Mercurial > repos > matthias > stacks2_clonefilter
changeset 6:b707e9def9ff draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f507c4eaca0fe04e730d7c3bbb9e9d2488239a9f
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--- a/macros.xml Wed Feb 27 10:03:16 2019 -0500 +++ b/macros.xml Thu Jun 20 08:18:09 2019 -0400 @@ -7,7 +7,7 @@ </requirements> </xml> - <token name="@STACKS_VERSION@">2.3c</token> + <token name="@STACKS_VERSION@">2.4</token> <token name="@WRAPPER_VERSION@">0</token> <!-- fix to 18.01 since https://github.com/galaxyproject/galaxy/pull/7032 --> <token name="@PROFILE@">18.01</token> @@ -116,7 +116,7 @@ #end if ]]></token> <xml name="in_log"> - <param name="add_log" type="boolean" checked="false" truevalue="yes" falsevalue="no" label="Add log output as dataset" /> + <param name="add_log" type="boolean" checked="true" truevalue="yes" falsevalue="no" label="Add log output as dataset" /> </xml> <xml name="out_log"> <data format="txt" name="output_log" label="${tool.name} on ${on_string} log file"> @@ -138,7 +138,7 @@ <param name="input_bam" format="bam" type="data" multiple="true" optional="false" label="Aligned data" help="either the matches to the catalog (bam), i.e. tsv2bam, or reads aligned to a reference" /> </xml> <xml name="input_aln_macro"> - <param name="input_aln" format="tabular,txt" type="data_collection" collection_type="list" label="Assembled contigs and variant sites" help="output from previous Stacks pipeline steps (e.g. gstacks, denovo_map, or refmap)" argument="-P" /> + <param name="input_aln" format="vcf,fasta.gz" type="data_collection" collection_type="list" label="Assembled contigs and variant sites" help="output from previous Stacks pipeline steps (e.g. gstacks, denovo_map, or refmap)" argument="-P" /> </xml> <!-- code for creating links to the data sets from previous pipeline steps @@ -212,7 +212,7 @@ <xml name="fastq_input_bc_file" token_multiple="false" token_listtype="paired"> <expand macro="fastq_input_bc" multiple="@MULTIPLE@" listtype="@LISTTYPE@"> - <param name="barcode" argument="-b" type="data" format="tabular,txt" label="Barcode file" /> + <param name="barcode" argument="-b" type="data" format="tabular,txt" label="Barcode file" /> </expand> </xml> @@ -509,6 +509,10 @@ <filter>populations_output['plink']</filter> </data> + <!--structure populations.hzar--> + <data format="tabular" name="out_hzar" label="${tool.name} on ${on_string} hzar format" from_work_dir="stacks_outputs/populations.hzar.csv"> + <filter>populations_output['hzar']</filter> + </data> <!--structure populations.structure--> <data format="tabular" name="out_structure" label="${tool.name} on ${on_string} Structure format" from_work_dir="stacks_outputs/populations.structure"> <filter>populations_output['structure']</filter> @@ -560,9 +564,13 @@ </expand> </xml> - <!-- variant calling option for use in gstacks and denovomap --> - <xml name="variant_calling_options_vg"> - <param argument="--var-alpha" name="var_alpha" type="float" value="0.01" min="0" label="Alpha threshold for discovering SNPs" /> + <!-- variant calling option for use in gstacks and denovomap + default for var_alpha is 0.01 if model == marukilow (which is the case in denovomap and refmap) + otherwise no default is is available and gstacks will output and error + "Error: No value was provided for \-\-var-alpha and there is no default for this model)" + --> + <xml name="variant_calling_options_vg" token_varalpha_default=""> + <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." /> <param argument="--gt-alpha" name="gt_alpha" type="float" value="0.05" min="0" label="Alpha threshold for calling genotypes" /> </xml>
--- a/stacks_clonefilter.xml Wed Feb 27 10:03:16 2019 -0500 +++ b/stacks_clonefilter.xml Thu Jun 20 08:18:09 2019 -0400 @@ -36,6 +36,8 @@ ## only supports fastq.gz output since the ## the program outputs empty files for fasta/fastq -y gzfastq +@TEE_APPEND_LOG@ +@CAT_LOG_TO_STDERR@ ## move outputs such that Galaxy can find them #if $capture: @@ -59,8 +61,10 @@ <param name="oligo_len_1" type="integer" value="0" label="Length of the single-end oligo sequence in dataset"/> <param name="oligo_len_2" optional="true" type="integer" label="Length of the paired-end oligo sequence in dataset"/> <param argument="--retain_oligo" type="boolean" checked="false" truevalue="--retain_oligo" falsevalue="" label="Do not trim off the random oligo sequence (if oligo is inline)" /> + <expand macro="in_log"/> </inputs> <outputs> + <expand macro="out_log"/> <data format="fastqsanger.gz" name="clean" from_work_dir="outputs/R1.fq.gz" label="${tool.name} on ${on_string}"> <filter>input_type['input_type_select'] == 'single'</filter> </data> @@ -82,6 +86,8 @@ <param name="fqinputs" ftype="fastqsanger.gz" value="clonefilter/R1_0001.1.fq.gz" /> </conditional> <param name="oligo_len_1" value="6" /> + <param name="add_log" value="yes" /> + <output name="output_log" ftype="txt" file="clonefilter/clonefilter.log" lines_diff="8"/> <output name="clean" compare="sim_size" file="clonefilter/Removed1_0001.1.1.fq.single.gz"/> </test> <!-- single end, alt BCencoding, capture-->
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/clonefilter/clonefilter.log Thu Jun 20 08:18:09 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.
--- a/test-data/cstacks/catalog.alleles.tsv Wed Feb 27 10:03:16 2019 -0500 +++ b/test-data/cstacks/catalog.alleles.tsv Thu Jun 20 08:18:09 2019 -0400 @@ -1,3 +1,3 @@ -# cstacks version 2.3b; catalog generated on 2019-02-21 19:57:38 +# cstacks version 2.4; catalog generated on 2019-06-18 10:34:45 0 1 AC 0 0 0 1 CA 0 0
--- a/test-data/cstacks/catalog.snps.tsv Wed Feb 27 10:03:16 2019 -0500 +++ b/test-data/cstacks/catalog.snps.tsv Thu Jun 20 08:18:09 2019 -0400 @@ -1,3 +1,3 @@ -# cstacks version 2.3b; catalog generated on 2019-02-21 19:57:38 +# 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 - -
--- a/test-data/cstacks/catalog.tags.tsv Wed Feb 27 10:03:16 2019 -0500 +++ b/test-data/cstacks/catalog.tags.tsv Thu Jun 20 08:18:09 2019 -0400 @@ -1,4 +1,4 @@ -# cstacks version 2.3b; catalog generated on 2019-02-21 19:57:38 +# 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_3 AATTCTCTACACCACAGCATCAATTCTAAAAATGACTACCAGAGAGACAACTCCGCAGTTAAACACTCTGACTGCCACGCCAGCTACCTCTAGA 0 0 0 -0 3 consensus 0 1_3,2_2 AATTCGGCTTGCAACGCAAGTGACGATTCCCACGGACATAACTGATCTAAGTAACTTCCAAATCTGGGAATGGGATTTCATAATTAAGGACTAT 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
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/denovo_map/denovo_map.log Thu Jun 20 08:18:09 2019 -0400 @@ -0,0 +1,309 @@ +denovo_map.pl version 2.4 started at 2019-06-18 10:34:45 +/home/berntm/miniconda3/envs/mulled-v1-2b57e7596f85ebb3b321e6c9681e8fd9250523a80d97945c46ac7743359454e7/bin/denovo_map.pl --samples demultiplexed --popmap denovo_map/popmap_cstacks.tsv -o stacks_outputs --paired + +ustacks +========== + +Sample 1 of 2 'PopA_01' +---------- +ustacks -t fastq -f demultiplexed/PopA_01.1.fq -o stacks_outputs -i 1 --name PopA_01 +ustacks parameters selected: + Input file: 'demultiplexed/PopA_01.1.fq' + 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. + +Sample 2 of 2 'PopA_02' +---------- +ustacks -t fastq -f demultiplexed/PopA_02.1.fq -o stacks_outputs -i 2 --name PopA_02 +ustacks parameters selected: + Input file: 'demultiplexed/PopA_02.1.fq' + 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. + +Depths of Coverage for Processed Samples: +PopA_01: 22.00x +PopA_02: 20.00x + +cstacks +========== +cstacks -P stacks_outputs -M denovo_map/popmap_cstacks.tsv + +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_outputs/PopA_01.tags.tsv + Parsing stacks_outputs/PopA_01.snps.tsv + Parsing stacks_outputs/PopA_01.alleles.tsv + 3 loci were newly added to the catalog. + +Processing sample stacks_outputs/PopA_02 [2 of 2] + Parsing stacks_outputs/PopA_02.tags.tsv + Parsing stacks_outputs/PopA_02.snps.tsv + Parsing stacks_outputs/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_outputs/'. +Final catalog contains 3 loci. +cstacks is done. + +sstacks +========== +sstacks -P stacks_outputs -M denovo_map/popmap_cstacks.tsv + +Searching for matches by sequence identity... + Parsing stacks_outputs/catalog.tags.tsv + Parsing stacks_outputs/catalog.snps.tsv + Parsing stacks_outputs/catalog.alleles.tsv +Populating kmer dictionary for exact matches...done. +Populating kmer dictionary for gapped alignments...done. + +Processing sample 'stacks_outputs/PopA_01' [1 of 2] + Parsing stacks_outputs/PopA_01.tags.tsv + Parsing stacks_outputs/PopA_01.snps.tsv + Parsing stacks_outputs/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_outputs/PopA_01.matches.tsv + +Processing sample 'stacks_outputs/PopA_02' [2 of 2] + Parsing stacks_outputs/PopA_02.tags.tsv + Parsing stacks_outputs/PopA_02.snps.tsv + Parsing stacks_outputs/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_outputs/PopA_02.matches.tsv + +sstacks is done. + +tsv2bam +========== +tsv2bam -P stacks_outputs -M denovo_map/popmap_cstacks.tsv -R demultiplexed/ + +Logging to 'stacks_outputs/tsv2bam.log'. +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. + +gstacks +========== +gstacks -P stacks_outputs -M denovo_map/popmap_cstacks.tsv + +Logging to 'stacks_outputs/gstacks.log'. +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. + +populations +========== +populations -P stacks_outputs -M denovo_map/popmap_cstacks.tsv + +Logging to 'stacks_outputs/populations.log'. +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. +denovo_map.pl is done. + +denovo_map.pl completed at 2019-06-18 10:34:45
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/gentest.sh Thu Jun 20 08:18:09 2019 -0400 @@ -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
--- a/test-data/gstacks/catalog.calls.vcf Wed Feb 27 10:03:16 2019 -0500 +++ b/test-data/gstacks/catalog.calls.vcf Thu Jun 20 08:18:09 2019 -0400 @@ -1,6 +1,6 @@ ##fileformat=VCFv4.2 -##fileDate=20190222 -##source="Stacks v2.3b" +##fileDate=20190618 +##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"> @@ -106,492 +106,492 @@ 1 92 . G . . . DP=30;AD=30 DP 18 12 1 93 . A . . . DP=30;AD=30 DP 18 12 1 94 . C . . . DP=30;AD=30 DP 18 12 -1 105 . C . . . DP=22;AD=22 DP 14 8 -1 106 . G . . . DP=22;AD=22 DP 14 8 -1 107 . T . . . DP=22;AD=22 DP 14 8 -1 108 . C . . . DP=22;AD=22 DP 14 8 -1 109 . A . . . DP=22;AD=22 DP 14 8 -1 110 . G . . . DP=22;AD=22 DP 14 8 -1 111 . A . . . DP=22;AD=22 DP 14 8 -1 112 . G . . . DP=22;AD=22 DP 14 8 -1 113 . G . . . DP=22;AD=22 DP 14 8 -1 114 . G . . . DP=22;AD=22 DP 14 8 -1 115 . C . . . DP=22;AD=22 DP 14 8 -1 116 . T . . . DP=22;AD=22 DP 14 8 -1 117 . T . . . DP=22;AD=22 DP 14 8 -1 118 . A . . . DP=22;AD=22 DP 14 8 -1 119 . T . . . DP=22;AD=22 DP 14 8 -1 120 . A . . . DP=22;AD=22 DP 14 8 -1 121 . T . . . DP=22;AD=22 DP 14 8 -1 122 . C . . . DP=22;AD=22 DP 14 8 -1 123 . G . . . DP=22;AD=22 DP 14 8 -1 124 . T . . . DP=22;AD=22 DP 14 8 -1 125 . G . . . DP=22;AD=22 DP 14 8 -1 126 . A . . . DP=22;AD=22 DP 14 8 -1 127 . G . . . DP=22;AD=22 DP 14 8 -1 128 . T . . . DP=22;AD=22 DP 14 8 -1 129 . G . . . DP=22;AD=22 DP 14 8 -1 130 . A . . . DP=22;AD=22 DP 14 8 -1 131 . T . . . DP=22;AD=22 DP 14 8 -1 132 . A . . . DP=22;AD=22 DP 14 8 -1 133 . G . . . DP=22;AD=22 DP 14 8 -1 134 . C . . . DP=22;AD=22 DP 14 8 -1 135 . A . . . DP=22;AD=22 DP 14 8 -1 136 . G . . . DP=22;AD=22 DP 14 8 -1 137 . C . . . DP=22;AD=22 DP 14 8 -1 138 . A . . . DP=22;AD=22 DP 14 8 -1 139 . G . . . DP=22;AD=22 DP 14 8 -1 140 . T . . . DP=22;AD=22 DP 14 8 -1 141 . T . . . DP=22;AD=22 DP 14 8 -1 142 . T . . . DP=22;AD=22 DP 14 8 -1 143 . C . . . DP=22;AD=22 DP 14 8 -1 144 . T . . . DP=22;AD=22 DP 14 8 -1 145 . C . . . DP=22;AD=22 DP 14 8 -1 146 . T . . . DP=22;AD=22 DP 14 8 -1 147 . C . . . DP=22;AD=22 DP 14 8 -1 148 . T . . . DP=22;AD=22 DP 14 8 -1 149 . A . . . DP=22;AD=22 DP 14 8 -1 150 . C . . . DP=22;AD=22 DP 14 8 -1 151 . C . . . DP=22;AD=22 DP 14 8 -1 152 . A . . . DP=22;AD=22 DP 14 8 -1 153 . C . . . DP=22;AD=22 DP 14 8 -1 154 . A . . . DP=22;AD=22 DP 14 8 -1 155 . T . . . DP=22;AD=22 DP 14 8 -1 156 . A . . . DP=22;AD=21 DP 14 8 -1 157 . G . . . DP=22;AD=22 DP 14 8 -1 158 . T . . . DP=22;AD=22 DP 14 8 -1 159 . T . . . DP=22;AD=22 DP 14 8 -1 160 . A . . . DP=22;AD=22 DP 14 8 -1 161 . T . . . DP=22;AD=22 DP 14 8 -1 162 . A . . . DP=22;AD=22 DP 14 8 -1 163 . C . . . DP=22;AD=22 DP 14 8 -1 164 . A . . . DP=22;AD=22 DP 14 8 -1 165 . C . . . DP=22;AD=22 DP 14 8 -1 166 . C . . . DP=22;AD=22 DP 14 8 -1 167 . A . . . DP=19;AD=19 DP 14 5 -1 168 . T . . . DP=22;AD=22 DP 14 8 -1 169 . T . . . DP=22;AD=21 DP 14 8 -1 170 . G . . . DP=22;AD=19 DP 14 8 -1 171 . G . . . DP=22;AD=22 DP 14 8 -1 172 . G . . . DP=22;AD=22 DP 14 8 -1 173 . C . . . DP=22;AD=22 DP 14 8 -1 174 . C . . . DP=22;AD=22 DP 14 8 -1 175 . A . . . DP=22;AD=22 DP 14 8 -1 176 . G . . . DP=22;AD=22 DP 14 8 -1 177 . C . . . DP=22;AD=22 DP 14 8 -1 178 . T . . . DP=22;AD=22 DP 14 8 -1 179 . C . . . DP=22;AD=22 DP 14 8 -1 180 . G . . . DP=22;AD=22 DP 14 8 -1 181 . T . . . DP=22;AD=22 DP 14 8 -1 182 . T . . . DP=22;AD=22 DP 14 8 -1 183 . G . . . DP=22;AD=22 DP 14 8 -1 184 . A . . . DP=22;AD=22 DP 14 8 -1 185 . A . . . DP=22;AD=22 DP 14 8 -1 186 . A . . . DP=22;AD=22 DP 14 8 -1 187 . A . . . DP=22;AD=22 DP 14 8 -1 188 . C . . . DP=22;AD=22 DP 14 8 -1 189 . T . . . DP=22;AD=22 DP 14 8 -1 190 . A . . . DP=22;AD=22 DP 14 8 -1 191 . C . . . DP=22;AD=21 DP 14 8 -1 192 . T . . . DP=22;AD=22 DP 14 8 -1 193 . G . . . DP=22;AD=22 DP 14 8 -1 194 . A . . . DP=22;AD=22 DP 14 8 -1 195 . T . . . DP=22;AD=22 DP 14 8 -1 196 . G . . . DP=22;AD=22 DP 14 8 -1 197 . C . . . DP=22;AD=22 DP 14 8 -1 198 . T . . . DP=22;AD=22 DP 14 8 -1 199 . G . . . DP=22;AD=22 DP 14 8 -1 200 . A . . . DP=22;AD=22 DP 14 8 -1 201 . T . . . DP=22;AD=22 DP 14 8 -1 202 . C . . . DP=22;AD=22 DP 14 8 -1 203 . G . . . DP=22;AD=22 DP 14 8 -1 204 . G . . . DP=22;AD=22 DP 14 8 -2 1 . A . . . DP=40;AD=40 DP 20 20 -2 2 . A . . . DP=40;AD=40 DP 20 20 -2 3 . T . . . DP=40;AD=40 DP 20 20 -2 4 . T . . . DP=40;AD=40 DP 20 20 -2 5 . C . . . DP=40;AD=40 DP 20 20 -2 6 . T . . . DP=40;AD=40 DP 20 20 -2 7 . C . . . DP=40;AD=40 DP 20 20 -2 8 . T . . . DP=40;AD=40 DP 20 20 -2 9 . A . . . DP=40;AD=40 DP 20 20 -2 10 . C . . . DP=40;AD=40 DP 20 20 -2 11 . A . . . DP=40;AD=40 DP 20 20 -2 12 . C . . . DP=40;AD=40 DP 20 20 -2 13 . C . . . DP=40;AD=40 DP 20 20 -2 14 . A . . . DP=40;AD=40 DP 20 20 -2 15 . C . . . DP=40;AD=40 DP 20 20 -2 16 . A . . . DP=40;AD=39 DP 20 20 -2 17 . G . . . DP=40;AD=40 DP 20 20 -2 18 . C . . . DP=40;AD=40 DP 20 20 -2 19 . A . . . DP=40;AD=40 DP 20 20 -2 20 . T . . . DP=40;AD=40 DP 20 20 -2 21 . C . . . DP=40;AD=40 DP 20 20 -2 22 . A . . . DP=40;AD=40 DP 20 20 -2 23 . A . . . DP=40;AD=40 DP 20 20 -2 24 . T . . . DP=40;AD=40 DP 20 20 -2 25 . T . . . DP=40;AD=40 DP 20 20 -2 26 . C . . . DP=40;AD=40 DP 20 20 -2 27 . T . . . DP=40;AD=40 DP 20 20 -2 28 . A . . . DP=40;AD=40 DP 20 20 -2 29 . A . . . DP=40;AD=40 DP 20 20 -2 30 . A . . . DP=40;AD=40 DP 20 20 -2 31 . A . . . DP=40;AD=40 DP 20 20 -2 32 . A . . . DP=40;AD=40 DP 20 20 -2 33 . T . . . DP=40;AD=40 DP 20 20 -2 34 . G . . . DP=40;AD=40 DP 20 20 -2 35 . A . . . DP=40;AD=40 DP 20 20 -2 36 . C . . . DP=40;AD=40 DP 20 20 -2 37 . T . . . DP=40;AD=40 DP 20 20 -2 38 . A . . . DP=40;AD=40 DP 20 20 -2 39 . C . . . DP=40;AD=40 DP 20 20 -2 40 . C . . . DP=40;AD=40 DP 20 20 -2 41 . A . . . DP=40;AD=40 DP 20 20 -2 42 . G . . . DP=40;AD=40 DP 20 20 -2 43 . A . . . DP=40;AD=40 DP 20 20 -2 44 . G . . . DP=40;AD=40 DP 20 20 -2 45 . A . . . DP=40;AD=40 DP 20 20 -2 46 . G . . . DP=40;AD=40 DP 20 20 -2 47 . A . . . DP=40;AD=40 DP 20 20 -2 48 . C . . . DP=40;AD=40 DP 20 20 -2 49 . A . . . DP=40;AD=40 DP 20 20 -2 50 . A . . . DP=40;AD=40 DP 20 20 -2 51 . C . . . DP=40;AD=40 DP 20 20 -2 52 . T . . . DP=40;AD=40 DP 20 20 -2 53 . C . . . DP=40;AD=40 DP 20 20 -2 54 . C . . . DP=40;AD=40 DP 20 20 -2 55 . G . . . DP=40;AD=40 DP 20 20 -2 56 . C . . . DP=40;AD=40 DP 20 20 -2 57 . A . . . DP=40;AD=40 DP 20 20 -2 58 . G . . . DP=40;AD=40 DP 20 20 -2 59 . T . . . DP=40;AD=40 DP 20 20 -2 60 . T . . . DP=40;AD=39 DP 20 20 -2 61 . A . . . DP=40;AD=40 DP 20 20 -2 62 . A . . . DP=40;AD=40 DP 20 20 -2 63 . A . . . DP=40;AD=40 DP 20 20 -2 64 . C . . . DP=40;AD=40 DP 20 20 -2 65 . A . . . DP=40;AD=40 DP 20 20 -2 66 . C . . . DP=40;AD=40 DP 20 20 -2 67 . T . . . DP=40;AD=40 DP 20 20 -2 68 . C . . . DP=40;AD=40 DP 20 20 -2 69 . T . . . DP=40;AD=40 DP 20 20 -2 70 . G . . . DP=40;AD=40 DP 20 20 -2 71 . A . . . DP=40;AD=40 DP 20 20 -2 72 . C . . . DP=40;AD=40 DP 20 20 -2 73 . T . . . DP=40;AD=40 DP 20 20 -2 74 . G . . . DP=40;AD=40 DP 20 20 -2 75 . C . . . DP=40;AD=40 DP 20 20 -2 76 . C . . . DP=40;AD=40 DP 20 20 -2 77 . A . . . DP=40;AD=40 DP 20 20 -2 78 . C . . . DP=40;AD=40 DP 20 20 -2 79 . G . . . DP=40;AD=40 DP 20 20 -2 80 . C . . . DP=40;AD=40 DP 20 20 -2 81 . C . . . DP=40;AD=40 DP 20 20 -2 82 . A . . . DP=40;AD=40 DP 20 20 -2 83 . G . . . DP=40;AD=40 DP 20 20 -2 84 . C . . . DP=40;AD=40 DP 20 20 -2 85 . T . . . DP=40;AD=40 DP 20 20 -2 86 . A . . . DP=40;AD=40 DP 20 20 -2 87 . C . . . DP=40;AD=40 DP 20 20 -2 88 . C . . . DP=40;AD=40 DP 20 20 -2 89 . T . . . DP=40;AD=40 DP 20 20 -2 90 . C . . . DP=40;AD=40 DP 20 20 -2 91 . T . . . DP=40;AD=39 DP 20 20 -2 92 . A . . . DP=40;AD=40 DP 20 20 -2 93 . G . . . DP=40;AD=40 DP 20 20 -2 94 . A . . . DP=40;AD=40 DP 20 20 -2 105 . G . . . DP=30;AD=30 DP 17 13 -2 106 . G . . . DP=30;AD=30 DP 17 13 -2 107 . C . . . DP=30;AD=30 DP 17 13 -2 108 . T . . . DP=30;AD=30 DP 17 13 -2 109 . G . . . DP=30;AD=30 DP 17 13 -2 110 . C . . . DP=30;AD=30 DP 17 13 -2 111 . T . . . DP=30;AD=30 DP 17 13 -2 112 . G . . . DP=30;AD=30 DP 17 13 -2 113 . G . . . DP=30;AD=30 DP 17 13 -2 114 . A . . . DP=30;AD=30 DP 17 13 -2 115 . C . . . DP=30;AD=30 DP 17 13 -2 116 . G . . . DP=30;AD=30 DP 17 13 -2 117 . T . . . DP=30;AD=30 DP 17 13 -2 118 . C . . . DP=30;AD=30 DP 17 13 -2 119 . C . . . DP=30;AD=30 DP 17 13 -2 120 . T . . . DP=30;AD=30 DP 17 13 -2 121 . T . . . DP=30;AD=30 DP 17 13 -2 122 . C . . . DP=30;AD=30 DP 17 13 -2 123 . G . . . DP=30;AD=30 DP 17 13 -2 124 . C . . . DP=30;AD=30 DP 17 13 -2 125 . T . . . DP=30;AD=30 DP 17 13 -2 126 . C . . . DP=30;AD=30 DP 17 13 -2 127 . G . . . DP=30;AD=30 DP 17 13 -2 128 . G . . . DP=30;AD=30 DP 17 13 -2 129 . T . . . DP=30;AD=30 DP 17 13 -2 130 . A . . . DP=30;AD=30 DP 17 13 -2 131 . C . . . DP=30;AD=30 DP 17 13 -2 132 . C . . . DP=30;AD=29 DP 17 13 -2 133 . T . . . DP=30;AD=30 DP 17 13 -2 134 . T . . . DP=30;AD=30 DP 17 13 -2 135 . G . . . DP=30;AD=30 DP 17 13 -2 136 . A . . . DP=30;AD=30 DP 17 13 -2 137 . C . . . DP=30;AD=30 DP 17 13 -2 138 . T . . . DP=30;AD=30 DP 17 13 -2 139 . G . . . DP=30;AD=30 DP 17 13 -2 140 . G . . . DP=30;AD=30 DP 17 13 -2 141 . A . . . DP=30;AD=30 DP 17 13 -2 142 . T . . . DP=30;AD=30 DP 17 13 -2 143 . T . . . DP=30;AD=30 DP 17 13 -2 144 . A . . . DP=30;AD=30 DP 17 13 -2 145 . T C 40 . DP=30;AD=16,14;AF=0.467 GT:PS:FT:GQ:DP:AD:GL 1|0:145:.:40:17:8,9:-20.29,0.00,-17.57 1|0:145:.:40:13:8,5:-10.39,-0.00,-18.77 -2 146 . A . . . DP=30;AD=30 DP 17 13 -2 147 . T . . . DP=30;AD=30 DP 17 13 -2 148 . A . . . DP=30;AD=30 DP 17 13 -2 149 . G . . . DP=30;AD=30 DP 17 13 -2 150 . C . . . DP=30;AD=30 DP 17 13 -2 151 . A . . . DP=30;AD=30 DP 17 13 -2 152 . T . . . DP=30;AD=30 DP 17 13 -2 153 . T . . . DP=30;AD=30 DP 17 13 -2 154 . C . . . DP=30;AD=30 DP 17 13 -2 155 . C . . . DP=30;AD=30 DP 17 13 -2 156 . T . . . DP=30;AD=29 DP 17 13 -2 157 . T G 40 . DP=30;AD=16,14;AF=0.467 GT:PS:FT:GQ:DP:AD:GL 1|0:145:.:40:17:8,9:-20.29,0.00,-17.57 1|0:145:.:40:13:8,5:-10.39,-0.00,-18.77 -2 158 . A . . . DP=30;AD=30 DP 17 13 -2 159 . G . . . DP=30;AD=30 DP 17 13 -2 160 . T . . . DP=30;AD=30 DP 17 13 -2 161 . T . . . DP=30;AD=30 DP 17 13 -2 162 . C . . . DP=30;AD=30 DP 17 13 -2 163 . A . . . DP=30;AD=30 DP 17 13 -2 164 . C . . . DP=30;AD=30 DP 17 13 -2 165 . G . . . DP=30;AD=30 DP 17 13 -2 166 . G . . . DP=30;AD=30 DP 17 13 -2 167 . C . . . DP=30;AD=30 DP 17 13 -2 168 . C . . . DP=30;AD=30 DP 17 13 -2 169 . A . . . DP=30;AD=30 DP 17 13 -2 170 . A . . . DP=30;AD=30 DP 17 13 -2 171 . T . . . DP=30;AD=30 DP 17 13 -2 172 . A . . . DP=30;AD=30 DP 17 13 -2 173 . T . . . DP=30;AD=30 DP 17 13 -2 174 . C . . . DP=30;AD=30 DP 17 13 -2 175 . G . . . DP=30;AD=30 DP 17 13 -2 176 . C . . . DP=30;AD=30 DP 17 13 -2 177 . C . . . DP=30;AD=30 DP 17 13 -2 178 . A . . . DP=30;AD=30 DP 17 13 -2 179 . A . . . DP=30;AD=30 DP 17 13 -2 180 . C . . . DP=30;AD=30 DP 17 13 -2 181 . C . . . DP=30;AD=30 DP 17 13 -2 182 . G . . . DP=30;AD=30 DP 17 13 -2 183 . T . . . DP=30;AD=30 DP 17 13 -2 184 . T . . . DP=30;AD=30 DP 17 13 -2 185 . G . . . DP=30;AD=30 DP 17 13 -2 186 . A . . . DP=30;AD=30 DP 17 13 -2 187 . G . . . DP=30;AD=30 DP 17 13 -2 188 . T . . . DP=30;AD=30 DP 17 13 -2 189 . G . . . DP=30;AD=30 DP 17 13 -2 190 . A . . . DP=30;AD=30 DP 17 13 -2 191 . G . . . DP=30;AD=30 DP 17 13 -2 192 . T . . . DP=30;AD=30 DP 17 13 -2 193 . T . . . DP=30;AD=30 DP 17 13 -2 194 . T . . . DP=30;AD=30 DP 17 13 -2 195 . A . . . DP=30;AD=30 DP 17 13 -2 196 . G . . . DP=30;AD=30 DP 17 13 -2 197 . T . . . DP=30;AD=30 DP 17 13 -2 198 . G . . . DP=30;AD=30 DP 17 13 -2 199 . A . . . DP=30;AD=30 DP 17 13 -2 200 . A . . . DP=30;AD=30 DP 17 13 -2 201 . C . . . DP=30;AD=30 DP 17 13 -2 202 . C . . . DP=30;AD=30 DP 17 13 -2 203 . G . . . DP=30;AD=30 DP 17 13 -2 204 . G . . . DP=30;AD=30 DP 17 13 -3 1 . A . . . DP=56;AD=56 DP 28 28 -3 2 . A . . . DP=56;AD=56 DP 28 28 -3 3 . T . . . DP=56;AD=56 DP 28 28 -3 4 . T . . . DP=56;AD=56 DP 28 28 -3 5 . C . . . DP=56;AD=56 DP 28 28 -3 6 . G . . . DP=56;AD=56 DP 28 28 -3 7 . G . . . DP=56;AD=56 DP 28 28 -3 8 . C . . . DP=56;AD=56 DP 28 28 -3 9 . T . . . DP=56;AD=56 DP 28 28 -3 10 . T . . . DP=56;AD=56 DP 28 28 -3 11 . G . . . DP=56;AD=56 DP 28 28 -3 12 . C . . . DP=56;AD=56 DP 28 28 -3 13 . A . . . DP=56;AD=56 DP 28 28 -3 14 . A . . . DP=56;AD=56 DP 28 28 -3 15 . C . . . DP=56;AD=56 DP 28 28 -3 16 . G . . . DP=56;AD=56 DP 28 28 -3 17 . C . . . DP=56;AD=56 DP 28 28 -3 18 . A . . . DP=56;AD=56 DP 28 28 -3 19 . A . . . DP=56;AD=56 DP 28 28 -3 20 . G . . . DP=56;AD=56 DP 28 28 -3 21 . T . . . DP=56;AD=56 DP 28 28 -3 22 . G . . . DP=56;AD=56 DP 28 28 -3 23 . A . . . DP=56;AD=56 DP 28 28 -3 24 . C . . . DP=56;AD=56 DP 28 28 -3 25 . G . . . DP=56;AD=56 DP 28 28 -3 26 . A . . . DP=56;AD=56 DP 28 28 -3 27 . T . . . DP=56;AD=56 DP 28 28 -3 28 . T . . . DP=56;AD=56 DP 28 28 -3 29 . C . . . DP=56;AD=56 DP 28 28 -3 30 . C . . . DP=56;AD=56 DP 28 28 -3 31 . C . . . DP=56;AD=56 DP 28 28 -3 32 . A . . . DP=56;AD=55 DP 28 28 -3 33 . C . . . DP=56;AD=56 DP 28 28 -3 34 . G . . . DP=56;AD=56 DP 28 28 -3 35 . G . . . DP=56;AD=56 DP 28 28 -3 36 . A . . . DP=56;AD=56 DP 28 28 -3 37 . C . . . DP=56;AD=56 DP 28 28 -3 38 . A . . . DP=56;AD=56 DP 28 28 -3 39 . T . . . DP=56;AD=56 DP 28 28 -3 40 . A . . . DP=56;AD=56 DP 28 28 -3 41 . A . . . DP=56;AD=56 DP 28 28 -3 42 . C . . . DP=56;AD=56 DP 28 28 -3 43 . T . . . DP=56;AD=56 DP 28 28 -3 44 . G . . . DP=56;AD=56 DP 28 28 -3 45 . A . . . DP=56;AD=56 DP 28 28 -3 46 . T . . . DP=56;AD=56 DP 28 28 -3 47 . C . . . DP=56;AD=56 DP 28 28 -3 48 . T . . . DP=56;AD=56 DP 28 28 -3 49 . A . . . DP=56;AD=56 DP 28 28 -3 50 . A . . . DP=56;AD=56 DP 28 28 -3 51 . G . . . DP=56;AD=56 DP 28 28 -3 52 . T . . . DP=56;AD=56 DP 28 28 -3 53 . A . . . DP=56;AD=56 DP 28 28 -3 54 . A . . . DP=56;AD=55 DP 28 28 -3 55 . C . . . DP=56;AD=56 DP 28 28 -3 56 . T . . . DP=56;AD=56 DP 28 28 -3 57 . T . . . DP=56;AD=56 DP 28 28 -3 58 . C . . . DP=56;AD=56 DP 28 28 -3 59 . C . . . DP=56;AD=56 DP 28 28 -3 60 . A . . . DP=56;AD=56 DP 28 28 -3 61 . A . . . DP=56;AD=56 DP 28 28 -3 62 . A . . . DP=56;AD=55 DP 28 28 -3 63 . T . . . DP=56;AD=56 DP 28 28 -3 64 . C . . . DP=56;AD=56 DP 28 28 -3 65 . T . . . DP=56;AD=56 DP 28 28 -3 66 . G . . . DP=56;AD=56 DP 28 28 -3 67 . G . . . DP=56;AD=56 DP 28 28 -3 68 . G . . . DP=56;AD=56 DP 28 28 -3 69 . A . . . DP=56;AD=56 DP 28 28 -3 70 . A . . . DP=56;AD=56 DP 28 28 -3 71 . T . . . DP=56;AD=56 DP 28 28 -3 72 . G . . . DP=56;AD=56 DP 28 28 -3 73 . G . . . DP=56;AD=56 DP 28 28 -3 74 . G . . . DP=56;AD=56 DP 28 28 -3 75 . A . . . DP=56;AD=56 DP 28 28 -3 76 . T . . . DP=56;AD=56 DP 28 28 -3 77 . T . . . DP=56;AD=56 DP 28 28 -3 78 . T . . . DP=56;AD=56 DP 28 28 -3 79 . C . . . DP=56;AD=56 DP 28 28 -3 80 . A . . . DP=56;AD=56 DP 28 28 -3 81 . T . . . DP=56;AD=56 DP 28 28 -3 82 . A . . . DP=56;AD=56 DP 28 28 -3 83 . A . . . DP=56;AD=56 DP 28 28 -3 84 . T . . . DP=56;AD=56 DP 28 28 -3 85 . T . . . DP=56;AD=56 DP 28 28 -3 86 . A . . . DP=56;AD=56 DP 28 28 -3 87 . A . . . DP=56;AD=56 DP 28 28 -3 88 . G . . . DP=56;AD=56 DP 28 28 -3 89 . G . . . DP=56;AD=56 DP 28 28 -3 90 . A . . . DP=56;AD=56 DP 28 28 -3 91 . C . . . DP=56;AD=56 DP 28 28 -3 92 . T . . . DP=56;AD=56 DP 28 28 -3 93 . A . . . DP=56;AD=56 DP 28 28 -3 94 . T . . . DP=56;AD=56 DP 28 28 -3 105 . T . . . DP=12;AD=12 DP . 