Repository 'bcftools_call'
hg clone https://toolshed.g2.bx.psu.edu/repos/iuc/bcftools_call

Changeset 14:912a8ff07fc9 (2021-10-14)
Previous changeset 13:072f606e2e69 (2021-02-05) Next changeset 15:d267bcfdc8fe (2022-01-15)
Commit message:
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit d5a01866d60f9775392420988259f1e79c464163"
modified:
bcftools_call.xml
macros.xml
removed:
test-data/annotate4.vcf
test-data/annots4.tab
test-data/annots4.vcf
test-data/concat.3.0.vcf
test-data/concat.3.a.vcf
test-data/concat.3.b.vcf
test-data/concat.3.c.vcf
test-data/concat.3.d.vcf
test-data/concat.3.e.vcf
test-data/concat.3.f.vcf
test-data/consensus.1.chain
test-data/consensus.1.out
test-data/filter.4.vcf
test-data/mpileup.4.bam
test-data/mpileup.c.X.vcf
test-data/mpileup.c.vcf
test-data/mpileup.regions.bed
test-data/mpileup.regions.tab
test-data/mpileup.tab
test-data/query.filter.vcf
test-data/vcf2sex.vcf
test-data/view.filter.vcf
test-data/view.vcf_bgzip
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diff -r 072f606e2e69 -r 912a8ff07fc9 bcftools_call.xml
--- a/bcftools_call.xml Fri Feb 05 19:28:02 2021 +0000
+++ b/bcftools_call.xml Thu Oct 14 10:22:59 2021 +0000
b
@@ -1,6 +1,7 @@
 <?xml version='1.0' encoding='utf-8'?>
 <tool name="bcftools @EXECUTABLE@" id="bcftools_@EXECUTABLE@" version="@TOOL_VERSION@">
     <description>SNP/indel variant calling from VCF/BCF</description>
+    <expand macro="bio_tools" />
     <macros>
         <token name="@EXECUTABLE@">call</token>
         <import>macros.xml</import>
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diff -r 072f606e2e69 -r 912a8ff07fc9 macros.xml
--- a/macros.xml Fri Feb 05 19:28:02 2021 +0000
+++ b/macros.xml Thu Oct 14 10:22:59 2021 +0000
b
@@ -1,5 +1,10 @@
 <macros>
   <token name="@TOOL_VERSION@">1.10</token>
+  <xml name="bio_tools">
+      <xrefs>
+          <xref type="bio.tools">bcftools</xref>
+      </xrefs>
+  </xml>
   <xml name="requirements">
     <requirements>
       <requirement type="package" version="@TOOL_VERSION@">bcftools</requirement>
@@ -11,7 +16,7 @@
       <requirement type="package" version="1.10">samtools</requirement>
   </xml>
   <xml name="matplotlib_requirement">
-      <requirement type="package" version="3.1.0">matplotlib</requirement>
+      <requirement type="package" version="3.4.3">matplotlib</requirement>
   </xml>
   <xml name="version_command">
     <version_command>bcftools 2&gt;&amp;1 | grep 'Version:'</version_command>
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diff -r 072f606e2e69 -r 912a8ff07fc9 test-data/annotate4.vcf
--- a/test-data/annotate4.vcf Fri Feb 05 19:28:02 2021 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
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@@ -1,13 +0,0 @@
-##fileformat=VCFv4.2
-##INFO=<ID=FR,Number=R,Type=Float,Description="test">
-##INFO=<ID=FA,Number=A,Type=Float,Description="test">
-##INFO=<ID=IA,Number=A,Type=Integer,Description="test">
-##INFO=<ID=IR,Number=R,Type=Integer,Description="test">
-##INFO=<ID=SA,Number=A,Type=String,Description="test">
-##INFO=<ID=SR,Number=R,Type=String,Description="test">
-##contig=<ID=1,assembly=b37,length=249250621>
-##reference=file:///lustre/scratch105/projects/g1k/ref/main_project/human_g1k_v37.fasta
-#CHROM POS ID REF ALT QUAL FILTER INFO
-1 1 . C T . . .
-1 2 . C T,G . . FA=.,9.9;FR=.,9.9,.;IA=.,99;IR=.,99,.;SA=.,99;SR=.,99,.
-1 3 . C A,T . . .
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diff -r 072f606e2e69 -r 912a8ff07fc9 test-data/annots4.tab
--- a/test-data/annots4.tab Fri Feb 05 19:28:02 2021 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
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@@ -1,3 +0,0 @@
-1 1 C A,T,G 0,1.1,0 1.1,0,2.2,0 0,1,0 1,0,2,0 X,11,XXX 1,XX,222,XXX
-1 2 C T,G 1.1,2.2 1.1,2.2,3.3 1,2 1,2,3 11,2 111,22,3
-1 3 C T 1.1 1.1,2.2 1 1,2 11 11,2
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diff -r 072f606e2e69 -r 912a8ff07fc9 test-data/annots4.vcf
--- a/test-data/annots4.vcf Fri Feb 05 19:28:02 2021 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
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@@ -1,13 +0,0 @@
-##fileformat=VCFv4.2
-##INFO=<ID=FA,Number=A,Type=Float,Description="test">
-##INFO=<ID=FR,Number=R,Type=Float,Description="test">
-##INFO=<ID=IA,Number=A,Type=Integer,Description="test">
-##INFO=<ID=IR,Number=R,Type=Integer,Description="test">
-##INFO=<ID=SA,Number=A,Type=String,Description="test">
-##INFO=<ID=SR,Number=R,Type=String,Description="test">
-##contig=<ID=1,assembly=b37,length=249250621>
-##reference=file:///lustre/scratch105/projects/g1k/ref/main_project/human_g1k_v37.fasta
-#CHROM POS ID REF ALT QUAL FILTER INFO
