| Previous changeset 13:98d5499ead46 (2021-04-13) Next changeset 15:e1a2389af238 (2022-01-15) |
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Commit message:
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit d5a01866d60f9775392420988259f1e79c464163" |
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modified:
bcftools_view.xml macros.xml |
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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 98d5499ead46 -r 1d1762860d7e bcftools_view.xml --- a/bcftools_view.xml Tue Apr 13 15:19:30 2021 +0000 +++ b/bcftools_view.xml Thu Oct 14 10:21:57 2021 +0000 |
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| @@ -1,6 +1,7 @@ <?xml version='1.0' encoding='utf-8'?> <tool name="bcftools @EXECUTABLE@" id="bcftools_@EXECUTABLE@" version="@TOOL_VERSION@"> <description>VCF/BCF conversion, view, subset and filter VCF/BCF files</description> + <expand macro="bio_tools" /> <macros> <token name="@EXECUTABLE@">view</token> <import>macros.xml</import> |
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| diff -r 98d5499ead46 -r 1d1762860d7e macros.xml --- a/macros.xml Tue Apr 13 15:19:30 2021 +0000 +++ b/macros.xml Thu Oct 14 10:21:57 2021 +0000 |
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| @@ -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>&1 | grep 'Version:'</version_command> |
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| diff -r 98d5499ead46 -r 1d1762860d7e test-data/annotate4.vcf --- a/test-data/annotate4.vcf Tue Apr 13 15:19:30 2021 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -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 98d5499ead46 -r 1d1762860d7e test-data/annots4.tab --- a/test-data/annots4.tab Tue Apr 13 15:19:30 2021 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -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 98d5499ead46 -r 1d1762860d7e test-data/annots4.vcf --- a/test-data/annots4.vcf Tue Apr 13 15:19:30 2021 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -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 |
| b |
| diff -r 98d5499ead46 -r 1d1762860d7e test-data/concat.3.0.vcf --- a/test-data/concat.3.0.vcf Tue Apr 13 15:19:30 2021 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -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 |
| b |
| diff -r 98d5499ead46 -r 1d1762860d7e test-data/concat.3.a.vcf --- a/test-data/concat.3.a.vcf Tue Apr 13 15:19:30 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 98d5499ead46 -r 1d1762860d7e test-data/concat.3.b.vcf --- a/test-data/concat.3.b.vcf Tue Apr 13 15:19:30 2021 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| 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 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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 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header">\n-##INFO=<ID=T197,Number=1,Type=Integer,Description="Test Tag: Big header">\n-##INFO=<ID=T198,Number=1,Type=Integer,Description="Test Tag: Big header">\n-##INFO=<ID=T199,Number=1,Type=Integer,Description="Test Tag: Big header">\n-##INFO=<ID=DP,Number=1,Type=Integer,Description="Total Depth">\n-##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">\n-##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality">\n-##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read Depth">\n-##FILTER=<ID=q10,Description="Quality below 10">\n-##contig=<ID=2,length=62435964>\n-#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT\tA\tB\n-2\t170\t.\tT\tA\t246\tPASS\tDP=10\tGT\t1|0\t0|1\n-2\t180\t.\tT\tA\t246\tPASS\tDP=10\tGT\t1|0\t0|1\n-2\t190\t.