| Previous changeset 31:57def2d7c093 (2021-11-27) Next changeset 33:04fa42777df9 (2021-12-03) |
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Commit message:
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit cce7fcdd5e8ba8636c751f9f974bf07a6845ba1c" |
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modified:
freebayes.xml macros.xml test-data/freebayes-hxb2-test5.vcf test-data/freebayes-hxb2-test6.vcf test-data/freebayes-hxb2-test7.vcf test-data/freebayes-phix174-test1.vcf test-data/freebayes-phix174-test2.vcf test-data/freebayes-phix174-test3.vcf test-data/freebayes-phix174-test4.vcf test-data/left-align-output.bam |
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added:
test-data/freebayes-phix174.cram |
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| diff -r 57def2d7c093 -r 8a7a42541080 freebayes.xml --- a/freebayes.xml Sat Nov 27 09:38:13 2021 +0000 +++ b/freebayes.xml Wed Dec 01 21:50:06 2021 +0000 |
| [ |
| @@ -1,4 +1,4 @@ -<tool id="freebayes" name="FreeBayes" version="@TOOL_VERSION@+galaxy1"> +<tool id="freebayes" name="FreeBayes" version="@TOOL_VERSION@+galaxy0"> <description>bayesian genetic variant detector</description> <xrefs> <xref type="bio.tools">freebayes</xref> @@ -7,8 +7,8 @@ <import>macros.xml</import> </macros> <expand macro="requirements"> - <requirement type="package" version="4.1.3">gawk</requirement> - <requirement type="package" version="20170422">parallel</requirement> + <requirement type="package" version="5.1.0">gawk</requirement> + <requirement type="package" version="20211022">parallel</requirement> </expand> <command detect_errors="exit_code"><![CDATA[ ##set up input files @@ -29,8 +29,13 @@ #end if #for $bam_count, $input_bam in enumerate( $input_bamfiles ): - ln -s -f '${input_bam}' 'b_${bam_count}.bam' && - ln -s -f '${input_bam.metadata.bam_index}' 'b_${bam_count}.bam.bai' && + #if $input_bam.ext == 'bam': + ln -s -f '${input_bam}' 'b_${bam_count}.bam' && + ln -s -f '${input_bam.metadata.bam_index}' 'b_${bam_count}.bam.bai' && + #elif $input_bam.ext == 'cram': + ln -s -f '${input_bam}' 'b_${bam_count}.cram' && + ln -s -f '${input_bam.metadata.cram_index}' 'b_${bam_count}.cram.crai' && + #end if #end for ## Tabixize optional input_variant_vcf file (for --variant-input option) @@ -47,7 +52,7 @@ #else ##divide up the regions in the bam file for efficient processing #for $bam_count, $input_bam in enumerate( $input_bamfiles ): - samtools view -H b_${bam_count}.bam | + samtools view -H b_${bam_count}.${input_bam.ext}| grep '^@SQ' | cut -f 2- | awk '{ gsub("^SN:","",$1); gsub("^LN:","",$2); print $1"\t0\t"$2; }' >> regions_all.bed && @@ -73,7 +78,7 @@ --region '\$i' #for $bam_count, $input_bam in enumerate( $input_bamfiles ): - --bam 'b_${bam_count}.bam' + --bam 'b_${bam_count}.${input_bam.ext}' #end for --fasta-reference '${reference_fasta_filename}' @@ -135,6 +140,7 @@ #if $options_type.optional_inputs.contamination_estimates: --contamination-estimates '${options_type.optional_inputs.contamination_estimates}' #end if + $options_type.optional_inputs.trim_complex_tail #end if ## REPORTING @@ -332,7 +338,7 @@ <conditional name="optional_inputs"> <param name="optional_inputs_selector" type="select" label="Additional inputs" - help="Sets --samples, --populations, --cnv-map, --trace, --failed-alleles, --variant-input, --only-use-input-alleles, --haplotype-basis-alleles, --report-all-haplotype-alleles, --report-monomorphic options, --observation-bias, and --contamination-estimates"> + help="Sets --samples, --populations, --cnv-map, --trace, --failed-alleles, --variant-input, --only-use-input-alleles, --haplotype-basis-alleles, --report-all-haplotype-alleles, --report-monomorphic options, --observation-bias, --contamination-estimates and --trim-complex-tail"> <option value="do_not_set" selected="true">Do not provide additional inputs</option> <option value="set">Provide additional inputs</option> </param> @@ -375,6 +381,8 @@ <param name="contamination_estimates" argument="--contamination-estimates" type="data" format="tabular" optional="true" label="Upload per-sample estimates of contamination from" help="The format should be: sample p(read=R|genotype=AR) p(read=A|genotype=AA) Sample '*' can be used to set default contamination estimates" /> + <param name="trim_complex_tail" argument="--trim-complex-tail" type="boolean" truevalue="--trim-complex-tail" falsevalue="" + label="Trim trailing reference matches" /> </when> <when value="do_not_set" /> </conditional> @@ -649,6 +657,7 @@ <param name="options_type_selector" value="full"/> <param name="population_model_selector" value="set"/> <param name="P" value="1"/> + <param name="trim_complex_tail" value="--trim-complex-tail"/> <output name="output_vcf" file="freebayes-phix174-test4.vcf" lines_diff="4" /> </test> <test> @@ -681,6 +690,14 @@ <param name="skip_coverage" value="100" /> <output name="output_vcf" file="freebayes-hxb2-test7.vcf" lines_diff="4" /> </test> + <test> <!-- Test with CRAM --> + <param name="reference_source_selector" value="history" /> + <param name="processmode" value="individual" /> + <param name="ref_file" ftype="fasta" value="freebayes-phix174.fasta"/> + <param name="input_bams" ftype="cram" value="freebayes-phix174.cram"/> + <param name="options_type_selector" value="simple"/> + <output name="output_vcf" file="freebayes-phix174-test1.vcf" lines_diff="4" /> + </test> </tests> <help><![CDATA[ **What it does** |
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| diff -r 57def2d7c093 -r 8a7a42541080 macros.xml --- a/macros.xml Sat Nov 27 09:38:13 2021 +0000 +++ b/macros.xml Wed Dec 01 21:50:06 2021 +0000 |
| b |
| @@ -1,9 +1,9 @@ <macros> - <token name="@TOOL_VERSION@">1.3.1</token> + <token name="@TOOL_VERSION@">1.3.5</token> <xml name="requirements"> <requirements> <requirement type="package" version="@TOOL_VERSION@">freebayes</requirement> - <requirement type="package" version="1.9">samtools</requirement> + <requirement type="package" version="1.12">samtools</requirement> <yield /> </requirements> </xml> @@ -32,12 +32,12 @@ <option value="merge">Merge output VCFs</option> </param> <when value="individual"> - <param name="input_bams" type="data" format="bam" label="BAM dataset"> + <param name="input_bams" type="data" format="bam,cram" label="BAM or CRAM dataset"> <yield /> </param> </when> <when value="merge"> - <param name="input_bams" type="data" format="bam" multiple="true" label="BAM dataset(s)"> + <param name="input_bams" type="data" format="bam,cram" multiple="true" label="BAM or CRAM dataset(s)"> <yield /> </param> </when> |