-1 1 . C A,T,G . . FA=0,1.1,0;FR=1.1,0,2.2,0;IA=0,1,0;IR=1,0,2,0;SA=X,11,XXX;SR=1,XX,222,XXX
-1 2 . C T,G . . FA=1.1,2.2;FR=1.1,2.2,3.3;IA=1,2;IR=1,2,3;SA=11,2;SR=111,22,3
-1 3 . C T . . FA=1.1;FR=1.1,2.2;IA=1;IR=1,2;SA=11;SR=11,2
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diff -r 072f606e2e69 -r 912a8ff07fc9 test-data/concat.3.0.vcf
--- a/test-data/concat.3.0.vcf Fri Feb 05 19:28:02 2021 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
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@@ -1,8 +0,0 @@
-##fileformat=VCFv4.0
-##INFO=<ID=DP,Number=1,Type=Integer,Description="Total Depth">
-##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
-##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality">
-##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read Depth">
-##FILTER=<ID=q10,Description="Quality below 10">
-##contig=<ID=2,length=62435964>
-#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT A B
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diff -r 072f606e2e69 -r 912a8ff07fc9 test-data/concat.3.a.vcf
--- a/test-data/concat.3.a.vcf Fri Feb 05 19:28:02 2021 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
b
@@ -1,27 +0,0 @@
-##fileformat=VCFv4.0
-##INFO=<ID=DP,Number=1,Type=Integer,Description="Total Depth">
-##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
-##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality">
-##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read Depth">
-##FILTER=<ID=q10,Description="Quality below 10">
-##contig=<ID=9,length=62435964>
-##contig=<ID=1,length=62435964>
-#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT A B
-9 202 . GTTT G 1806 q10 DP=35 GT:GQ:DP 0|1:409:35 0|1
-9 212 . C T,G 1792 PASS DP=32 GT:GQ:DP 0|1:245:32 0|1
-9 212 . CAAA C 1792 PASS DP=32 GT:GQ:DP 0|1:245:32 0|1
-9 222 . GA G 628 q10 DP=21 GT:GQ:DP 0|1:21:21 0|1
-9 232 . G T 1016 PASS DP=22 GT:GQ:DP 0|1:212:22 0|1
-9 232 . GAA GG 1016 PASS DP=22 GT:GQ:DP 0|1:212:22 0|1
-9 242 . GT G 727 PASS DP=30 GT:GQ:DP 0|1:150:30 0|1
-9 252 . TAAAA TA,T 246 PASS DP=10 GT:GQ:DP 0|1:12:10 0|1
-9 262 . TAAAA TA,T 246 PASS DP=10 GT:GQ:DP 0|1:12:10 0|1
-1 100 . GTTT G 1806 q10 DP=35 GT:GQ:DP 0|1:409:35 0|1
-1 110 . C T,G 1792 PASS DP=32 GT:GQ:DP 0|1:245:32 0|1
-1 110 . CAAA C 1792 PASS DP=32 GT:GQ:DP 0|1:245:32 0|1
-1 120 . GA G 628 q10 DP=21 GT:GQ:DP 0|1:21:21 0|1
-1 130 . G T 1016 PASS DP=22 GT:GQ:DP 0|1:212:22 0|1
-1 130 . GAA GG 1016 PASS DP=22 GT:GQ:DP 0|1:212:22 0|1
-1 140 . GT G 727 PASS DP=30 GT:GQ:DP 0|1:150:30 0|1
-1 150 . TAAAA TA,T 246 PASS DP=10 GT:GQ:DP 0|1:12:10 0|1
-1 160 . TAAAA TA,T 246 PASS DP=10 GT:GQ:DP 0|1:12:10 0|1
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diff -r 072f606e2e69 -r 912a8ff07fc9 test-data/concat.3.b.vcf
--- a/test-data/concat.3.b.vcf Fri Feb 05 19:28:02 2021 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
b
b'@@ -1,223 +0,0 @@\n-##fileformat=VCFv4.0\n-##INFO=<ID=T1,Number=1,Type=Integer,Description="Test Tag: Big header">\n-##INFO=<ID=T2,Number=1,Type=Integer,Description="Test Tag: Big header">\n-##INFO=<ID=T3,Number=1,Type=Integer,Description="Test Tag: Big header">\n-##INFO=<ID=T4,Number=1,Type=Integer,Description="Test Tag: Big header">\n-##INFO=<ID=T5,Number=1,Type=Integer,Description="Test Tag: Big header">\n-##INFO=<ID=T6,Number=1,Type=Integer,Description="Test Tag: Big header">\n-##INFO=<ID=T7,Number=1,Type=Integer,Description="Test Tag: Big header">\n-##INFO=<ID=T8,Number=1,Type=Integer,Description="Test Tag: Big header">\n-##INFO=<ID=T9,Number=1,Type=Integer,Description="Test Tag: Big header">\n-##INFO=<ID=T10,Number=1,Type=Integer,Description="Test Tag: Big header">\n-##INFO=<ID=T11,Number=1,Type=Integer,Description="Test Tag: Big header">\n-##INFO=<ID=T12,Number=1,Type=Integer,Description="Test Tag: Big header">\n-##INFO=<ID=T13,Number=1,Type=Integer,Description="Test Tag: Big header">\n-##INFO=<ID=T14,Number=1,Type=Integer,Description="Test Tag: Big header">\n-##INFO=<ID=T15,Number=1,Type=Integer,Description="Test Tag: Big header">\n-##INFO=<ID=T16,Number=1,Type=Integer,Description="Test Tag: Big header">\n-##INFO=<ID=T17,Number=1,Type=Integer,Description="Test Tag: Big header">\n-##INFO=<ID=T18,Number=1,Type=Integer,Description="Test Tag: Big header">\n-##INFO=<ID=T19,Number=1,Type=Integer,Description="Test Tag: Big header">\n-##INFO=<ID=T20,Number=1,Type=Integer,Description="Test Tag: Big header">\n-##INFO=<ID=T21,Number=1,Type=Integer,Description="Test Tag: Big header">\n-##INFO=<ID=T22,Number=1,Type=Integer,Description="Test Tag: Big header">\n-##INFO=<ID=T23,Number=1,Type=Integer,Description="Test Tag: Big header">\n-##INFO=<ID=T24,Number=1,Type=Integer,Description="Test