| Previous changeset 3:eb784fa07f80 (2021-04-27) Next changeset 5:f6e91108b7b1 (2022-04-14) |
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Commit message:
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 75f83e7b16127aecc68a58df2cb75062f2a9296a" |
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modified:
macros.xml stacks_gstacks.xml test-data/cstacks/catalog.alleles.tsv test-data/cstacks/catalog.snps.tsv test-data/cstacks/catalog.tags.tsv test-data/denovo_map/denovo_map.log 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/gstacks.log test-data/gstacks/gstacks.log.distribs test-data/populations/populations.log test-data/sstacks/PopA_01.matches.tsv test-data/sstacks/PopA_02.matches.tsv 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 |
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| diff -r eb784fa07f80 -r 7370bb65bad4 macros.xml --- a/macros.xml Tue Apr 27 09:31:18 2021 +0000 +++ b/macros.xml Wed Sep 01 11:29:04 2021 +0000 |
| [ |
| @@ -10,8 +10,8 @@ </xml> <token name="@STACKS_VERSION@">2.55</token> - <token name="@WRAPPER_VERSION@">0</token> - <token name="@PROFILE@">20.01</token> + <token name="@WRAPPER_VERSION@">1</token> + <token name="@PROFILE@">20.05</token> <xml name="citation"> <citations> @@ -424,11 +424,11 @@ <filter>add_log_distribs</filter> </data> <collection name="gstacks_alns_out" type="list" label="${tool.name} @TOOLADD@ on ${on_string} Read alignments"> - <discover_datasets pattern="(?P<name>.*).alns.bam$" ext="bam" directory="stacks_outputs"/> - <filter>mode_cond['mode_select'] == 'denovo' and mode_cond['advanced_cond']['advanced_select'] == "yes" and mode_cond['advanced_cond']['write_alignments'] != "" and popmap!=None</filter> + <discover_datasets pattern="(?P<name>.*).alns.bam$" format="bam" directory="stacks_outputs"/> + <filter>mode_cond['mode_select'] == 'denovo' and mode_cond['advanced_cond']['advanced_select'] == "yes" and mode_cond['advanced_cond']['write_alignments'] and popmap!=None</filter> </collection> <data name="gstacks_aln_out" format="bam" label="${tool.name} @TOOLADD@ on ${on_string} Read alignment" from_work_dir="stacks_outputs/alignments.bam"> - <filter>mode_cond['mode_select'] == 'denovo' and mode_cond['advanced_cond']['advanced_select'] == "yes" and mode_cond['advanced_cond']['write_alignments'] != "" and popmap==None</filter> + <filter>mode_cond['mode_select'] == 'denovo' and mode_cond['advanced_cond']['advanced_select'] == "yes" and mode_cond['advanced_cond']['write_alignments'] and popmap==None</filter> </data> </xml> <xml name="gstacks_outputs_macro" token_tooladd=""> |
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| diff -r eb784fa07f80 -r 7370bb65bad4 stacks_gstacks.xml --- a/stacks_gstacks.xml Tue Apr 27 09:31:18 2021 +0000 +++ b/stacks_gstacks.xml Wed Sep 01 11:29:04 2021 +0000 |
| [ |
| b'@@ -4,7 +4,7 @@\n <import>macros.xml</import>\n </macros>\n <expand macro="requirements">\n- <requirement type="package" version="1.9">samtools</requirement>\n+ <requirement type="package" version="1.13">samtools</requirement>\n </expand>\n <expand macro="version_cmd"/>\n <command detect_errors="aggressive"><![CDATA[\n@@ -88,11 +88,11 @@\n ## exit codes and stderr output) this adds the samtools requirement\n ## for later versions where this is fixed the output bam files could just be moved\n ## to stacks_outputs if this is still necessary\n-#if $mode_cond.mode_select == "denovo" and $mode_cond.advanced_cond.advanced_select == "yes" and $mode_cond.advanced_cond.write_alignments != ""\n+#if $mode_cond.mode_select == "denovo" and $mode_cond.advanced_cond.advanced_select == "yes" and $mode_cond.advanced_cond.write_alignments\n #if $popmap:\n- && for b in stacks_outputs/*alns.bam; do (samtools view -b "\\$b" || true) 2> /dev/null > tmp && mv tmp "\\$b"; done\n+ && for b in stacks_outputs/*alns.bam; do (samtools view --no-PG -b "\\$b" || true) 2> /dev/null > tmp && mv tmp "\\$b"; done\n #else\n- && (samtools view -b stacks_outputs/alignments.bam || true) 2> /dev/null > tmp && mv tmp stacks_outputs/alignments.bam\n+ && (samtools view --no-PG -b stacks_outputs/alignments.bam || true) 2> /dev/null > tmp && mv tmp stacks_outputs/alignments.bam\n #end if\n #end if\n \n@@ -117,17 +117,17 @@\n <option value="refbased">Reference-based</option>\n </param>\n <when value="denovo">\n- <param argument="--ignore-pe-reads" name="ignore_pe_reads" type="boolean" checked="false" truevalue="--ignore-pe-reads" falsevalue="" label="Ignore paired-end reads" help="ignore paired-end reads even if present in the input"/>\n+ <param argument="--ignore-pe-reads" type="boolean" checked="false" truevalue="--ignore-pe-reads" falsevalue="" label="Ignore paired-end reads" help="ignore paired-end reads even if present in the input"/>\n <conditional name="advanced_cond">\n <param name="advanced_select" type="select" label="Advanced options">\n <option value="no">No</option>\n <option value="yes">Yes</option>\n </param>\n <when value="yes">\n- <param argument="--kmer-length" name="kmer_length" type="integer" value="31" min="2" max="31" label="K-mer length for the de Bruijn graph"/>\n- <param argument="--max-debruijn-reads" name="max_debruijn_reads" type="integer" value="1000" min="1" label="Maximum number of reads to use in the de Bruijn graph"/>\n- <param argument="--min-kmer-cov" name="min_kmer_cov" type="integer" value="2" label="Minimum coverage to consider a kmer"/>\n- <param argument="--write-alignments" name="write_alignments" type="boolean" checked="false" truevalue="--write-alignments" falsevalue="" label="save read alignments" help="heavy BAM files"/>\n+ <param argument="--kmer-length" type="integer" value="31" min="2" max="31" label="K-mer length for the de Bruijn graph"/>\n+ <param argument="--max-debruijn-reads" type="integer" value="1000" min="1" label="Maximum number of reads to use in the de Bruijn graph"/>\n+ <param argument="--min-kmer-cov" type="integer" value="2" label="Minimum coverage to consider a kmer"/>\n+ <param argument="--write-alignments" type="boolean" checked="false" truevalue="--write-alignments" falsevalue="" label="save read alignments" help="heavy BAM files"/>\n </when>\n <when value="no"/>\n </conditional>\n@@ -140,8 +140,8 @@\n <option value="--ignore-pe-reads" selected="true">ignore paired-end reads (--ignore-pe-reads)</option>\n </'..b'type="boolean" checked="false" truevalue="--rm-unpaired-reads" falsevalue="" label="Discard unpaired reads"/>\n+ <param argument="--rm-pcr-duplicates" type="boolean" checked="false" truevalue="--rm-pcr-duplicates" falsevalue="" label="Remove read pairs of the same sample that have the same insert length" help="implies --rm-unpaired-reads"/>\n </when>\n <when value="--unpaired"/>\n <when value="--ignore-pe-reads"/>\n@@ -152,13 +152,13 @@\n <option value="yes">Yes</option>\n </param>\n <when value="yes">\n- <param argument="--min-mapq" name="min_mapq" type="integer" value="10" min="0" max="255" label="Minimum PHRED-scaled mapping quality to consider a read"/>\n- <param argument="--max-clipped" name="max_clipped" type="float" value="0.2" min="0.0" max="1.1" label="Maximum soft-clipping level" help="in fraction of read length"/>\n- <param argument="--max-insert-len" name="max_insert_len" type="integer" value="1000" min="0" label="Maximum allowed sequencing insert length"/>\n+ <param argument="--min-mapq" type="integer" value="10" min="0" max="255" label="Minimum PHRED-scaled mapping quality to consider a read"/>\n+ <param argument="--max-clipped" type="float" value="0.2" min="0.0" max="1.1" label="Maximum soft-clipping level" help="in fraction of read length"/>\n+ <param argument="--max-insert-len" type="integer" value="1000" min="0" label="Maximum allowed sequencing insert length"/>\n <param argument="--details" type="boolean" checked="false" truevalue="--details" falsevalue="" label="Write a heaview output"/>\n <param name="phasing_cooccurrences_thr_min" type="integer" value="1" min="0" label="Edge coverage min" help="(--phasing-cooccurrences-thr-range)"/>\n <param name="phasing_cooccurrences_thr_max" type="integer" value="2" min="0" label="Edge coverage max" help="range of edge coverage thresholds to iterate over when building the graph of allele cooccurrences for SNP phasing (--phasing-cooccurrences-thr-range)"/>\n- <param argument="--phasing-dont-prune-hets" name="phasing_dont_prune_hets" type="boolean" checked="false" truevalue="--phasing-dont-prune-hets" falsevalue="" label="Don\'t try to ignore dubious heterozygote genotypes during phasing"/>\n+ <param argument="--phasing-dont-prune-hets" type="boolean" checked="false" truevalue="--phasing-dont-prune-hets" falsevalue="" label="Don\'t try to ignore dubious heterozygote genotypes during phasing"/>\n </when>\n <when value="no"/>\n </conditional>\n@@ -203,7 +203,7 @@\n <output name="distribs" ftype="txt" file="gstacks/gstacks.log.distribs" compare="sim_size" delta="10"/>\n <output_collection name="gstacks_out" type="list" count="2">\n <element name="catalog.calls.vcf" file="gstacks/catalog.calls.vcf" ftype="vcf" lines_diff="4"/>\n- <element name="catalog.fa.gz" file="gstacks/catalog.fa.gz" ftype="fasta.gz" compare="diff"/>\n+ <element name="catalog.fa.gz" file="gstacks/catalog.fa.gz" ftype="fasta.gz" decompress="true" compare="diff"/>\n </output_collection>\n </test>\n <!-- denovomode, w popmap, write alignments -->\n@@ -214,7 +214,7 @@\n <param name="mode_select" value="denovo"/>\n <conditional name="advanced_cond">\n <param name="advanced_select" value="yes"/>\n- <param name="write_alignments" value="--write-alignments"/>\n+ <param name="write_alignments" value="true"/>\n </conditional>\n </conditional>\n <param name="add_log" value="yes"/>\n' |
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| diff -r eb784fa07f80 -r 7370bb65bad4 test-data/cstacks/catalog.alleles.tsv --- a/test-data/cstacks/catalog.alleles.tsv Tue Apr 27 09:31:18 2021 +0000 +++ b/test-data/cstacks/catalog.alleles.tsv Wed Sep 01 11:29:04 2021 +0000 |
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| @@ -1,4 +1,4 @@ -# cstacks version 2.52; catalog generated on 2020-03-16 15:39:40 +# cstacks version 2.55; catalog generated on 2021-08-24 13:29:01 0 1 AC 0 0 0 1 CA 0 0 -# cstacks completed on 2020-03-16 15:39:40 +# cstacks completed on 2021-08-24 13:29:01 |