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| diff -r 57def2d7c093 -r 8a7a42541080 test-data/freebayes-hxb2-test5.vcf --- a/test-data/freebayes-hxb2-test5.vcf Sat Nov 27 09:38:13 2021 +0000 +++ b/test-data/freebayes-hxb2-test5.vcf Wed Dec 01 21:50:06 2021 +0000 |
| b |
| @@ -1,6 +1,6 @@ ##fileformat=VCFv4.2 -##fileDate=20191101 -##source=freeBayes v1.3.1-dirty +##fileDate=20211130 +##source=freeBayes v1.3.5 ##reference=localref.fa ##contig=<ID=K03455,length=9719> ##phasing=none @@ -65,10 +65,10 @@ K03455 2728 . T A 4.41787e-14 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=25;CIGAR=1X;DP=459;DPB=459;DPRA=0;EPP=28.1125;EPPR=3.87378;GTI=0;LEN=1;MEANALT=3;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=475.527;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=444;QR=13384;RO=425;RPL=21;RPP=28.1125;RPPR=38.2086;RPR=4;RUN=1;SAF=25;SAP=57.2971;SAR=0;SRF=356;SRP=423.862;SRR=69;TYPE=snp;technology.ILLUMINA=1 GT:DP:AD:RO:QR:AO:QA:GL 0/0:459:425,25:425:13384:25:444:0,-95.5268,-1164.2 K03455 2797 . G A 20542.6 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=666;CIGAR=1X;DP=666;DPB=666;DPRA=0;EPP=133.429;EPPR=0;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=0;NS=1;NUMALT=1;ODDS=927.877;PAIRED=1;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=23333;QR=0;RO=0;RPL=319;RPP=5.56651;RPPR=0;RPR=347;RUN=1;SAF=474;SAP=262.296;SAR=192;SRF=0;SRP=0;SRR=0;TYPE=snp;technology.ILLUMINA=1 GT:DP:AD:RO:QR:AO:QA:GL 1/1:666:0,666:0:0:666:23333:-2098.99,-200.486,0 K03455 2802 . C A 3.80909e-14 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=57;CIGAR=1X;DP=672;DPB=672;DPRA=0;EPP=126.784;EPPR=65.6713;GTI=0;LEN=1;MEANALT=3;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=627.193;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=1084;QR=20184;RO=613;RPL=56;RPP=118.251;RPPR=63.8009;RPR=1;RUN=1;SAF=56;SAP=118.251;SAR=1;SRF=403;SRP=134.96;SRR=210;TYPE=snp;technology.ILLUMINA=1 GT:DP:AD:RO:QR:AO:QA:GL 0/0:672:613,57:613:20184:57:1084:0,-104.146,-1718.1 -K03455 2848 . TAAAAAAGAAAAAATC TAAAAAAAGAAAAAATC 18102 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=630;CIGAR=1M1I15M;DP=722;DPB=774.875;DPRA=0;EPP=43.2136;EPPR=13.8677;GTI=0;LEN=1;MEANALT=40;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=830.486;PAIRED=1;PAIREDR=1;PAO=22;PQA=531.5;PQR=553.5;PRO=23;QA=20369;QR=158;RO=5;RPL=282;RPP=18.0245;RPPR=3.44459;RPR=348;RUN=1;SAF=333;SAP=7.47733;SAR=297;SRF=3;SRP=3.44459;SRR=2;TYPE=ins;technology.ILLUMINA=1 GT:DP:AD:RO:QR:AO:QA:GL 1/1:722:5,630:5:158:630:20369:-1818.16,-176.934,0 +K03455 2848 . TAAAAAAGAAA TAAAAAAAGAAA 19553.7 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=694;CIGAR=1M1I10M;DP=781;DPB=850.818;DPRA=0;EPP=71.5462;EPPR=13.8677;GTI=0;LEN=1;MEANALT=35;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=918.93;PAIRED=1;PAIREDR=1;PAO=2.5;PQA=50.5;PQR=50.5;PRO=2.5;QA=22027;QR=157;RO=5;RPL=325;RPP=9.06789;RPPR=3.44459;RPR=369;RUN=1;SAF=392;SAP=28.3546;SAR=302;SRF=3;SRP=3.44459;SRR=2;TYPE=ins;technology.ILLUMINA=1 GT:DP:AD:RO:QR:AO:QA:GL 1/1:781:5,694:5:157:694:22027:-1967.45,-196.288,0 K03455 2873 . AC AT 21993.4 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=754;CIGAR=1M1X;DP=773;DPB=775.5;DPRA=0;EPP=5.26817;EPPR=5.18177;GTI=0;LEN=1;MEANALT=5;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=1039.03;PAIRED=1;PAIREDR=1;PAO=2.5;PQA=63;PQR=63;PRO=2.5;QA=24534;QR=37;RO=1;RPL=357;RPP=7.6182;RPPR=5.18177;RPR=397;RUN=1;SAF=378;SAP=3.02182;SAR=376;SRF=0;SRP=5.18177;SRR=1;TYPE=snp;technology.ILLUMINA=1 