 3 48 O 27.73 A - +1 3 49 O 27.73 A - +1 3 50 O 27.73 C - +1 3 51 O 27.73 T - +1 3 52 O 27.73 C - +1 3 53 O 27.73 C - +1 3 54 O 27.73 G - +1 3 55 O 27.73 C - +1 3 56 O 27.73 A - +1 3 57 O 27.73 G - +1 3 58 O 27.73 T - +1 3 59 O 17.59 T - +1 3 60 O 27.73 A - +1 3 61 O 27.73 A - +1 3 62 O 27.73 A - +1 3 63 O 27.73 C - +1 3 64 O 27.73 A - +1 3 65 O 27.73 C - +1 3 66 O 27.73 T - +1 3 67 O 27.73 C - +1 3 68 O 27.73 T - +1 3 69 O 27.73 G - +1 3 70 O 27.73 A - +1 3 71 O 27.73 C - +1 3 72 O 27.73 T - +1 3 73 O 27.73 G - +1 3 74 O 27.73 C - +1 3 75 O 27.73 C - +1 3 76 O 27.73 A - +1 3 77 O 27.73 C - +1 3 78 O 27.73 G - +1 3 79 O 27.73 C - +1 3 80 O 27.73 C - +1 3 81 O 27.73 A - +1 3 82 O 27.73 G - +1 3 83 O 27.73 C - +1 3 84 O 27.73 T - +1 3 85 O 27.73 A - +1 3 86 O 27.73 C - +1 3 87 O 27.73 C - +1 3 88 O 27.73 T - +1 3 89 O 27.73 C - +1 3 90 O 17.59 T - +1 3 91 O 27.73 A - +1 3 92 O 27.73 G - +1 3 93 O 27.73 A - |
| b |
| diff -r 000000000000 -r b2e3553e1be2 test-data/ustacks/PopA_01.tags.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/ustacks/PopA_01.tags.tsv Mon Jul 01 10:58:28 2019 -0400 |
| b |
| b'@@ -0,0 +1,73 @@\n+# ustacks version 2.4; generated on 2019-06-18 10:34:45\n+1\t1\tconsensus\t\t\tAATTCGTTTGCTGCTTCAGGAATCTCTCGTATAATCTGAGTATGTGCGTACGTACGCTATTTAGATGGATAACCGACGCTGCCAGACGAGAGAC\t0\t0\t0\n+1\t1\tmodel\t\t\tOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOEOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOEOOOOO\t\t\t\n+1\t1\tprimary\t0\tlane1_fakedata7_0 1:N:0:/1\tAATTCGTTTGCTGCTTCAGGAATCTCTCGTATACTCTGAGTATGTGCGTACGTACGCTATTTAGATGGATAACCGACGCTGCCAGACGAGAGAC\t\t\t\n+1\t1\tprimary\t0\tlane1_fakedata7_1 1:N:0:/1\tAATTCGTTTGCTGCTTCAGGAATCTCTCGTATACTCTGAGTATGTGCGTACGTACGCTATTTAGATGGATAACCGACGCTGCCAGACGAGAGAC\t\t\t\n+1\t1\tprimary\t0\tlane1_fakedata7_2 1:N:0:/1\tAATTCGTTTGCTGCTTCAGGAATCTCTCGTATACTCTGAGTATGTGCGTACGTACGCTATTTAGATGGATAACCGACGCTGCCAGACGAGAGAC\t\t\t\n+1\t1\tprimary\t0\tlane1_fakedata7_3 1:N:0:/1\tAATTCGTTTGCTGCTTCAGGAATCTCTCGTATACTCTGAGTATGTGCGTACGTACGCTATTTAGATGGATAACCGACGCTGCCAGACGAGAGAC\t\t\t\n+1\t1\tprimary\t0\tlane1_fakedata7_4 1:N:0:/1\tAATTCGTTTGCTGCTTCAGGAATCTCTCGTATACTCTGAGTATGTGCGTACGTACGCTATTTAGATGGATAACCGACGCTGCCAGACGAGAGAC\t\t\t\n+1\t1\tprimary\t0\tlane1_fakedata7_5 1:N:0:/1\tAATTCGTTTGCTGCTTCAGGAATCTCTCGTATACTCTGAGTATGTGCGTACGTACGCTATTTAGATGGATAACCGACGCTGCCAGACGAGAGAC\t\t\t\n+1\t1\tprimary\t0\tlane1_fakedata7_6 1:N:0:/1\tAATTCGTTTGCTGCTTCAGGAATCTCTCGTATACTCTGAGTATGTGCGTACGTACGCTATTTAGATGGATAACCGACGCTGCCAGACGAGAGAC\t\t\t\n+1\t1\tprimary\t0\tlane1_fakedata7_7 1:N:0:/1\tAATTCGTTTGCTGCTTCAGGAATCTCTCGTATACTCTGAGTATGTGCGTACGTACGCTATTTAGATGGATAACCGACGCTGCCAGACGAGAGAC\t\t\t\n+1\t1\tprimary\t0\tlane1_fakedata7_8 1:N:0:/1\tAATTCGTTTGCTGCTTCAGGAATCTCTCGTATACTCTGAGTATGTGCGTACGTACGCTATTTAGATGGATAACCGACGCTGCCAGACGAGAGAC\t\t\t\n+1\t1\tprimary\t1\tlane1_fakedata7_9 1:N:0:/1\tAATTCGTTTGCTGCTTCAGGAATCTCTCGTATAATCTGAGTATGTGCGTACGTACGCTATTTAGATGGATAACCGACGCTGCCAGACGCGAGAC\t\t\t\n+1\t1\tprimary\t1\tlane1_fakedata7_10 1:N:0:/1\tAATTCGTTTGCTGCTTCAGGAATCTCTCGTATAATCTGAGTATGTGCGTACGTACGCTATTTAGATGGATAACCGACGCTGCCAGACGCGAGAC\t\t\t\n+1\t1\tprimary\t1\tlane1_fakedata7_11 1:N:0:/1\tAATTCGTTTGCTGCTTCAGGAATCTCTCGTATAATCTGAGTATGTGCGTACGTACGCTATTTAGATGGATAACCGACGCTGCCAGACGCGAGAC\t\t\t\n+1\t1\tprimary\t1\tlane1_fakedata7_12 1:N:0:/1\tAATTCGTTTGCTGCTTCAGGAATCTCTCGTATAATCTGAGTATGTGCGTACGTACGCTATTTAGATGGATAACCGACGCTGCCAGACGCGAGAC\t\t\t\n+1\t1\tprimary\t1\tlane1_fakedata7_13 1:N:0:/1\tAATTCGTTTGCTGCTTCAGGAATCTCTCGTATAATCTGAGTATGTGCGTACGTACGCTATTTAGATGGATAACCGACGCTGCCAGACGCGAGAC\t\t\t\n+1\t1\tprimary\t1\tlane1_fakedata7_14 