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| diff -r eb784fa07f80 -r 7370bb65bad4 test-data/cstacks/catalog.snps.tsv --- a/test-data/cstacks/catalog.snps.tsv Tue Apr 27 09:31:18 2021 +0000 +++ b/test-data/cstacks/catalog.snps.tsv Wed Sep 01 11:29:04 2021 +0000 |
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| @@ -1,4 +1,4 @@ -# cstacks version 2.52; catalog generated on 2020-03-16 15:39:40 +# cstacks version 2.55; catalog generated on 2021-08-24 13:29:01 0 1 33 E 0 A C - - 0 1 88 E 0 A C - - -# cstacks completed on 2020-03-16 15:39:40 +# cstacks completed on 2021-08-24 13:29:01 |
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| diff -r eb784fa07f80 -r 7370bb65bad4 test-data/cstacks/catalog.tags.tsv --- a/test-data/cstacks/catalog.tags.tsv Tue Apr 27 09:31:18 2021 +0000 +++ b/test-data/cstacks/catalog.tags.tsv Wed Sep 01 11:29:04 2021 +0000 |
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| @@ -1,5 +1,5 @@ -# cstacks version 2.52; catalog generated on 2020-03-16 15:39:40 +# cstacks version 2.55; catalog generated on 2021-08-24 13:29:01 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 -# cstacks completed on 2020-03-16 15:39:40 +# cstacks completed on 2021-08-24 13:29:01 |
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| diff -r eb784fa07f80 -r 7370bb65bad4 test-data/denovo_map/denovo_map.log --- a/test-data/denovo_map/denovo_map.log Tue Apr 27 09:31:18 2021 +0000 +++ b/test-data/denovo_map/denovo_map.log Wed Sep 01 11:29:04 2021 +0000 |
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| @@ -1,5 +1,5 @@ -denovo_map.pl version 2.52 started at 2020-03-16 15:39:40 -/home/berntm/miniconda3/envs/__stacks@2.52/bin/denovo_map.pl --samples demultiplexed --popmap denovo_map/popmap_cstacks.tsv -o stacks_outputs --paired +denovo_map.pl version 2.55 started at 2021-08-24 13:29:01 +/home/berntm/miniconda3/envs/mulled-v1-4cbe4390dde1292aa8dbfc7f3537b788791787f5ad55cd86edeadacb1e3df63a/bin/denovo_map.pl --samples demultiplexed --popmap denovo_map/popmap_cstacks.tsv -o stacks_outputs --paired ustacks ========== @@ -305,4 +305,4 @@ Populations is done. denovo_map.pl is done. -denovo_map.pl completed at 2020-03-16 15:39:40 +denovo_map.pl completed at 2021-08-24 13:29:01 |
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| diff -r eb784fa07f80 -r 7370bb65bad4 test-data/gentest.sh --- a/test-data/gentest.sh Tue Apr 27 09:31:18 2021 +0000 +++ b/test-data/gentest.sh Wed Sep 01 11:29:04 2021 +0000 |
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| @@ -1,9 +1,6 @@ #!/usr/bin/env bash -eval "$(conda shell.bash hook)" -conda activate __stacks@2.52 - - - +#eval "$(conda shell.bash hook)" +#conda activate __stacks@2.52 mkdir stacks_outputs denovo_map.pl --samples demultiplexed --popmap denovo_map/popmap_cstacks.tsv -o stacks_outputs --paired && |
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| diff -r eb784fa07f80 -r 7370bb65bad4 test-data/gstacks/PopA_01.alns.bam |
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| Binary file test-data/gstacks/PopA_01.alns.bam has changed |
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| diff -r eb784fa07f80 -r 7370bb65bad4 test-data/gstacks/PopA_02.alns.bam |
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| Binary file test-data/gstacks/PopA_02.alns.bam has changed |
