| Next changeset 1:8c2617661c49 (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_tsv2bam.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 1b270fc77c81 macros.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros.xml Mon Jul 01 10:59:53 2019 -0400 |
| [ |
| 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 1b270fc77c81 macros_process.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros_process.xml Mon Jul 01 10:59:53 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 1b270fc77c81 stacks_tsv2bam.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/stacks_tsv2bam.xml Mon Jul 01 10:59:53 2019 -0400 |
| [ |
| b'@@ -0,0 +1,254 @@\n+<tool id="stacks2_tsv2bam" name="Stacks2: tsv2bam" profile="@PROFILE@" version="@STACKS_VERSION@+galaxy@WRAPPER_VERSION@">\n+ <description>Sort reads by RAD locus</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+@LINK_STACKS_INPUT@\n+@LINK_CAT_INPUT@\n+@LINK_MATCHES_INPUT@\n+\n+## link fastq files into stacks_inputs/\n+#set $paired_reads=False\n+#for $sample in $input_type.fqinputs:\n+ #if not $sample:\n+ #continue\n+ #end if\n+ #set $paired_reads=True\n+ #set ($link_cmd, $data_path, $name, $inputype) = $fastq_input_foo($sample, "reverse", ".2")\n+ $link_cmd\n+#end for\n+\n+tsv2bam\n+-P stacks_inputs\n+#if $popmap\n+ -M \'$popmap\'\n+#else\n+ #for $sample in $samples\n+ -s \'$sample\'\n+ #end for\n+#end if\n+#if $paired_reads\n+ --pe-reads-dir stacks_inputs\n+#end if\n+-t \\${GALAXY_SLOTS:-1}\n+## tsv2bam writes to stdout and creates a log file\n+## - make stdout stderr\n+## - move the additional log file\n+2>&1\n+\n+#if $output_log\n+ && mv stacks_inputs/tsv2bam.log $output_log\n+#end if\n+&& mv stacks_inputs/*matches.bam stacks_outputs\n+]]></command>\n+\n+ <inputs>\n+ <expand macro="input_stacks_macro"/>\n+ <expand macro="input_cat_macro"/>\n+ <expand macro="input_matches_macro"/>\n+ <!-- TODO add BAM? -->\n+ <expand macro="fastq_input" fastq_optional="true" se_option="reverse reads" help="Paired end data or reverse reads. If a paired list is provided only the reverse reads are used in tsv2bam. Leave selection empty if you analyse single end data."/>\n+ <param name="popmap" type="data" format="tabular,txt" label="Population map" help="If set, matching will be done only for samples listed in this file" optional="true" argument="-M" />\n+ <expand macro="in_log"/>\n+ </inputs>\n+\n+ <outputs>\n+ <expand macro="out_log"/>\n+ <expand macro="tsv2bam_outputs_macro"/>\n+ </outputs>\n+\n+ <tests>\n+ <!-- test wo paired end data -->\n+ <test>\n+ <param name="input_cat">\n+ <collection type="list">\n+ <element name="catalog.alleles" ftype="tabular" value="cstacks/catalog.alleles.tsv" />\n+ <element name="catalog.snps" ftype="tabular" value="cstacks/catalog.snps.tsv" />\n+ <element name="catalog.tags" ftype="tabular" value="cstacks/catalog.tags.tsv" />\n+ </collection>\n+ </param>\n+ <param name="input_stacks">\n+ <collection type="list">\n+ <element name="PopA_01.alleles" ftype="tabular" value="ustacks/PopA_01.alleles.tsv" />\n+ <element name="PopA_01.snps" ftype="tabular" value="ustacks/PopA_01.snps.tsv" />\n+ <element name="PopA_01.tags" ftype="tabular" value="ustacks/PopA_01.tags.tsv" />\n+ <element name="PopA_02.alleles" ftype="tabular" value="ustacks/PopA_02.alleles.tsv" />\n+ <element name="PopA_02.snps" ftype="tabular" value="ustacks/PopA_02.snps.tsv" />\n+ <element name="PopA_02.tags" ftype="tabular" value="ustacks/PopA_02.tags.tsv" />\n+ </collection>\n+ </param>\n+ <param name="input_matches">\n+ <collection type="list">\n+ <element name="PopA_01.matches" ftype="tabular" value="sstacks/PopA_01.matches.tsv" />\n+ <element name="PopA_02.matches" ftype="tabular" value="sstacks/PopA_02.matches.tsv" />\n+ </collection>\n+ </param>\n+ <param name="add_log" value="yes" />\n+ <output name="output_log" ftype="txt" file="tsv2bam/tsv2bam.log" lines_diff="14"/>\n+ <output_collection name="bams" type="list" count="2">\n+ <element name="PopA_01.matches'..b'ame="input_cat">\n+ <collection type="list">\n+ <element name="catalog.alleles" ftype="tabular" value="cstacks/catalog.alleles.tsv" />\n+ <element name="catalog.snps" ftype="tabular" value="cstacks/catalog.snps.tsv" />\n+ <element name="catalog.tags" ftype="tabular" value="cstacks/catalog.tags.tsv" />\n+ </collection>\n+ </param>\n+ <param name="input_stacks">\n+ <collection type="list">\n+ <element name="PopA_01.alleles" ftype="tabular" value="ustacks/PopA_01.alleles.tsv" />\n+ <element name="PopA_01.snps" ftype="tabular" value="ustacks/PopA_01.snps.tsv" />\n+ <element name="PopA_01.tags" ftype="tabular" value="ustacks/PopA_01.tags.tsv" />\n+ <element name="PopA_02.alleles" ftype="tabular" value="ustacks/PopA_02.alleles.tsv" />\n+ <element name="PopA_02.snps" ftype="tabular" value="ustacks/PopA_02.snps.tsv" />\n+ <element name="PopA_02.tags" ftype="tabular" value="ustacks/PopA_02.tags.tsv" />\n+ </collection>\n+ </param>\n+ <param name="input_matches">\n+ <collection type="list">\n+ <element name="PopA_01.matches" ftype="tabular" value="sstacks/PopA_01.matches.tsv" />\n+ <element name="PopA_02.matches" ftype="tabular" value="sstacks/PopA_02.matches.tsv" />\n+ </collection>\n+ </param>\n+ <param name="input_type|input_type_select" value="paired"/>\n+ <param name="input_type|fqinputs">\n+ <collection type="list:paired">\n+ <element name="PopA_01">\n+ <collection type="paired">\n+ <element name="forward" value="demultiplexed/PopA_01.1.fq" ftype="fastqsanger" />\n+ <element name="reverse" value="demultiplexed/PopA_01.2.fq" ftype="fastqsanger"/>\n+ </collection>\n+ </element>\n+ <element name="PopA_02">\n+ <collection type="paired">\n+ <element name="forward" value="demultiplexed/PopA_02.1.fq" ftype="fastqsanger" />\n+ <element name="reverse" value="demultiplexed/PopA_02.2.fq" ftype="fastqsanger"/>\n+ </collection>\n+ </element>\n+ </collection>\n+ </param>\n+ <param name="add_log" value="yes" />\n+ <output name="output_log"><assert_contents><has_text text="done." /></assert_contents></output>\n+ <output_collection name="bams" type="list" count="2"/>\n+ </test>\n+ </tests>\n+\n+ <help>\n+<![CDATA[\n+.. class:: infomark\n+\n+**What it does**\n+\n+The unique stacks program will take as input a set of short-read sequences and align them into exactly-matching stacks. Comparing the stacks it will form a set of loci and detect SNPs at each locus using a maximum likelihood framework\n+\n+--------\n+\n+**Input files**\n+\n+FASTQ, FASTA\n+\n+**Output files**\n+\n+- XXX.tags.tsv file:\n+\n+See `Stacks output description <http://catchenlab.life.illinois.edu/stacks/manual/#files>`_\n+\n+Notes: For the tags file, each stack will start in the file with a consensus sequence for the entire stack followed by the flags for that stack. Then, each individual read that was merged into that stack will follow. The next stack will start with another consensus sequence.\n+\n+\n+- XXX.snps.tsv file:\n+\n+See `Stacks output description <http://catchenlab.life.illinois.edu/stacks/manual/#files>`_\n+\n+Notes: If a stack has two SNPs called within it, then there will be two lines in this file listing each one.\n+\n+\n+- XXX.alleles.tsv file:\n+\n+See `Stacks output description <http://catchenlab.life.illinois.edu/stacks/manual/#files>`_\n+\n+@STACKS_INFOS@\n+]]>\n+ </help>\n+ <expand macro="citation" />\n+</tool>\n' |
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| diff -r 000000000000 -r 1b270fc77c81 test-data/clonefilter/Removed2_0001.2.2.fq.gz |
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| diff -r 000000000000 -r 1b270fc77c81 test-data/clonefilter/clonefilter.log --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/clonefilter/clonefilter.log Mon Jul 01 10:59:53 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 1b270fc77c81 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 10:59:53 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 1b270fc77c81 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 10:59:53 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 1b270fc77c81 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 10:59:53 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 1b270fc77c81 test-data/cstacks/cstacks.log --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/cstacks/cstacks.log Mon Jul 01 10:59:53 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 1b270fc77c81 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 10:59:53 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 1b270fc77c81 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 1b270fc77c81 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 10:59:53 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 1b270fc77c81 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 10:59:53 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 1b270fc77c81 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 1b270fc77c81 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 10:59:53 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 1b270fc77c81 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 10:59:53 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 1b270fc77c81 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 1b270fc77c81 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 1b270fc77c81 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 10:59:53 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 1b270fc77c81 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 10:59:53 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 1b270fc77c81 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 10:59:53 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 1b270fc77c81 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 10:59:53 2019 -0400 |
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| @@ -0,0 +1,2 @@ +PopA_01 1 +PopA_02 1 |
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| diff -r 000000000000 -r 1b270fc77c81 test-data/gentest.sh --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/gentest.sh Mon Jul 01 10:59:53 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 1b270fc77c81 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 10:59:53 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 1b270fc77c81 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 1b270fc77c81 test-data/gstacks/gstacks.log --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/gstacks/gstacks.log Mon Jul 01 10:59:53 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 1b270fc77c81 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 10:59:53 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 1b270fc77c81 test-data/kmerfilter/kfreqdist.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/kmerfilter/kfreqdist.tsv Mon Jul 01 10:59:53 2019 -0400 |
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| @@ -0,0 +1,3 @@ +# KmerFrequency Count +1 408 +2 136 |