GT:DP:AD:RO:QR:AO:QA:GL 1/1:773:1,754:1:37:754:24534:-2203.73,-223.941,0 K03455 2882 . G T 21924 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=721;CIGAR=1X;DP=736;DPB=736;DPRA=0;EPP=36.2149;EPPR=22.5536;GTI=0;LEN=1;MEANALT=3;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=945.018;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=24583;QR=177;RO=9;RPL=353;RPP=3.68794;RPPR=9.04217;RPR=368;RUN=1;SAF=363;SAP=3.08559;SAR=358;SRF=7;SRP=9.04217;SRR=2;TYPE=snp;technology.ILLUMINA=1 GT:DP:AD:RO:QR:AO:QA:GL 1/1:736:9,721:9:177:721:24583:-2195.37,-203.838,0 -K03455 2883 . GGT GGG 2.65192e-14 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=46;CIGAR=2M1X;DP=726;DPB=731;DPRA=0;EPP=86.2815;EPPR=8.74455;GTI=0;LEN=1;MEANALT=6;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=660.068;PAIRED=1;PAIREDR=1;PAO=3.5;PQA=112;PQR=112;PRO=4.5;QA=1167;QR=22483;RO=668;RPL=43;RPP=78.5398;RPPR=3.12733;RPR=3;RUN=1;SAF=45;SAP=94.401;SAR=1;SRF=316;SRP=7.22322;SRR=352;TYPE=snp;technology.ILLUMINA=1 GT:DP:AD:RO:QR:AO:QA:GL 0/0:726:668,46:668:22483:46:1167:0,-109.931,-1917.55 +K03455 2883 . GGT GGG 2.63987e-14 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=46;CIGAR=2M1X;DP=726;DPB=731;DPRA=0;EPP=86.2815;EPPR=8.74455;GTI=0;LEN=1;MEANALT=6;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=660.068;PAIRED=1;PAIREDR=1;PAO=3.5;PQA=112;PQR=112;PRO=4.5;QA=1167;QR=22483;RO=668;RPL=43;RPP=78.5398;RPPR=3.12733;RPR=3;RUN=1;SAF=45;SAP=94.401;SAR=1;SRF=316;SRP=7.22322;SRR=352;TYPE=snp;technology.ILLUMINA=1 GT:DP:AD:RO:QR:AO:QA:GL 0/0:726:668,46:668:22483:46:1167:0,-109.931,-1917.55 K03455 2894 . T C 21733.9 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=717;CIGAR=1X;DP=723;DPB=723;DPRA=0;EPP=10.8876;EPPR=5.18177;GTI=0;LEN=1;MEANALT=3;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=991.951;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=24231;QR=17;RO=1;RPL=373;RPP=5.55731;RPPR=5.18177;RPR=344;RUN=1;SAF=354;SAP=3.25561;SAR=363;SRF=1;SRP=5.18177;SRR=0;TYPE=snp;technology.ILLUMINA=1 GT:DP:AD:RO:QR:AO:QA:GL 1/1:723:1,717:1:17:717:24231:-2178.13,-214.613,0 K03455 2906 . C T 20694.7 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=650;CIGAR=1X;DP=653;DPB=653;DPRA=0;EPP=3.86553;EPPR=3.0103;GTI=0;LEN=1;MEANALT=2;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=885.229;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=23147;QR=65;RO=2;RPL=368;RPP=27.7183;RPPR=7.35324;RPR=282;RUN=1;SAF=301;SAP=10.7073;SAR=349;SRF=1;SRP=3.0103;SRR=1;TYPE=snp;technology.ILLUMINA=1 GT:DP:AD:RO:QR:AO:QA:GL 1/1:653:2,650:2:65:650:23147:-2076.11,-190.301,0 K03455 2913 . G A 20816.6 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=638;CIGAR=1X;DP=639;DPB=639;DPRA=0;EPP=3.0103;EPPR=5.18177;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=878.93;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=23329;QR=31;RO=1;RPL=402;RPP=96.7988;RPPR=5.18177;RPR=236;RUN=1;SAF=297;SAP=9.5996;SAR=341;SRF=1;SRP=5.18177;SRR=0;TYPE=snp;technology.ILLUMINA=1 GT:DP:AD:RO:QR:AO:QA:GL 1/1:639:1,638:1:31:638:23329:-2095.39,-189.259,0 |
| b |
| diff -r 57def2d7c093 -r 8a7a42541080 test-data/freebayes-hxb2-test6.vcf --- a/test-data/freebayes-hxb2-test6.vcf Sat Nov 27 09:38:13 2021 +0000 +++ b/test-data/freebayes-hxb2-test6.vcf Wed Dec 01 21:50:06 2021 +0000 |