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| diff -r eb784fa07f80 -r 7370bb65bad4 test-data/gstacks/alignments.bam |
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| Binary file test-data/gstacks/alignments.bam has changed |
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| diff -r eb784fa07f80 -r 7370bb65bad4 test-data/gstacks/catalog.calls.vcf --- a/test-data/gstacks/catalog.calls.vcf Tue Apr 27 09:31:18 2021 +0000 +++ b/test-data/gstacks/catalog.calls.vcf Wed Sep 01 11:29:04 2021 +0000 |
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| @@ -1,6 +1,6 @@ ##fileformat=VCFv4.2 -##fileDate=20200316 -##source="Stacks v2.52" +##fileDate=20210824 +##source="Stacks v2.55" ##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"> |
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| diff -r eb784fa07f80 -r 7370bb65bad4 test-data/gstacks/gstacks.log --- a/test-data/gstacks/gstacks.log Tue Apr 27 09:31:18 2021 +0000 +++ b/test-data/gstacks/gstacks.log Wed Sep 01 11:29:04 2021 +0000 |
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| @@ -1,4 +1,4 @@ -gstacks v2.52, executed 2020-03-16 15:39:40 (zlib-1.2.11) +gstacks v2.55, executed 2021-08-24 13:29:01 (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'. |
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| diff -r eb784fa07f80 -r 7370bb65bad4 test-data/gstacks/gstacks.log.distribs --- a/test-data/gstacks/gstacks.log.distribs Tue Apr 27 09:31:18 2021 +0000 +++ b/test-data/gstacks/gstacks.log.distribs Wed Sep 01 11:29:04 2021 +0000 |
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| @@ -19,25 +19,25 @@ Num. threads: 1 Parallel time: 0.0 Average thread time spent: - 0.0 reading (3.0%) - 0.0 processing (95.7%) - 0.0 pre-alignments block (74.4%) - 0.0 reformatting fw-reads (0.2%) - 0.0 assembling (27.3%) - 0.0 initializing alignments (8.7%) - 0.0 aligning (36.6%) + 0.0 reading (2.8%) + 0.0 processing (95.9%) + 0.0 pre-alignments block (76.1%) + 0.0 reformatting fw-reads (0.1%) + 0.0 assembling (17.5%) + 0.0 initializing alignments (4.0%) + 0.0 aligning (52.9%) 0.0 merging read pairs (1.6%) - 0.0 post-alignments block (19.8%) + 0.0 post-alignments block (18.7%) 0.0 filtering reads (0.0%) - 0.0 counting nucleotides (3.2%) - 0.0 genotyping (1.5%) - 0.0 haplotyping (0.9%) + 0.0 counting nucleotides (2.8%) + 0.0 genotyping (1.2%) + 0.0 haplotyping (1.0%) 0.0 computing consensus (0.1%) 0.0 building_fa (0.1%) - 0.0 building_vcf (14.0%) + 0.0 building_vcf (13.4%) 0.0 writing_fa (0.0%) 0.0 writing_vcf (0.9%) - 0.0 clocking (0.1%) -Total time spent writing vcf: 0.0 (0.8%) + 0.0 clocking (0.2%) +Total time spent writing vcf: 0.0 (0.9%) VCFwrite block size: mean=1.0(n=3); max=1 END clockings |
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| diff -r eb784fa07f80 -r 7370bb65bad4 test-data/populations/populations.log --- a/test-data/populations/populations.log Tue Apr 27 09:31:18 2021 +0000 +++ b/test-data/populations/populations.log Wed Sep 01 11:29:04 2021 +0000 |
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| @@ -1,4 +1,4 @@ -populations v2.52, executed 2020-03-16 15:39:40 (zlib-1.2.11) +populations v2.55, executed 2021-08-24 13:29:01 (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: |