12 -3 106 . A . . . DP=46;AD=46 DP 23 23 -3 107 . C . . . DP=46;AD=46 DP 23 23 -3 108 . G . . . DP=46;AD=46 DP 23 23 -3 109 . A . . . DP=46;AD=46 DP 23 23 -3 110 . C . . . DP=46;AD=46 DP 23 23 -3 111 . G . . . DP=46;AD=46 DP 23 23 -3 112 . A . . . DP=46;AD=46 DP 23 23 -3 113 . G . . . DP=46;AD=46 DP 23 23 -3 114 . C . . . DP=46;AD=46 DP 23 23 -3 115 . A . . . DP=46;AD=46 DP 23 23 -3 116 . A . . . DP=46;AD=46 DP 23 23 -3 117 . T . . . DP=46;AD=46 DP 23 23 -3 118 . C . . . DP=46;AD=46 DP 23 23 -3 119 . C . . . DP=46;AD=46 DP 23 23 -3 120 . A . . . DP=46;AD=46 DP 23 23 -3 121 . C . . . DP=46;AD=46 DP 23 23 -3 122 . A . . . DP=46;AD=46 DP 23 23 -3 123 . G . . . DP=46;AD=46 DP 23 23 -3 124 . A . . . DP=46;AD=46 DP 23 23 -3 125 . C . . . DP=46;AD=46 DP 23 23 -3 126 . C . . . DP=46;AD=45 DP 23 23 -3 127 . T . . . DP=46;AD=46 DP 23 23 -3 128 . A . . . DP=46;AD=46 DP 23 23 -3 129 . G . . . DP=46;AD=46 DP 23 23 -3 130 . G . . . DP=46;AD=46 DP 23 23 -3 131 . C . . . DP=46;AD=46 DP 23 23 -3 132 . C . . . DP=46;AD=46 DP 23 23 -3 133 . C . . . DP=46;AD=46 DP 23 23 -3 134 . A . . . DP=46;AD=46 DP 23 23 -3 135 . T . . . DP=46;AD=46 DP 23 23 -3 136 . C . . . DP=46;AD=46 DP 23 23 -3 137 . G . . . DP=46;AD=46 DP 23 23 -3 138 . A . . . DP=46;AD=46 DP 23 23 -3 139 . A . . . DP=46;AD=46 DP 23 23 -3 140 . G . . . DP=46;AD=46 DP 23 23 -3 141 . C . . . DP=46;AD=46 DP 23 23 -3 142 . G . . . DP=46;AD=46 DP 23 23 -3 143 . T . . . DP=46;AD=46 DP 23 23 -3 144 . C . . . DP=46;AD=46 DP 23 23 -3 145 . T . . . DP=46;AD=46 DP 23 23 -3 146 . T . . . DP=46;AD=46 DP 23 23 -3 147 . A . . . DP=46;AD=46 DP 23 23 -3 148 . T . . . DP=46;AD=46 DP 23 23 -3 149 . G . . . DP=46;AD=46 DP 23 23 -3 150 . A . . . DP=46;AD=46 DP 23 23 -3 151 . T . . . DP=46;AD=46 DP 23 23 -3 152 . T . . . DP=46;AD=46 DP 23 23 -3 153 . G . . . DP=46;AD=46 DP 23 23 -3 154 . A . . . DP=46;AD=46 DP 23 23 -3 155 . T . . . DP=46;AD=46 DP 23 23 -3 156 . A . . . DP=46;AD=46 DP 23 23 -3 157 . A . . . DP=46;AD=46 DP 23 23 -3 158 . C . . . DP=46;AD=46 DP 23 23 -3 159 . A . . . DP=46;AD=46 DP 23 23 -3 160 . T . . . DP=46;AD=46 DP 23 23 -3 161 . C . . . DP=46;AD=46 DP 23 23 -3 162 . A . . . DP=46;AD=46 DP 23 23 -3 163 . G A 40 . DP=46;AD=34,12;AF=0.261 GT:PS:FT:GQ:DP:AD:GL 0/0:.:.:40:23:23,0:-0.00,-6.89,-68.45 1|0:163:.:40:23:11,12:-28.67,0.00,-25.99 -3 164 . A . . . DP=46;AD=46 DP 23 23 -3 165 . G . . . DP=46;AD=46 DP 23 23 -3 166 . G . . . DP=46;AD=46 DP 23 23 -3 167 . G . . . DP=46;AD=46 DP 23 23 -3 168 . G . . . DP=46;AD=46 DP 23 23 -3 169 . G . . . DP=46;AD=46 DP 23 23 -3 170 . A . . . DP=46;AD=46 DP 23 23 -3 171 . T . . . DP=46;AD=46 DP 23 23 -3 172 . G . . . DP=46;AD=46 DP 23 23 -3 173 . G . . . DP=46;AD=46 DP 23 23 -3 174 . G . . . DP=46;AD=46 DP 23 23 -3 175 . A . . . DP=46;AD=46 DP 23 23 -3 176 . G . . . DP=46;AD=45 DP 23 23 -3 177 . G . . . DP=46;AD=46 DP 23 23 -3 178 . T . . . DP=46;AD=46 DP 23 23 -3 179 . C . . . DP=46;AD=46 DP 23 23 -3 180 . C . . . DP=46;AD=46 DP 23 23 -3 181 . T . . . DP=46;AD=46 DP 23 23 -3 182 . G A 40 . DP=46;AD=34,12;AF=0.261 GT:PS:FT:GQ:DP:AD:GL 0/0:.:.:40:23:23,0:-0.00,-6.89,-68.45 1|0:163:.:40:23:11,12:-28.67,0.00,-25.99 -3 183 . C . . . DP=46;AD=46 DP 23 23 -3 184 . T . . . DP=46;AD=46 DP 23 23 -3 185 . G . . . DP=46;AD=46 DP 23 23 -3 186 . T . . . DP=46;AD=45 DP 23 23 -3 187 . C . . . DP=46;AD=46 DP 23 23 -3 188 . G . . . DP=46;AD=46 DP 23 23 -3 189 . C . . . DP=46;AD=46 DP 23 23 -3 190 . A . . . DP=46;AD=46 DP 23 23 -3 191 . T . . . DP=46;AD=46 DP 23 23 -3 192 . G . . . DP=46;AD=46 DP 23 23 -3 193 . G . . . DP=46;AD=46 DP 23 23 -3 194 . G . . . DP=46;AD=45 DP 23 23 -3 195 . A . . . DP=46;AD=46 DP 23 23 -3 196 . G . . . DP=46;AD=46 DP 23 23 -3 197 . A . . . DP=46;AD=46 DP 23 23 -3 198 . A . . . DP=46;AD=46 DP 23 23 -3 199 . T . . . DP=46;AD=46 DP 23 23 -3 200 . A . . . DP=46;AD=46 DP 23 23 -3 201 . C . . . DP=46;AD=46 DP 23 23 -3 202 . A . . . DP=34;AD=34 DP 23 11 -3 203 . C . . . DP=34;AD=34 DP 23 11 -3 204 . G . . . DP=34;AD=34 DP 23 11 -3 205 . G . . . DP=34;AD=34 DP 23 11 +1 105 . C . . . DP=19;AD=19 DP 11 8 +1 106 . G . . . DP=19;AD=19 DP 11 8 +1 107 . T . . . DP=19;AD=19 DP 11 8 +1 108 . C . . . DP=19;AD=19 DP 11 8 +1 109 . A . . . DP=19;AD=19 DP 11 8 +1 110 . G . . . DP=19;AD=19 DP 11 8 +1 111 . A . . . DP=19;AD=19 DP 11 8 +1 112 . G . . . DP=19;AD=19 DP 11 8 +1 113 . G . . . DP=19;AD=19 DP 11 8 +1 114 . G . . . DP=19;AD=19 DP 11 8 +1 115 . C . . . DP=19;AD=19 DP 11 8 +1 116 . T . . . DP=19;AD=19 DP 11 8 +1 117 . T . . . DP=19;AD=19 DP 11 8 +1 118 . A . . . DP=19;AD=19 DP 11 8 +1 119 . T . . . DP=19;AD=19 DP 11 8 +1 120 . A . . . DP=19;AD=19 DP 11 8 +1 121 . T . . . DP=19;AD=19 DP 11 8 +1 122 . C . . . DP=19;AD=19 DP 11 8 +1 123 . G . . . DP=19;AD=19 DP 11 8 +1 124 . T . . . DP=19;AD=19 DP 11 8 +1 125 . G . . . DP=19;AD=19 DP 11 8 +1 126 . A . . . DP=19;AD=19 DP 11 8 +1 127 . G . . . DP=19;AD=19 DP 11 8 +1 128 . T . . . DP=19;AD=19 DP 11 8 +1 129 . G . . . DP=19;AD=19 DP 11 8 +1 130 . A . . . DP=19;AD=19 DP 11 8 +1 131 . T . . . DP=19;AD=19 DP 11 8 +1 132 . A . . . DP=19;AD=19 DP 11 8 +1 133 . G . . . DP=19;AD=19 DP 11 8 +1 134 . C . . . DP=19;AD=19 DP 11 8 +1 135 . A . . . DP=19;AD=19 DP 11 8 +1 136 . G . . . DP=19;AD=19 DP 11 8 +1 137 . C . . . DP=19;AD=19 DP 11 8 +1 138 . A . . . DP=19;AD=19 DP 11 8 +1 139 . G . . . DP=19;AD=19 DP 11 8 +1 140 . T . . . DP=19;AD=19 DP 11 8 +1 141 . T . . . DP=19;AD=19 DP 11 8 +1 142 . T . . . DP=19;AD=19 DP 11 8 +1 143 . C . . . DP=19;AD=19 DP 11 8 +1 144 . T . . . DP=19;AD=19 DP 11 8 +1 145 . C . . . DP=19;AD=19 DP 11 8 +1 146 . T . . . DP=19;AD=19 DP 11 8 +1 147 . C . . . DP=19;AD=19 DP 11 8 +1 148 . T . . . DP=19;AD=19 DP 11 8 +1 149 . A . . . DP=19;AD=19 DP 11 8 +1 150 . C . . . DP=19;AD=19 DP 11 8 +1 151 . C . . . DP=19;AD=19 DP 11 8 +1 152 . A . . . DP=19;AD=19 DP 11 8 +1 153 . C . . . DP=19;AD=19 DP 11 8 +1 154 . A . . . DP=19;AD=19 DP 11 8 +1 155 . T . . . DP=19;AD=19 DP 11 8 +1 156 . A . . . DP=19;AD=18 DP 11 8 +1 157 . G . . . DP=19;AD=19 DP 11 8 +1 158 . T . . . DP=19;AD=19 DP 11 8 +1 159 . T . . . DP=19;AD=19 DP 11 8 +1 160 . A . . . DP=19;AD=19 DP 11 8 +1 161 . T . . . DP=19;AD=19 DP 11 8 +1 162 . A . . . DP=19;AD=19 DP 11 8 +1 163 . C . . . DP=19;AD=19 DP 11 8 +1 164 . A . . . DP=19;AD=19 DP 11 8 +1 165 . C . . . DP=19;AD=19 DP 11 8 +1 166 . C . . . DP=19;AD=19 DP 11 8 +1 167 . A . . . DP=16;AD=16 DP 11 5 +1 168 . T . . . DP=19;AD=19 DP 11 8 +1 169 . T . . . DP=19;AD=18 DP 11 8 +1 170 . G . . . DP=19;AD=16 DP 11 8 +1 171 . G . . . DP=19;AD=19 DP 11 8 +1 172 . G . . . DP=19;AD=19 DP 11 8 +1 173 . C . . . DP=19;AD=19 DP 11 8 +1 174 . C . . . DP=19;AD=19 DP 11 8 +1 175 . A . . . DP=19;AD=19 DP 11 8 +1 176 . G . . . DP=19;AD=19 DP 11 8 +1 177 . C . . . DP=19;AD=19 DP 11 8 +1 178 . T . . . DP=19;AD=19 DP 11 8 +1 179 . C . . . DP=19;AD=19 DP 11 8 +1 180 . G . . . DP=19;AD=19 DP 11 8 +1 181 . T . . . DP=19;AD=19 DP 11 8 +1 182 . T . . . DP=19;AD=19 DP 11 8 +1 183 . G . . . DP=19;AD=19 DP 11 8 +1 184 . A . . . DP=19;AD=19 DP 11 8 +1 185 . A . . . DP=19;AD=19 DP 11 8 +1 186 . A . . . DP=19;AD=19 DP 11 8 +1 187 . A . . . DP=19;AD=19 DP 11 8 +1 188 . C . . . DP=19;AD=19 DP 11 8 +1 189 . T . . . DP=19;AD=19 DP 11 8 +1 190 . A . . . DP=19;AD=19 DP 11 8 +1 191 . C . . . DP=19;AD=18 DP 11 8 +1 192 . T . . . DP=19;AD=19 DP 11 8 +1 193 . G . . . DP=19;AD=19 DP 11 8 +1 194 . A . . . DP=19;AD=19 DP 11 8 +1 195 . T . . . DP=19;AD=19 DP 11 8 +1 196 . G . . . DP=19;AD=19 DP 11 8 +1 197 . C . . . DP=19;AD=19 DP 11 8 +1 198 . T . . . DP=19;AD=19 DP 11 8 +1 199 . G . . . DP=19;AD=19 DP 11 8 +1 200 . A . . . DP=19;AD=19 DP 11 8 +1 201 . T . . . DP=19;AD=19 DP 11 8 +1 202 . C . . . DP=19;AD=19 DP 11 8 +1 203 . G . . . DP=19;AD=19 DP 11 8 +1 204 . G . . . DP=19;AD=19 DP 11 8 +2 1 . A . . . DP=56;AD=56 DP 28 28 +2 2 . A . . . DP=56;AD=56 DP 28 28 +2 3 . T . . . DP=56;AD=56 DP 28 28 +2 4 . T . . . DP=56;AD=56 DP 28 28 +2 5 . C . . . DP=56;AD=56 DP 28 28 +2 6 . G . . . DP=56;AD=56 DP 28 28 +2 7 . G . . . DP=56;AD=56 DP 28 28 +2 8 . C . . . DP=56;AD=56 DP 28 28 +2 9 . T . . . DP=56;AD=56 DP 28 28 +2 10 . T . . . DP=56;AD=56 DP 28 28 +2 11 . G . . . DP=56;AD=56 DP 28 28 +2 12 . C . . . DP=56;AD=56 DP 28 28 +2 13 . A . . . DP=56;AD=56 DP 28 28 +2 14 . A . . . DP=56;AD=56 DP 28 28 +2 15 . C . . . DP=56;AD=56 DP 28 28 +2 16 . G . . . DP=56;AD=56 DP 28 28 +2 17 . C . . . DP=56;AD=56 DP 28 28 +2 18 . A . . . DP=56;AD=56 DP 28 28 +2 19 . A . . . DP=56;AD=56 DP 28 28 +2 20 . G . . . DP=56;AD=56 DP 28 28 +2 21 . T . . . DP=56;AD=56 DP 28 28 +2 22 . G . . . DP=56;AD=56 DP 28 28 +2 23 . A . . . DP=56;AD=56 DP 28 28 +2 24 . C . . . DP=56;AD=56 DP 28 28 +2 25 . G . . . DP=56;AD=56 DP 28 28 +2 26 . A . . . DP=56;AD=56 DP 28 28 +2 27 . T . . . DP=56;AD=56 DP 28 28 +2 28 . T . . . DP=56;AD=56 DP 28 28 +2 29 . C . . . DP=56;AD=56 DP 28 28 +2 30 . C . . . DP=56;AD=56 DP 28 28 +2 31 . C . . . DP=56;AD=56 DP 28 28 +2 32 . A . . . DP=56;AD=55 DP 28 28 +2 33 . C . . . DP=56;AD=56 DP 28 28 +2 34 . G . . . DP=56;AD=56 DP 28 28 +2 35 . G . . . DP=56;AD=56 DP 28 28 +2 36 . A . . . DP=56;AD=56 DP 28 28 +2 37 . C . . . DP=56;AD=56 DP 28 28 +2 38 . A . . . DP=56;AD=56 DP 28 28 +2 39 . T . . . DP=56;AD=56 DP 28 28 +2 40 . A . . . DP=56;AD=56 DP 28 28 +2 41 . A . . . DP=56;AD=56 DP 28 28 +2 42 . C . . . DP=56;AD=56 DP 28 28 +2 43 . T . . . DP=56;AD=56 DP 28 28 +2 44 . G . . . DP=56;AD=56 DP 28 28 +2 45 . A . . . DP=56;AD=56 DP 28 28 +2 46 . T . . . DP=56;AD=56 DP 28 28 +2 47 . C . . . DP=56;AD=56 DP 28 28 +2 48 . T . . . DP=56;AD=56 DP 28 28 +2 49 . A . . . DP=56;AD=56 DP 28 28 +2 50 . A . . . DP=56;AD=56 DP 28 28 +2 51 . G . . . DP=56;AD=56 DP 28 28 +2 52 . T . . . DP=56;AD=56 DP 28 28 +2 53 . A . . . DP=56;AD=56 DP 28 28 +2 54 . A . . . DP=56;AD=55 DP 28 28 +2 55 . C . . . DP=56;AD=56 DP 28 28 +2 56 . T . . . DP=56;AD=56 DP 28 28 +2 57 . T . . . DP=56;AD=56 DP 28 28 +2 58 . C . . . DP=56;AD=56 DP 28 28 +2 59 . C . . . DP=56;AD=56 DP 28 28 +2 60 . A . . . DP=56;AD=56 DP 28 28 +2 61 . A . . . DP=56;AD=56 DP 28 28 +2 62 . A . . . DP=56;AD=55 DP 28 28 +2 63 . T . . . DP=56;AD=56 DP 28 28 +2 64 . C . . . DP=56;AD=56 DP 28 28 +2 65 . T . . . DP=56;AD=56 DP 28 28 +2 66 . G . . . DP=56;AD=56 DP 28 28 +2 67 . G . . . DP=56;AD=56 DP 28 28 +2 68 . G . . . DP=56;AD=56 DP 28 28 +2 69 . A . . . DP=56;AD=56 DP 28 28 +2 70 . A . . . DP=56;AD=56 DP 28 28 +2 71 . T . . . DP=56;AD=56 DP 28 28 +2 72 . G . . . DP=56;AD=56 DP 28 28 +2 73 . G . . . DP=56;AD=56 DP 28 28 +2 74 . G . . . DP=56;AD=56 DP 28 28 +2 75 . A . . . DP=56;AD=56 DP 28 28 +2 76 . T . . . DP=56;AD=56 DP 28 28 +2 77 . T . . . DP=56;AD=56 DP 28 28 +2 78 . T . . . DP=56;AD=56 DP 28 28 +2 79 . C . . . DP=56;AD=56 DP 28 28 +2 80 . A . . . DP=56;AD=56 DP 28 28 +2 81 . T . . . DP=56;AD=56 DP 28 28 +2 82 . A . . . DP=56;AD=56 DP 28 28 +2 83 . A . . . DP=56;AD=56 DP 28 28 +2 84 . T . . . DP=56;AD=56 DP 28 28 +2 85 . T . . . DP=56;AD=56 DP 28 28 +2 86 . A . . . DP=56;AD=56 DP 28 28 +2 87 . A . . . DP=56;AD=56 DP 28 28 +2 88 . G . . . DP=56;AD=56 DP 28 28 +2 89 . G . . . DP=56;AD=56 DP 28 28 +2 90 . A . . . DP=56;AD=56 DP 28 28 +2 91 . C . . . DP=56;AD=56 DP 28 28 +2 92 . T . . . DP=56;AD=56 DP 28 28 +2 93 . A . . . DP=56;AD=56 DP 28 28 +2 94 . T . . . DP=56;AD=56 DP 28 28 +2 105 . T . . . DP=12;AD=12 DP . 