\tT\tA\t246\tPASS\tDP=10\tGT\t1|0\t0|1\n-2\t200\t.\tT\tA\t246\tPASS\tDP=10\tGT\t1|0\t0|1\n-2\t210\t.\tT\tA\t246\tPASS\tDP=10\tGT\t1|0\t0|1\n-2\t220\t.\tT\tA\t246\tPASS\tDP=10\tGT\t1|0\t0|1\n-2\t230\t.\tT\tA\t246\tPASS\tDP=10\tGT\t1|0\t0|1\n-2\t240\t.\tT\tA\t246\tPASS\tDP=10\tGT\t1|0\t0|1\n-2\t250\t.\tT\tA\t246\tPASS\tDP=10\tGT\t1|0\t0|1\n-2\t260\t.\tT\tA\t246\tPASS\tDP=10\tGT\t1|0\t0|1\n-2\t270\t.\tT\tA\t246\tPASS\tDP=10\tGT\t1|0\t0|1\n-2\t280\t.\tT\tA\t246\tPASS\tDP=10\tGT\t1|0\t0|1\n-2\t290\t.\tT\tA\t246\tPASS\tDP=10\tGT\t1|0\t0|1\n-2\t300\t.\tT\tA\t246\tPASS\tDP=10\tGT\t1|0\t0|1\n-2\t310\t.\tT\tA\t246\tPASS\tDP=10\tGT\t1|0\t0|1\n-2\t320\t.\tT\tA\t246\tPASS\tDP=10\tGT\t1|0\t0|1\n' |
| b |
| diff -r 98d5499ead46 -r 1d1762860d7e test-data/concat.3.c.vcf --- a/test-data/concat.3.c.vcf Tue Apr 13 15:19:30 2021 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,22 +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 -2 280 . T A 246 PASS DP=10 GT 1|0 0|1 -2 290 . T A 246 PASS DP=10 GT 1|0 1|0 -2 300 . T A 246 PASS DP=10 GT 0|1 1|0 -2 310 . T A 246 PASS DP=10 GT 0|1 1|0 -2 320 . T A 246 PASS DP=10 GT 0|1 1|0 -2 330 . T A 246 PASS DP=10 GT 0|1 1|0 -2 340 . T A 246 PASS DP=10 GT 0|1 1|0 -2 350 . T A 246 PASS DP=10 GT 0|1 1|0 -2 360 . T A 246 PASS DP=10 GT 0|1 1|0 -2 370 . T A 246 PASS DP=10 GT 0|1 1|0 -2 380 . T A 246 PASS DP=10 GT 0|1 1|0 -2 390 . T A 246 PASS DP=10 GT 0|1 1|0 -2 400 . T A 246 PASS DP=10 GT 0|1 1|0 -2 410 . T A 246 PASS DP=10 GT 0|1 1|0 |
| b |
| diff -r 98d5499ead46 -r 1d1762860d7e test-data/concat.3.d.vcf --- a/test-data/concat.3.d.vcf Tue Apr 13 15:19:30 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 -2 300 . 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 98d5499ead46 -r 1d1762860d7e test-data/concat.3.e.vcf --- a/test-data/concat.3.e.vcf Tue Apr 13 15:19:30 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 98d5499ead46 -r 1d1762860d7e test-data/concat.3.f.vcf --- a/test-data/concat.3.f.vcf Tue Apr 13 15:19:30 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 98d5499ead46 -r 1d1762860d7e test-data/consensus.1.chain --- a/test-data/consensus.1.chain Tue Apr 13 15:19:30 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 98d5499ead46 -r 1d1762860d7e test-data/consensus.1.out --- a/test-data/consensus.1.out Tue Apr 13 15:19:30 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 98d5499ead46 -r 1d1762860d7e test-data/filter.4.vcf --- a/test-data/filter.4.vcf Tue Apr 13 15:19:30 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 98d5499ead46 -r 1d1762860d7e test-data/mpileup.4.bam |
| b |
| Binary file test-data/mpileup.4.bam has changed |
| b |
| diff -r 98d5499ead46 -r 1d1762860d7e test-data/mpileup.c.X.vcf --- a/test-data/mpileup.c.X.vcf Tue Apr 13 15:19:30 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 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|
| b |
| diff -r 98d5499ead46 -r 1d1762860d7e test-data/mpileup.c.vcf --- a/test-data/mpileup.c.vcf Tue Apr 13 15:19:30 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 98d5499ead46 -r 1d1762860d7e test-data/mpileup.regions.bed --- a/test-data/mpileup.regions.bed Tue Apr 13 15:19:30 2021 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,1 +0,0 @@ -17 99 110 |
| b |
| diff -r 98d5499ead46 -r 1d1762860d7e test-data/mpileup.regions.tab --- a/test-data/mpileup.regions.tab Tue Apr 13 15:19:30 2021 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,1 +0,0 @@ -17 100 110 |
| b |