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| diff -r eb784fa07f80 -r 7370bb65bad4 test-data/sstacks/PopA_01.matches.tsv --- a/test-data/sstacks/PopA_01.matches.tsv Tue Apr 27 09:31:18 2021 +0000 +++ b/test-data/sstacks/PopA_01.matches.tsv Wed Sep 01 11:29:04 2021 +0000 |
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| @@ -1,6 +1,6 @@ -# sstacks version 2.52; generated on 2020-03-16 15:39:40 +# sstacks version 2.55; generated on 2021-08-24 13:29:01 1 1 1 AC 9 94M 1 1 1 CA 9 94M 2 1 2 consensus 28 94M 3 1 3 consensus 20 94M -# sstacks completed on 2020-03-16 15:39:40 +# sstacks completed on 2021-08-24 13:29:01 |
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| diff -r eb784fa07f80 -r 7370bb65bad4 test-data/sstacks/PopA_02.matches.tsv --- a/test-data/sstacks/PopA_02.matches.tsv Tue Apr 27 09:31:18 2021 +0000 +++ b/test-data/sstacks/PopA_02.matches.tsv Wed Sep 01 11:29:04 2021 +0000 |
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| @@ -1,6 +1,6 @@ -# sstacks version 2.52; generated on 2020-03-16 15:39:40 +# sstacks version 2.55; generated on 2021-08-24 13:29:01 1 2 1 AC 6 94M 1 2 1 CA 6 94M 2 2 2 consensus 28 94M 3 2 3 consensus 20 94M -# sstacks completed on 2020-03-16 15:39:40 +# sstacks completed on 2021-08-24 13:29:01 |
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| diff -r eb784fa07f80 -r 7370bb65bad4 test-data/tsv2bam/tsv2bam.log --- a/test-data/tsv2bam/tsv2bam.log Tue Apr 27 09:31:18 2021 +0000 +++ b/test-data/tsv2bam/tsv2bam.log Wed Sep 01 11:29:04 2021 +0000 |
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| @@ -1,4 +1,4 @@ -tsv2bam v2.52, executed 2020-03-16 15:39:40 (zlib-1.2.11) +tsv2bam v2.55, executed 2021-08-24 13:29:01 (zlib-1.2.11) tsv2bam -P stacks_outputs -M denovo_map/popmap_cstacks.tsv -R demultiplexed/ Configuration for this run: Stacks directory: 'stacks_outputs/' |
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| diff -r eb784fa07f80 -r 7370bb65bad4 test-data/ustacks/PopA_01.alleles.tsv --- a/test-data/ustacks/PopA_01.alleles.tsv Tue Apr 27 09:31:18 2021 +0000 +++ b/test-data/ustacks/PopA_01.alleles.tsv Wed Sep 01 11:29:04 2021 +0000 |
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| @@ -1,4 +1,4 @@ -# ustacks version 2.52; generated on 2020-03-16 15:39:40 +# ustacks version 2.55; generated on 2021-08-24 13:29:01 1 1 AC 50.00 9 1 1 CA 50.00 9 -# ustacks completed on 2020-03-16 15:39:40 +# ustacks completed on 2021-08-24 13:29:01 |
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| diff -r eb784fa07f80 -r 7370bb65bad4 test-data/ustacks/PopA_01.snps.tsv --- a/test-data/ustacks/PopA_01.snps.tsv Tue Apr 27 09:31:18 2021 +0000 +++ b/test-data/ustacks/PopA_01.snps.tsv Wed Sep 01 11:29:04 2021 +0000 |
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| @@ -1,4 +1,4 @@ -# ustacks version 2.52; generated on 2020-03-16 15:39:40 +# ustacks version 2.55; generated on 2021-08-24 13:29:01 1 1 0 O 24.95 A - 1 1 1 O 24.95 A - 1 1 2 O 24.95 T - @@ -281,4 +281,4 @@ 1 3 91 O 27.73 A - 1 3 92 O 27.73 G - 1 3 93 O 27.73 A - -# ustacks completed on 2020-03-16 15:39:40 +# ustacks completed on 2021-08-24 13:29:01 |
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| diff -r eb784fa07f80 -r 7370bb65bad4 test-data/ustacks/PopA_01.tags.tsv --- a/test-data/ustacks/PopA_01.tags.tsv Tue Apr 27 09:31:18 2021 +0000 +++ b/test-data/ustacks/PopA_01.tags.tsv Wed Sep 01 11:29:04 2021 +0000 |