12 +2 106 . A . . . DP=46;AD=46 DP 23 23 +2 107 . C . . . DP=46;AD=46 DP 23 23 +2 108 . G . . . DP=46;AD=46 DP 23 23 +2 109 . A . . . DP=46;AD=46 DP 23 23 +2 110 . C . . . DP=46;AD=46 DP 23 23 +2 111 . G . . . DP=46;AD=46 DP 23 23 +2 112 . A . . . DP=46;AD=46 DP 23 23 +2 113 . G . . . DP=46;AD=46 DP 23 23 +2 114 . C . . . DP=46;AD=46 DP 23 23 +2 115 . A . . . DP=46;AD=46 DP 23 23 +2 116 . A . . . DP=46;AD=46 DP 23 23 +2 117 . T . . . DP=46;AD=46 DP 23 23 +2 118 . C . . . DP=46;AD=46 DP 23 23 +2 119 . C . . . DP=46;AD=46 DP 23 23 +2 120 . A . . . DP=46;AD=46 DP 23 23 +2 121 . C . . . DP=46;AD=46 DP 23 23 +2 122 . A . . . DP=46;AD=46 DP 23 23 +2 123 . G . . . DP=46;AD=46 DP 23 23 +2 124 . A . . . DP=46;AD=46 DP 23 23 +2 125 . C . . . DP=46;AD=46 DP 23 23 +2 126 . C . . . DP=46;AD=45 DP 23 23 +2 127 . T . . . DP=46;AD=46 DP 23 23 +2 128 . A . . . DP=46;AD=46 DP 23 23 +2 129 . G . . . DP=46;AD=46 DP 23 23 +2 130 . G . . . DP=46;AD=46 DP 23 23 +2 131 . C . . . DP=46;AD=46 DP 23 23 +2 132 . C . . . DP=46;AD=46 DP 23 23 +2 133 . C . . . DP=46;AD=46 DP 23 23 +2 134 . A . . . DP=46;AD=46 DP 23 23 +2 135 . T . . . DP=46;AD=46 DP 23 23 +2 136 . C . . . DP=46;AD=46 DP 23 23 +2 137 . G . . . DP=46;AD=46 DP 23 23 +2 138 . A . . . DP=46;AD=46 DP 23 23 +2 139 . A . . . DP=46;AD=46 DP 23 23 +2 140 . G . . . DP=46;AD=46 DP 23 23 +2 141 . C . . . DP=46;AD=46 DP 23 23 +2 142 . G . . . DP=46;AD=46 DP 23 23 +2 143 . T . . . DP=46;AD=46 DP 23 23 +2 144 . C . . . DP=46;AD=46 DP 23 23 +2 145 . T . . . DP=46;AD=46 DP 23 23 +2 146 . T . . . DP=46;AD=46 DP 23 23 +2 147 . A . . . DP=46;AD=46 DP 23 23 +2 148 . T . . . DP=46;AD=46 DP 23 23 +2 149 . G . . . DP=46;AD=46 DP 23 23 +2 150 . A . . . DP=46;AD=46 DP 23 23 +2 151 . T . . . DP=46;AD=46 DP 23 23 +2 152 . T . . . DP=46;AD=46 DP 23 23 +2 153 . G . . . DP=46;AD=46 DP 23 23 +2 154 . A . . . DP=46;AD=46 DP 23 23 +2 155 . T . . . DP=46;AD=46 DP 23 23 +2 156 . A . . . DP=46;AD=46 DP 23 23 +2 157 . A . . . DP=46;AD=46 DP 23 23 +2 158 . C . . . DP=46;AD=46 DP 23 23 +2 159 . A . . . DP=46;AD=46 DP 23 23 +2 160 . T . . . DP=46;AD=46 DP 23 23 +2 161 . C . . . DP=46;AD=46 DP 23 23 +2 162 . A . . . DP=46;AD=46 DP 23 23 +2 163 . G A 40 . DP=46;AD=34,12;AF=0.261 GT:PS:FT:GQ:DP:AD:GL 0/0:.:.:40:23:23,0:-0.00,-6.89,-68.45 1|0:163:.:40:23:11,12:-28.67,0.00,-25.99 +2 164 . A . . . DP=46;AD=46 DP 23 23 +2 165 . G . . . DP=46;AD=46 DP 23 23 +2 166 . G . . . DP=46;AD=46 DP 23 23 +2 167 . G . . . DP=46;AD=46 DP 23 23 +2 168 . G . . . DP=46;AD=46 DP 23 23 +2 169 . G . . . DP=46;AD=46 DP 23 23 +2 170 . A . . . DP=46;AD=46 DP 23 23 +2 171 . T . . . DP=46;AD=46 DP 23 23 +2 172 . G . . . DP=46;AD=46 DP 23 23 +2 173 . G . . . DP=46;AD=46 DP 23 23 +2 174 . G . . . DP=46;AD=46 DP 23 23 +2 175 . A . . . DP=46;AD=46 DP 23 23 +2 176 . G . . . DP=46;AD=45 DP 23 23 +2 177 . G . . . DP=46;AD=46 DP 23 23 +2 178 . T . . . DP=46;AD=46 DP 23 23 +2 179 . C . . . DP=46;AD=46 DP 23 23 +2 180 . C . . . DP=46;AD=46 DP 23 23 +2 181 . T . . . DP=46;AD=46 DP 23 23 +2 182 . G A 40 . DP=46;AD=34,12;AF=0.261 GT:PS:FT:GQ:DP:AD:GL 0/0:.:.:40:23:23,0:-0.00,-6.89,-68.45 1|0:163:.:40:23:11,12:-28.67,0.00,-25.99 +2 183 . C . . . DP=46;AD=46 DP 23 23 +2 184 . T . . . DP=46;AD=46 DP 23 23 +2 185 . G . . . DP=46;AD=46 DP 23 23 +2 186 . T . . . DP=46;AD=45 DP 23 23 +2 187 . C . . . DP=46;AD=46 DP 23 23 +2 188 . G . . . DP=46;AD=46 DP 23 23 +2 189 . C . . . DP=46;AD=46 DP 23 23 +2 190 . A . . . DP=46;AD=46 DP 23 23 +2 191 . T . . . DP=46;AD=46 DP 23 23 +2 192 . G . . . DP=46;AD=46 DP 23 23 +2 193 . G . . . DP=46;AD=46 DP 23 23 +2 194 . G . . . DP=46;AD=45 DP 23 23 +2 195 . A . . . DP=46;AD=46 DP 23 23 +2 196 . G . . . DP=46;AD=46 DP 23 23 +2 197 . A . . . DP=46;AD=46 DP 23 23 +2 198 . A . . . DP=46;AD=46 DP 23 23 +2 199 . T . . . DP=46;AD=46 DP 23 23 +2 200 . A . . . DP=46;AD=46 DP 23 23 +2 201 . C . . . DP=46;AD=46 DP 23 23 +2 202 . A . . . DP=34;AD=34 DP 23 11 +2 203 . C . . . DP=34;AD=34 DP 23 11 +2 204 . G . . . DP=34;AD=34 DP 23 11 +2 205 . G . . . DP=34;AD=34 DP 23 11 +3 1 . A . . . DP=40;AD=40 DP 20 20 +3 2 . A . . . DP=40;AD=40 DP 20 20 +3 3 . T . . . DP=40;AD=40 DP 20 20 +3 4 . T . . . DP=40;AD=40 DP 20 20 +3 5 . C . . . DP=40;AD=40 DP 20 20 +3 6 . T . . . DP=40;AD=40 DP 20 20 +3 7 . C . . . DP=40;AD=40 DP 20 20 +3 8 . T . . . DP=40;AD=40 DP 20 20 +3 9 . A . . . DP=40;AD=40 DP 20 20 +3 10 . C . . . DP=40;AD=40 DP 20 20 +3 11 . A . . . DP=40;AD=40 DP 20 20 +3 12 . C . . . DP=40;AD=40 DP 20 20 +3 13 . C . . . DP=40;AD=40 DP 20 20 +3 14 . A . . . DP=40;AD=40 DP 20 20 +3 15 . C . . . DP=40;AD=40 DP 20 20 +3 16 . A . . . DP=40;AD=39 DP 20 20 +3 17 . G . . . DP=40;AD=40 DP 20 20 +3 18 . C . . . DP=40;AD=40 DP 20 20 +3 19 . A . . . DP=40;AD=40 DP 20 20 +3 20 . T . . . DP=40;AD=40 DP 20 20 +3 21 . C . . . DP=40;AD=40 DP 20 20 +3 22 . A . . . DP=40;AD=40 DP 20 20 +3 23 . A . . . DP=40;AD=40 DP 20 20 +3 24 . T . . . DP=40;AD=40 DP 20 20 +3 25 . T . . . DP=40;AD=40 DP 20 20 +3 26 . C . . . DP=40;AD=40 DP 20 20 +3 27 . T . . . DP=40;AD=40 DP 20 20 +3 28 . A . . . DP=40;AD=40 DP 20 20 +3 29 . A . . . DP=40;AD=40 DP 20 20 +3 30 . A . . . DP=40;AD=40 DP 20 20 +3 31 . A . . . DP=40;AD=40 DP 20 20 +3 32 . A . . . DP=40;AD=40 DP 20 20 +3 33 . T . . . DP=40;AD=40 DP 20 20 +3 34 . G . . . DP=40;AD=40 DP 20 20 +3 35 . A . . . DP=40;AD=40 DP 20 20 +3 36 . C . . . DP=40;AD=40 DP 20 20 +3 37 . T . . . DP=40;AD=40 DP 20 20 +3 38 . A . . . DP=40;AD=40 DP 20 20 +3 39 . C . . . DP=40;AD=40 DP 20 20 +3 40 . C . . . DP=40;AD=40 DP 20 20 +3 41 . A . . . DP=40;AD=40 DP 20 20 +3 42 . G . . . DP=40;AD=40 DP 20 20 +3 43 . A . . . DP=40;AD=40 DP 20 20 +3 44 . G . . . DP=40;AD=40 DP 20 20 +3 45 . A . . . DP=40;AD=40 DP 20 20 +3 46 . G . . . DP=40;AD=40 DP 20 20 +3 47 . A . . . DP=40;AD=40 DP 20 20 +3 48 . C . . . DP=40;AD=40 DP 20 20 +3 49 . A . . . DP=40;AD=40 DP 20 20 +3 50 . A . . . DP=40;AD=40 DP 20 20 +3 51 . C . . . DP=40;AD=40 DP 20 20 +3 52 . T . . . DP=40;AD=40 DP 20 20 +3 53 . C . . . DP=40;AD=40 DP 20 20 +3 54 . C . . . DP=40;AD=40 DP 20 20 +3 55 . G . . . DP=40;AD=40 DP 20 20 +3 56 . C . . . DP=40;AD=40 DP 20 20 +3 57 . A . . . DP=40;AD=40 DP 20 20 +3 58 . G . . . DP=40;AD=40 DP 20 20 +3 59 . T . . . DP=40;AD=40 DP 20 20 +3 60 . T . . . DP=40;AD=39 DP 20 20 +3 61 . A . . . DP=40;AD=40 DP 20 20 +3 62 . A . . . DP=40;AD=40 DP 20 20 +3 63 . A . . . DP=40;AD=40 DP 20 20 +3 64 . C . . . DP=40;AD=40 DP 20 20 +3 65 . A . . . DP=40;AD=40 DP 20 20 +3 66 . C . . . DP=40;AD=40 DP 20 20 +3 67 . T . . . DP=40;AD=40 DP 20 20 +3 68 . C . . . DP=40;AD=40 DP 20 20 +3 69 . T . . . DP=40;AD=40 DP 20 20 +3 70 . G . . . DP=40;AD=40 DP 20 20 +3 71 . A . . . DP=40;AD=40 DP 20 20 +3 72 . C . . . DP=40;AD=40 DP 20 20 +3 73 . T . . . DP=40;AD=40 DP 20 20 +3 74 . G . . . DP=40;AD=40 DP 20 20 +3 75 . C . . . DP=40;AD=40 DP 20 20 +3 76 . C . . . DP=40;AD=40 DP 20 20 +3 77 . A . . . DP=40;AD=40 DP 20 20 +3 78 . C . . . DP=40;AD=40 DP 20 20 +3 79 . G . . . DP=40;AD=40 DP 20 20 +3 80 . C . . . DP=40;AD=40 DP 20 20 +3 81 . C . . . DP=40;AD=40 DP 20 20 +3 82 . A . . . DP=40;AD=40 DP 20 20 +3 83 . G . . . DP=40;AD=40 DP 20 20 +3 84 . C . . . DP=40;AD=40 DP 20 20 +3 85 . T . . . DP=40;AD=40 DP 20 20 +3 86 . A . . . DP=40;AD=40 DP 20 20 +3 87 . C . . . DP=40;AD=40 DP 20 20 +3 88 . C . . . DP=40;AD=40 DP 20 20 +3 89 . T . . . DP=40;AD=40 DP 20 20 +3 90 . C . . . DP=40;AD=40 DP 20 20 +3 91 . T . . . DP=40;AD=39 DP 20 20 +3 92 . A . . . DP=40;AD=40 DP 20 20 +3 93 . G . . . DP=40;AD=40 DP 20 20 +3 94 . A . . . DP=40;AD=40 DP 20 20 +3 105 . G . . . DP=30;AD=30 DP 17 13 +3 106 . G . . . DP=30;AD=30 DP 17 13 +3 107 . C . . . DP=30;AD=30 DP 17 13 +3 108 . T . . . DP=30;AD=30 DP 17 13 +3 109 . G . . . DP=30;AD=30 DP 17 13 +3 110 . C . . . DP=30;AD=30 DP 17 13 +3 111 . T . . . DP=30;AD=30 DP 17 13 +3 112 . G . . . DP=30;AD=30 DP 17 13 +3 113 . G . . . DP=30;AD=30 DP 17 13 +3 114 . A . . . DP=30;AD=30 DP 17 13 +3 115 . C . . . DP=30;AD=30 DP 17 13 +3 116 . G . . . DP=30;AD=30 DP 17 13 +3 117 . T . . . DP=30;AD=30 DP 17 13 +3 118 . C . . . DP=30;AD=30 DP 17 13 +3 119 . C . . . DP=30;AD=30 DP 17 13 +3 120 . T . . . DP=30;AD=30 DP 17 13 +3 121 . T . . . DP=30;AD=30 DP 17 13 +3 122 . C . . . DP=30;AD=30 DP 17 13 +3 123 . G . . . DP=30;AD=30 DP 17 13 +3 124 . C . . . DP=30;AD=30 DP 17 13 +3 125 . T . . . DP=30;AD=30 DP 17 13 +3 126 . C . . . DP=30;AD=30 DP 17 13 +3 127 . G . . . DP=30;AD=30 DP 17 13 +3 128 . G . . . DP=30;AD=30 DP 17 13 +3 129 . T . . . DP=30;AD=30 DP 17 13 +3 130 . A . . . DP=30;AD=30 DP 17 13 +3 131 . C . . . DP=30;AD=30 DP 17 13 +3 132 . C . . . DP=30;AD=29 DP 17 13 +3 133 . T . . . DP=30;AD=30 DP 17 13 +3 134 . T . . . DP=30;AD=30 DP 17 13 +3 135 . G . . . DP=30;AD=30 DP 17 13 +3 136 . A . . . DP=30;AD=30 DP 17 13 +3 137 . C . . . DP=30;AD=30 DP 17 13 +3 138 . T . . . DP=30;AD=30 DP 17 13 +3 139 . G . . . DP=30;AD=30 DP 17 13 +3 140 . G . . . DP=30;AD=30 DP 17 13 +3 141 . A . . . DP=30;AD=30 DP 17 13 +3 142 . T . . . DP=30;AD=30 DP 17 13 +3 143 . T . . . DP=30;AD=30 DP 17 13 +3 144 . A . . . DP=30;AD=30 DP 17 13 +3 145 . T C 40 . DP=30;AD=16,14;AF=0.467 GT:PS:FT:GQ:DP:AD:GL 1|0:145:.:40:17:8,9:-20.29,0.00,-17.57 1|0:145:.:40:13:8,5:-10.39,-0.00,-18.77 +3 146 . A . . . DP=30;AD=30 DP 17 13 +3 147 . T . . . DP=30;AD=30 DP 17 13 +3 148 . A . . . DP=30;AD=30 DP 17 13 +3 149 . G . . . DP=30;AD=30 DP 17 13 +3 150 . C . . . DP=30;AD=30 DP 17 13 +3 151 . A . . . DP=30;AD=30 DP 17 13 +3 152 . T . . . DP=30;AD=30 DP 17 13 +3 153 . T . . . DP=30;AD=30 DP 17 13 +3 154 . C . . . DP=30;AD=30 DP 17 13 +3 155 . C . . . DP=30;AD=30 DP 17 13 +3 156 . T . . . DP=30;AD=29 DP 17 13 +3 157 . T G 40 . DP=30;AD=16,14;AF=0.467 GT:PS:FT:GQ:DP:AD:GL 1|0:145:.:40:17:8,9:-20.29,0.00,-17.57 1|0:145:.:40:13:8,5:-10.39,-0.00,-18.77 +3 158 . A . . . DP=30;AD=30 DP 17 13 +3 159 . G . . . DP=30;AD=30 DP 17 13 +3 160 . T . . . DP=30;AD=30 DP 17 13 +3 161 . T . . . DP=30;AD=30 DP 17 13 +3 162 . C . . . DP=30;AD=30 DP 17 13 +3 163 . A . . . DP=30;AD=30 DP 17 13 +3 164 . C . . . DP=30;AD=30 DP 17 13 +3 165 . G . . . DP=30;AD=30 DP 17 13 +3 166 . G . . . DP=30;AD=30 DP 17 13 +3 167 . C . . . DP=30;AD=30 DP 17 13 +3 168 . C . . . DP=30;AD=30 DP 17 13 +3 169 . A . . . DP=30;AD=30 DP 17 13 +3 170 . A . . . DP=30;AD=30 DP 17 13 +3 171 . T . . . DP=30;AD=30 DP 17 13 +3 172 . A . . . DP=30;AD=30 DP 17 13 +3 173 . T . . . DP=30;AD=30 DP 17 13 +3 174 . C . . . DP=30;AD=30 DP 17 13 +3 175 . G . . . DP=30;AD=30 DP 17 13 +3 176 . C . . . DP=30;AD=30 DP 17 13 +3 177 . C . . . DP=30;AD=30 DP 17 13 +3 178 . A . . . DP=30;AD=30 DP 17 13 +3 179 . A . . . DP=30;AD=30 DP 17 13 +3 180 . C . . . DP=30;AD=30 DP 17 13 +3 181 . C . . . DP=30;AD=30 DP 17 13 +3 182 . G . . . DP=30;AD=30 DP 17 13 +3 183 . T . . . DP=30;AD=30 DP 17 13 +3 184 . T . . . DP=30;AD=30 DP 17 13 +3 185 . G . . . DP=30;AD=30 DP 17 13 +3 186 . A . . . DP=30;AD=30 DP 17 13 +3 187 . G . . . DP=30;AD=30 DP 17 13 +3 188 . T . . . DP=30;AD=30 DP 17 13 +3 189 . G . . . DP=30;AD=30 DP 17 13 +3 190 . A . . . DP=30;AD=30 DP 17 13 +3 191 . G . . . DP=30;AD=30 DP 17 13 +3 192 . T . . . DP=30;AD=30 DP 17 13 +3 193 . T . . . DP=30;AD=30 DP 17 13 +3 194 . T . . . DP=30;AD=30 DP 17 13 +3 195 . A . . . DP=30;AD=30 DP 17 13 +3 196 . G . . . DP=30;AD=30 DP 17 13 +3 197 . T . . . DP=30;AD=30 DP 17 13 +3 198 . G . . . DP=30;AD=30 DP 17 13 +3 199 . A . . . DP=30;AD=30 DP 17 13 +3 200 . A . . . DP=30;AD=30 DP 17 13 +3 201 . C . . . DP=30;AD=30 DP 17 13 +3 202 . C . . . DP=30;AD=30 DP 17 13 +3 203 . G . . . DP=30;AD=30 DP 17 13 +3 204 . G . . . DP=30;AD=30 DP 17 13
--- a/test-data/gstacks/gstacks.log Wed Feb 27 10:03:16 2019 -0500 +++ b/test-data/gstacks/gstacks.log Thu Jun 20 08:18:09 2019 -0400 @@ -1,11 +1,11 @@ -gstacks v2.3b, executed 2019-02-22 12:51:51 -gstacks -P bam_inputs -M /tmp/tmpZcvUSM/files/000/dataset_3.dat -O stacks_outputs -t 1 --model marukilow --var-alpha 0.01 --gt-alpha 0.05 +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: '/tmp/tmpZcvUSM/files/000/dataset_3.dat' - Input files: 2, e.g. 'bam_inputs/PopA_01.matches.bam' + 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)