1:N:0:/1\tAATTCGTTTGCTGCTTCAGGAATCTCTCGTATAATCTGAGTATGTGCGTACGTACGCTATTTAGATGGATAACCGACGCTGCCAGACGCGAGAC\t\t\t\n+1\t1\tprimary\t1\tlane1_fakedata7_15 1:N:0:/1\tAATTCGTTTGCTGCTTCAGGAATCTCTCGTATAATCTGAGTATGTGCGTACGTACGCTATTTAGATGGATAACCGACGCTGCCAGACGCGAGAC\t\t\t\n+1\t1\tprimary\t1\tlane1_fakedata7_16 1:N:0:/1\tAATTCGTTTGCTGCTTCAGGAATCTCTCGTATAATCTGAGTATGTGCGTACGTACGCTATTTAGATGGATAACCGACGCTGCCAGACGCGAGAC\t\t\t\n+1\t1\tprimary\t1\tlane1_fakedata7_17 1:N:0:/1\tAATTCGTTTGCTGCTTCAGGAATCTCTCGTATAATCTGAGTATGTGCGTACGTACGCTATTTAGATGGATAACCGACGCTGCCAGACGCGAGAC\t\t\t\n+1\t2\tconsensus\t\t\tAATTCGGCTTGCAACGCAAGTGACGATTCCCACGGACATAACTGATCTAAGTAACTTCCAAATCTGGGAATGGGATTTCATAATTAAGGACTAT\t0\t0\t0\n+1\t2\tmodel\t\t\tOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOO\t\t\t\n+1\t2\tprimary\t0\tlane1_fakedata0_0 1:N:0:/1\tAATTCGGCTTGCAACGCAAGTGACGATTCCCACGGACATAACTGATCTAAGTAACTTCCAAATCTGGGAATGGGATTTCATAATTAAGGACTAT\t\t\t\n+1\t2\tprimary\t0\tlane1_fakedata0_1 1:N:0:/1\tAATTCGGCTTGCAACGCAAGTGACGATTCCCACGGACATAACTGATCTAAGTAACTTCCAAATCTGGGAATGGGATTTCATAATTAAGGACTAT\t\t\t\n+1\t2\tprimary\t0\tlane1_fakedata0_2 1:N:0:/1\tAATTCGGCTTGCAACGCAAGTGACGATTCCCACGGACATAACTGATCTAAGTAACTTCCAAATCTGGGAATGGGATTTCATAATTAAGGACTAT\t\t\t\n+1\t2\tprimary\t0\tlane1_fakedata0_3 1:N:0:/1\tAATTCGGCTTGCAACGCAAGTGACGATTCCCACGGACATAACTGATCTAAGTAACTTCCAAATCTGGGAATGGGATTTCATAATTAAGGACTAT\t\t\t\n+1\t2\tprimary\t0\tlane1_fakedata0_4 1:N:0:/1\tAATTCGGCTTGCAACGCAAGTGACGATTCCCACGGACATAACTGATCTAAGTAACTTCCAAATCTGGGAATGGGATTTCATAATTAAGGACTAT\t\t\t\n+1\t2\tprimary\t0\tlane1_fakedata0_5 1:N:0:/1\tAATTCGGCTTGCAACGCAAGTGACGATTCCCACGGACATAACTGATCTAAGTAACTTCCAAATCTGGGAATGGGATTTCATAATTAAGGACTAT\t\t\t\n+1\t2\tprimary\t0\tlane1_fakedata0_6 1:N:0:/1\tAATTCGGCTTGCAACGCAAGTGACGATTCCCACGGACATAACTGATCTAAGTAACTT'..b'_22 1:N:0:/1\tAATTCGGCTTGCAACGCAAGTGACGATTCCCACGGACATAACTGATCTAAGTAACTTCCAAATCTGGGAATGGGATTTCATAATTAAGGACTAT\t\t\t\n+1\t2\tprimary\t0\tlane1_fakedata0_23 1:N:0:/1\tAATTCGGCTTGCAACGCAAGTGACGATTCCCACGGACATAACTGATCTAAGTAACTTCCAAATCTGGGAATGGGATTTCATAATTAAGGACTAT\t\t\t\n+1\t2\tprimary\t0\tlane1_fakedata0_24 1:N:0:/1\tAATTCGGCTTGCAACGCAAGTGACGATTCCCACGGACATAACTGATCTAAGTAACTTCCAAATCTGGGAATGGGATTTCATAATTAAGGACTAT\t\t\t\n+1\t2\tprimary\t0\tlane1_fakedata0_25 1:N:0:/1\tAATTCGGCTTGCAACGCAAGTGACGATTCCCACGGACATAACTGATCTAAGTAACTTCCAAATCTGGGAATGGGATTTCATAATTAAGGACTAT\t\t\t\n+1\t2\tprimary\t0\tlane1_fakedata0_26 1:N:0:/1\tAATTCGGCTTGCAACGCAAGTGACGATTCCCACGGACATAACTGATCTAAGTAACTTCCAAATCTGGGAATGGGATTTCATAATTAAGGACTAT\t\t\t\n+1\t2\tprimary\t0\tlane1_fakedata0_27 1:N:0:/1\tAATTCGGCTTGCAACGCAAGTGACGATTCCCACGGACATAACTGATCTAAGTAACTTCCAAATCTGGGAATGGGATTTCATAATTAAGGACTAT\t\t\t\n+1\t2\tsecondary\t\tlane1_fakedata0_15 1:N:0:/1\tAATTCGGCTTGCAACGCAAGTGACGATTCCCACGGACATAACTGATCTAAGTAACTTCCAAGTCTGGGAATGGGATTTCATAATTAAGGACTAT\t\t\t\n+1\t3\tconsensus\t\t\tAATTCTCTACACCACAGCATCAATTCTAAAAATGACTACCAGAGAGACAACTCCGCAGTTAAACACTCTGACTGCCACGCCAGCTACCTCTAGA\t0\t0\t0\n+1\t3\tmodel\t\t\tOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOO\t\t\t\n+1\t3\tprimary\t0\tlane1_fakedata2_0 1:N:0:/1\tAATTCTCTACACCACAGCATCAATTCTAAAAATGACTACCAGAGAGACAACTCCGCAGTTAAACACTCTGACTGCCACGCCAGCTACCTCTAGA\t\t\t\n+1\t3\tprimary\t0\tlane1_fakedata2_1 1:N:0:/1\tAATTCTCTACACCACAGCATCAATTCTAAAAATGACTACCAGAGAGACAACTCCGCAGTTAAACACTCTGACTGCCACGCCAGCTACCTCTAGA\t\t\t\n+1\t3\tprimary\t0\tlane1_fakedata2_2 1:N:0:/1\tAATTCTCTACACCACAGCATCAATTCTAAAAATGACTACCAGAGAGACAACTCCGCAGTTAAACACTCTGACTGCCACGCCAGCTACCTCTAGA\t\t\t\n+1\t3\tprimary\t0\tlane1_fakedata2_3 