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| diff -r 000000000000 -r 1b270fc77c81 test-data/kmerfilter/kmerfilter.log --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/kmerfilter/kmerfilter.log Mon Jul 01 10:59:53 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 1b270fc77c81 test-data/populations/blacklist.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/populations/blacklist.tsv Mon Jul 01 10:59:53 2019 -0400 |
| b |
| @@ -0,0 +1,1 @@ +666 |
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| diff -r 000000000000 -r 1b270fc77c81 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 10:59:53 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 1b270fc77c81 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 10:59:53 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 1b270fc77c81 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 10:59:53 2019 -0400 |
| b |
| @@ -0,0 +1,1 @@ + 1 |
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| diff -r 000000000000 -r 1b270fc77c81 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 10:59:53 2019 -0400 |
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| @@ -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 1b270fc77c81 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 10:59:53 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 1b270fc77c81 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 10:59:53 2019 -0400 |
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| @@ -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 1b270fc77c81 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 10:59:53 2019 -0400 |
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| @@ -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 1b270fc77c81 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 10:59:53 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 1b270fc77c81 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 10:59:53 2019 -0400 |
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| @@ -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 1b270fc77c81 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 10:59:53 2019 -0400 |
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| @@ -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 1b270fc77c81 test-data/populations/populations.log --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/populations/populations.log Mon Jul 01 10:59:53 2019 -0400 |
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| @@ -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 1b270fc77c81 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 10:59:53 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 1b270fc77c81 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 10:59:53 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; |
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| diff -r 000000000000 -r 1b270fc77c81 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 10:59:53 2019 -0400 |
| b |
| @@ -0,0 +1,5 @@ +# Phi_st Means + 1 + +# Fst' Means + 1 |
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| diff -r 000000000000 -r 1b270fc77c81 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 10:59:53 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 1b270fc77c81 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 10:59:53 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 |
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| diff -r 000000000000 -r 1b270fc77c81 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 10:59:53 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 1b270fc77c81 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 10:59:53 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 1b270fc77c81 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 10:59:53 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 1b270fc77c81 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 10:59:53 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 1b270fc77c81 test-data/populations/populations.structure --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/populations/populations.structure Mon Jul 01 10:59:53 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 1b270fc77c81 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 10:59:53 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 1b270fc77c81 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 10:59:53 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 1b270fc77c81 test-data/populations/populations.treemix --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/populations/populations.treemix Mon Jul 01 10:59:53 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 1b270fc77c81 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 10:59:53 2019 -0400 |
| b |
| @@ -0,0 +1,3 @@ +1 6 +1 MMYKRR +# Stacks v2.4; Phylip sequential; June 17, 2019 |
| b |
| diff -r 000000000000 -r 1b270fc77c81 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 10:59:53 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 1b270fc77c81 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 10:59:53 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 1b270fc77c81 test-data/procrad/R1.fq --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/procrad/R1.fq Mon Jul 01 10:59:53 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 1b270fc77c81 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 10:59:53 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 1b270fc77c81 test-data/procrad/R1.fq.gzip |
| b |
| Binary file test-data/procrad/R1.fq.gzip has changed |
| b |