--- a/test-data/gstacks/gstacks.log.distribs Wed Feb 27 10:03:16 2019 -0500 +++ b/test-data/gstacks/gstacks.log.distribs Thu Jun 20 08:18:09 2019 -0400 @@ -19,25 +19,25 @@ Num. threads: 1 Parallel time: 0.0 Average thread time spent: - 0.0 reading (2.9%) - 0.0 processing (95.7%) - 0.0 pre-alignments block (69.1%) - 0.0 reformatting fw-reads (0.2%) - 0.0 assembling (21.2%) - 0.0 initializing alignments (4.4%) - 0.0 aligning (41.3%) - 0.0 merging read pairs (2.0%) - 0.0 post-alignments block (25.2%) + 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 (4.0%) + 0.0 counting nucleotides (3.5%) 0.0 genotyping (1.9%) - 0.0 haplotyping (1.2%) + 0.0 haplotyping (1.0%) 0.0 computing consensus (0.1%) 0.0 building_fa (0.1%) - 0.0 building_vcf (17.8%) + 0.0 building_vcf (14.6%) 0.0 writing_fa (0.1%) - 0.0 writing_vcf (1.0%) + 0.0 writing_vcf (1.3%) 0.0 clocking (0.2%) -Total time spent writing vcf: 0.0 (1.0%) +Total time spent writing vcf: 0.0 (1.3%) VCFwrite block size: mean=1.0(n=3); max=1 END clockings
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/kmerfilter/kmerfilter.log Thu Jun 20 08:18:09 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.
--- a/test-data/populations/populations.fixed.phylip Wed Feb 27 10:03:16 2019 -0500 +++ b/test-data/populations/populations.fixed.phylip Thu Jun 20 08:18:09 2019 -0400 @@ -1,3 +1,3 @@ 1 0 1 -# Stacks v2.3b; Phylip sequential; February 25, 2019 +# Stacks v2.4; Phylip sequential; June 17, 2019
--- a/test-data/populations/populations.fixed.phylip.log Wed Feb 27 10:03:16 2019 -0500 +++ b/test-data/populations/populations.fixed.phylip.log Thu Jun 20 08:18:09 2019 -0400 @@ -1,2 +1,2 @@ -# Stacks v2.3b; Phylip sequential; February 25, 2019 +# Stacks v2.4; Phylip sequential; June 17, 2019 # Seq Pos Locus ID Column Population
--- a/test-data/populations/populations.haplotypes.tsv Wed Feb 27 10:03:16 2019 -0500 +++ b/test-data/populations/populations.haplotypes.tsv Thu Jun 20 08:18:09 2019 -0400 @@ -1,4 +1,4 @@ # Catalog Locus ID Cnt PopA_01 PopA_02 -1 0 AC/CA AC/CA -2 0 CG/TT CG/TT -3 0 GG/GG AA/GG +1 2 AC/CA AC/CA +2 2 GG/GG AA/GG +3 2 CG/TT CG/TT
--- a/test-data/populations/populations.haps.genepop Wed Feb 27 10:03:16 2019 -0500 +++ b/test-data/populations/populations.haps.genepop Thu Jun 20 08:18:09 2019 -0400 @@ -1,4 +1,4 @@ -Stacks v2.3b; GenePop v4.1.3; February 25, 2019 +Stacks v2.4; GenePop v4.1.3; June 17, 2019 1,2,3 pop PopA_01, 0102 0102 0101
--- a/test-data/populations/populations.haps.vcf Wed Feb 27 10:03:16 2019 -0500 +++ b/test-data/populations/populations.haps.vcf Thu Jun 20 08:18:09 2019 -0400 @@ -1,6 +1,6 @@ ##fileformat=VCFv4.2 -##fileDate=20190225 -##source="Stacks v2.3b" +##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">
--- a/test-data/populations/populations.hapstats.tsv Wed Feb 27 10:03:16 2019 -0500 +++ b/test-data/populations/populations.hapstats.tsv Thu Jun 20 08:18:09 2019 -0400 @@ -1,5 +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 -201 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 3 1 4 2 0.66667 0.00000 0.00000 1.33333 0.00000 0.00000 0.00000 0.00000 CG:2;TT:2 -3 un 206 1 4 2 0.50000 0.00000 0.00000 1.00000 0.00000 0.00000 0.00000 0.00000 AA:1;GG:3 +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
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/populations/populations.hzar.csv Thu Jun 20 08:18:09 2019 -0400 @@ -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
--- a/test-data/populations/populations.loci.fa Wed Feb 27 10:03:16 2019 -0500 +++ b/test-data/populations/populations.loci.fa Thu Jun 20 08:18:09 2019 -0400 @@ -1,4 +1,4 @@ -Stacks version 2.3b; February 25, 2019 +# Stacks version 2.4; June 17, 2019 >CLocus_1 AATTCGTTTGCTGCTTCAGGAATCTCTCGTATAATCTGAGTATGTGCGTACGTACGCTATTTAGATGGATAACCGACGCTGCCAGACGAGAGACNNNNNNNNNNCGTCAGAGGGCTTATATCGTGAGTGATAGCAGCAGTTTCTCTCTACCACATAGTTATACACCATTGGGCCAGCTCGTTGAAAACTACTGATGCTGATCGG >CLocus_2
--- a/test-data/populations/populations.log Wed Feb 27 10:03:16 2019 -0500 +++ b/test-data/populations/populations.log Thu Jun 20 08:18:09 2019 -0400 @@ -1,5 +1,5 @@ -populations v2.3b, executed 2019-02-25 23:06:32 -populations -t 1 -P stacks_inputs -O stacks_outputs -M /tmp/tmp4FNQre/files/000/dataset_3.dat -p 1 -r 0.0 --min_maf 0.0 --min_mac 0 --merge_prune_lim 1.0 +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
--- a/test-data/populations/populations.log.distribs Wed Feb 27 10:03:16 2019 -0500 +++ b/test-data/populations/populations.log.distribs Thu Jun 20 08:18:09 2019 -0400 @@ -8,14 +8,13 @@ BEGIN samples_per_loc_prefilters # Distribution of valid samples matched to a catalog locus prior to filtering. n_samples n_loci -0 3 +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 -2 3 +0 3 END missing_samples_per_loc_prefilters BEGIN snps_per_loc_prefilters @@ -27,14 +26,13 @@ BEGIN samples_per_loc_postfilters # Distribution of valid samples matched to a catalog locus after filtering. n_samples n_loci -0 3 +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 -2 3 +0 3 END missing_samples_per_loc_postfilters BEGIN snps_per_loc_postfilters
--- a/test-data/populations/populations.markers.tsv Wed Feb 27 10:03:16 2019 -0500 +++ b/test-data/populations/populations.markers.tsv Thu Jun 20 08:18:09 2019 -0400 @@ -1,4 +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 2 100.00000 ab:2(100.0%); 0.00000 1.00000 CG:a;TT:b; -3 2 50.00000 aa:1(50.0%);ab:1(50.0%); 0.00000 1.00000 AA:b;GG:a; +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;
--- a/test-data/populations/populations.plink.map Wed Feb 27 10:03:16 2019 -0500 +++ b/test-data/populations/populations.plink.map Thu Jun 20 08:18:09 2019 -0400 @@ -1,7 +1,7 @@ -# Stacks v2.3b; PLINK v1.07; February 25, 2019 -un 1_33 0 35 -un 1_88 0 90 -un 2_144 0 350 -un 2_156 0 362 -un 3_162 0 572 -un 3_181 0 591 +# 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
--- a/test-data/populations/populations.plink.ped Wed Feb 27 10:03:16 2019 -0500 +++ b/test-data/populations/populations.plink.ped Thu Jun 20 08:18:09 2019 -0400 @@ -1,3 +1,3 @@ -# Stacks v2.3b; PLINK v1.07; February 25, 2019 +# 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
--- a/test-data/populations/populations.samples-raw.fa Wed Feb 27 10:03:16 2019 -0500 +++ b/test-data/populations/populations.samples-raw.fa Thu Jun 20 08:18:09 2019 -0400 @@ -1,4 +1,4 @@ -Stacks version 2.3b; February 25, 2019 +# 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]
--- a/test-data/populations/populations.samples.fa Wed Feb 27 10:03:16 2019 -0500 +++ b/test-data/populations/populations.samples.fa Thu Jun 20 08:18:09 2019 -0400 @@ -1,4 +1,4 @@ -Stacks version 2.3b; February 25, 2019 +# 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]
--- a/test-data/populations/populations.snps.genepop Wed Feb 27 10:03:16 2019 -0500 +++ b/test-data/populations/populations.snps.genepop Thu Jun 20 08:18:09 2019 -0400 @@ -1,4 +1,4 @@ -# Stacks v2.3b; GenePop v4.1.3; February 25, 2019 +# 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
--- a/test-data/populations/populations.snps.vcf Wed Feb 27 10:03:16 2019 -0500 +++ b/test-data/populations/populations.snps.vcf Thu Jun 20 08:18:09 2019 -0400 @@ -1,6 +1,6 @@ ##fileformat=VCFv4.2 -##fileDate=20190225 -##source="Stacks v2.3b" +##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">
--- a/test-data/populations/populations.structure Wed Feb 27 10:03:16 2019 -0500 +++ b/test-data/populations/populations.structure Thu Jun 20 08:18:09 2019 -0400 @@ -1,4 +1,4 @@ -# Stacks v2.3b; Structure v2.3; February 25, 2019 +# 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
--- a/test-data/populations/populations.sumstats.tsv Wed Feb 27 10:03:16 2019 -0500 +++ b/test-data/populations/populations.sumstats.tsv Thu Jun 20 08:18:09 2019 -0400 @@ -1,8 +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 35 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 90 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 350 144 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 -2 un 362 156 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 -3 un 572 162 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 -3 un 591 181 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 +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
--- a/test-data/populations/populations.treemix Wed Feb 27 10:03:16 2019 -0500 +++ b/test-data/populations/populations.treemix Thu Jun 20 08:18:09 2019 -0400 @@ -1,3 +1,4 @@ +# Stacks v2.4; TreeMix v1.1; June 17, 2019 1 2,2 2,2
--- a/test-data/populations/populations.var.phylip Wed Feb 27 10:03:16 2019 -0500 +++ b/test-data/populations/populations.var.phylip Thu Jun 20 08:18:09 2019 -0400 @@ -1,3 +1,3 @@ 1 6 1 MMYKRR -# Stacks v2.3b; Phylip sequential; February 25, 2019 +# Stacks v2.4; Phylip sequential; June 17, 2019
--- a/test-data/populations/populations.var.phylip.log Wed Feb 27 10:03:16 2019 -0500 +++ b/test-data/populations/populations.var.phylip.log Thu Jun 20 08:18:09 2019 -0400 @@ -1,4 +1,4 @@ -# Stacks v2.3b; Phylip sequential; February 25, 2019 +# Stacks v2.4; Phylip sequential; June 17, 2019 # Seq Pos Locus ID Column Population 0 1 33 1:M, 1 1 88 1:M,
--- a/test-data/refmap/catalog.calls.vcf Wed Feb 27 10:03:16 2019 -0500 +++ b/test-data/refmap/catalog.calls.vcf Thu Jun 20 08:18:09 2019 -0400 @@ -1,6 +1,6 @@ ##fileformat=VCFv4.2 -##fileDate=20190225 -##source="Stacks v2.3b" +##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">
--- a/test-data/refmap/populations.haplotypes.tsv Wed Feb 27 10:03:16 2019 -0500 +++ b/test-data/refmap/populations.haplotypes.tsv Thu Jun 20 08:18:09 2019 -0400 @@ -1,14 +1,14 @@ # Catalog Locus ID Cnt PopA_01 PopA_02 -1 0 consensus consensus -2 0 consensus consensus -3 0 consensus consensus -4 0 consensus consensus -5 0 consensus consensus -6 0 consensus consensus -7 0 consensus consensus -8 0 consensus consensus -9 0 consensus consensus -10 0 AC/CA AC/CA -11 0 consensus consensus -12 0 AC/CA AC/CA -13 0 AC/CA AC/CA +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
--- a/test-data/refmap/populations.hapstats.tsv Wed Feb 27 10:03:16 2019 -0500 +++ b/test-data/refmap/populations.hapstats.tsv Thu Jun 20 08:18:09 2019 -0400 @@ -1,5 +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 -92 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 -92 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 -92 1 4 2 0.66667 0.00000 0.00000 1.33333 0.00000 0.00000 0.00000 0.00000 AC:2;CA:2 +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
--- a/test-data/refmap/populations.log.distribs Wed Feb 27 10:03:16 2019 -0500 +++ b/test-data/refmap/populations.log.distribs Thu Jun 20 08:18:09 2019 -0400 @@ -21,14 +21,13 @@ BEGIN samples_per_loc_prefilters # Distribution of valid samples matched to a catalog locus prior to filtering. n_samples n_loci -0 13 +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 -2 13 +0 13 END missing_samples_per_loc_prefilters BEGIN snps_per_loc_prefilters @@ -41,14 +40,13 @@ BEGIN samples_per_loc_postfilters # Distribution of valid samples matched to a catalog locus after filtering. n_samples n_loci -0 13 +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 -2 13 +0 13 END missing_samples_per_loc_postfilters BEGIN snps_per_loc_postfilters
--- a/test-data/sstacks/PopA_01.matches.tsv Wed Feb 27 10:03:16 2019 -0500 +++ b/test-data/sstacks/PopA_01.matches.tsv Thu Jun 20 08:18:09 2019 -0400 @@ -1,5 +1,5 @@ -# sstacks version 2.3b; generated on 2019-02-21 19:57:38 +# 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 20 94M -3 1 3 consensus 28 94M +2 1 2 consensus 28 94M +3 1 3 consensus 20 94M
--- a/test-data/sstacks/PopA_02.matches.tsv Wed Feb 27 10:03:16 2019 -0500 +++ b/test-data/sstacks/PopA_02.matches.tsv Thu Jun 20 08:18:09 2019 -0400 @@ -1,5 +1,5 @@ -# sstacks version 2.3b; generated on 2019-02-21 19:57:38 +# sstacks version 2.4; generated on 2019-06-18 10:34:45 1 2 1 AC 6 94M 1 2 1 CA 6 94M -3 2 2 consensus 28 94M -2 2 3 consensus 20 94M +2 2 2 consensus 28 94M +3 2 3 consensus 20 94M
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/stacks_outputs/tsv2bam.log Thu Jun 20 08:18:09 2019 -0400 @@ -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.