1:N:0:/1\tAATTCTCTACACCACAGCATCAATTCTAAAAATGACTACCAGAGAGACAACTCCGCAGTTAAACACTCTGACTGCCACGCCAGCTACCTCTAGA\t\t\t\n+1\t3\tprimary\t0\tlane1_fakedata2_4 1:N:0:/1\tAATTCTCTACACCACAGCATCAATTCTAAAAATGACTACCAGAGAGACAACTCCGCAGTTAAACACTCTGACTGCCACGCCAGCTACCTCTAGA\t\t\t\n+1\t3\tprimary\t0\tlane1_fakedata2_6 1:N:0:/1\tAATTCTCTACACCACAGCATCAATTCTAAAAATGACTACCAGAGAGACAACTCCGCAGTTAAACACTCTGACTGCCACGCCAGCTACCTCTAGA\t\t\t\n+1\t3\tprimary\t0\tlane1_fakedata2_7 1:N:0:/1\tAATTCTCTACACCACAGCATCAATTCTAAAAATGACTACCAGAGAGACAACTCCGCAGTTAAACACTCTGACTGCCACGCCAGCTACCTCTAGA\t\t\t\n+1\t3\tprimary\t0\tlane1_fakedata2_8 1:N:0:/1\tAATTCTCTACACCACAGCATCAATTCTAAAAATGACTACCAGAGAGACAACTCCGCAGTTAAACACTCTGACTGCCACGCCAGCTACCTCTAGA\t\t\t\n+1\t3\tprimary\t0\tlane1_fakedata2_9 1:N:0:/1\tAATTCTCTACACCACAGCATCAATTCTAAAAATGACTACCAGAGAGACAACTCCGCAGTTAAACACTCTGACTGCCACGCCAGCTACCTCTAGA\t\t\t\n+1\t3\tprimary\t0\tlane1_fakedata2_10 1:N:0:/1\tAATTCTCTACACCACAGCATCAATTCTAAAAATGACTACCAGAGAGACAACTCCGCAGTTAAACACTCTGACTGCCACGCCAGCTACCTCTAGA\t\t\t\n+1\t3\tprimary\t0\tlane1_fakedata2_11 1:N:0:/1\tAATTCTCTACACCACAGCATCAATTCTAAAAATGACTACCAGAGAGACAACTCCGCAGTTAAACACTCTGACTGCCACGCCAGCTACCTCTAGA\t\t\t\n+1\t3\tprimary\t0\tlane1_fakedata2_12 1:N:0:/1\tAATTCTCTACACCACAGCATCAATTCTAAAAATGACTACCAGAGAGACAACTCCGCAGTTAAACACTCTGACTGCCACGCCAGCTACCTCTAGA\t\t\t\n+1\t3\tprimary\t0\tlane1_fakedata2_13 1:N:0:/1\tAATTCTCTACACCACAGCATCAATTCTAAAAATGACTACCAGAGAGACAACTCCGCAGTTAAACACTCTGACTGCCACGCCAGCTACCTCTAGA\t\t\t\n+1\t3\tprimary\t0\tlane1_fakedata2_14 1:N:0:/1\tAATTCTCTACACCACAGCATCAATTCTAAAAATGACTACCAGAGAGACAACTCCGCAGTTAAACACTCTGACTGCCACGCCAGCTACCTCTAGA\t\t\t\n+1\t3\tprimary\t0\tlane1_fakedata2_15 1:N:0:/1\tAATTCTCTACACCACAGCATCAATTCTAAAAATGACTACCAGAGAGACAACTCCGCAGTTAAACACTCTGACTGCCACGCCAGCTACCTCTAGA\t\t\t\n+1\t3\tprimary\t0\tlane1_fakedata2_16 1:N:0:/1\tAATTCTCTACACCACAGCATCAATTCTAAAAATGACTACCAGAGAGACAACTCCGCAGTTAAACACTCTGACTGCCACGCCAGCTACCTCTAGA\t\t\t\n+1\t3\tprimary\t0\tlane1_fakedata2_18 1:N:0:/1\tAATTCTCTACACCACAGCATCAATTCTAAAAATGACTACCAGAGAGACAACTCCGCAGTTAAACACTCTGACTGCCACGCCAGCTACCTCTAGA\t\t\t\n+1\t3\tprimary\t0\tlane1_fakedata2_19 1:N:0:/1\tAATTCTCTACACCACAGCATCAATTCTAAAAATGACTACCAGAGAGACAACTCCGCAGTTAAACACTCTGACTGCCACGCCAGCTACCTCTAGA\t\t\t\n+1\t3\tsecondary\t\tlane1_fakedata2_5 1:N:0:/1\tAATTCTCTACACCACAGCATCAATTCTAAAAATGACTACCAGAGAGACAACTCCGCAGTAAAACACTCTGACTGCCACGCCAGCTACCTCTAGA\t\t\t\n+1\t3\tsecondary\t\tlane1_fakedata2_17 1:N:0:/1\tAATTCTCTACACCACAGCATCAATTCTAAAAATGACTACCAGAGAGACAACTCCGCAGTTAAACACTCTGACTGCCACGCCAGCTACCTCCAGA\t\t\t\n' |
| b |
| diff -r 000000000000 -r b2e3553e1be2 test-data/ustacks/PopA_02.alleles.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/ustacks/PopA_02.alleles.tsv Mon Jul 01 10:58:28 2019 -0400 |
| b |
| @@ -0,0 +1,3 @@ +# ustacks version 2.4; generated on 2019-06-18 10:34:45 +2 1 AC 50.00 6 +2 1 CA 50.00 6 |
| b |
| diff -r 000000000000 -r b2e3553e1be2 test-data/ustacks/PopA_02.snps.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/ustacks/PopA_02.snps.tsv Mon Jul 01 10:58:28 2019 -0400 |
| b |
| @@ -0,0 +1,283 @@ +# ustacks version 2.4; generated on 2019-06-18 10:34:45 +2 1 0 O 16.64 A - +2 1 1 O 16.64 A - +2 1 2 O 16.64 T - +2 1 3 O 16.64 T - +2 1 4 O 16.64 C - +2 1 5 O 16.64 G - +2 1 6 O 16.64 T - +2 1 7 O 16.64 T - +2 1 8 O 16.64 T - +2 1 9 O 16.64 G - +2 1 10 O 16.64 C - +2 1 11 O 16.64 T - +2 1 12 O 16.64 G - +2 1 13 O 16.64 C - +2 1 14 O 16.64 T - +2 1 15 O 16.64 T - +2 1 16 O 16.64 C - +2 1 17 O 16.64 A - +2 1 18 O 16.64 G - +2 1 19 O 16.64 G - +2 1 20 O 16.64 A - +2 1 21 O 16.64 A - +2 1 22 O 7.55 T - +2 1 23 O 16.64 C - +2 1 24 O 16.64 T - +2 1 25 O 7.55 C - +2 1 26 O 