| b |
| @@ -1,6 +1,6 @@ ##fileformat=VCFv4.2 -##fileDate=20191106 -##source=freeBayes v1.3.1-dirty +##fileDate=20211130 +##source=freeBayes v1.3.5 ##reference=localref.fa ##contig=<ID=K03455,length=9719> ##phasing=none @@ -67,10 +67,9 @@ K03455 2728 . T A 4.41787e-14 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=25;CIGAR=1X;DP=459;DPB=459;DPRA=0;EPP=28.1125;EPPR=3.87378;GTI=0;LEN=1;MEANALT=3;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=475.527;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=444;QR=13384;RO=425;RPL=21;RPP=28.1125;RPPR=38.2086;RPR=4;RUN=1;SAF=25;SAP=57.2971;SAR=0;SRF=356;SRP=423.862;SRR=69;TYPE=snp;technology.ILLUMINA=1 GT:DP:AD:RO:QR:AO:QA:GL 0/0:459:425,25:425:13384:25:444:0,-95.5268,-1164.2 K03455 2797 . G A 20542.6 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=666;CIGAR=1X;DP=666;DPB=666;DPRA=0;EPP=133.429;EPPR=0;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=0;NS=1;NUMALT=1;ODDS=927.877;PAIRED=1;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=23333;QR=0;RO=0;RPL=319;RPP=5.56651;RPPR=0;RPR=347;RUN=1;SAF=474;SAP=262.296;SAR=192;SRF=0;SRP=0;SRR=0;TYPE=snp;technology.ILLUMINA=1 GT:DP:AD:RO:QR:AO:QA:GL 1/1:666:0,666:0:0:666:23333:-2098.99,-200.486,0 K03455 2802 . C A 3.80909e-14 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=57;CIGAR=1X;DP=672;DPB=672;DPRA=0;EPP=126.784;EPPR=65.6713;GTI=0;LEN=1;MEANALT=3;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=627.193;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=1084;QR=20184;RO=613;RPL=56;RPP=118.251;RPPR=63.8009;RPR=1;RUN=1;SAF=56;SAP=118.251;SAR=1;SRF=403;SRP=134.96;SRR=210;TYPE=snp;technology.ILLUMINA=1 GT:DP:AD:RO:QR:AO:QA:GL 0/0:672:613,57:613:20184:57:1084:0,-104.146,-1718.1 -K03455 2848 . TAAAAAAGAAAAAATC TAAAAAAAGAAAAAATC 18102 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=630;CIGAR=1M1I15M;DP=722;DPB=774.875;DPRA=0;EPP=43.2136;EPPR=13.8677;GTI=0;LEN=1;MEANALT=40;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=830.486;PAIRED=1;PAIREDR=1;PAO=22;PQA=531.5;PQR=553.5;PRO=23;QA=20369;QR=158;RO=5;RPL=282;RPP=18.0245;RPPR=3.44459;RPR=348;RUN=1;SAF=333;SAP=7.47733;SAR=297;SRF=3;SRP=3.44459;SRR=2;TYPE=ins;technology.ILLUMINA=1 GT:DP:AD:RO:QR:AO:QA:GL 1/1:722:5,630:5:158:630:20369:-1818.16,-176.934,0 -K03455 2873 . AC AT 21993.4 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=754;CIGAR=1M1X;DP=773;DPB=775.5;DPRA=0;EPP=5.26817;EPPR=5.18177;GTI=0;LEN=1;MEANALT=5;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=1039.03;PAIRED=1;PAIREDR=1;PAO=2.5;PQA=63;PQR=63;PRO=2.5;QA=24534;QR=37;RO=1;RPL=357;RPP=7.6182;RPPR=5.18177;RPR=397;RUN=1;SAF=378;SAP=3.02182;SAR=376;SRF=0;SRP=5.18177;SRR=1;TYPE=snp;technology.ILLUMINA=1 GT:DP:AD:RO:QR:AO:QA:GL 1/1:773:1,754:1:37:754:24534:-2203.73,-223.941,0 -K03455 2882 . G T 21924 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=721;CIGAR=1X;DP=736;DPB=736;DPRA=0;EPP=36.2149;EPPR=22.5536;GTI=0;LEN=1;MEANALT=3;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=945.018;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=24583;QR=177;RO=9;RPL=353;RPP=3.68794;RPPR=9.04217;RPR=368;RUN=1;SAF=363;SAP=3.08559;SAR=358;SRF=7;SRP=9.04217;SRR=2;TYPE=snp;technology.ILLUMINA=1 GT:DP:AD:RO:QR:AO:QA:GL 