Tag: Big header">\n-##INFO=<ID=T25,Number=1,Type=Integer,Description="Test Tag: Big header">\n-##INFO=<ID=T26,Number=1,Type=Integer,Description="Test Tag: Big header">\n-##INFO=<ID=T27,Number=1,Type=Integer,Description="Test Tag: Big header">\n-##INFO=<ID=T28,Number=1,Type=Integer,Description="Test Tag: Big header">\n-##INFO=<ID=T29,Number=1,Type=Integer,Description="Test Tag: Big header">\n-##INFO=<ID=T30,Number=1,Type=Integer,Description="Test Tag: Big header">\n-##INFO=<ID=T31,Number=1,Type=Integer,Description="Test Tag: Big header">\n-##INFO=<ID=T32,Number=1,Type=Integer,Description="Test Tag: Big header">\n-##INFO=<ID=T33,Number=1,Type=Integer,Description="Test Tag: Big header">\n-##INFO=<ID=T34,Number=1,Type=Integer,Description="Test Tag: Big header">\n-##INFO=<ID=T35,Number=1,Type=Integer,Description="Test Tag: Big header">\n-##INFO=<ID=T36,Number=1,Type=Integer,Description="Test Tag: Big header">\n-##INFO=<ID=T37,Number=1,Type=Integer,Description="Test Tag: Big header">\n-##INFO=<ID=T38,Number=1,Type=Integer,Description="Test Tag: Big header">\n-##INFO=<ID=T39,Number=1,Type=Integer,Description="Test Tag: Big header">\n-##INFO=<ID=T40,Number=1,Type=Integer,Description="Test Tag: Big header">\n-##INFO=<ID=T41,Number=1,Type=Integer,Description="Test Tag: Big header">\n-##INFO=<ID=T42,Number=1,Type=Integer,Description="Test Tag: Big header">\n-##INFO=<ID=T43,Number=1,Type=Integer,Description="Test Tag: Big header">\n-##INFO=<ID=T44,Number=1,Type=Integer,Description="Test Tag: Big header">\n-##INFO=<ID=T45,Number=1,Type=Integer,Description="Test Tag: Big header">\n-##INFO=<ID=T46,Number=1,Type=Integer,Description="Test Tag: Big header">\n-##INFO=<ID=T47,Number=1,Type=Integer,Description="Test Tag: Big header">\n-##INFO=<ID=T48,Number=1,Type=Integer,Description="Test Tag: Big header">\n-##INFO=<ID=T49,Number=1,Type=Integer,Description="Test Tag: Big header">\n-##INFO=<ID=T50,Number=1,Type=Integer,Description="Test Tag: Big header">\n-##INFO=<ID=T51,Number=1,Type=Integer,Description="Test Tag: Big header">\n-##INFO=<ID=T52,Number=1,Type=Integer,Description="Test Tag: Big header">\n-##INFO=<ID=T53,Number=1,Type=Integer,Description="Test Tag: Big header">\n-##INFO=<ID=T54,Number=1,Type=Integer,Descript'..b'er=1,Type=Integer,Description="Test Tag: Big header">\n-##INFO=<ID=T161,Number=1,Type=Integer,Description="Test Tag: Big header">\n-##INFO=<ID=T162,Number=1,Type=Integer,Description="Test Tag: Big header">\n-##INFO=<ID=T163,Number=1,Type=Integer,Description="Test Tag: Big header">\n-##INFO=<ID=T164,Number=1,Type=Integer,Description="Test Tag: Big header">\n-##INFO=<ID=T165,Number=1,Type=Integer,Description="Test Tag: Big header">\n-##INFO=<ID=T166,Number=1,Type=Integer,Description="Test Tag: Big header">\n-##INFO=<ID=T167,Number=1,Type=Integer,Description="Test Tag: Big header">\n-##INFO=<ID=T168,Number=1,Type=Integer,Description="Test Tag: Big header">\n-##INFO=<ID=T169,Number=1,Type=Integer,Description="Test Tag: Big header">\n-##INFO=<ID=T170,Number=1,Type=Integer,Description="Test Tag: Big header">\n-##INFO=<ID=T171,Number=1,Type=Integer,Description="Test Tag: Big header">\n-##INFO=<ID=T172,Number=1,Type=Integer,Descripti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diff -r 072f606e2e69 -r 912a8ff07fc9 test-data/concat.3.c.vcf
--- a/test-data/concat.3.c.vcf Fri Feb 05 19:28:02 2021 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
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@@ -1,22 +0,0 @@
-##fileformat=VCFv4.0
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-##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
-##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality">
-##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read Depth">
-##FILTER=<ID=q10,Description="Quality below 10">
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-#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT A B
-2 280 . T A 246 PASS DP=10 GT 1|0 0|1
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-2 410 . T A 246 PASS DP=10 GT 0|1 1|0
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diff -r 072f606e2e69 -r 912a8ff07fc9 test-data/concat.3.d.vcf
--- a/test-data/concat.3.d.vcf Fri Feb 05 19:28:02 2021 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
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@@ -1,20 +0,0 @@
-##fileformat=VCFv4.0
-##INFO=<ID=DP,Number=1,Type=Integer,Description="Total Depth">
-##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
-##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality">
-##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read Depth">
-##FILTER=<ID=q10,Description="Quality below 10">