16.64 T - +2 1 27 O 16.64 C - +2 1 28 O 16.64 G - +2 1 29 O 16.64 T - +2 1 30 O 16.64 A - +2 1 31 O 16.64 T - +2 1 32 O 16.64 A - +2 1 33 E -13.18 A C +2 1 34 O 16.64 T - +2 1 35 O 16.64 C - +2 1 36 O 16.64 T - +2 1 37 O 16.64 G - +2 1 38 O 16.64 A - +2 1 39 O 16.64 G - +2 1 40 O 16.64 T - +2 1 41 O 16.64 A - +2 1 42 O 16.64 T - +2 1 43 O 16.64 G - +2 1 44 O 16.64 T - +2 1 45 O 16.64 G - +2 1 46 O 16.64 C - +2 1 47 O 16.64 G - +2 1 48 O 16.64 T - +2 1 49 O 16.64 A - +2 1 50 O 16.64 C - +2 1 51 O 16.64 G - +2 1 52 O 16.64 T - +2 1 53 O 16.64 A - +2 1 54 O 16.64 C - +2 1 55 O 16.64 G - +2 1 56 O 16.64 C - +2 1 57 O 16.64 T - +2 1 58 O 16.64 A - +2 1 59 O 16.64 T - +2 1 60 O 16.64 T - +2 1 61 O 16.64 T - +2 1 62 O 16.64 A - +2 1 63 O 16.64 G - +2 1 64 O 16.64 A - +2 1 65 O 16.64 T - +2 1 66 O 16.64 G - +2 1 67 O 16.64 G - +2 1 68 O 16.64 A - +2 1 69 O 16.64 T - +2 1 70 O 16.64 A - +2 1 71 O 16.64 A - +2 1 72 O 16.64 C - +2 1 73 O 16.64 C - +2 1 74 O 16.64 G - +2 1 75 O 16.64 A - +2 1 76 O 16.64 C - +2 1 77 O 16.64 G - +2 1 78 O 16.64 C - +2 1 79 O 16.64 T - +2 1 80 O 16.64 G - +2 1 81 O 16.64 C - +2 1 82 O 16.64 C - +2 1 83 O 16.64 A - +2 1 84 O 16.64 G - +2 1 85 O 16.64 A - +2 1 86 O 16.64 C - +2 1 87 O 16.64 G - +2 1 88 E -13.18 A C +2 1 89 O 16.64 G - +2 1 90 O 16.64 A - +2 1 91 O 16.64 G - +2 1 92 O 16.64 A - +2 1 93 O 16.64 C - +2 2 0 O 38.82 A - +2 2 1 O 38.82 A - +2 2 2 O 38.82 T - +2 2 3 O 38.82 T - +2 2 4 O 38.82 C - +2 2 5 O 38.82 G - +2 2 6 O 38.82 G - +2 2 7 O 38.82 C - +2 2 8 O 38.82 T - +2 2 9 O 38.82 T - +2 2 10 O 38.82 G - +2 2 11 O 38.82 C - +2 2 12 O 38.82 A - +2 2 13 O 38.82 A - +2 2 14 O 38.82 C - +2 2 15 O 38.82 G - +2 2 16 O 38.82 C - +2 2 17 O 38.82 A - +2 2 18 O 38.82 A - +2 2 19 O 38.82 G - +2 2 20 O 38.82 T - +2 2 21 O 38.82 G - +2 2 22 O 38.82 A - +2 2 23 O 38.82 C - +2 2 24 O 38.82 G - +2 2 25 O 38.82 A - +2 2 26 O 38.82 T - +2 2 27 O 38.82 T - +2 2 28 O 38.82 C - +2 2 29 O 38.82 C - +2 2 30 O 38.82 C - +2 2 31 O 27.99 A - +2 2 32 O 38.82 C - +2 2 33 O 38.82 G - +2 2 34 O 38.82 G - +2 2 35 O 38.82 A - +2 2 36 O 38.82 C - +2 2 37 O 38.82 A - +2 2 38 O 38.82 T - +2 2 39 O 38.82 A - +2 2 40 O 38.82 A - +2 2 41 O 38.82 C - +2 2 42 O 38.82 T - +2 2 43 O 38.82 G - +2 2 44 O 38.82 A - +2 2 45 O 38.82 T - +2 2 46 O 38.82 C - +2 2 47 O 38.82 T - +2 2 48 O 38.82 A - +2 2 49 O 38.82 A - +2 2 50 O 38.82 G - +2 2 51 O 38.82 T - +2 2 52 O 38.82 A - +2 2 53 O 27.99 A - +2 2 54 O 38.82 C - +2 2 55 O 38.82 T - +2 2 56 O 38.82 T - +2 2 57 O 38.82 C - +2 2 58 O 38.82 C - +2 2 59 O 38.82 A - +2 2 60 O 38.82 A - +2 2 61 O 38.82 A - +2 2 62 O 38.82 T - +2 2 63 O 38.82 C - +2 2 64 O 38.82 T - +2 2 65 O 38.82 G - +2 2 66 O 38.82 G - +2 2 67 O 38.82 G - +2 2 68 O 38.82 A - +2 2 69 O 38.82 A - +2 2 70 O 38.82 T - +2 2 71 O 38.82 G - +2 2 72 O 38.82 G - +2 2 73 O 38.82 G - +2 2 74 O 38.82 A - +2 2 75 O 38.82 T - +2 2 76 O 38.82 T - +2 2 77 O 38.82 T - +2 2 78 O 38.82 C - +2 2 79 O 38.82 A - +2 2 80 O 38.82 T - +2 2 81 O 38.82 A - +2 2 82 O 38.82 A - +2 2 83 O 38.82 T - +2 2 84 O 38.82 T - +2 2 85 O 38.82 A - +2 2 86 O 38.82 A - +2 2 87 O 38.82 G - +2 2 88 O 38.82 G - +2 2 89 O 38.82 A - +2 2 90 O 38.82 C - +2 2 91 O 38.82 T - +2 2 92 O 38.82 A - +2 2 93 O 38.82 T - +2 3 0 O 27.73 A - +2 3 1 O 27.73 A - +2 3 2 O 27.73 T - +2 3 3 O 27.73 T - +2 3 4 O 27.73 C - +2 3 5 O 27.73 T - +2 3 6 O 27.73 C - +2 3 7 O 27.73 T - +2 3 8 O 27.73 A - +2 3 9 O 27.73 C - +2 3 10 O 27.73 A - +2 3 11 O 27.73 C - +2 3 12 O 27.73 C - +2 3 13 O 27.73 A - +2 3 14 O 27.73 C - +2 3 15 O 17.59 A - +2 3 16 O 27.73 G - +2 3 17 