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mcshanemcshane
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Merge pull request samtools#271 from samtools/feature/fix.84
fix.84
2 parents dbb7dda + b2163f5 commit b3bfc34

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-67
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9 files changed

+222
-67
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‎test/norm.fa‎

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@@ -22,3 +22,5 @@ ACTGGACACGTGGACACACACACACACACACACACACACACAGTCAAACCACCTACCAGA
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TCCCCTCTTGACCTCTCTCTATTTTTTTTTTTTTTTCTGAGATGGATTTTTGCTCTTGTT
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>5 20:18724313-18724343
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GTCTCAAAAAAAAAAAAAAAAAAAAGAAAAG
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>21
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TTTATTATTATTATTATTAAATTGAATTTATTTAGTGTACATACATTCATGTGTATTGTG

‎test/norm.fa.fai‎

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@@ -4,3 +4,4 @@
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3 60 902 60 61
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4 60 985 60 61
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5 31 1070 31 32
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21 60 1106 60 61

‎test/norm.merge.2.out‎

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##fileformat=VCFv4.1
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##FILTER=<ID=PASS,Description="All filters passed">
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##INFO=<ID=INDEL,Number=0,Type=Flag,Description="Indicates that the variant is an INDEL.">
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##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
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##FORMAT=<ID=PL,Number=G,Type=Integer,Description="Phred-scaled likelihood">
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##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Depth">
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##contig=<ID=1,length=2147483647>
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##contig=<ID=2,length=2147483647>
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##contig=<ID=20,length=2147483647>
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##INFO=<ID=DP,Number=1,Type=Integer,Description="Total Depth">
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##INFO=<ID=AC,Number=A,Type=Integer,Description="Allele count in genotypes">
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##INFO=<ID=AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes">
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##INFO=<ID=XRF,Number=R,Type=Float,Description="Test Number=AGR in INFO">
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##INFO=<ID=XAF,Number=A,Type=Float,Description="Test Number=AGR in INFO">
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##INFO=<ID=XGF,Number=G,Type=Float,Description="Test Number=AGR in INFO">
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##INFO=<ID=XRI,Number=R,Type=Integer,Description="Test Number=AGR in INFO">
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##INFO=<ID=XAI,Number=A,Type=Integer,Description="Test Number=AGR in INFO">
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##INFO=<ID=XGI,Number=G,Type=Integer,Description="Test Number=AGR in INFO">
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##INFO=<ID=XRS,Number=R,Type=String,Description="Test Number=AGR in INFO">
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##INFO=<ID=XAS,Number=A,Type=String,Description="Test Number=AGR in INFO">
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##INFO=<ID=XGS,Number=G,Type=String,Description="Test Number=AGR in INFO">
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##FORMAT=<ID=FRF,Number=R,Type=Float,Description="Test Number=AGR in FORMAT">
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##FORMAT=<ID=FAF,Number=A,Type=Float,Description="Test Number=AGR in FORMAT">
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##FORMAT=<ID=FGF,Number=G,Type=Float,Description="Test Number=AGR in FORMAT">
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##FORMAT=<ID=FRI,Number=R,Type=Integer,Description="Test Number=AGR in FORMAT">
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##FORMAT=<ID=FAI,Number=A,Type=Integer,Description="Test Number=AGR in FORMAT">
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##FORMAT=<ID=FGI,Number=G,Type=Integer,Description="Test Number=AGR in FORMAT">
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##FORMAT=<ID=FRS,Number=R,Type=String,Description="Test Number=AGR in FORMAT">
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##FORMAT=<ID=FAS,Number=A,Type=String,Description="Test Number=AGR in FORMAT">
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##FORMAT=<ID=FGS,Number=G,Type=String,Description="Test Number=AGR in FORMAT">
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##FORMAT=<ID=FSTR,Number=1,Type=String,Description="Test String in FORMAT">
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##INFO=<ID=ISTR,Number=1,Type=String,Description="Test String in INFO">
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##FILTER=<ID=FAIL1,Description="Failed filter 1">
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##FILTER=<ID=FAIL2,Description="Failed filter 2">
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#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT XY00001 XY00002 XY00003
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1 105 . T C 999 PASS . GT:FGI:FRI 1:1,2:3,4 0/1:5,6,7:8,9 0/1:.:.,.
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1 110 . C A 999 PASS . GT:FGI 1:1,2 0:3,4 0:.
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1 150 . A C 999 PASS . GT:FGI 1:1,2 0:. 0:3,4