1/1:736:9,721:9:177:721:24583:-2195.37,-203.838,0 -K03455 2883 . GGT GGG 2.65192e-14 . AB=0;ABP=0;AC=0;AF=0;AN=2;AO=46;CIGAR=2M1X;DP=726;DPB=731;DPRA=0;EPP=86.2815;EPPR=8.74455;GTI=0;LEN=1;MEANALT=6;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=660.068;PAIRED=1;PAIREDR=1;PAO=3.5;PQA=112;PQR=112;PRO=4.5;QA=1167;QR=22483;RO=668;RPL=43;RPP=78.5398;RPPR=3.12733;RPR=3;RUN=1;SAF=45;SAP=94.401;SAR=1;SRF=316;SRP=7.22322;SRR=352;TYPE=snp;technology.ILLUMINA=1 GT:DP:AD:RO:QR:AO:QA:GL 0/0:726:668,46:668:22483:46:1167:0,-109.931,-1917.55 +K03455 2848 . TAAAAAAGAAA TAAAAAAAGAAA 19553.7 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=694;CIGAR=1M1I10M;DP=781;DPB=850.818;DPRA=0;EPP=71.5462;EPPR=13.8677;GTI=0;LEN=1;MEANALT=35;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=918.93;PAIRED=1;PAIREDR=1;PAO=2.5;PQA=50.5;PQR=50.5;PRO=2.5;QA=22027;QR=157;RO=5;RPL=325;RPP=9.06789;RPPR=3.44459;RPR=369;RUN=1;SAF=392;SAP=28.3546;SAR=302;SRF=3;SRP=3.44459;SRR=2;TYPE=ins;technology.ILLUMINA=1 GT:DP:AD:RO:QR:AO:QA:GL 1/1:781:5,694:5:157:694:22027:-1967.45,-196.288,0 +K03455 2872 . TAC TAT 20668.8 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=697;CIGAR=2M1X;DP=765;DPB=766.667;DPRA=0;EPP=3.53681;EPPR=5.18177;GTI=0;LEN=1;MEANALT=9;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=960.516;PAIRED=1;PAIREDR=1;PAO=4;PQA=118.5;PQR=16.5;PRO=1;QA=23075;QR=35;RO=1;RPL=314;RPP=17.843;RPPR=5.18177;RPR=383;RUN=1;SAF=328;SAP=8.24738;SAR=369;SRF=0;SRP=5.18177;SRR=1;TYPE=snp;technology.ILLUMINA=1 GT:DP:AD:RO:QR:AO:QA:GL 1/1:765:1,697:1:35:697:23075:-2072.59,-206.969,0 +K03455 2882 . GGGT TGGT 20548.4 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=659;CIGAR=1X3M;DP=724;DPB=728.75;DPRA=0;EPP=7.52129;EPPR=7.35324;GTI=0;LEN=1;MEANALT=11;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=655.711;PAIRED=1;PAIREDR=1;PAO=3.5;PQA=98.5;PQR=193;PRO=6.5;QA=22947;QR=55;RO=2;RPL=326;RPP=3.17176;RPPR=3.0103;RPR=333;RUN=1;SAF=311;SAP=7.52129;SAR=348;SRF=1;SRP=3.0103;SRR=1;TYPE=snp;technology.ILLUMINA=1 GT:DP:AD:RO:QR:AO:QA:GL 1/1:724:2,659:2:55:659:22947:-2059.07,-194.031,0 K03455 2894 . T C 21733.9 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=717;CIGAR=1X;DP=723;DPB=723;DPRA=0;EPP=10.8876;EPPR=5.18177;GTI=0;LEN=1;MEANALT=3;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=991.951;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=24231;QR=17;RO=1;RPL=373;RPP=5.55731;RPPR=5.18177;RPR=344;RUN=1;SAF=354;SAP=3.25561;SAR=363;SRF=1;SRP=5.18177;SRR=0;TYPE=snp;technology.ILLUMINA=1 GT:DP:AD:RO:QR:AO:QA:GL 1/1:723:1,717:1:17:717:24231:-2178.13,-214.613,0 K03455 2906 . C T 20694.7 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=650;CIGAR=1X;DP=653;DPB=653;DPRA=0;EPP=3.86553;EPPR=3.0103;GTI=0;LEN=1;MEANALT=2;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=885.229;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=23147;QR=65;RO=2;RPL=368;RPP=27.7183;RPPR=7.35324;RPR=282;RUN=1;SAF=301;SAP=10.7073;SAR=349;SRF=1;SRP=3.0103;SRR=1;TYPE=snp;technology.ILLUMINA=1 GT:DP:AD:RO:QR:AO:QA:GL 1/1:653:2,650:2:65:650:23147:-2076.11,-190.301,0 K03455 2913 . G A 20816.6 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=638;CIGAR=1X;DP=639;DPB=639;DPRA=0;EPP=3.0103;EPPR=5.18177;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=878.93;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=23329;QR=31;RO=1;RPL=402;RPP=96.7988;RPPR=5.18177;RPR=236;RUN=1;SAF=297;SAP=9.5996;SAR=341;SRF=1;SRP=5.18177;SRR=0;TYPE=snp;technology.ILLUMINA=1 GT:DP:AD:RO:QR:AO:QA:GL 1/1:639:1,638:1:31:638:23329:-2095.39,-189.259,0 |