O 27.73 C - +2 3 18 O 27.73 A - +2 3 19 O 27.73 T - +2 3 20 O 27.73 C - +2 3 21 O 27.73 A - +2 3 22 O 27.73 A - +2 3 23 O 27.73 T - +2 3 24 O 27.73 T - +2 3 25 O 27.73 C - +2 3 26 O 27.73 T - +2 3 27 O 27.73 A - +2 3 28 O 27.73 A - +2 3 29 O 27.73 A - +2 3 30 O 27.73 A - +2 3 31 O 27.73 A - +2 3 32 O 27.73 T - +2 3 33 O 27.73 G - +2 3 34 O 27.73 A - +2 3 35 O 27.73 C - +2 3 36 O 27.73 T - +2 3 37 O 27.73 A - +2 3 38 O 27.73 C - +2 3 39 O 27.73 C - +2 3 40 O 27.73 A - +2 3 41 O 27.73 G - +2 3 42 O 27.73 A - +2 3 43 O 27.73 G - +2 3 44 O 27.73 A - +2 3 45 O 27.73 G - +2 3 46 O 27.73 A - +2 3 47 O 27.73 C - +2 3 48 O 27.73 A - +2 3 49 O 27.73 A - +2 3 50 O 27.73 C - +2 3 51 O 27.73 T - +2 3 52 O 27.73 C - +2 3 53 O 27.73 C - +2 3 54 O 27.73 G - +2 3 55 O 27.73 C - +2 3 56 O 27.73 A - +2 3 57 O 27.73 G - +2 3 58 O 27.73 T - +2 3 59 O 27.73 T - +2 3 60 O 27.73 A - +2 3 61 O 27.73 A - +2 3 62 O 27.73 A - +2 3 63 O 27.73 C - +2 3 64 O 27.73 A - +2 3 65 O 27.73 C - +2 3 66 O 27.73 T - +2 3 67 O 27.73 C - +2 3 68 O 27.73 T - +2 3 69 O 27.73 G - +2 3 70 O 27.73 A - +2 3 71 O 27.73 C - +2 3 72 O 27.73 T - +2 3 73 O 27.73 G - +2 3 74 O 27.73 C - +2 3 75 O 27.73 C - +2 3 76 O 27.73 A - +2 3 77 O 27.73 C - +2 3 78 O 27.73 G - +2 3 79 O 27.73 C - +2 3 80 O 27.73 C - +2 3 81 O 27.73 A - +2 3 82 O 27.73 G - +2 3 83 O 27.73 C - +2 3 84 O 27.73 T - +2 3 85 O 27.73 A - +2 3 86 O 27.73 C - +2 3 87 O 27.73 C - +2 3 88 O 27.73 T - +2 3 89 O 27.73 C - +2 3 90 O 27.73 T - +2 3 91 O 27.73 A - +2 3 92 O 27.73 G - +2 3 93 O 27.73 A - |
| b |
| diff -r 000000000000 -r b2e3553e1be2 test-data/ustacks/PopA_02.tags.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/ustacks/PopA_02.tags.tsv Mon Jul 01 10:58:28 2019 -0400 |
| b |
| b'@@ -0,0 +1,67 @@\n+# ustacks version 2.4; generated on 2019-06-18 10:34:45\n+2\t1\tconsensus\t\t\tAATTCGTTTGCTGCTTCAGGAATCTCTCGTATAATCTGAGTATGTGCGTACGTACGCTATTTAGATGGATAACCGACGCTGCCAGACGAGAGAC\t0\t0\t0\n+2\t1\tmodel\t\t\tOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOEOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOEOOOOO\t\t\t\n+2\t1\tprimary\t0\tlane1_fakedata7_7 1:N:0:/1\tAATTCGTTTGCTGCTTCAGGAATCTCTCGTATACTCTGAGTATGTGCGTACGTACGCTATTTAGATGGATAACCGACGCTGCCAGACGAGAGAC\t\t\t\n+2\t1\tprimary\t0\tlane1_fakedata7_8 1:N:0:/1\tAATTCGTTTGCTGCTTCAGGAATCTCTCGTATACTCTGAGTATGTGCGTACGTACGCTATTTAGATGGATAACCGACGCTGCCAGACGAGAGAC\t\t\t\n+2\t1\tprimary\t0\tlane1_fakedata7_9 1:N:0:/1\tAATTCGTTTGCTGCTTCAGGAATCTCTCGTATACTCTGAGTATGTGCGTACGTACGCTATTTAGATGGATAACCGACGCTGCCAGACGAGAGAC\t\t\t\n+2\t1\tprimary\t0\tlane1_fakedata7_11 1:N:0:/1\tAATTCGTTTGCTGCTTCAGGAATCTCTCGTATACTCTGAGTATGTGCGTACGTACGCTATTTAGATGGATAACCGACGCTGCCAGACGAGAGAC\t\t\t\n+2\t1\tprimary\t1\tlane1_fakedata7_0 1:N:0:/1\tAATTCGTTTGCTGCTTCAGGAATCTCTCGTATAATCTGAGTATGTGCGTACGTACGCTATTTAGATGGATAACCGACGCTGCCAGACGCGAGAC\t\t\t\n+2\t1\tprimary\t1\tlane1_fakedata7_1 1:N:0:/1\tAATTCGTTTGCTGCTTCAGGAATCTCTCGTATAATCTGAGTATGTGCGTACGTACGCTATTTAGATGGATAACCGACGCTGCCAGACGCGAGAC\t\t\t\n+2\t1\tprimary\t1\tlane1_fakedata7_2 1:N:0:/1\tAATTCGTTTGCTGCTTCAGGAATCTCTCGTATAATCTGAGTATGTGCGTACGTACGCTATTTAGATGGATAACCGACGCTGCCAGACGCGAGAC\t\t\t\n+2\t1\tprimary\t1\tlane1_fakedata7_3 1:N:0:/1\tAATTCGTTTGCTGCTTCAGGAATCTCTCGTATAATCTGAGTATGTGCGTACGTACGCTATTTAGATGGATAACCGACGCTGCCAGACGCGAGAC\t\t\t\n+2\t1\tprimary\t1\tlane1_fakedata7_4 1:N:0:/1\tAATTCGTTTGCTGCTTCAGGAATCTCTCGTATAATCTGAGTATGTGCGTACGTACGCTATTTAGATGGATAACCGACGCTGCCAGACGCGAGAC\t\t\t\n+2\t1\tprimary\t1\tlane1_fakedata7_5 1:N:0:/1\tAATTCGTTTGCTGCTTCAGGAATCTCTCGTATAATCTGAGTATGTGCGTACGTACGCTATTTAGATGGATAACCGACGCTGCCAGACGCGAGAC\t\t\t\n+2\t1\tsecondary\t\tlane1_fakedata7_6 