-##contig=<ID=2,length=62435964>
-#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT A B
-2 300 . T A 246 PASS DP=10 GT 1|0 1|0
-2 320 . T A 246 PASS DP=10 GT 1|0 1|0
-2 330 . T A 246 PASS DP=10 GT 1|0 1|0
-2 340 . T A 246 PASS DP=10 GT 1|0 1|0
-2 350 . T A 246 PASS DP=10 GT 1|0 1|0
-2 360 . T A 246 PASS DP=10 GT 1|0 1|0
-2 370 . T A 246 PASS DP=10 GT 1|0 1|0
-2 380 . T A 246 PASS DP=10 GT 1|0 1|0
-2 390 . T A 246 PASS DP=10 GT 1|0 1|0
-2 490 . T A 246 PASS DP=10 GT 1|0 1|0
-2 500 . T A 246 PASS DP=10 GT 1|0 1|0
-2 510 . T A 246 PASS DP=10 GT 1|0 1|0
b
diff -r 072f606e2e69 -r 912a8ff07fc9 test-data/concat.3.e.vcf
--- a/test-data/concat.3.e.vcf Fri Feb 05 19:28:02 2021 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
b
@@ -1,20 +0,0 @@
-##fileformat=VCFv4.0
-##INFO=<ID=DP,Number=1,Type=Integer,Description="Total Depth">
-##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
-##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality">
-##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read Depth">
-##FILTER=<ID=q10,Description="Quality below 10">
-##contig=<ID=2,length=62435964>
-#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT A B
-2 310 . T A 246 PASS DP=10 GT 0|1 0|1
-2 320 . T A 246 PASS DP=10 GT 0|1 0|1
-2 330 . T A 246 PASS DP=10 GT 0|1 0|1
-2 340 . T A 246 PASS DP=10 GT 0|1 0|1
-2 350 . T A 246 PASS DP=10 GT 0|1 0|1
-2 360 . T A 246 PASS DP=10 GT 0|1 0|1
-2 370 . T A 246 PASS DP=10 GT 0|1 0|1
-2 380 . T A 246 PASS DP=10 GT 0|1 0|1
-2 390 . T A 246 PASS DP=10 GT 0|1 0|1
-2 490 . T A 246 PASS DP=10 GT 0|1 0|1
-2 500 . T A 246 PASS DP=10 GT 0|1 0|1
-2 510 . T A 246 PASS DP=10 GT 0|1 0|1
b
diff -r 072f606e2e69 -r 912a8ff07fc9 test-data/concat.3.f.vcf
--- a/test-data/concat.3.f.vcf Fri Feb 05 19:28:02 2021 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
b
@@ -1,20 +0,0 @@
-##fileformat=VCFv4.0
-##INFO=<ID=DP,Number=1,Type=Integer,Description="Total Depth">
-##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
-##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality">
-##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read Depth">
-##FILTER=<ID=q10,Description="Quality below 10">
-##contig=<ID=3,length=62435964>
-#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT A B
-3 380 . T A 246 PASS DP=10 GT 1|0 1|0
-3 390 . T A 246 PASS DP=10 GT 1|0 1|0
-3 400 . T A 246 PASS DP=10 GT 1|0 1|0
-3 410 . T A 246 PASS DP=10 GT 1|0 1|0
-3 420 . T A 246 PASS DP=10 GT 1|0 1|0
-3 430 . T A 246 PASS DP=10 GT 1|0 1|0
-3 440 . T A 246 PASS DP=10 GT 1|0 1|0
-3 450 . T A 246 PASS DP=10 GT 1|0 1|0
-3 460 . T A 246 PASS DP=10 GT 1|0 1|0
-3 470 . T A 246 PASS DP=10 GT 1|0 1|0
-3 480 . T A 246 PASS DP=10 GT 1|0 1|0
-3 490 . T A 246 PASS DP=10 GT 1|0 1|0
b
diff -r 072f606e2e69 -r 912a8ff07fc9 test-data/consensus.1.chain
--- a/test-data/consensus.1.chain Fri Feb 05 19:28:02 2021 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
b
@@ -1,12 +0,0 @@
-chain 497 1 501 + 1 501 1 502 + 1 502 1
-11 3 1
-1 0 3
-485
-
-chain 485 2 501 + 0 501 2 495 + 0 495 2
-61 3 1
-54 3 1
-58 0 8
-21 10 0
-291
-
b
diff -r 072f606e2e69 -r 912a8ff07fc9 test-data/consensus.1.out
--- a/test-data/consensus.1.out Fri Feb 05 19:28:02 2021 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
b
@@ -1,20 +0,0 @@
->1:2-501
-TACAAAATATGATAAAATCAAAAAGAACATAACCTACGTATCAACTAAAGTGGTTGTTTG
-AAGAAAAGGAAGACTTAAAAAGAGTCAGTACTAACCTACATAATATATACAATGTTCATT
-AAATAATAAAATGAGCTCATCATACTTAGGTCATCATAAATATATCTGAAATTCACAAAT
-ATTGATCAAATGGTAAAATAGACAAGTAGATTTTAATAGGTTAAACAATTACTGATTCTC
-TTGAAAGAATAAATTTAATATGAGACCTATTTCATTATAATGAACTCACAAATTAGAAAC
-TTCACACTGGGGGCTGGAGAGATGGCTCAGTAGTTAAGAACACTGACTGCTCTTCTGAAG
-GTCCTGAGTTCAAATCCCAGCAACCACATGGTGACTTACAACCATCTGTAATGACATCTG
-NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
-TTTAAAAACAAAAAAAAAGAA
->2
-NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
-AAATTAGTGATTTTCCATATTCTTTAAGTCATTTTAGAGTAATGTGTTCTTAAGATTTCA
-GAAAAACAAAAACTTGTGCTTTCCTGTTTGAAAAACAAACAGCTGTGGGGAATGGACGTA
-CGTTGTCGGGACAGCCTTTTTATAAAATAATGTTGAGGCTTTGATACGTCAAAGNNNNNN
-NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNTTTGCT
-GCTGCCAATGACAGCACACCCTGGGAATGCCCCAACTACTTACTACAAAGCAGTGTTACA
-TGGAGAAGATCTTCAAGAGTCTTTTTGCTAGATCTTTCCTTGGCTTTTGATGTGACTCCT
-CTCAATAAAATCCACAGTAATATAGTGAGTGGTCTCCTGCTCCAAACCAGTATTCCAGAC
-ACAGTTAATCCAGAC
b
diff -r 072f606e2e69 -r 912a8ff07fc9 test-data/filter.4.vcf
--- a/test-data/filter.4.vcf Fri Feb 05 19:28:02 2021 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
b
@@ -1,10 +0,0 @@
-##fileformat=VCFv4.1
-##contig=<ID=chr1,length=135006516>
-##INFO=<ID=TEST1,Number=1,Type=Integer,Description="Test1">
-##INFO=<ID=TEST2,Number=1,Type=Float,Description="Test2">