--- a/test-data/tsv2bam/tsv2bam.log Wed Feb 27 10:03:16 2019 -0500 +++ b/test-data/tsv2bam/tsv2bam.log Thu Jun 20 08:18:09 2019 -0400 @@ -1,14 +1,17 @@ -tsv2bam v2.2, executed 2018-11-27 13:20:44 -tsv2bam -P stacks_inputs -s PopA_01 -s PopA_02 -t 1 +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_inputs/' + 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; wrote 66 records. -Sample 'PopA_02': matched 3 sample loci to 3 catalog loci; wrote 60 records. +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.
--- a/test-data/ustacks/PopA_01.alleles.tsv Wed Feb 27 10:03:16 2019 -0500 +++ b/test-data/ustacks/PopA_01.alleles.tsv Thu Jun 20 08:18:09 2019 -0400 @@ -1,3 +1,3 @@ -# ustacks version 2.3b; generated on 2019-02-21 19:57:38 +# ustacks version 2.4; generated on 2019-06-18 10:34:45 1 1 AC 50.00 9 1 1 CA 50.00 9
--- a/test-data/ustacks/PopA_01.snps.tsv Wed Feb 27 10:03:16 2019 -0500 +++ b/test-data/ustacks/PopA_01.snps.tsv Thu Jun 20 08:18:09 2019 -0400 @@ -1,4 +1,4 @@ -# ustacks version 2.3b; generated on 2019-02-21 19:57:38 +# 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 - @@ -93,191 +93,191 @@ 1 1 91 O 24.95 G - 1 1 92 O 24.95 A - 1 1 93 O 24.95 C - -1 2 0 O 27.73 A - -1 2 1 O 27.73 A - -1 2 2 O 27.73 T - -1 2 3 O 27.73 T - -1 2 4 O 27.73 C - -1 2 5 O 27.73 T - -1 2 6 O 27.73 C - -1 2 7 O 27.73 T - -1 2 8 O 27.73 A - -1 2 9 O 27.73 C - -1 2 10 O 27.73 A - -1 2 11 O 27.73 C - -1 2 12 O 27.73 C - -1 2 13 O 27.73 A - -1 2 14 O 27.73 C - -1 2 15 O 27.73 A - -1 2 16 O 27.73 G - -1 2 17 O 27.73 C - -1 2 18 O 27.73 A - -1 2 19 O 27.73 T - -1 2 20 O 27.73 C - -1 2 21 O 27.73 A - -1 2 22 O 27.73 A - -1 2 23 O 27.73 T - -1 2 24 O 27.73 T - -1 2 25 O 27.73 C - -1 2 26 O 27.73 T - -1 2 27 O 27.73 A - -1 2 28 O 27.73 A - -1 2 29 O 27.73 A - -1 2 30 O 27.73 A - 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+1 2 45 O 38.82 T - +1 2 46 O 38.82 C - +1 2 47 O 38.82 T - +1 2 48 O 38.82 A - +1 2 49 O 38.82 A - +1 2 50 O 38.82 G - +1 2 51 O 38.82 T - +1 2 52 O 38.82 A - +1 2 53 O 38.82 A - +1 2 54 O 38.82 C - +1 2 55 O 38.82 T - +1 2 56 O 38.82 T - +1 2 57 O 38.82 C - +1 2 58 O 38.82 C - +1 2 59 O 38.82 A - +1 2 60 O 38.82 A - +1 2 61 O 27.99 A - +1 2 62 O 38.82 T - +1 2 63 O 38.82 C - +1 2 64 O 38.82 T - +1 2 65 O 38.82 G - +1 2 66 O 38.82 G - +1 2 67 O 38.82 G - +1 2 68 O 38.82 A - +1 2 69 O 38.82 A - +1 2 70 O 38.82 T - +1 2 71 O 38.82 G - +1 2 72 O 38.82 G - +1 2 73 O 38.82 G - +1 2 74 O 38.82 A - +1 2 75 O 38.82 T - +1 2 76 O 38.82 T - +1 2 77 O 38.82 T - +1 2 78 O 38.82 C - +1 2 79 O 38.82 A - +1 2 80 O 38.82 T - +1 2 81 O 38.82 A - +1 2 82 O 38.82 A - +1 2 83 O 38.82 T - +1 2 84 O 38.82 T - +1 2 85 O 38.82 A - +1 2 86 O 38.82 A - +1 2 87 O 38.82 G - +1 2 88 O 38.82 G - +1 2 89 O 38.82 A - +1 2 90 O 38.82 C - +1 2 91 O 38.82 T - +1 2 92 O 38.82 A - +1 2 93 O 38.82 T - +1 3 0 O 27.73 A - +1 3 1 O 27.73 A - +1 3 2 O 27.73 T - +1 3 3 O 27.73 T - +1 3 4 O 27.73 C - +1 3 5 O 27.73 T - +1 3 6 O 27.73 C - +1 3 7 O 27.73 T - +1 3 8 O 27.73 A - +1 3 9 O 27.73 C - +1 3 10 O 27.73 A - +1 3 11 O 27.73 C - +1 3 12 O 27.73 C - +1 3 13 O 27.73 A - +1 3 14 O 27.73 C - +1 3 15 O 27.73 A - +1 3 16 O 27.73 G - +1 3 17 O 27.73 C - +1 3 18 O 27.73 A - +1 3 19 O 27.73 T - +1 3 20 O 27.73 C - +1 3 21 O 27.73 A - +1 3 22 O 27.73 A - +1 3 23 O 27.73 T - +1 3 24 O 27.73 T - +1 3 25 O 27.73 C - +1 3 26 O 27.73 T - +1 3 27 O 27.73 A - +1 3 28 O 27.73 A - +1 3 29 O 27.73 A - +1 3 30 O 27.73 A - +1 3 31 O 27.73 A - +1 3 32 O 27.73 T - +1 3 33 O 27.73 G - +1 3 34 O 27.73 A - +1 3 35 O 27.73 C - +1 3 36 O 27.73 T - +1 3 37 O 27.73 A - +1 3 38 O 27.73 C - +1 3 39 O 27.73 C - +1 3 40 O 27.73 A - +1 3 41 O 27.73 G - +1 3 42 O 27.73 A - +1 3 43 O 27.73 G - +1 3 44 O 27.73 A - +1 3 45 O 27.73 G - +1 3 46 O 27.73 A - +1 3 47 O 27.73 C - +1 3 48 O 27.73 A - +1 3 49 O 27.73 A - +1 3 50 O 27.73 C - +1 3 51 O 27.73 T - +1 3 52 O 27.73 C - +1 3 53 O 27.73 C - +1 3 54 O 27.73 G - +1 3 55 O 27.73 C - +1 3 56 O 27.73 A - +1 3 57 O 27.73 G - +1 3 58 O 27.73 T - +1 3 59 O 17.59 T - +1 3 60 O 27.73 A - +1 3 61 O 27.73 A - +1 3 62 O 27.73 A - +1 3 63 O 27.73 C - +1 3 64 O 27.73 A - +1 3 65 O 27.73 C - +1 3 66 O 27.73 T - +1 3 67 O 27.73 C - +1 3 68 O 27.73 T - +1 3 69 O 27.73 G - +1 3 70 O 27.73 A - +1 3 71 O 27.73 C - +1 3 72 O 27.73 T - +1 3 73 O 27.73 G - +1 3 74 O 27.73 C - +1 3 75 O 27.73 C - +1 3 76 O 27.73 A - +1 3 77 O 27.73 C - +1 3 78 O 27.73 G - +1 3 79 O 27.73 C - +1 3 80 O 27.73 C - +1 3 81 O 27.73 A - +1 3 82 O 27.73 G - +1 3 83 O 27.73 C - +1 3 84 O 27.73 T - +1 3 85 O 27.73 A - +1 3 86 O 27.73 C - +1 3 87 O 27.73 C - +1 3 88 O 27.73 T - +1 3 89 O 27.73 C - +1 3 90 O 17.59 T - +1 3 91 O 27.73 A - +1 3 92 O 27.73 G - +1 3 93 O 27.73 A -
--- a/test-data/ustacks/PopA_01.tags.tsv Wed Feb 27 10:03:16 2019 -0500 +++ b/test-data/ustacks/PopA_01.tags.tsv Thu Jun 20 08:18:09 2019 -0400 @@ -1,73 +1,73 @@ -# ustacks version 2.3b; generated on 2019-02-21 19:57:38 +# ustacks version 2.4; generated on 2019-06-18 10:34:45 1 1 consensus AATTCGTTTGCTGCTTCAGGAATCTCTCGTATAATCTGAGTATGTGCGTACGTACGCTATTTAGATGGATAACCGACGCTGCCAGACGAGAGAC 0 0 0 1 1 model OOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOEOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOEOOOOO -1 1 primary 0 lane1_fakedata7_9 1:N:0:/1 AATTCGTTTGCTGCTTCAGGAATCTCTCGTATAATCTGAGTATGTGCGTACGTACGCTATTTAGATGGATAACCGACGCTGCCAGACGCGAGAC -1 1 primary 0 lane1_fakedata7_10 1:N:0:/1 AATTCGTTTGCTGCTTCAGGAATCTCTCGTATAATCTGAGTATGTGCGTACGTACGCTATTTAGATGGATAACCGACGCTGCCAGACGCGAGAC -1 1 primary 0 lane1_fakedata7_11 1:N:0:/1 AATTCGTTTGCTGCTTCAGGAATCTCTCGTATAATCTGAGTATGTGCGTACGTACGCTATTTAGATGGATAACCGACGCTGCCAGACGCGAGAC -1 1 primary 0 lane1_fakedata7_12 1:N:0:/1 AATTCGTTTGCTGCTTCAGGAATCTCTCGTATAATCTGAGTATGTGCGTACGTACGCTATTTAGATGGATAACCGACGCTGCCAGACGCGAGAC -1 1 primary 0 lane1_fakedata7_13 1:N:0:/1 AATTCGTTTGCTGCTTCAGGAATCTCTCGTATAATCTGAGTATGTGCGTACGTACGCTATTTAGATGGATAACCGACGCTGCCAGACGCGAGAC -1 1 primary 0 lane1_fakedata7_14 1:N:0:/1 AATTCGTTTGCTGCTTCAGGAATCTCTCGTATAATCTGAGTATGTGCGTACGTACGCTATTTAGATGGATAACCGACGCTGCCAGACGCGAGAC -1 1 primary 0 lane1_fakedata7_15 1:N:0:/1 AATTCGTTTGCTGCTTCAGGAATCTCTCGTATAATCTGAGTATGTGCGTACGTACGCTATTTAGATGGATAACCGACGCTGCCAGACGCGAGAC -1 1 primary 0 lane1_fakedata7_16 1:N:0:/1 AATTCGTTTGCTGCTTCAGGAATCTCTCGTATAATCTGAGTATGTGCGTACGTACGCTATTTAGATGGATAACCGACGCTGCCAGACGCGAGAC -1 1 primary 0 lane1_fakedata7_17 1:N:0:/1 AATTCGTTTGCTGCTTCAGGAATCTCTCGTATAATCTGAGTATGTGCGTACGTACGCTATTTAGATGGATAACCGACGCTGCCAGACGCGAGAC -1 1 primary 1 lane1_fakedata7_0 1:N:0:/1 AATTCGTTTGCTGCTTCAGGAATCTCTCGTATACTCTGAGTATGTGCGTACGTACGCTATTTAGATGGATAACCGACGCTGCCAGACGAGAGAC -1 1 primary 1 lane1_fakedata7_1 1:N:0:/1 AATTCGTTTGCTGCTTCAGGAATCTCTCGTATACTCTGAGTATGTGCGTACGTACGCTATTTAGATGGATAACCGACGCTGCCAGACGAGAGAC -1 1 primary 1 lane1_fakedata7_2 1:N:0:/1 AATTCGTTTGCTGCTTCAGGAATCTCTCGTATACTCTGAGTATGTGCGTACGTACGCTATTTAGATGGATAACCGACGCTGCCAGACGAGAGAC -1 1 primary 1 lane1_fakedata7_3 1:N:0:/1 AATTCGTTTGCTGCTTCAGGAATCTCTCGTATACTCTGAGTATGTGCGTACGTACGCTATTTAGATGGATAACCGACGCTGCCAGACGAGAGAC -1 1 primary 1 lane1_fakedata7_4 1:N:0:/1 AATTCGTTTGCTGCTTCAGGAATCTCTCGTATACTCTGAGTATGTGCGTACGTACGCTATTTAGATGGATAACCGACGCTGCCAGACGAGAGAC -1 1 primary 1 lane1_fakedata7_5 1:N:0:/1 AATTCGTTTGCTGCTTCAGGAATCTCTCGTATACTCTGAGTATGTGCGTACGTACGCTATTTAGATGGATAACCGACGCTGCCAGACGAGAGAC -1 1 primary 1 lane1_fakedata7_6 1:N:0:/1 AATTCGTTTGCTGCTTCAGGAATCTCTCGTATACTCTGAGTATGTGCGTACGTACGCTATTTAGATGGATAACCGACGCTGCCAGACGAGAGAC -1 1 primary 1 lane1_fakedata7_7 1:N:0:/1 AATTCGTTTGCTGCTTCAGGAATCTCTCGTATACTCTGAGTATGTGCGTACGTACGCTATTTAGATGGATAACCGACGCTGCCAGACGAGAGAC -1 1 primary 1 lane1_fakedata7_8 1:N:0:/1 AATTCGTTTGCTGCTTCAGGAATCTCTCGTATACTCTGAGTATGTGCGTACGTACGCTATTTAGATGGATAACCGACGCTGCCAGACGAGAGAC -1 2 consensus AATTCTCTACACCACAGCATCAATTCTAAAAATGACTACCAGAGAGACAACTCCGCAGTTAAACACTCTGACTGCCACGCCAGCTACCTCTAGA 0 0 0 +1 1 primary 0 lane1_fakedata7_0 1:N:0:/1 AATTCGTTTGCTGCTTCAGGAATCTCTCGTATACTCTGAGTATGTGCGTACGTACGCTATTTAGATGGATAACCGACGCTGCCAGACGAGAGAC +1 1 primary 0 lane1_fakedata7_1 1:N:0:/1 AATTCGTTTGCTGCTTCAGGAATCTCTCGTATACTCTGAGTATGTGCGTACGTACGCTATTTAGATGGATAACCGACGCTGCCAGACGAGAGAC +1 1 primary 0 lane1_fakedata7_2 1:N:0:/1 AATTCGTTTGCTGCTTCAGGAATCTCTCGTATACTCTGAGTATGTGCGTACGTACGCTATTTAGATGGATAACCGACGCTGCCAGACGAGAGAC +1 1 primary 0 lane1_fakedata7_3 1:N:0:/1 AATTCGTTTGCTGCTTCAGGAATCTCTCGTATACTCTGAGTATGTGCGTACGTACGCTATTTAGATGGATAACCGACGCTGCCAGACGAGAGAC +1 1 primary 0 lane1_fakedata7_4 1:N:0:/1 AATTCGTTTGCTGCTTCAGGAATCTCTCGTATACTCTGAGTATGTGCGTACGTACGCTATTTAGATGGATAACCGACGCTGCCAGACGAGAGAC +1 1 primary 0 lane1_fakedata7_5 1:N:0:/1 AATTCGTTTGCTGCTTCAGGAATCTCTCGTATACTCTGAGTATGTGCGTACGTACGCTATTTAGATGGATAACCGACGCTGCCAGACGAGAGAC +1 1 primary 0 lane1_fakedata7_6 1:N:0:/1 