1:N:0:/1\tAATTCGTTTGCTGCTTCAGGAACCTCTCGTATACTCTGAGTATGTGCGTACGTACGCTATTTAGATGGATAACCGACGCTGCCAGACGAGAGAC\t\t\t\n+2\t1\tsecondary\t\tlane1_fakedata7_10 1:N:0:/1\tAATTCGTTTGCTGCTTCAGGAATCTTTCGTATACTCTGAGTATGTGCGTACGTACGCTATTTAGATGGATAACCGACGCTGCCAGACGAGAGAC\t\t\t\n+2\t2\tconsensus\t\t\tAATTCGGCTTGCAACGCAAGTGACGATTCCCACGGACATAACTGATCTAAGTAACTTCCAAATCTGGGAATGGGATTTCATAATTAAGGACTAT\t0\t0\t0\n+2\t2\tmodel\t\t\tOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOO\t\t\t\n+2\t2\tprimary\t0\tlane1_fakedata0_0 1:N:0:/1\tAATTCGGCTTGCAACGCAAGTGACGATTCCCACGGACATAACTGATCTAAGTAACTTCCAAATCTGGGAATGGGATTTCATAATTAAGGACTAT\t\t\t\n+2\t2\tprimary\t0\tlane1_fakedata0_1 1:N:0:/1\tAATTCGGCTTGCAACGCAAGTGACGATTCCCACGGACATAACTGATCTAAGTAACTTCCAAATCTGGGAATGGGATTTCATAATTAAGGACTAT\t\t\t\n+2\t2\tprimary\t0\tlane1_fakedata0_2 1:N:0:/1\tAATTCGGCTTGCAACGCAAGTGACGATTCCCACGGACATAACTGATCTAAGTAACTTCCAAATCTGGGAATGGGATTTCATAATTAAGGACTAT\t\t\t\n+2\t2\tprimary\t0\tlane1_fakedata0_3 1:N:0:/1\tAATTCGGCTTGCAACGCAAGTGACGATTCCCACGGACATAACTGATCTAAGTAACTTCCAAATCTGGGAATGGGATTTCATAATTAAGGACTAT\t\t\t\n+2\t2\tprimary\t0\tlane1_fakedata0_4 1:N:0:/1\tAATTCGGCTTGCAACGCAAGTGACGATTCCCACGGACATAACTGATCTAAGTAACTTCCAAATCTGGGAATGGGATTTCATAATTAAGGACTAT\t\t\t\n+2\t2\tprimary\t0\tlane1_fakedata0_5 1:N:0:/1\tAATTCGGCTTGCAACGCAAGTGACGATTCCCACGGACATAACTGATCTAAGTAACTTCCAAATCTGGGAATGGGATTTCATAATTAAGGACTAT\t\t\t\n+2\t2\tprimary\t0\tlane1_fakedata0_6 1:N:0:/1\tAATTCGGCTTGCAACGCAAGTGACGATTCCCACGGACATAACTGATCTAAGTAACTTCCAAATCTGGGAATGGGATTTCATAATTAAGGACTAT\t\t\t\n+2\t2\tprimary\t0\tlane1_fakedata0_7 1:N:0:/1\tAATTCGGCTTGCAACGCAAGTGACGATTCCCACGGACATAACTGATCTAAGTAACTTCCAAATCTGGGAATGGGATTTCATAATTAAGGACTAT\t\t\t\n+2\t2\tprimary\t0\tlane1_fakedata0_8 1:N:0:/1\tAATTCGGCTTGCAACGCAAGTGACGATTCCCACGGACATAACTGATCTAAGTAACTTCCAAATCTGGGAATGGGATTTCATAATTAAGGACTAT\t\t\t\n+2\t2\tprimary\t0\tlane1_fakedata0_9 1:N:0:/1\tAATTCGGCTTGCAACGCAAGTGACGATTCCCACGGACATAACTGATCTAAGTAACTTCCAAATCTGGGAATGGGATTTCATAATTAAGGACTAT\t\t\t\n+2\t2\tprimary\t0\tlane1_fakedata0_10 1:N:0:/1\tAATTCGGCTTGCAACGCAAGTGACGATTCCCACGGACATAACTGATCTAAGTAACTTCCAAATCTGGGAATGGGATTTCATAATTAAGGACTAT\t\t\t\n+2\t2\tprimary\t0\tlane1_fakedata0_11 1:N:0:/1\tAATTCGGCTTGCAACGCAAGTGACGATTCCCACGGACATAACTGATCTAAGTAACTTCCAAATCTGGGAATGGGATTTCATAATTAAGGACTAT\t\t\t\n+2\t2\tprimary\t0\tlane1_fakedata0_12 1:N:0:/1\tAATTCGGCTTGCAACGCAAGTGACGATTCCCACGGACATAACTGATCTAAGTAACTTC'..b'_21 1:N:0:/1\tAATTCGGCTTGCAACGCAAGTGACGATTCCCACGGACATAACTGATCTAAGTAACTTCCAAATCTGGGAATGGGATTTCATAATTAAGGACTAT\t\t\t\n+2\t2\tprimary\t0\tlane1_fakedata0_23 1:N:0:/1\tAATTCGGCTTGCAACGCAAGTGACGATTCCCACGGACATAACTGATCTAAGTAACTTCCAAATCTGGGAATGGGATTTCATAATTAAGGACTAT\t\t\t\n+2\t2\tprimary\t0\tlane1_fakedata0_24 1:N:0:/1\tAATTCGGCTTGCAACGCAAGTGACGATTCCCACGGACATAACTGATCTAAGTAACTTCCAAATCTGGGAATGGGATTTCATAATTAAGGACTAT\t\t\t\n+2\t2\tprimary\t0\tlane1_fakedata0_25 1:N:0:/1\tAATTCGGCTTGCAACGCAAGTGACGATTCCCACGGACATAACTGATCTAAGTAACTTCCAAATCTGGGAATGGGATTTCATAATTAAGGACTAT\t\t\t\n+2\t2\tprimary\t0\tlane1_fakedata0_27 1:N:0:/1\tAATTCGGCTTGCAACGCAAGTGACGATTCCCACGGACATAACTGATCTAAGTAACTTCCAAATCTGGGAATGGGATTTCATAATTAAGGACTAT\t\t\t\n+2\t2\tsecondary\t\tlane1_fakedata0_22 1:N:0:/1\tAATTCGGCTTGCAACGCAAGTGACGATTCCCCCGGACATAACTGATCTAAGTAACTTCCAAATCTGGGAATGGGATTTCATAATTAAGGACTAT\t\t\t\n+2\t2\tsecondary\t\tlane1_fakedata0_26 1:N:0:/1\tAATTCGGCTTGCAACGCAAGTGACGATTCCCACGGACATAACTGATCTAAGTATCTTCCAAATCTGGGAATGGGATTTCATAATTAAGGACTAT\t\t\t\n+2\t3\tconsensus\t\t\tAATTCTCTACACCACAGCATCAATTCTAAAAATGACTACCAGAGAGACAACTCCGCAGTTAAACACTCTGACTGCCACGCCAGCTACCTCTAGA\t0\t0\t0\n+2\t3\tmodel\t\t\tOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOO\t\t\t\n+2\t3\tprimary\t0\tlane1_fakedata2_0 