-##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
-##FORMAT=<ID=TEST3,Number=1,Type=Integer,Description="Test3">
-##FORMAT=<ID=TEST4,Number=1,Type=Float,Description="Test4">
-#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT sample1 sample2
-chr1 1 . A T 100 . TEST1=10;TEST2=10 GT:TEST3:TEST4 0/1:10:10 0/1:30:30
-chr1 2 . A T 100 . TEST1=50;TEST2=50 GT:TEST3:TEST4 0/1:20:20 0/1:40:40
b
diff -r 072f606e2e69 -r 912a8ff07fc9 test-data/mpileup.4.bam
b
Binary file test-data/mpileup.4.bam has changed
b
diff -r 072f606e2e69 -r 912a8ff07fc9 test-data/mpileup.c.X.vcf
--- a/test-data/mpileup.c.X.vcf Fri Feb 05 19:28:02 2021 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
b
b'@@ -1,4127 +0,0 @@\n-##fileformat=VCFv4.2\n-##FILTER=<ID=PASS,Description="All filters passed">\n-##samtoolsVersion=1.1-19-g6b249e2+htslib-1.1-74-g845c515\n-##samtoolsCommand=samtools mpileup -uvDV -b xxx//mpileup.bam.list -f xxx//mpileup.ref.fa.gz\n-##reference=file://xxx//mpileup.ref.fa.gz\n-##contig=<ID=X,length=81195210>\n-##ALT=<ID=X,Description="Represents allele(s) other than observed.">\n-##INFO=<ID=INDEL,Number=0,Type=Flag,Description="Indicates that the variant is an INDEL.">\n-##INFO=<ID=IDV,Number=1,Type=Integer,Description="Maximum number of reads supporting an indel">\n-##INFO=<ID=IMF,Number=1,Type=Float,Description="Maximum fraction of reads supporting an indel">\n-##INFO=<ID=DP,Number=1,Type=Integer,Description="Raw read depth">\n-##INFO=<ID=VDB,Number=1,Type=Float,Description="Variant Distance Bias for filtering splice-site artefacts in RNA-seq data (bigger is better)",Version="3">\n-##INFO=<ID=RPB,Number=1,Type=Float,Description="Mann-Whitney U test of Read Position Bias (bigger is better)">\n-##INFO=<ID=MQB,Number=1,Type=Float,Description="Mann-Whitney U test of Mapping Quality Bias (bigger is better)">\n-##INFO=<ID=BQB,Number=1,Type=Float,Description="Mann-Whitney U test of Base Quality Bias (bigger is better)">\n-##INFO=<ID=MQSB,Number=1,Type=Float,Description="Mann-Whitney U test of Mapping Quality vs Strand Bias (bigger is better)">\n-##INFO=<ID=SGB,Number=1,Type=Float,Description="Segregation based metric.">\n-##INFO=<ID=MQ0F,Number=1,Type=Float,Description="Fraction of MQ0 reads (smaller is better)">\n-##INFO=<ID=I16,Number=16,Type=Float,Description="Auxiliary tag used for calling, see description of bcf_callret1_t in bam2bcf.h">\n-##INFO=<ID=QS,Number=R,Type=Float,Description="Auxiliary tag used for calling">\n-##FORMAT=<ID=PL,Number=G,Type=Integer,Description="List of Phred-scaled genotype likelihoods">\n-##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Number of high-quality bases">\n-##FORMAT=<ID=DV,Number=1,Type=Integer,Description="Number of high-quality non-reference bases">\n-#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT\tHG00100\tHG00101\tHG00102\n-X\t1\t.\tA\t<*>\t0\t.\tDP=11;I16=11,0,0,0,452,18594,0,0,319,9251,0,0,223,4959,0,0;QS=3,0;MQ0F=0\tPL:DP:DV\t0,15,100:5:0\t0,9,72:3:0\t0,9,72:3:0\n-X\t2\t.\tA\t<*>\t0\t.\tDP=11;I16=11,0,0,0,439,17587,0,0,319,9251,0,0,226,5030,0,0;QS=3,0;MQ0F=0\tPL:DP:DV\t0,15,100:5:0\t0,9,72:3:0\t0,9,72:3:0\n-X\t3\t.\tG\t<*>\t0\t.\tDP=11;I16=11,0,0,0,431,16971,0,0,319,9251,0,0,229,5111,0,0;QS=3,0;MQ0F=0\tPL:DP:DV\t0,15,100:5:0\t0,9,72:3:0\t0,9,72:3:0\n-X\t4\t.\tC\t<*>\t0\t.\tDP=11;I16=11,0,0,0,423,16417,0,0,319,9251,0,0,232,5202,0,0;QS=3,0;MQ0F=0\tPL:DP:DV\t0,15,100:5:0\t0,9,72:3:0\t0,9,71:3:0\n-X\t5\t.\tT\t<*>\t0\t.\tDP=11;I16=11,0,0,0,450,18520,0,0,319,9251,0,0,234,5252,0,0;QS=3,0;MQ0F=0\tPL:DP:DV\t0,15,100:5:0\t0,9,72:3:0\t0,9,72:3:0\n-X\t6\t.\tT\t<*>\t0\t.\tDP=11;I16=11,0,0,0,403,14847,0,0,319,9251,0,0,236,5310,0,0;QS=3,0;MQ0F=0\tPL:DP:DV\t0,15,100:5:0\t0,9,72:3:0\t0,9,72:3:0\n-X\t7\t.\tC\t<*>\t0\t.\tDP=11;I16=11,0,0,0,446,18114,0,0,319,9251,0,0,237,5327,0,0;QS=3,0;MQ0F=0\tPL:DP:DV\t0,15,100:5:0\t0,9,72:3:0\t0,9,72:3:0\n-X\t8\t.\tT\t<*>\t0\t.\tDP=11;I16=11,0,0,0,465,19677,0,0,319,9251,0,0,238,5354,0,0;QS=3,0;MQ0F=0\tPL:DP:DV\t0,15,100:5:0\t0,9,72:3:0\t0,9,72:3:0\n-X\t9\t.\tC\t<*>\t0\t.\tDP=11;I16=11,0,0,0,447,18205,0,0,319,9251,0,0,239,5391,0,0;QS=3,0;MQ0F=0\tPL:DP:DV\t0,15,100:5:0\t0,9,72:3:0\t0,9,72:3:0\n-X\t10\t.\tA\t<*>\t0\t.\tDP=11;I16=11,0,0,0,426,16756,0,0,319,9251,0,0,240,5438,0,0;QS=3,0;MQ0F=0\tPL:DP:DV\t0,15,100:5:0\t0,9,72:3:0\t0,9,69:3:0\n-X\t11\t.\tC\t<*>\t0\t.\tDP=11;I16=11,0,0,0,413,15603,0,0,319,9251,0,0,241,5495,0,0;QS=3,0;MQ0F=0\tPL:DP:DV\t0,15,100:5:0\t0,9,72:3:0\t0,9,72:3:0\n-X\t12\t.\tC\t<*>\t0\t.\tDP=11;I16=11,0,0,0,438,17506,0,0,319,9251,0,0,242,5562,0,0;QS=3,0;MQ0F=0\tPL:DP:DV\t0,15,100:5:0\t0,9,72:3:0\t0,9,72:3:0\n-X\t13\t.\tC\t<*>\t0\t.\tDP=11;I16=11,0,0,0,437,17463,0,0,319,9251,0,0,243,5639,0,0;QS=3,0;MQ0F=0\tPL:DP:DV\t0,15,100:5:0\t0,9,72:3:0\t0,9,72:3:0\n-X\t14\t.