| diff -r 000000000000 -r 1b270fc77c81 test-data/procrad/R2.fq --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/procrad/R2.fq Mon Jul 01 10:59:53 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 1b270fc77c81 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 10:59:53 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 1b270fc77c81 test-data/procrad/R2.fq.gzip |
| b |
| Binary file test-data/procrad/R2.fq.gzip has changed |
| b |
| diff -r 000000000000 -r 1b270fc77c81 test-data/procrad/barcodes --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/procrad/barcodes Mon Jul 01 10:59:53 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 1b270fc77c81 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 10:59:53 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 1b270fc77c81 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 10:59:53 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 1b270fc77c81 test-data/refmap/PopA_01.bam |
| b |
| Binary file test-data/refmap/PopA_01.bam has changed |
| b |
| diff -r 000000000000 -r 1b270fc77c81 test-data/refmap/PopA_02.bam |
| b |
| Binary file test-data/refmap/PopA_02.bam has changed |
| b |
| diff -r 000000000000 -r 1b270fc77c81 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 10:59:53 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 1b270fc77c81 test-data/refmap/catalog.fa.gz |
| b |
| Binary file test-data/refmap/catalog.fa.gz has changed |
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| diff -r 000000000000 -r 1b270fc77c81 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 10:59:53 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 |
| b |
| diff -r 000000000000 -r 1b270fc77c81 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 10:59:53 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 1b270fc77c81 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 10:59:53 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 1b270fc77c81 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 10:59:53 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 1b270fc77c81 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 10:59:53 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 1b270fc77c81 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 10:59:53 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 1b270fc77c81 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 1b270fc77c81 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 10:59:53 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 1b270fc77c81 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 1b270fc77c81 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 1b270fc77c81 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 1b270fc77c81 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 10:59:53 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 1b270fc77c81 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 10:59:53 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 1b270fc77c81 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 10:59:53 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 1b270fc77c81 test-data/sstacks/sstacks.log --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/sstacks/sstacks.log Mon Jul 01 10:59:53 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 1b270fc77c81 test-data/stacks_outputs/catalog.calls |
| b |
| Binary file test-data/stacks_outputs/catalog.calls has changed |
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| diff -r 000000000000 -r 1b270fc77c81 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 10:59:53 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 1b270fc77c81 test-data/tsv2bam/PopA_01.bam |
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| Binary file test-data/tsv2bam/PopA_01.bam has changed |
| b |
| diff -r 000000000000 -r 1b270fc77c81 test-data/tsv2bam/PopA_01.matches.bam |
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| Binary file test-data/tsv2bam/PopA_01.matches.bam has changed |
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| diff -r 000000000000 -r 1b270fc77c81 test-data/tsv2bam/PopA_02.bam |
| b |
| Binary file test-data/tsv2bam/PopA_02.bam has changed |
| b |
| diff -r 000000000000 -r 1b270fc77c81 test-data/tsv2bam/PopA_02.matches.bam |
| b |
| Binary file test-data/tsv2bam/PopA_02.matches.bam has changed |
| b |
| diff -r 000000000000 -r 1b270fc77c81 test-data/tsv2bam/tsv2bam.log --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/tsv2bam/tsv2bam.log Mon Jul 01 10:59:53 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 1b270fc77c81 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 10:59:53 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 1b270fc77c81 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 10:59:53 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 - 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+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 1b270fc77c81 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 10:59:53 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 1b270fc77c81 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 10:59:53 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 1b270fc77c81 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 10:59:53 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 1b270fc77c81 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 10:59:53 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 1b270fc77c81 test-data/ustacks/ustacks.log --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/ustacks/ustacks.log Mon Jul 01 10:59:53 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. |