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changeset 32:8a7a42541080 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit cce7fcdd5e8ba8636c751f9f974bf07a6845ba1c"
author iuc
date Wed, 01 Dec 2021 21:50:06 +0000
parents 57def2d7c093
children 04fa42777df9
files 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/freebayes-phix174.cram test-data/left-align-output.bam
diffstat 11 files changed, 43 insertions(+), 27 deletions(-) [+]
line wrap: on
line diff
--- 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**
--- a/macros.xml	Sat Nov 27 09:38:13 2021 +0000
+++ b/macros.xml	Wed Dec 01 21:50:06 2021 +0000
@@ -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>
--- 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
@@ -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 @@
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-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
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 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
--- 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
@@ -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
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-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
--- 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
@@ -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
--- 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
@@ -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
--- 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
@@ -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
--- 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
@@ -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
--- 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
@@ -1,6 +1,6 @@
 ##fileformat=VCFv4.2
 ##fileDate=20191030
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+##source=freeBayes v1.3.5
 ##reference=localref.fa
 ##contig=<ID=phiX174,length=5386>
 ##phasing=none
Binary file test-data/freebayes-phix174.cram has changed
Binary file test-data/left-align-output.bam has changed