\tT\t<*>\t0\t.\tDP=11;I16=11,0,0,0,453,18715,0,0,319,9251,0,0,242,5628,0,0;QS=3,0;MQ0F=0\tPL:DP:DV\t0,15,100:5:0\t0,9,72:3:0\t0,9,72:3:0\n-X\t15\t.\tG\t<*>\t0\t.\tDP=11;I1'..b'1,0;MQSB=0.333333;MQ0F=0\tPL:DP:DV\t0,15,142:5:0\t0,0,0:0:0\t0,0,0:0:0\n-X\t4072\t.\tG\t<*>\t0\t.\tDP=5;I16=2,2,0,0,138,4974,0,0,194,9938,0,0,55,987,0,0;QS=1,0;MQSB=0;MQ0F=0\tPL:DP:DV\t0,12,122:4:0\t0,0,0:0:0\t0,0,0:0:0\n-X\t4073\t.\tG\t<*>\t0\t.\tDP=5;I16=3,2,0,0,156,5082,0,0,254,13538,0,0,60,994,0,0;QS=1,0;MQSB=0.333333;MQ0F=0\tPL:DP:DV\t0,15,136:5:0\t0,0,0:0:0\t0,0,0:0:0\n-X\t4074\t.\tC\t<*>\t0\t.\tDP=5;I16=3,2,0,0,160,5602,0,0,254,13538,0,0,56,928,0,0;QS=1,0;MQSB=0.333333;MQ0F=0\tPL:DP:DV\t0,15,142:5:0\t0,0,0:0:0\t0,0,0:0:0\n-X\t4075\t.\tT\t<*>\t0\t.\tDP=5;I16=3,2,0,0,187,7069,0,0,254,13538,0,0,52,870,0,0;QS=1,0;MQSB=0.333333;MQ0F=0\tPL:DP:DV\t0,15,155:5:0\t0,0,0:0:0\t0,0,0:0:0\n-X\t4076\t.\tG\t<*>\t0\t.\tDP=5;I16=3,2,0,0,174,6298,0,0,254,13538,0,0,48,820,0,0;QS=1,0;MQ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b
diff -r 072f606e2e69 -r 912a8ff07fc9 test-data/mpileup.c.vcf
--- a/test-data/mpileup.c.vcf Fri Feb 05 19:28:02 2021 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
b
b'@@ -1,4127 +0,0 @@\n-##fileformat=VCFv4.2\n-##FILTER=<ID=PASS,Description="All filters passed">\n-##samtoolsVersion=1.1-19-g6b249e2+htslib-1.1-74-g845c515\n-##samtoolsCommand=samtools mpileup -uvDV -b xxx//mpileup.bam.list -f xxx//mpileup.ref.fa.gz\n-##reference=file://xxx//mpileup.ref.fa.gz\n-##contig=<ID=17,length=81195210>\n-##ALT=<ID=X,Description="Represents allele(s) other than observed.">\n-##INFO=<ID=INDEL,Number=0,Type=Flag,Description="Indicates that the variant is an INDEL.">\n-##INFO=<ID=IDV,Number=1,Type=Integer,Description="Maximum number of reads supporting an indel">\n-##INFO=<ID=IMF,Number=1,Type=Float,Description="Maximum fraction of reads supporting an indel">\n-##INFO=<ID=DP,Number=1,Type=Integer,Description="Raw read depth">\n-##INFO=<ID=VDB,Number=1,Type=Float,Description="Variant Distance Bias for filtering splice-site artefacts in RNA-seq data (bigger is better)",Version="3">\n-##INFO=<ID=RPB,Number=1,Type=Float,Description="Mann-Whitney U test of Read Position Bias (bigger is better)">\n-##INFO=<ID=MQB,Number=1,Type=Float,Description="Mann-Whitney U test of Mapping Quality Bias (bigger is better)">\n-##INFO=<ID=BQB,Number=1,Type=Float,Description="Mann-Whitney U test of Base Quality Bias (bigger is better)">\n-##INFO=<ID=MQSB,Number=1,Type=Float,Description="Mann-Whitney U test of Mapping Quality vs Strand Bias (bigger is better)">\n-##INFO=<ID=SGB,Number=1,Type=Float,Description="Segregation based metric.">\n-##INFO=<ID=MQ0F,Number=1,Type=Float,Description="Fraction of MQ0 reads (smaller is better)">\n-##INFO=<ID=I16,Number=16,Type=Float,Description="Auxiliary tag used for calling, see description of bcf_callret1_t in bam2bcf.h">\n-##INFO=<ID=QS,Number=R,Type=Float,Description="Auxiliary tag used for calling">\n-##FORMAT=<ID=PL,Number=G,Type=Integer,Description="List of Phred-scaled genotype likelihoods">\n-##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Number of high-quality bases">\n-##FORMAT=<ID=DV,Number=1,Type=Integer,Description="Number of high-quality non-reference bases">\n-#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT\tHG00100\tHG00101\tHG00102\n-17\t1\t.\tA\t<X>\t0\t.\tDP=11;I16=11,0,0,0,452,18594,0,0,319,9251,0,0,223,4959,0,0;QS=3,0;MQ0F=0\tPL:DP:DV\t0,15,100:5:0\t0,9,72:3:0\t0,9,72:3:0\n-17\t2\t.\tA\t<X>\t0\t.\tDP=11;I16=11,0,0,0,439,17587,0,0,319,9251,0,0,226,5030,0,0;QS=3,0;MQ0F=0\tPL:DP:DV\t0,15,100:5:0\t0,9,72:3:0\t0,9,72:3:0\n-17\t3\t.\tG\t<X>\t0\t.\tDP=11;I16=11,0,0,0,431,16971,0,0,319,9251,0,0,229,5111,0,0;QS=3,0;MQ0F=0\tPL:DP:DV\t0,15,100:5:0\t0,9,72:3:0\t0,9,72:3:0\n-17\t4\t.\tC\t<X>\t0\t.\tDP=11;I16=11,0,0,0,423,16417,0,0,319,9251,0,0,232,5202,0,0;QS=3,0;MQ0F=0\tPL:DP:DV\t0,15,100:5:0\t0,9,72:3:0\t0,9,71:3:0\n-17\t5\t.\tT\t<X>\t0\t.\tDP=11;I16=11,0,0,0,450,18520,0,0,319,9251,0,0,234,5252,0,0;QS=3,0;MQ0F=0\tPL:DP:DV\t0,15,100:5:0\t0,9,72:3:0\t0,9,72:3:0\n-17\t6\t.\tT\t<X>\t0\t.\tDP=11;I16=11,0,0,0,403,14847,0,0,319,9251,0,0,236,5310,0,0;QS=3,0;MQ0F=0\tPL:DP:DV\t0,15,100:5:0\t0,9,72:3:0\t0,9,72:3:0\n-17\t7\t.\tC\t<X>\t0\t.\tDP=11;I16=11,0,0,0,446,18114,0,0,319,9251,0,0,237,5327,0,0;QS=3,0;MQ0F=0\tPL:DP:DV\t0,15,100:5:0\t0,9,72:3:0\t0,9,72:3:0\n-17\t8\t.\tT\t<X>\t0\t.\tDP=11;I16=11,0,0,0,465,19677,0,0,319,9251,0,0,238,5354,0,0;QS=3,0;MQ0F=0\tPL:DP:DV\t0,15,100:5:0\t0,9,72:3:0\t0,9,72:3:0\n-17\t9\t.\tC\t<X>\t0\t.\tDP=11;I16=11,0,0,0,447,18205,0,0,319,9251,0,0,239,5391,0,0;QS=3,0;MQ0F=0\tPL:DP:DV\t0,15,100:5:0\t0,9,72:3:0\t0,9,72:3:0\n-17\t10\t.