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| @@ -1,4 +1,4 @@ -# ustacks version 2.52; generated on 2020-03-16 15:39:40 +# ustacks version 2.55; generated on 2021-08-24 13:29:01 1 1 consensus AATTCGTTTGCTGCTTCAGGAATCTCTCGTATAATCTGAGTATGTGCGTACGTACGCTATTTAGATGGATAACCGACGCTGCCAGACGAGAGAC 0 0 0 1 1 model OOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOEOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOEOOOOO 1 1 primary 0 lane1_fakedata7_0 1:N:0:/1 AATTCGTTTGCTGCTTCAGGAATCTCTCGTATACTCTGAGTATGTGCGTACGTACGCTATTTAGATGGATAACCGACGCTGCCAGACGAGAGAC @@ -71,4 +71,4 @@ 1 3 primary 0 lane1_fakedata2_19 1:N:0:/1 AATTCTCTACACCACAGCATCAATTCTAAAAATGACTACCAGAGAGACAACTCCGCAGTTAAACACTCTGACTGCCACGCCAGCTACCTCTAGA 1 3 secondary lane1_fakedata2_5 1:N:0:/1 AATTCTCTACACCACAGCATCAATTCTAAAAATGACTACCAGAGAGACAACTCCGCAGTAAAACACTCTGACTGCCACGCCAGCTACCTCTAGA 1 3 secondary lane1_fakedata2_17 1:N:0:/1 AATTCTCTACACCACAGCATCAATTCTAAAAATGACTACCAGAGAGACAACTCCGCAGTTAAACACTCTGACTGCCACGCCAGCTACCTCCAGA -# ustacks completed on 2020-03-16 15:39:40 +# ustacks completed on 2021-08-24 13:29:01 |
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| diff -r eb784fa07f80 -r 7370bb65bad4 test-data/ustacks/PopA_02.alleles.tsv --- a/test-data/ustacks/PopA_02.alleles.tsv Tue Apr 27 09:31:18 2021 +0000 +++ b/test-data/ustacks/PopA_02.alleles.tsv Wed Sep 01 11:29:04 2021 +0000 |
| b |
| @@ -1,4 +1,4 @@ -# ustacks version 2.52; generated on 2020-03-16 15:39:40 +# ustacks version 2.55; generated on 2021-08-24 13:29:01 2 1 AC 50.00 6 2 1 CA 50.00 6 -# ustacks completed on 2020-03-16 15:39:40 +# ustacks completed on 2021-08-24 13:29:01 |
| b |
| diff -r eb784fa07f80 -r 7370bb65bad4 test-data/ustacks/PopA_02.snps.tsv --- a/test-data/ustacks/PopA_02.snps.tsv Tue Apr 27 09:31:18 2021 +0000 +++ b/test-data/ustacks/PopA_02.snps.tsv Wed Sep 01 11:29:04 2021 +0000 |
| b |
| @@ -1,4 +1,4 @@ -# ustacks version 2.52; generated on 2020-03-16 15:39:40 +# ustacks version 2.55; generated on 2021-08-24 13:29:01 2 1 0 O 16.64 A - 2 1 1 O 16.64 A - 2 1 2 O 16.64 T - @@ -281,4 +281,4 @@ 2 3 91 O 27.73 A - 2 3 92 O 27.73 G - 2 3 93 O 27.73 A - -# ustacks completed on 2020-03-16 15:39:40 +# ustacks completed on 2021-08-24 13:29:01 |
| b |
| diff -r eb784fa07f80 -r 7370bb65bad4 test-data/ustacks/PopA_02.tags.tsv --- a/test-data/ustacks/PopA_02.tags.tsv Tue Apr 27 09:31:18 2021 +0000 +++ b/test-data/ustacks/PopA_02.tags.tsv Wed Sep 01 11:29:04 2021 +0000 |
| b |
| @@ -1,4 +1,4 @@ -# ustacks version 2.52; generated on 2020-03-16 15:39:40 +# ustacks version 2.55; generated on 2021-08-24 13:29:01 2 1 consensus AATTCGTTTGCTGCTTCAGGAATCTCTCGTATAATCTGAGTATGTGCGTACGTACGCTATTTAGATGGATAACCGACGCTGCCAGACGAGAGAC 0 0 0 2 1 model OOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOEOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOEOOOOO 2 1 primary 0 lane1_fakedata7_7 1:N:0:/1 AATTCGTTTGCTGCTTCAGGAATCTCTCGTATACTCTGAGTATGTGCGTACGTACGCTATTTAGATGGATAACCGACGCTGCCAGACGAGAGAC @@ -65,4 +65,4 @@ 2 3 primary 0 lane1_fakedata2_18 1:N:0:/1 AATTCTCTACACCACAGCATCAATTCTAAAAATGACTACCAGAGAGACAACTCCGCAGTTAAACACTCTGACTGCCACGCCAGCTACCTCTAGA 2 3 primary 0 lane1_fakedata2_19 1:N:0:/1 AATTCTCTACACCACAGCATCAATTCTAAAAATGACTACCAGAGAGACAACTCCGCAGTTAAACACTCTGACTGCCACGCCAGCTACCTCTAGA 2 3 secondary lane1_fakedata2_1 1:N:0:/1 AATTCTCTACACCACTGCATCAATTCTAAAAATGACTACCAGAGAGACAACTCCGCAGTTAAACACTCTGACTGCCACGCCAGCTACCTCTAGA -# ustacks completed on 2020-03-16 15:39:40 +# ustacks completed on 2021-08-24 13:29:01 |