1:N:0:/1\tAATTCTCTACACCACAGCATCAATTCTAAAAATGACTACCAGAGAGACAACTCCGCAGTTAAACACTCTGACTGCCACGCCAGCTACCTCTAGA\t\t\t\n+2\t3\tprimary\t0\tlane1_fakedata2_2 1:N:0:/1\tAATTCTCTACACCACAGCATCAATTCTAAAAATGACTACCAGAGAGACAACTCCGCAGTTAAACACTCTGACTGCCACGCCAGCTACCTCTAGA\t\t\t\n+2\t3\tprimary\t0\tlane1_fakedata2_3 1:N:0:/1\tAATTCTCTACACCACAGCATCAATTCTAAAAATGACTACCAGAGAGACAACTCCGCAGTTAAACACTCTGACTGCCACGCCAGCTACCTCTAGA\t\t\t\n+2\t3\tprimary\t0\tlane1_fakedata2_4 1:N:0:/1\tAATTCTCTACACCACAGCATCAATTCTAAAAATGACTACCAGAGAGACAACTCCGCAGTTAAACACTCTGACTGCCACGCCAGCTACCTCTAGA\t\t\t\n+2\t3\tprimary\t0\tlane1_fakedata2_5 1:N:0:/1\tAATTCTCTACACCACAGCATCAATTCTAAAAATGACTACCAGAGAGACAACTCCGCAGTTAAACACTCTGACTGCCACGCCAGCTACCTCTAGA\t\t\t\n+2\t3\tprimary\t0\tlane1_fakedata2_6 1:N:0:/1\tAATTCTCTACACCACAGCATCAATTCTAAAAATGACTACCAGAGAGACAACTCCGCAGTTAAACACTCTGACTGCCACGCCAGCTACCTCTAGA\t\t\t\n+2\t3\tprimary\t0\tlane1_fakedata2_7 1:N:0:/1\tAATTCTCTACACCACAGCATCAATTCTAAAAATGACTACCAGAGAGACAACTCCGCAGTTAAACACTCTGACTGCCACGCCAGCTACCTCTAGA\t\t\t\n+2\t3\tprimary\t0\tlane1_fakedata2_8 1:N:0:/1\tAATTCTCTACACCACAGCATCAATTCTAAAAATGACTACCAGAGAGACAACTCCGCAGTTAAACACTCTGACTGCCACGCCAGCTACCTCTAGA\t\t\t\n+2\t3\tprimary\t0\tlane1_fakedata2_9 1:N:0:/1\tAATTCTCTACACCACAGCATCAATTCTAAAAATGACTACCAGAGAGACAACTCCGCAGTTAAACACTCTGACTGCCACGCCAGCTACCTCTAGA\t\t\t\n+2\t3\tprimary\t0\tlane1_fakedata2_10 1:N:0:/1\tAATTCTCTACACCACAGCATCAATTCTAAAAATGACTACCAGAGAGACAACTCCGCAGTTAAACACTCTGACTGCCACGCCAGCTACCTCTAGA\t\t\t\n+2\t3\tprimary\t0\tlane1_fakedata2_11 1:N:0:/1\tAATTCTCTACACCACAGCATCAATTCTAAAAATGACTACCAGAGAGACAACTCCGCAGTTAAACACTCTGACTGCCACGCCAGCTACCTCTAGA\t\t\t\n+2\t3\tprimary\t0\tlane1_fakedata2_12 1:N:0:/1\tAATTCTCTACACCACAGCATCAATTCTAAAAATGACTACCAGAGAGACAACTCCGCAGTTAAACACTCTGACTGCCACGCCAGCTACCTCTAGA\t\t\t\n+2\t3\tprimary\t0\tlane1_fakedata2_13 1:N:0:/1\tAATTCTCTACACCACAGCATCAATTCTAAAAATGACTACCAGAGAGACAACTCCGCAGTTAAACACTCTGACTGCCACGCCAGCTACCTCTAGA\t\t\t\n+2\t3\tprimary\t0\tlane1_fakedata2_14 1:N:0:/1\tAATTCTCTACACCACAGCATCAATTCTAAAAATGACTACCAGAGAGACAACTCCGCAGTTAAACACTCTGACTGCCACGCCAGCTACCTCTAGA\t\t\t\n+2\t3\tprimary\t0\tlane1_fakedata2_15 1:N:0:/1\tAATTCTCTACACCACAGCATCAATTCTAAAAATGACTACCAGAGAGACAACTCCGCAGTTAAACACTCTGACTGCCACGCCAGCTACCTCTAGA\t\t\t\n+2\t3\tprimary\t0\tlane1_fakedata2_16 1:N:0:/1\tAATTCTCTACACCACAGCATCAATTCTAAAAATGACTACCAGAGAGACAACTCCGCAGTTAAACACTCTGACTGCCACGCCAGCTACCTCTAGA\t\t\t\n+2\t3\tprimary\t0\tlane1_fakedata2_17 1:N:0:/1\tAATTCTCTACACCACAGCATCAATTCTAAAAATGACTACCAGAGAGACAACTCCGCAGTTAAACACTCTGACTGCCACGCCAGCTACCTCTAGA\t\t\t\n+2\t3\tprimary\t0\tlane1_fakedata2_18 1:N:0:/1\tAATTCTCTACACCACAGCATCAATTCTAAAAATGACTACCAGAGAGACAACTCCGCAGTTAAACACTCTGACTGCCACGCCAGCTACCTCTAGA\t\t\t\n+2\t3\tprimary\t0\tlane1_fakedata2_19 1:N:0:/1\tAATTCTCTACACCACAGCATCAATTCTAAAAATGACTACCAGAGAGACAACTCCGCAGTTAAACACTCTGACTGCCACGCCAGCTACCTCTAGA\t\t\t\n+2\t3\tsecondary\t\tlane1_fakedata2_1 1:N:0:/1\tAATTCTCTACACCACTGCATCAATTCTAAAAATGACTACCAGAGAGACAACTCCGCAGTTAAACACTCTGACTGCCACGCCAGCTACCTCTAGA\t\t\t\n' |
| b |
| diff -r 000000000000 -r b2e3553e1be2 test-data/ustacks/ustacks.log --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/ustacks/ustacks.log Mon Jul 01 10:58:28 2019 -0400 |
| b |