\tA\t<X>\t0\t.\tDP=11;I16=11,0,0,0,426,16756,0,0,319,9251,0,0,240,5438,0,0;QS=3,0;MQ0F=0\tPL:DP:DV\t0,15,100:5:0\t0,9,72:3:0\t0,9,69:3:0\n-17\t11\t.\tC\t<X>\t0\t.\tDP=11;I16=11,0,0,0,413,15603,0,0,319,9251,0,0,241,5495,0,0;QS=3,0;MQ0F=0\tPL:DP:DV\t0,15,100:5:0\t0,9,72:3:0\t0,9,72:3:0\n-17\t12\t.\tC\t<X>\t0\t.\tDP=11;I16=11,0,0,0,438,17506,0,0,319,9251,0,0,242,5562,0,0;QS=3,0;MQ0F=0\tPL:DP:DV\t0,15,100:5:0\t0,9,72:3:0\t0,9,72:3:0\n-17\t13\t.\tC\t<X>\t0\t.\tDP=11;I16=11,0,0,0,437,17463,0,0,319,9251,0,0,243,5639,0,0;QS=3,0;MQ0F=0\tPL:DP:DV\t0,15,100:5:0\t0,9,72:3:0\t0,9,72:3:0\n-17\t14\t.\tT\t<X>\t0\t.\tDP=11;I16=11,0,0,0,453,18715,0,0,319,9251,0,0,242,5628,0,0;QS=3,0;MQ0F=0\tPL:DP:DV\t0,15,100:5:0\t0,9,72:3:0\t0,9,72:3:0\n-17\t15\t.\tG\t'..b':DV\t0,15,142:5:0\t0,0,0:0:0\t0,0,0:0:0\n-17\t4072\t.\tG\t<X>\t0\t.\tDP=5;I16=2,2,0,0,138,4974,0,0,194,9938,0,0,55,987,0,0;QS=1,0;MQSB=0;MQ0F=0\tPL:DP:DV\t0,12,122:4:0\t0,0,0:0:0\t0,0,0:0:0\n-17\t4073\t.\tG\t<X>\t0\t.\tDP=5;I16=3,2,0,0,156,5082,0,0,254,13538,0,0,60,994,0,0;QS=1,0;MQSB=0.333333;MQ0F=0\tPL:DP:DV\t0,15,136:5:0\t0,0,0:0:0\t0,0,0:0:0\n-17\t4074\t.\tC\t<X>\t0\t.\tDP=5;I16=3,2,0,0,160,5602,0,0,254,13538,0,0,56,928,0,0;QS=1,0;MQSB=0.333333;MQ0F=0\tPL:DP:DV\t0,15,142:5:0\t0,0,0:0:0\t0,0,0:0:0\n-17\t4075\t.\tT\t<X>\t0\t.\tDP=5;I16=3,2,0,0,187,7069,0,0,254,13538,0,0,52,870,0,0;QS=1,0;MQSB=0.333333;MQ0F=0\tPL:DP:DV\t0,15,155:5:0\t0,0,0:0:0\t0,0,0:0:0\n-17\t4076\t.\tG\t<X>\t0\t.\tDP=5;I16=3,2,0,0,174,6298,0,0,254,13538,0,0,48,820,0,0;QS=1,0;MQSB=0.333333;MQ0F=0\tPL:DP:DV\t0,15,149:5:0\t0,0,0:0:0\t0,0,0:0:0\n-17\t4077\t.\tA\t<X>\t0\t.\tDP=4;I16=3,1,0,0,138,4810,0,0,194,9938,0,0,44,728,0,0;QS=1,0;MQSB=1;MQ0F=0\tPL:DP:DV\t0,12,121:4:0\t0,0,0:0:0\t0,0,0:0:0\n-17\t4078\t.\tT\t<X>\t0\t.\tDP=4;I16=3,1,0,0,143,5173,0,0,194,9938,0,0,40,644,0,0;QS=1,0;MQSB=1;MQ0F=0\tPL:DP:DV\t0,12,124:4:0\t0,0,0:0:0\t0,0,0:0:0\n-17\t4079\t.\tA\t<X>\t0\t.\tDP=4;I16=3,1,0,0,121,3847,0,0,194,9938,0,0,36,568,0,0;QS=1,0;MQSB=1;MQ0F=0\tPL:DP:DV\t0,12,107:4:0\t0,0,0:0:0\t0,0,0:0:0\n-17\t4080\t.\tT\t<X>\t0\t.\tDP=4;I16=3,0,0,0,106,3778,0,0,134,6338,0,0,25,451,0,0;QS=1,0;MQ0F=0\tPL:DP:DV\t0,9,87:3:0\t0,0,0:0:0\t0,0,0:0:0\n-17\t4081\t.\tT\t<X>\t0\t.\tDP=4;I16=3,1,0,0,106,2934,0,0,194,9938,0,0,28,440,0,0;QS=1,0;MQSB=1;MQ0F=0\tPL:DP:DV\t0,12,94:4:0\t0,0,0:0:0\t0,0,0:0:0\n-17\t4082\t.\tC\t<X>\t0\t.\tDP=3;I16=2,1,0,0,110,4042,0,0,134,6338,0,0,25,387,0,0;QS=1,0;MQSB=1;MQ0F=0\tPL:DP:DV\t0,9,103:3:0\t0,0,0:0:0\t0,0,0:0:0\n-17\t4083\t.\tC\t<X>\t0\t.\tDP=3;I16=2,1,0,0,104,3648,0,0,134,6338,0,0,22,340,0,0;QS=1,0;MQSB=1;MQ0F=0\tPL:DP:DV\t0,9,98:3:0\t0,0,0:0:0\t0,0,0:0:0\n-17\t4084\t.\tA\t<X>\t0\t.\tDP=2;I16=1,1,0,0,78,3050,0,0,97,4969,0,0,20,298,0,0;QS=1,0;MQSB=1;MQ0F=0\tPL:DP:DV\t0,6,74:2:0\t0,0,0:0:0\t0,0,0:0:0\n-17\t4085\t.\tC\t<X>\t0\t.\tDP=2;I16=1,1,0,0,62,1940,0,0,97,4969,0,0,18,260,0,0;QS=1,0;MQSB=1;MQ0F=0\tPL:DP:DV\t0,6,62:2:0\t0,0,0:0:0\t0,0,0:0:0\n-17\t4086\t.\tG\t<X>\t0\t.\tDP=2;I16=1,1,0,0,56,1640,0,0,97,4969,0,0,16,226,0,0;QS=1,0;MQSB=1;MQ0F=0\tPL:DP:DV\t0,6,56:2:0\t0,0,0:0:0\t0,0,0:0:0\n-17\t4087\t.\tC\t<X>\t0\t.\tDP=2;I16=1,1,0,0,69,2405,0,0,97,4969,0,0,14,196,0,0;QS=1,0;MQSB=1;MQ0F=0\tPL:DP:DV\t0,6,68:2:0\t0,0,0:0:0\t0,0,0:0:0\n-17\t4088\t.\tA\t<X>\t0\t.\tDP=1;I16=1,0,0,0,39,1521,0,0,37,1369,0,0,13,169,0,0;QS=1,0;MQ0F=0\tPL:DP:DV\t0,3,37:1:0\t0,0,0:0:0\t0,0,0:0:0\n-17\t4089\t.\tC\t<X>\t0\t.\tDP=1;I16=1,0,0,0,36,1296,0,0,37,1369,0,0,12,144,0,0;QS=1,0;MQ0F=0\tPL:DP:DV\t0,3,36:1:0\t0,0,0:0:0\t0,0,0:0:0\n-17\t4090\t.\tC\t<X>\t0\t.\tDP=1;I16=1,0,0,0,33,1089,0,0,37,1369,0,0,11,121,0,0;QS=1,0;MQ0F=0\tPL:DP:DV\t0,3,33:1:0\t0,0,0:0:0\t0,0,0:0:0\n-17\t4091\t.\tT\t<X>\t0\t.\tDP=1;I16=1,0,0,0,36,1296,0,0,37,1369,0,0,10,100,0,0;QS=1,0;MQ0F=0\tPL:DP:DV\t0,3,36:1:0\t0,0,0:0:0\t0,0,0:0:0\n-17\t4092\t.\tG\t<X>\t0\t.\tDP=1;I16=1,0,0,0,37,1369,0,0,37,1369,0,0,9,81,0,0;QS=1,0;MQ0F=0\tPL:DP:DV\t0,3,37:1:0\t0,0,0:0:0\t0,0,0:0:0\n-17\t4093\t.\tC\t<X>\t0\t.\tDP=1;I16=1,0,0,0,35,1225,0,0,37,1369,0,0,8,64,0,0;QS=1,0;MQ0F=0\tPL:DP:DV\t0,3,35:1:0\t0,0,0:0:0\t0,0,0:0:0\n-17\t4094\t.\tT\t<X>\t0\t.\tDP=1;I16=1,0,0,0,40,1600,0,0,37,1369,0,0,7,49,0,0;QS=1,0;MQ0F=0\tPL:DP:DV\t0,3,37:1:0\t0,0,0:0:0\t0,0,0:0:0\n-17\t4095\t.\tA\t<X>\t0\t.\tDP=1;I16=1,0,0,0,35,1225,0,0,37,1369,0,0,6,36,0,0;QS=1,0;MQ0F=0\tPL:DP:DV\t0,3,35:1:0\t0,0,0:0:0\t0,0,0:0:0\n-17\t4096\t.\tC\t<X>\t0\t.\tDP=1;I16=1,0,0,0,32,1024,0,0,37,1369,0,0,5,25,0,0;QS=1,0;MQ0F=0\tPL:DP:DV\t0,3,32:1:0\t0,0,0:0:0\t0,0,0:0:0\n-17\t4097\t.\tA\t<X>\t0\t.\tDP=1;I16=1,0,0,0,35,1225,0,0,37,1369,0,0,4,16,0,0;QS=1,0;MQ0F=0\tPL:DP:DV\t0,3,35:1:0\t0,0,0:0:0\t0,0,0:0:0\n-17\t4098\t.\tC\t<X>\t0\t.\tDP=1;I16=1,0,0,0,31,961,0,0,37,1369,0,0,3,9,0,0;QS=1,0;MQ0F=0\tPL:DP:DV\t0,3,31:1:0\t0,0,0:0:0\t0,0,0:0:0\n-17\t4099\t.\tT\t<X>\t0\t.\tDP=1;I16=1,0,0,0,32,1024,0,0,37,1369,0,0,2,4,0,0;QS=1,0;MQ0F=0\tPL:DP:DV\t0,3,32:1:0\t0,0,0:0:0\t0,0,0:0:0\n-17\t4100\t.\tC\t<X>\t0\t.\tDP=1;I16=1,0,0,0,27,729,0,0,37,1369,0,0,1,1,0,0;QS=1,0;MQ0F=0\tPL:DP:DV\t0,3,27:1:0\t0,0,0:0:0\t0,0,0:0:0\n-17\t4101\t.\tC\t<X>\t0\t.\tDP=1;I16=1,0,0,0,26,676,0,0,37,1369,0,0,0,0,0,0;QS=1,0;MQ0F=0\tPL:DP:DV\t0,3,26:1:0\t0,0,0:0:0\t0,0,0:0:0\n'