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| diff -r 57def2d7c093 -r 8a7a42541080 test-data/freebayes-hxb2-test7.vcf --- a/test-data/freebayes-hxb2-test7.vcf Sat Nov 27 09:38:13 2021 +0000 +++ b/test-data/freebayes-hxb2-test7.vcf Wed Dec 01 21:50:06 2021 +0000 |
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| @@ -1,6 +1,6 @@ ##fileformat=VCFv4.2 ##fileDate=20191030 -##source=freeBayes v1.3.1-dirty +##source=freeBayes v1.3.5 ##reference=localref.fa ##contig=<ID=K03455,length=9719> ##phasing=none |
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| diff -r 57def2d7c093 -r 8a7a42541080 test-data/freebayes-phix174-test1.vcf --- a/test-data/freebayes-phix174-test1.vcf Sat Nov 27 09:38:13 2021 +0000 +++ b/test-data/freebayes-phix174-test1.vcf Wed Dec 01 21:50:06 2021 +0000 |
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| @@ -1,6 +1,6 @@ ##fileformat=VCFv4.2 ##fileDate=20191030 -##source=freeBayes v1.3.1-dirty +##source=freeBayes v1.3.5 ##reference=localref.fa ##contig=<ID=phiX174,length=5386> ##phasing=none |
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| diff -r 57def2d7c093 -r 8a7a42541080 test-data/freebayes-phix174-test2.vcf --- a/test-data/freebayes-phix174-test2.vcf Sat Nov 27 09:38:13 2021 +0000 +++ b/test-data/freebayes-phix174-test2.vcf Wed Dec 01 21:50:06 2021 +0000 |
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| @@ -1,6 +1,6 @@ ##fileformat=VCFv4.2 ##fileDate=20191031 -##source=freeBayes v1.3.1-dirty +##source=freeBayes v1.3.5 ##reference=localref.fa ##contig=<ID=phiX174,length=5386> ##phasing=none |
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| diff -r 57def2d7c093 -r 8a7a42541080 test-data/freebayes-phix174-test3.vcf --- a/test-data/freebayes-phix174-test3.vcf Sat Nov 27 09:38:13 2021 +0000 +++ b/test-data/freebayes-phix174-test3.vcf Wed Dec 01 21:50:06 2021 +0000 |
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| @@ -1,6 +1,6 @@ ##fileformat=VCFv4.2 ##fileDate=20191031 -##source=freeBayes v1.3.1-dirty +##source=freeBayes v1.3.5 ##reference=localref.fa ##contig=<ID=phiX174,length=5386> ##phasing=none |
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| diff -r 57def2d7c093 -r 8a7a42541080 test-data/freebayes-phix174-test4.vcf --- a/test-data/freebayes-phix174-test4.vcf Sat Nov 27 09:38:13 2021 +0000 +++ b/test-data/freebayes-phix174-test4.vcf Wed Dec 01 21:50:06 2021 +0000 |
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| @@ -1,6 +1,6 @@ ##fileformat=VCFv4.2 ##fileDate=20191030 -##source=freeBayes v1.3.1-dirty +##source=freeBayes v1.3.5 ##reference=localref.fa ##contig=<ID=phiX174,length=5386> ##phasing=none |
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| diff -r 57def2d7c093 -r 8a7a42541080 test-data/freebayes-phix174.cram |
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| Binary file test-data/freebayes-phix174.cram has changed |
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| diff -r 57def2d7c093 -r 8a7a42541080 test-data/left-align-output.bam |
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| Binary file test-data/left-align-output.bam has changed |