| @@ -0,0 +1,92 @@ +ustacks parameters selected: + Input file: 'stacks_inputs/PopA_01.1.fastq' + Sample ID: 1 + Min depth of coverage to create a stack (m): 3 + Repeat removal algorithm: enabled + Max distance allowed between stacks (M): 2 + Max distance allowed to align secondary reads: 4 + Max number of stacks allowed per de novo locus: 3 + Deleveraging algorithm: disabled + Gapped assembly: enabled + Minimum alignment length: 0.8 + Model type: SNP + Alpha significance level for model: 0.05 + +Loading RAD-Tags... + +Loaded 66 reads; formed: + 4 stacks representing 63 primary reads (95.5%) + 3 secondary stacks representing 3 secondary reads (4.5%) + +Stack coverage: mean=15.75; stdev=7.46; max=27; n_reads=63(95.5%) +Removing repetitive stacks: cov > 39 (mean+3*stdev)... + Blacklisted 0 stacks. +Coverage after repeat removal: mean=15.75; stdev=7.46; max=27; n_reads=63(95.5%) + +Assembling stacks (max. dist. M=2)... + Assembled 4 stacks into 3; blacklisted 0 stacks. +Coverage after assembling stacks: mean=21.00; stdev=4.24; max=27; n_reads=63(95.5%) + +Merging secondary stacks (max. dist. N=4 from consensus)... + Merged 3 out of 3 secondary reads (100.0%), 1 merged with gapped alignments. +Coverage after merging secondary stacks: mean=22.00; stdev=4.32; max=28; n_reads=66(100.0%) + +Assembling stacks, allowing for gaps (min. match length 80.0%)... + Assembled 3 stacks into 3 stacks. +Coverage after gapped assembly: mean=22.00; stdev=4.32; max=28; n_reads=66(100.0%) + +Merging secondary stacks, allowing for gaps (min. match length 80.0%)... + Merged 0 out of 0 secondary reads (-nan%). +Coverage after merging gapped secondary stacks: mean=22.00; stdev=4.32; max=28; n_reads=66(100.0%) + +Final coverage: mean=22.00; stdev=4.32; max=28; n_reads=66(100.0%) +Calling consensus sequences and haplotypes for catalog assembly... +Writing tags, SNPs, and alleles files... +Refetching read IDs...done. +ustacks is done. +ustacks parameters selected: + Input file: 'stacks_inputs/PopA_02.1.fastq' + Sample ID: 2 + Min depth of coverage to create a stack (m): 3 + Repeat removal algorithm: enabled + Max distance allowed between stacks (M): 2 + Max distance allowed to align secondary reads: 4 + Max number of stacks allowed per de novo locus: 3 + Deleveraging algorithm: disabled + Gapped assembly: enabled + Minimum alignment length: 0.8 + Model type: SNP + Alpha significance level for model: 0.05 + +Loading RAD-Tags... + +Loaded 60 reads; formed: + 4 stacks representing 55 primary reads (91.7%) + 5 secondary stacks representing 5 secondary reads (8.3%) + +Stack coverage: mean=13.75; stdev=9.12; max=26; n_reads=55(91.7%) +Removing repetitive stacks: cov > 42 (mean+3*stdev)... + Blacklisted 0 stacks. +Coverage after repeat removal: mean=13.75; stdev=9.12; max=26; n_reads=55(91.7%) + +Assembling stacks (max. dist. M=2)... + Assembled 4 stacks into 3; blacklisted 0 stacks. +Coverage after assembling stacks: mean=18.33; stdev=6.55; max=26; n_reads=55(91.7%) + +Merging secondary stacks (max. dist. N=4 from consensus)... + Merged 5 out of 5 secondary reads (100.0%), 0 merged with gapped alignments. +Coverage after merging secondary stacks: mean=20.00; stdev=6.53; max=28; n_reads=60(100.0%) + +Assembling stacks, allowing for gaps (min. match length 80.0%)... + Assembled 3 stacks into 3 stacks. +Coverage after gapped assembly: mean=20.00; stdev=6.53; max=28; n_reads=60(100.0%) + +Merging secondary stacks, allowing for gaps (min. match length 80.0%)... + Merged 0 out of 0 secondary reads (-nan%). +Coverage after merging gapped secondary stacks: mean=20.00; stdev=6.53; max=28; n_reads=60(100.0%) + +Final coverage: mean=20.00; stdev=6.53; max=28; n_reads=60(100.0%) +Calling consensus sequences and haplotypes for catalog assembly... +Writing tags, SNPs, and alleles files... +Refetching read IDs...done. +ustacks is done. |