b
diff -r 072f606e2e69 -r 912a8ff07fc9 test-data/mpileup.regions.bed
--- a/test-data/mpileup.regions.bed Fri Feb 05 19:28:02 2021 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
b
@@ -1,1 +0,0 @@
-17 99 110
b
diff -r 072f606e2e69 -r 912a8ff07fc9 test-data/mpileup.regions.tab
--- a/test-data/mpileup.regions.tab Fri Feb 05 19:28:02 2021 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
b
@@ -1,1 +0,0 @@
-17 100 110
b
diff -r 072f606e2e69 -r 912a8ff07fc9 test-data/mpileup.tab
--- a/test-data/mpileup.tab Fri Feb 05 19:28:02 2021 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
b
@@ -1,11 +0,0 @@
-17 1 A,G,T
-17 2 A,T,G
-17 3 A,C
-17 4 A,C,T,G
-17 5 A,G,T
-17 6 A,T,G
-17 7 A,T,G,C
-17 828 T,C
-17 1665 T,C
-17 2220 G,C
-17 2564 A,AG
b
diff -r 072f606e2e69 -r 912a8ff07fc9 test-data/query.filter.vcf
--- a/test-data/query.filter.vcf Fri Feb 05 19:28:02 2021 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
b
@@ -1,20 +0,0 @@
-##fileformat=VCFv4.1
-##INFO=<ID=TEST,Number=1,Type=Integer,Description="Testing Tag">
-##FORMAT=<ID=TT,Number=A,Type=Integer,Description="Testing Tag, with commas and \"escapes\" and escaped escapes combined with \\\"quotes\\\\\"">
-##INFO=<ID=DP4,Number=4,Type=Integer,Description="# high-quality ref-forward bases, ref-reverse, alt-forward and alt-reverse bases">
-##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
-##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality">
-##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read Depth">
-##FORMAT=<ID=GL,Number=G,Type=Float,Description="Genotype Likelihood">
-##FILTER=<ID=q10,Description="Quality below 10">
-##FILTER=<ID=test,Description="Testing filter">
-##contig=<ID=1,assembly=b37,length=249250621>
-##contig=<ID=2,assembly=b37,length=249250621>
-##contig=<ID=3,assembly=b37,length=198022430>
-##contig=<ID=4,assembly=b37,length=191154276>
-##reference=file:///lustre/scratch105/projects/g1k/ref/main_project/human_g1k_v37.fasta
-#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT A B
-1 3000150 . C T 59.2 PASS . GT 0 0
-1 3000151 . C T 59.2 PASS . GT 1 0
-1 3000152 . C T 59.2 PASS . GT 0 1
-1 3000153 . C T 59.2 PASS . GT 1 1
b
diff -r 072f606e2e69 -r 912a8ff07fc9 test-data/vcf2sex.vcf
--- a/test-data/vcf2sex.vcf Fri Feb 05 19:28:02 2021 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
b
@@ -1,24 +0,0 @@
-##fileformat=VCFv4.2
-##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
-##contig=<ID=X,assembly=b37,length=249250621>
-##contig=<ID=Y,assembly=b37,length=249250621>
-#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT MALE FEMALE
-X 1 . C A . PASS . GT 1 0/1
-X 12000 . C A . PASS . GT 0 0/1
-X 24000 . C A . PASS . GT 1 0/1
-X 36000 . C A . PASS . GT 0 0/1
-X 48000 . C A . PASS . GT 1 0/1
-X 60000 . C A . PASS . GT 0 0/1
-X 100000 . C A . PASS . GT 0/1 0/1
-X 2699521 . C A . PASS . GT 0 0/1
-X 33145825 . C A . PASS . GT 1 0/1
-X 63592129 . C A . PASS . GT 1 0/1
-X 94038433 . C A . PASS . GT 0 0/1
-X 124484737 . C A . PASS . GT 0 0/1
-X 154931043 . C A . PASS . GT 0/1 0/1
-Y 1 . C A . PASS . GT 0 .
-Y 11874713 . C A . PASS . GT 0 .
-Y 23749426 . C A . PASS . GT 0 .
-Y 35624139 . C A . PASS . GT 0 .
-Y 47498852 . C A . PASS . GT 0 .
-Y 59373565 . C A . PASS . GT 0 .
b
diff -r 072f606e2e69 -r 912a8ff07fc9 test-data/view.filter.vcf
--- a/test-data/view.filter.vcf Fri Feb 05 19:28:02 2021 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
b
@@ -1,42 +0,0 @@
-##fileformat=VCFv4.2
-##INFO=<ID=DP,Number=1,Type=Integer,Description="Total Depth">
-##INFO=<ID=DP4,Number=4,Type=Integer,Description="# high-quality ref-forward bases, ref-reverse, alt-forward and alt-reverse bases">
-##INFO=<ID=STR,Number=A,Type=String,Description="Testing string and Number=A in INFO">
-##INFO=<ID=TXT0,Number=1,Type=String,Description="Testing in INFO">
-##INFO=<ID=TXT,Number=.,Type=String,Description="Testing in INFO">
-##INFO=<ID=XRF,Number=R,Type=Float,Description="Test Number=AGR in INFO">
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b
diff -r 072f606e2e69 -r 912a8ff07fc9 test-data/view.vcf_bgzip
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Binary file test-data/view.vcf_bgzip has changed