| diff -r 98d5499ead46 -r 1d1762860d7e test-data/mpileup.tab --- a/test-data/mpileup.tab Tue Apr 13 15:19:30 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 98d5499ead46 -r 1d1762860d7e test-data/query.filter.vcf --- a/test-data/query.filter.vcf Tue Apr 13 15:19:30 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 98d5499ead46 -r 1d1762860d7e test-data/vcf2sex.vcf --- a/test-data/vcf2sex.vcf Tue Apr 13 15:19:30 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 98d5499ead46 -r 1d1762860d7e test-data/view.filter.vcf --- a/test-data/view.filter.vcf Tue Apr 13 15:19:30 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"> -##INFO=<ID=XAF,Number=A,Type=Float,Description="Test Number=AGR in INFO"> -##INFO=<ID=XGF,Number=G,Type=Float,Description="Test Number=AGR in INFO"> -##INFO=<ID=XRI,Number=R,Type=Integer,Description="Test Number=AGR in INFO"> -##INFO=<ID=XAI,Number=A,Type=Integer,Description="Test Number=AGR in INFO"> -##INFO=<ID=XGI,Number=G,Type=Integer,Description="Test Number=AGR in INFO"> -##INFO=<ID=XRS,Number=R,Type=String,Description="Test Number=AGR in INFO"> -##INFO=<ID=XAS,Number=A,Type=String,Description="Test Number=AGR in INFO"> -##INFO=<ID=XGS,Number=G,Type=String,Description="Test Number=AGR in INFO"> -##SAMPLE=<ID=NORMAL,SampleName=B,Description="Less-than (\"<\") and greater-than (\">\") quoting nonsense where double brackets would do just fine",softwareName=<Nonsense,Software>,softwareVer=<119,65>,softwareParam=<.>,MetadataResource=http://somewhere.com/path> -##INFO=<ID=CIGAR,Number=A,Type=String,Description="test"> -##INFO=<ID=AO,Number=A,Type=Integer,Description="Alternate allele observations, with partial observations recorded fractionally"> -##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=FGS,Number=G,Type=String,Description="Test Number=AGR in FORMAT"> -##FORMAT=<ID=FGI,Number=G,Type=Integer,Description="Test Number=AGR in FORMAT"> -##FORMAT=<ID=FGF,Number=G,Type=Float,Description="Test Number=AGR in FORMAT"> -##FORMAT=<ID=FAS,Number=A,Type=String,Description="Test Number=AGR in FORMAT"> -##FORMAT=<ID=FAI,Number=A,Type=Integer,Description="Test Number=AGR in FORMAT"> -##FORMAT=<ID=FAF,Number=A,Type=Float,Description="Test Number=AGR in FORMAT"> -##FORMAT=<ID=FRS,Number=R,Type=String,Description="Test Number=AGR in FORMAT"> -##FORMAT=<ID=FRI,Number=R,Type=Integer,Description="Test Number=AGR in FORMAT"> -##FORMAT=<ID=FRF,Number=R,Type=Float,Description="Test Number=AGR in FORMAT"> -##FORMAT=<ID=STR,Number=1,Type=String,Description="Test"> -##FILTER=<ID=q20,Description="Mapping quality below 20"> -##contig=<ID=1,assembly=b37,length=249250621> -##contig=<ID=2,assembly=b37,length=243199373> -##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 -##INFO=<ID=AC,Number=A,Type=Integer,Description="Allele count in genotypes"> -##INFO=<ID=AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes"> -#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT A B -1 3162006 . GAA G,GA 238 PASS DP=19;AN=4;AC=1,1;XRF=1e6,2e6,3e6;XRI=1111,2222,3333;XRS=ABC,DEF,GHI;XAF=1e6,2e6;XAI=1111,2222;XAS=ABC,DEF;XGF=1e6,2e6,3e6,4e6,5e6,6e6;XGI=11,22,33,44,55,66;XGS=ABC,DEF,GHI,JKL,MNO,PQR;TXT=ABC,DEF,GHI GT:GQ:DP:STR 0/1:589:19:XX 0/2:1:1:YY -1 3162007 . TAGGG CAGGG,CAGGT 238 PASS AO=52101,113;CIGAR=1X4M,1X3M1X;TXT0=text GT:FGS:FGI:FGF:FAS:FAI:FAF:FRS:FRI:FRF 0/1:AAAAAA,BBBBB,CCCC,DDD,EE,F:1,2,3,4,5,6:1e-1,2e-2,3e-3,4e-4,5e-5,6e-6:AAA,B:1,2:1e-1,2e-2:A,BB,CCC:1,2,3:1e-1,2e-2,3e-3 2:AAAAAA,BBB,C:1,2,3:1e-1,2e-2,3e-3:AAA,B:1,2:1e-1,2e-2:A,BB,CCC:1,2,3:1e-1,2e-2,3e-3 |
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| diff -r 98d5499ead46 -r 1d1762860d7e test-data/view.vcf_bgzip |
| b |
| Binary file test-data/view.vcf_bgzip has changed |