AATTCGTTTGCTGCTTCAGGAATCTCTCGTATACTCTGAGTATGTGCGTACGTACGCTATTTAGATGGATAACCGACGCTGCCAGACGAGAGAC +1 1 primary 0 lane1_fakedata7_7 1:N:0:/1 AATTCGTTTGCTGCTTCAGGAATCTCTCGTATACTCTGAGTATGTGCGTACGTACGCTATTTAGATGGATAACCGACGCTGCCAGACGAGAGAC +1 1 primary 0 lane1_fakedata7_8 1:N:0:/1 AATTCGTTTGCTGCTTCAGGAATCTCTCGTATACTCTGAGTATGTGCGTACGTACGCTATTTAGATGGATAACCGACGCTGCCAGACGAGAGAC +1 1 primary 1 lane1_fakedata7_9 1:N:0:/1 AATTCGTTTGCTGCTTCAGGAATCTCTCGTATAATCTGAGTATGTGCGTACGTACGCTATTTAGATGGATAACCGACGCTGCCAGACGCGAGAC +1 1 primary 1 lane1_fakedata7_10 1:N:0:/1 AATTCGTTTGCTGCTTCAGGAATCTCTCGTATAATCTGAGTATGTGCGTACGTACGCTATTTAGATGGATAACCGACGCTGCCAGACGCGAGAC +1 1 primary 1 lane1_fakedata7_11 1:N:0:/1 AATTCGTTTGCTGCTTCAGGAATCTCTCGTATAATCTGAGTATGTGCGTACGTACGCTATTTAGATGGATAACCGACGCTGCCAGACGCGAGAC +1 1 primary 1 lane1_fakedata7_12 1:N:0:/1 AATTCGTTTGCTGCTTCAGGAATCTCTCGTATAATCTGAGTATGTGCGTACGTACGCTATTTAGATGGATAACCGACGCTGCCAGACGCGAGAC +1 1 primary 1 lane1_fakedata7_13 1:N:0:/1 AATTCGTTTGCTGCTTCAGGAATCTCTCGTATAATCTGAGTATGTGCGTACGTACGCTATTTAGATGGATAACCGACGCTGCCAGACGCGAGAC +1 1 primary 1 lane1_fakedata7_14 1:N:0:/1 AATTCGTTTGCTGCTTCAGGAATCTCTCGTATAATCTGAGTATGTGCGTACGTACGCTATTTAGATGGATAACCGACGCTGCCAGACGCGAGAC +1 1 primary 1 lane1_fakedata7_15 1:N:0:/1 AATTCGTTTGCTGCTTCAGGAATCTCTCGTATAATCTGAGTATGTGCGTACGTACGCTATTTAGATGGATAACCGACGCTGCCAGACGCGAGAC +1 1 primary 1 lane1_fakedata7_16 1:N:0:/1 AATTCGTTTGCTGCTTCAGGAATCTCTCGTATAATCTGAGTATGTGCGTACGTACGCTATTTAGATGGATAACCGACGCTGCCAGACGCGAGAC +1 1 primary 1 lane1_fakedata7_17 1:N:0:/1 AATTCGTTTGCTGCTTCAGGAATCTCTCGTATAATCTGAGTATGTGCGTACGTACGCTATTTAGATGGATAACCGACGCTGCCAGACGCGAGAC +1 2 consensus AATTCGGCTTGCAACGCAAGTGACGATTCCCACGGACATAACTGATCTAAGTAACTTCCAAATCTGGGAATGGGATTTCATAATTAAGGACTAT 0 0 0 1 2 model OOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOO -1 2 primary 0 lane1_fakedata2_0 1:N:0:/1 AATTCTCTACACCACAGCATCAATTCTAAAAATGACTACCAGAGAGACAACTCCGCAGTTAAACACTCTGACTGCCACGCCAGCTACCTCTAGA -1 2 primary 0 lane1_fakedata2_1 1:N:0:/1 AATTCTCTACACCACAGCATCAATTCTAAAAATGACTACCAGAGAGACAACTCCGCAGTTAAACACTCTGACTGCCACGCCAGCTACCTCTAGA -1 2 primary 0 lane1_fakedata2_2 1:N:0:/1 AATTCTCTACACCACAGCATCAATTCTAAAAATGACTACCAGAGAGACAACTCCGCAGTTAAACACTCTGACTGCCACGCCAGCTACCTCTAGA -1 2 primary 0 lane1_fakedata2_3 1:N:0:/1 AATTCTCTACACCACAGCATCAATTCTAAAAATGACTACCAGAGAGACAACTCCGCAGTTAAACACTCTGACTGCCACGCCAGCTACCTCTAGA -1 2 primary 0 lane1_fakedata2_4 1:N:0:/1 AATTCTCTACACCACAGCATCAATTCTAAAAATGACTACCAGAGAGACAACTCCGCAGTTAAACACTCTGACTGCCACGCCAGCTACCTCTAGA -1 2 primary 0 lane1_fakedata2_6 1:N:0:/1 AATTCTCTACACCACAGCATCAATTCTAAAAATGACTACCAGAGAGACAACTCCGCAGTTAAACACTCTGACTGCCACGCCAGCTACCTCTAGA -1 2 primary 0 lane1_fakedata2_7 1:N:0:/1 AATTCTCTACACCACAGCATCAATTCTAAAAATGACTACCAGAGAGACAACTCCGCAGTTAAACACTCTGACTGCCACGCCAGCTACCTCTAGA -1 2 primary 0 lane1_fakedata2_8 1:N:0:/1 AATTCTCTACACCACAGCATCAATTCTAAAAATGACTACCAGAGAGACAACTCCGCAGTTAAACACTCTGACTGCCACGCCAGCTACCTCTAGA -1 2 primary 0 lane1_fakedata2_9 1:N:0:/1 AATTCTCTACACCACAGCATCAATTCTAAAAATGACTACCAGAGAGACAACTCCGCAGTTAAACACTCTGACTGCCACGCCAGCTACCTCTAGA -1 2 primary 0 lane1_fakedata2_10 1:N:0:/1 AATTCTCTACACCACAGCATCAATTCTAAAAATGACTACCAGAGAGACAACTCCGCAGTTAAACACTCTGACTGCCACGCCAGCTACCTCTAGA -1 2 primary 0 lane1_fakedata2_11 1:N:0:/1 AATTCTCTACACCACAGCATCAATTCTAAAAATGACTACCAGAGAGACAACTCCGCAGTTAAACACTCTGACTGCCACGCCAGCTACCTCTAGA -1 2 primary 0 lane1_fakedata2_12 1:N:0:/1 AATTCTCTACACCACAGCATCAATTCTAAAAATGACTACCAGAGAGACAACTCCGCAGTTAAACACTCTGACTGCCACGCCAGCTACCTCTAGA -1 2 primary 0 lane1_fakedata2_13 1:N:0:/1 AATTCTCTACACCACAGCATCAATTCTAAAAATGACTACCAGAGAGACAACTCCGCAGTTAAACACTCTGACTGCCACGCCAGCTACCTCTAGA -1 2 primary 0 lane1_fakedata2_14 1:N:0:/1 AATTCTCTACACCACAGCATCAATTCTAAAAATGACTACCAGAGAGACAACTCCGCAGTTAAACACTCTGACTGCCACGCCAGCTACCTCTAGA -1 2 primary 0 lane1_fakedata2_15 1:N:0:/1 AATTCTCTACACCACAGCATCAATTCTAAAAATGACTACCAGAGAGACAACTCCGCAGTTAAACACTCTGACTGCCACGCCAGCTACCTCTAGA -1 2 primary 0 lane1_fakedata2_16 1:N:0:/1 AATTCTCTACACCACAGCATCAATTCTAAAAATGACTACCAGAGAGACAACTCCGCAGTTAAACACTCTGACTGCCACGCCAGCTACCTCTAGA -1 2 primary 0 lane1_fakedata2_18 1:N:0:/1 AATTCTCTACACCACAGCATCAATTCTAAAAATGACTACCAGAGAGACAACTCCGCAGTTAAACACTCTGACTGCCACGCCAGCTACCTCTAGA -1 2 primary 0 lane1_fakedata2_19 1:N:0:/1 AATTCTCTACACCACAGCATCAATTCTAAAAATGACTACCAGAGAGACAACTCCGCAGTTAAACACTCTGACTGCCACGCCAGCTACCTCTAGA -1 2 secondary lane1_fakedata2_5 1:N:0:/1 AATTCTCTACACCACAGCATCAATTCTAAAAATGACTACCAGAGAGACAACTCCGCAGTAAAACACTCTGACTGCCACGCCAGCTACCTCTAGA -1 2 secondary lane1_fakedata2_17 1:N:0:/1 AATTCTCTACACCACAGCATCAATTCTAAAAATGACTACCAGAGAGACAACTCCGCAGTTAAACACTCTGACTGCCACGCCAGCTACCTCCAGA -1 3 consensus AATTCGGCTTGCAACGCAAGTGACGATTCCCACGGACATAACTGATCTAAGTAACTTCCAAATCTGGGAATGGGATTTCATAATTAAGGACTAT 0 0 0 +1 2 primary 0 lane1_fakedata0_0 1:N:0:/1 AATTCGGCTTGCAACGCAAGTGACGATTCCCACGGACATAACTGATCTAAGTAACTTCCAAATCTGGGAATGGGATTTCATAATTAAGGACTAT +1 2 primary 0 lane1_fakedata0_1 1:N:0:/1 AATTCGGCTTGCAACGCAAGTGACGATTCCCACGGACATAACTGATCTAAGTAACTTCCAAATCTGGGAATGGGATTTCATAATTAAGGACTAT +1 2 primary 0 lane1_fakedata0_2 1:N:0:/1 AATTCGGCTTGCAACGCAAGTGACGATTCCCACGGACATAACTGATCTAAGTAACTTCCAAATCTGGGAATGGGATTTCATAATTAAGGACTAT +1 2 primary 0 lane1_fakedata0_3 1:N:0:/1 AATTCGGCTTGCAACGCAAGTGACGATTCCCACGGACATAACTGATCTAAGTAACTTCCAAATCTGGGAATGGGATTTCATAATTAAGGACTAT +1 2 primary 0 lane1_fakedata0_4 1:N:0:/1 AATTCGGCTTGCAACGCAAGTGACGATTCCCACGGACATAACTGATCTAAGTAACTTCCAAATCTGGGAATGGGATTTCATAATTAAGGACTAT +1 2 primary 0 lane1_fakedata0_5 1:N:0:/1 AATTCGGCTTGCAACGCAAGTGACGATTCCCACGGACATAACTGATCTAAGTAACTTCCAAATCTGGGAATGGGATTTCATAATTAAGGACTAT +1 2 primary 0 lane1_fakedata0_6 1:N:0:/1 AATTCGGCTTGCAACGCAAGTGACGATTCCCACGGACATAACTGATCTAAGTAACTTCCAAATCTGGGAATGGGATTTCATAATTAAGGACTAT +1 2 primary 0 lane1_fakedata0_7 1:N:0:/1 AATTCGGCTTGCAACGCAAGTGACGATTCCCACGGACATAACTGATCTAAGTAACTTCCAAATCTGGGAATGGGATTTCATAATTAAGGACTAT +1 2 primary 0 lane1_fakedata0_8 1:N:0:/1 AATTCGGCTTGCAACGCAAGTGACGATTCCCACGGACATAACTGATCTAAGTAACTTCCAAATCTGGGAATGGGATTTCATAATTAAGGACTAT +1 2 primary 0 lane1_fakedata0_9 1:N:0:/1 AATTCGGCTTGCAACGCAAGTGACGATTCCCACGGACATAACTGATCTAAGTAACTTCCAAATCTGGGAATGGGATTTCATAATTAAGGACTAT +1 2 primary 0 lane1_fakedata0_10 1:N:0:/1 AATTCGGCTTGCAACGCAAGTGACGATTCCCACGGACATAACTGATCTAAGTAACTTCCAAATCTGGGAATGGGATTTCATAATTAAGGACTAT +1 2 primary 0 lane1_fakedata0_11 1:N:0:/1 AATTCGGCTTGCAACGCAAGTGACGATTCCCACGGACATAACTGATCTAAGTAACTTCCAAATCTGGGAATGGGATTTCATAATTAAGGACTAT +1 2 primary 0 lane1_fakedata0_12 1:N:0:/1 AATTCGGCTTGCAACGCAAGTGACGATTCCCACGGACATAACTGATCTAAGTAACTTCCAAATCTGGGAATGGGATTTCATAATTAAGGACTAT +1 2 primary 0 lane1_fakedata0_13 1:N:0:/1 AATTCGGCTTGCAACGCAAGTGACGATTCCCACGGACATAACTGATCTAAGTAACTTCCAAATCTGGGAATGGGATTTCATAATTAAGGACTAT +1 2 primary 0 lane1_fakedata0_14 1:N:0:/1 AATTCGGCTTGCAACGCAAGTGACGATTCCCACGGACATAACTGATCTAAGTAACTTCCAAATCTGGGAATGGGATTTCATAATTAAGGACTAT +1 2 primary 0 lane1_fakedata0_16 1:N:0:/1 AATTCGGCTTGCAACGCAAGTGACGATTCCCACGGACATAACTGATCTAAGTAACTTCCAAATCTGGGAATGGGATTTCATAATTAAGGACTAT +1 2 primary 0 lane1_fakedata0_17 1:N:0:/1 AATTCGGCTTGCAACGCAAGTGACGATTCCCACGGACATAACTGATCTAAGTAACTTCCAAATCTGGGAATGGGATTTCATAATTAAGGACTAT +1 2 primary 0 lane1_fakedata0_18 1:N:0:/1 AATTCGGCTTGCAACGCAAGTGACGATTCCCACGGACATAACTGATCTAAGTAACTTCCAAATCTGGGAATGGGATTTCATAATTAAGGACTAT +1 2 primary 0 lane1_fakedata0_19 1:N:0:/1 AATTCGGCTTGCAACGCAAGTGACGATTCCCACGGACATAACTGATCTAAGTAACTTCCAAATCTGGGAATGGGATTTCATAATTAAGGACTAT +1 2 primary 0 lane1_fakedata0_20 1:N:0:/1 AATTCGGCTTGCAACGCAAGTGACGATTCCCACGGACATAACTGATCTAAGTAACTTCCAAATCTGGGAATGGGATTTCATAATTAAGGACTAT +1 2 primary 0 lane1_fakedata0_21 1:N:0:/1 AATTCGGCTTGCAACGCAAGTGACGATTCCCACGGACATAACTGATCTAAGTAACTTCCAAATCTGGGAATGGGATTTCATAATTAAGGACTAT +1 2 primary 0 lane1_fakedata0_22 1:N:0:/1 AATTCGGCTTGCAACGCAAGTGACGATTCCCACGGACATAACTGATCTAAGTAACTTCCAAATCTGGGAATGGGATTTCATAATTAAGGACTAT +1 2 primary 0 lane1_fakedata0_23 1:N:0:/1 AATTCGGCTTGCAACGCAAGTGACGATTCCCACGGACATAACTGATCTAAGTAACTTCCAAATCTGGGAATGGGATTTCATAATTAAGGACTAT +1 2 primary 0 lane1_fakedata0_24 1:N:0:/1 AATTCGGCTTGCAACGCAAGTGACGATTCCCACGGACATAACTGATCTAAGTAACTTCCAAATCTGGGAATGGGATTTCATAATTAAGGACTAT +1 2 primary 0 lane1_fakedata0_25 1:N:0:/1 AATTCGGCTTGCAACGCAAGTGACGATTCCCACGGACATAACTGATCTAAGTAACTTCCAAATCTGGGAATGGGATTTCATAATTAAGGACTAT +1 2 primary 0 lane1_fakedata0_26 1:N:0:/1 AATTCGGCTTGCAACGCAAGTGACGATTCCCACGGACATAACTGATCTAAGTAACTTCCAAATCTGGGAATGGGATTTCATAATTAAGGACTAT +1 2 primary 0 lane1_fakedata0_27 1:N:0:/1 AATTCGGCTTGCAACGCAAGTGACGATTCCCACGGACATAACTGATCTAAGTAACTTCCAAATCTGGGAATGGGATTTCATAATTAAGGACTAT +1 2 secondary lane1_fakedata0_15 1:N:0:/1 AATTCGGCTTGCAACGCAAGTGACGATTCCCACGGACATAACTGATCTAAGTAACTTCCAAGTCTGGGAATGGGATTTCATAATTAAGGACTAT +1 3 consensus AATTCTCTACACCACAGCATCAATTCTAAAAATGACTACCAGAGAGACAACTCCGCAGTTAAACACTCTGACTGCCACGCCAGCTACCTCTAGA 0 0 0 1 3 model OOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOO -1 3 primary 0 lane1_fakedata0_0 1:N:0:/1 AATTCGGCTTGCAACGCAAGTGACGATTCCCACGGACATAACTGATCTAAGTAACTTCCAAATCTGGGAATGGGATTTCATAATTAAGGACTAT -1 3 primary 0 lane1_fakedata0_1 1:N:0:/1 AATTCGGCTTGCAACGCAAGTGACGATTCCCACGGACATAACTGATCTAAGTAACTTCCAAATCTGGGAATGGGATTTCATAATTAAGGACTAT -1 3 primary 0 lane1_fakedata0_2 1:N:0:/1 AATTCGGCTTGCAACGCAAGTGACGATTCCCACGGACATAACTGATCTAAGTAACTTCCAAATCTGGGAATGGGATTTCATAATTAAGGACTAT -1 3 primary 0 lane1_fakedata0_3 1:N:0:/1 AATTCGGCTTGCAACGCAAGTGACGATTCCCACGGACATAACTGATCTAAGTAACTTCCAAATCTGGGAATGGGATTTCATAATTAAGGACTAT -1 3 primary 0 lane1_fakedata0_4 1:N:0:/1 AATTCGGCTTGCAACGCAAGTGACGATTCCCACGGACATAACTGATCTAAGTAACTTCCAAATCTGGGAATGGGATTTCATAATTAAGGACTAT -1 3 primary 0 lane1_fakedata0_5 1:N:0:/1 AATTCGGCTTGCAACGCAAGTGACGATTCCCACGGACATAACTGATCTAAGTAACTTCCAAATCTGGGAATGGGATTTCATAATTAAGGACTAT -1 3 primary 0 lane1_fakedata0_6 1:N:0:/1 AATTCGGCTTGCAACGCAAGTGACGATTCCCACGGACATAACTGATCTAAGTAACTTCCAAATCTGGGAATGGGATTTCATAATTAAGGACTAT -1 3 primary 0 lane1_fakedata0_7 1:N:0:/1 AATTCGGCTTGCAACGCAAGTGACGATTCCCACGGACATAACTGATCTAAGTAACTTCCAAATCTGGGAATGGGATTTCATAATTAAGGACTAT -1 3 primary 0 lane1_fakedata0_8 1:N:0:/1 AATTCGGCTTGCAACGCAAGTGACGATTCCCACGGACATAACTGATCTAAGTAACTTCCAAATCTGGGAATGGGATTTCATAATTAAGGACTAT -1 3 primary 0 lane1_fakedata0_9 1:N:0:/1 AATTCGGCTTGCAACGCAAGTGACGATTCCCACGGACATAACTGATCTAAGTAACTTCCAAATCTGGGAATGGGATTTCATAATTAAGGACTAT -1 3 primary 0 lane1_fakedata0_10 1:N:0:/1 AATTCGGCTTGCAACGCAAGTGACGATTCCCACGGACATAACTGATCTAAGTAACTTCCAAATCTGGGAATGGGATTTCATAATTAAGGACTAT -1 3 primary 0 lane1_fakedata0_11 1:N:0:/1 AATTCGGCTTGCAACGCAAGTGACGATTCCCACGGACATAACTGATCTAAGTAACTTCCAAATCTGGGAATGGGATTTCATAATTAAGGACTAT -1 3 primary 0 lane1_fakedata0_12 1:N:0:/1 AATTCGGCTTGCAACGCAAGTGACGATTCCCACGGACATAACTGATCTAAGTAACTTCCAAATCTGGGAATGGGATTTCATAATTAAGGACTAT -1 3 primary 0 lane1_fakedata0_13 1:N:0:/1 AATTCGGCTTGCAACGCAAGTGACGATTCCCACGGACATAACTGATCTAAGTAACTTCCAAATCTGGGAATGGGATTTCATAATTAAGGACTAT -1 3 primary 0 lane1_fakedata0_14 1:N:0:/1 AATTCGGCTTGCAACGCAAGTGACGATTCCCACGGACATAACTGATCTAAGTAACTTCCAAATCTGGGAATGGGATTTCATAATTAAGGACTAT -1 3 primary 0 lane1_fakedata0_16 1:N:0:/1 AATTCGGCTTGCAACGCAAGTGACGATTCCCACGGACATAACTGATCTAAGTAACTTCCAAATCTGGGAATGGGATTTCATAATTAAGGACTAT -1 3 primary 0 lane1_fakedata0_17 1:N:0:/1 AATTCGGCTTGCAACGCAAGTGACGATTCCCACGGACATAACTGATCTAAGTAACTTCCAAATCTGGGAATGGGATTTCATAATTAAGGACTAT -1 3 primary 0 lane1_fakedata0_18 1:N:0:/1 AATTCGGCTTGCAACGCAAGTGACGATTCCCACGGACATAACTGATCTAAGTAACTTCCAAATCTGGGAATGGGATTTCATAATTAAGGACTAT -1 3 primary 0 lane1_fakedata0_19 1:N:0:/1 AATTCGGCTTGCAACGCAAGTGACGATTCCCACGGACATAACTGATCTAAGTAACTTCCAAATCTGGGAATGGGATTTCATAATTAAGGACTAT -1 3 primary 0 lane1_fakedata0_20 1:N:0:/1 AATTCGGCTTGCAACGCAAGTGACGATTCCCACGGACATAACTGATCTAAGTAACTTCCAAATCTGGGAATGGGATTTCATAATTAAGGACTAT -1 3 primary 0 lane1_fakedata0_21 1:N:0:/1 AATTCGGCTTGCAACGCAAGTGACGATTCCCACGGACATAACTGATCTAAGTAACTTCCAAATCTGGGAATGGGATTTCATAATTAAGGACTAT -1 3 primary 0 lane1_fakedata0_22 1:N:0:/1 AATTCGGCTTGCAACGCAAGTGACGATTCCCACGGACATAACTGATCTAAGTAACTTCCAAATCTGGGAATGGGATTTCATAATTAAGGACTAT -1 3 primary 0 lane1_fakedata0_23 1:N:0:/1 AATTCGGCTTGCAACGCAAGTGACGATTCCCACGGACATAACTGATCTAAGTAACTTCCAAATCTGGGAATGGGATTTCATAATTAAGGACTAT -1 3 primary 0 lane1_fakedata0_24 1:N:0:/1 AATTCGGCTTGCAACGCAAGTGACGATTCCCACGGACATAACTGATCTAAGTAACTTCCAAATCTGGGAATGGGATTTCATAATTAAGGACTAT -1 3 primary 0 lane1_fakedata0_25 1:N:0:/1 AATTCGGCTTGCAACGCAAGTGACGATTCCCACGGACATAACTGATCTAAGTAACTTCCAAATCTGGGAATGGGATTTCATAATTAAGGACTAT -1 3 primary 0 lane1_fakedata0_26 1:N:0:/1 AATTCGGCTTGCAACGCAAGTGACGATTCCCACGGACATAACTGATCTAAGTAACTTCCAAATCTGGGAATGGGATTTCATAATTAAGGACTAT -1 3 primary 0 lane1_fakedata0_27 1:N:0:/1 AATTCGGCTTGCAACGCAAGTGACGATTCCCACGGACATAACTGATCTAAGTAACTTCCAAATCTGGGAATGGGATTTCATAATTAAGGACTAT -1 3 secondary lane1_fakedata0_15 1:N:0:/1 AATTCGGCTTGCAACGCAAGTGACGATTCCCACGGACATAACTGATCTAAGTAACTTCCAAGTCTGGGAATGGGATTTCATAATTAAGGACTAT +1 3 primary 0 lane1_fakedata2_0 1:N:0:/1 AATTCTCTACACCACAGCATCAATTCTAAAAATGACTACCAGAGAGACAACTCCGCAGTTAAACACTCTGACTGCCACGCCAGCTACCTCTAGA +1 3 primary 0 lane1_fakedata2_1 1:N:0:/1 AATTCTCTACACCACAGCATCAATTCTAAAAATGACTACCAGAGAGACAACTCCGCAGTTAAACACTCTGACTGCCACGCCAGCTACCTCTAGA +1 3 primary 0 lane1_fakedata2_2 1:N:0:/1 AATTCTCTACACCACAGCATCAATTCTAAAAATGACTACCAGAGAGACAACTCCGCAGTTAAACACTCTGACTGCCACGCCAGCTACCTCTAGA +1 3 primary 0 lane1_fakedata2_3 1:N:0:/1 AATTCTCTACACCACAGCATCAATTCTAAAAATGACTACCAGAGAGACAACTCCGCAGTTAAACACTCTGACTGCCACGCCAGCTACCTCTAGA +1 3 primary 0 lane1_fakedata2_4 1:N:0:/1 AATTCTCTACACCACAGCATCAATTCTAAAAATGACTACCAGAGAGACAACTCCGCAGTTAAACACTCTGACTGCCACGCCAGCTACCTCTAGA +1 3 primary 0 lane1_fakedata2_6 1:N:0:/1 AATTCTCTACACCACAGCATCAATTCTAAAAATGACTACCAGAGAGACAACTCCGCAGTTAAACACTCTGACTGCCACGCCAGCTACCTCTAGA +1 3 primary 0 lane1_fakedata2_7 1:N:0:/1 AATTCTCTACACCACAGCATCAATTCTAAAAATGACTACCAGAGAGACAACTCCGCAGTTAAACACTCTGACTGCCACGCCAGCTACCTCTAGA +1 3 primary 0 lane1_fakedata2_8 1:N:0:/1 AATTCTCTACACCACAGCATCAATTCTAAAAATGACTACCAGAGAGACAACTCCGCAGTTAAACACTCTGACTGCCACGCCAGCTACCTCTAGA +1 3 primary 0 lane1_fakedata2_9 1:N:0:/1 AATTCTCTACACCACAGCATCAATTCTAAAAATGACTACCAGAGAGACAACTCCGCAGTTAAACACTCTGACTGCCACGCCAGCTACCTCTAGA +1 3 primary 0 lane1_fakedata2_10 1:N:0:/1 AATTCTCTACACCACAGCATCAATTCTAAAAATGACTACCAGAGAGACAACTCCGCAGTTAAACACTCTGACTGCCACGCCAGCTACCTCTAGA +1 3 primary 0 lane1_fakedata2_11 1:N:0:/1 AATTCTCTACACCACAGCATCAATTCTAAAAATGACTACCAGAGAGACAACTCCGCAGTTAAACACTCTGACTGCCACGCCAGCTACCTCTAGA +1 3 primary 0 lane1_fakedata2_12 1:N:0:/1 AATTCTCTACACCACAGCATCAATTCTAAAAATGACTACCAGAGAGACAACTCCGCAGTTAAACACTCTGACTGCCACGCCAGCTACCTCTAGA +1 3 primary 0 lane1_fakedata2_13 1:N:0:/1 AATTCTCTACACCACAGCATCAATTCTAAAAATGACTACCAGAGAGACAACTCCGCAGTTAAACACTCTGACTGCCACGCCAGCTACCTCTAGA +1 3 primary 0 lane1_fakedata2_14 1:N:0:/1 AATTCTCTACACCACAGCATCAATTCTAAAAATGACTACCAGAGAGACAACTCCGCAGTTAAACACTCTGACTGCCACGCCAGCTACCTCTAGA +1 3 primary 0 lane1_fakedata2_15 1:N:0:/1 AATTCTCTACACCACAGCATCAATTCTAAAAATGACTACCAGAGAGACAACTCCGCAGTTAAACACTCTGACTGCCACGCCAGCTACCTCTAGA +1 3 primary 0 lane1_fakedata2_16 1:N:0:/1 AATTCTCTACACCACAGCATCAATTCTAAAAATGACTACCAGAGAGACAACTCCGCAGTTAAACACTCTGACTGCCACGCCAGCTACCTCTAGA +1 3 primary 0 lane1_fakedata2_18 1:N:0:/1 AATTCTCTACACCACAGCATCAATTCTAAAAATGACTACCAGAGAGACAACTCCGCAGTTAAACACTCTGACTGCCACGCCAGCTACCTCTAGA +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
--- a/test-data/ustacks/PopA_02.alleles.tsv Wed Feb 27 10:03:16 2019 -0500 +++ b/test-data/ustacks/PopA_02.alleles.tsv Thu Jun 20 08:18:09 2019 -0400 @@ -1,3 +1,3 @@ -# ustacks version 2.3b; generated on 2019-02-21 19:57:38 +# ustacks version 2.4; generated on 2019-06-18 10:34:45 2 1 AC 50.00 6 2 1 CA 50.00 6
--- a/test-data/ustacks/PopA_02.snps.tsv Wed Feb 27 10:03:16 2019 -0500 +++ b/test-data/ustacks/PopA_02.snps.tsv Thu Jun 20 08:18:09 2019 -0400 @@ -1,4 +1,4 @@ -# ustacks version 2.3b; generated on 2019-02-21 19:57:38 +# 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 -
--- a/test-data/ustacks/PopA_02.tags.tsv Wed Feb 27 10:03:16 2019 -0500 +++ b/test-data/ustacks/PopA_02.tags.tsv Thu Jun 20 08:18:09 2019 -0400 @@ -1,4 +1,4 @@ -# ustacks version 2.3b; generated on 2019-02-21 19:57:38 +# ustacks version 2.4; generated on 2019-06-18 10:34:45 2 1 consensus AATTCGTTTGCTGCTTCAGGAATCTCTCGTATAATCTGAGTATGTGCGTACGTACGCTATTTAGATGGATAACCGACGCTGCCAGACGAGAGAC 0 0 0 2 1 model OOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOEOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOEOOOOO 2 1 primary 0 lane1_fakedata7_7 1:N:0:/1 AATTCGTTTGCTGCTTCAGGAATCTCTCGTATACTCTGAGTATGTGCGTACGTACGCTATTTAGATGGATAACCGACGCTGCCAGACGAGAGAC @@ -11,8 +11,8 @@ 2 1 primary 1 lane1_fakedata7_3 1:N:0:/1 AATTCGTTTGCTGCTTCAGGAATCTCTCGTATAATCTGAGTATGTGCGTACGTACGCTATTTAGATGGATAACCGACGCTGCCAGACGCGAGAC 2 1 primary 1 lane1_fakedata7_4 1:N:0:/1 AATTCGTTTGCTGCTTCAGGAATCTCTCGTATAATCTGAGTATGTGCGTACGTACGCTATTTAGATGGATAACCGACGCTGCCAGACGCGAGAC 2 1 primary 1 lane1_fakedata7_5 1:N:0:/1 AATTCGTTTGCTGCTTCAGGAATCTCTCGTATAATCTGAGTATGTGCGTACGTACGCTATTTAGATGGATAACCGACGCTGCCAGACGCGAGAC +2 1 secondary lane1_fakedata7_6 1:N:0:/1 AATTCGTTTGCTGCTTCAGGAACCTCTCGTATACTCTGAGTATGTGCGTACGTACGCTATTTAGATGGATAACCGACGCTGCCAGACGAGAGAC 2 1 secondary lane1_fakedata7_10 1:N:0:/1 AATTCGTTTGCTGCTTCAGGAATCTTTCGTATACTCTGAGTATGTGCGTACGTACGCTATTTAGATGGATAACCGACGCTGCCAGACGAGAGAC -2 1 secondary lane1_fakedata7_6 1:N:0:/1 AATTCGTTTGCTGCTTCAGGAACCTCTCGTATACTCTGAGTATGTGCGTACGTACGCTATTTAGATGGATAACCGACGCTGCCAGACGAGAGAC 2 2 consensus AATTCGGCTTGCAACGCAAGTGACGATTCCCACGGACATAACTGATCTAAGTAACTTCCAAATCTGGGAATGGGATTTCATAATTAAGGACTAT 0 0 0 2 2 model OOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOO 2 2 primary 0 lane1_fakedata0_0 1:N:0:/1 AATTCGGCTTGCAACGCAAGTGACGATTCCCACGGACATAACTGATCTAAGTAACTTCCAAATCTGGGAATGGGATTTCATAATTAAGGACTAT