‎test/norm.merge.2.vcf‎

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##fileformat=VCFv4.1
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##FILTER=<ID=PASS,Description="All filters passed">
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##INFO=<ID=INDEL,Number=0,Type=Flag,Description="Indicates that the variant is an INDEL.">
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##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
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##FORMAT=<ID=PL,Number=G,Type=Integer,Description="Phred-scaled likelihood">
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##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Depth">
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##contig=<ID=1,length=2147483647>
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##contig=<ID=2,length=2147483647>
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##contig=<ID=20,length=2147483647>
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##INFO=<ID=DP,Number=1,Type=Integer,Description="Total Depth">
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##INFO=<ID=AC,Number=A,Type=Integer,Description="Allele count in genotypes">
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##INFO=<ID=AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes">
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##INFO=<ID=XRF,Number=R,Type=Float,Description="Test Number=AGR in INFO">
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##INFO=<ID=XAF,Number=A,Type=Float,Description="Test Number=AGR in INFO">
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##INFO=<ID=XGF,Number=G,Type=Float,Description="Test Number=AGR in INFO">
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##INFO=<ID=XRI,Number=R,Type=Integer,Description="Test Number=AGR in INFO">
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##INFO=<ID=XAI,Number=A,Type=Integer,Description="Test Number=AGR in INFO">
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##INFO=<ID=XGI,Number=G,Type=Integer,Description="Test Number=AGR in INFO">
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##INFO=<ID=XRS,Number=R,Type=String,Description="Test Number=AGR in INFO">
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##INFO=<ID=XAS,Number=A,Type=String,Description="Test Number=AGR in INFO">
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##INFO=<ID=XGS,Number=G,Type=String,Description="Test Number=AGR in INFO">
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##FORMAT=<ID=FRF,Number=R,Type=Float,Description="Test Number=AGR in FORMAT">
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##FORMAT=<ID=FAF,Number=A,Type=Float,Description="Test Number=AGR in FORMAT">
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##FORMAT=<ID=FGF,Number=G,Type=Float,Description="Test Number=AGR in FORMAT">
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##FORMAT=<ID=FRI,Number=R,Type=Integer,Description="Test Number=AGR in FORMAT">
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##FORMAT=<ID=FAI,Number=A,Type=Integer,Description="Test Number=AGR in FORMAT">
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##FORMAT=<ID=FGI,Number=G,Type=Integer,Description="Test Number=AGR in FORMAT">
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##FORMAT=<ID=FRS,Number=R,Type=String,Description="Test Number=AGR in FORMAT">
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##FORMAT=<ID=FAS,Number=A,Type=String,Description="Test Number=AGR in FORMAT">
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##FORMAT=<ID=FGS,Number=G,Type=String,Description="Test Number=AGR in FORMAT">
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##FORMAT=<ID=FSTR,Number=1,Type=String,Description="Test String in FORMAT">
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##INFO=<ID=ISTR,Number=1,Type=String,Description="Test String in INFO">
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##FILTER=<ID=FAIL1,Description="Failed filter 1">
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##FILTER=<ID=FAIL2,Description="Failed filter 2">
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#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT XY00001 XY00002 XY00003
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1 105 . T . 999 PASS . GT:FGI:FRI 0:.:. 0/0:.:. 0/1:.:.
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1 105 . T C 999 PASS . GT:FGI:FRI 1:1,2:3,4 0/1:5,6,7:8,9 0/1:.:.
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1 110 . C . 999 PASS . GT:FGI 0:. 0:. 0:.
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1 110 . C A 999 PASS . GT:FGI 1:1,2 0:3,4 0:.
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1 150 . A . 999 PASS . GT:FGI 0:. 0:. 0:.
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1 150 . A C 999 PASS . GT:FGI 1:1,2 0:. 0:3,4

‎test/norm.split.out‎

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@@ -7,6 +7,7 @@
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##contig=<ID=1,length=2147483647>
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##contig=<ID=2,length=2147483647>
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##contig=<ID=20,length=2147483647>
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##contig=<ID=21,length=2147483647>
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##INFO=<ID=DP,Number=1,Type=Integer,Description="Total Depth">
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##INFO=<ID=AC,Number=A,Type=Integer,Description="Allele count in genotypes">
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##INFO=<ID=AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes">
@@ -55,5 +56,9 @@
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20 275 . A C 999 PASS INDEL;AN=2;AC=0 GT:PL:DP:FGF:FGI:FGS:FSTR 0:0,0:0:1e+06,2e+06:1111,2222:A,BB:WORD 0:0,0:0:1e+06,2e+06:1111,2222:A,BB:WORD
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20 275 . A G 999 PASS INDEL;AN=2;AC=2 GT:PL:DP:FGF:FGI:FGS:FSTR 1:0,0:0:1e+06,3e+06:1111,3333:A,CCC:WORD 1:0,0:0:1e+06,3e+06:1111,3333:A,CCC:WORD
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20 278 . AAAAAAAAAAAAAAAAA AAAAAAAAAAAAAAAAAAA 999 PASS INDEL;AN=0;AC=0 GT:PL:DP ./.:0,0,0:0 ./.:0,0,0:0
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20 300 . A C 999 PASS INDEL;AN=0;AC=0 GT:PL:DP ./.:0,0,0:0 ./.:0,0,0:0
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20 300 . A G 999 PASS INDEL;AN=0;AC=0 GT:PL:DP ./.:0,0,0:0 ./.:0,0,0:0
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20 300 . T C 999 PASS INDEL;AN=0;AC=0 GT:PL:DP ./.:0,0,0:0 ./.:0,0,0:0
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20 300 . T G 999 PASS INDEL;AN=0;AC=0 GT:PL:DP ./.:0,0,0:0 ./.:0,0,0:0
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21 1 id TTTA TTTATTATTA 999 PASS INDEL;AN=0;AC=0 GT:DP ./.:0 ./.:0
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21 1 id TTTA TTTATTATTATTATTATTATTA 999 PASS INDEL;AN=0;AC=0 GT:DP ./.:0 ./.:0
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21 1 id TTTA T 999 PASS INDEL;AN=0;AC=0 GT:DP ./.:0 ./.:0
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21 1 id TTTA TTATTATTA 999 PASS INDEL;AN=0;AC=0 GT:DP ./.:0 ./.:0

‎test/norm.split.vcf‎

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@@ -7,6 +7,7 @@
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##contig=<ID=1,length=2147483647>
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##contig=<ID=2,length=2147483647>
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##contig=<ID=20,length=2147483647>
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##contig=<ID=21,length=2147483647>
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##INFO=<ID=DP,Number=1,Type=Integer,Description="Total Depth">
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##INFO=<ID=AC,Number=A,Type=Integer,Description="Allele count in genotypes">
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##INFO=<ID=AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes">
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20 274 . AAAAAAAAA AAAAAAAAAAAAAAAAAAA 999 PASS INDEL;AN=0;AC=0 GT:PL:DP ./.:0,0,0:0 ./.:0,0,0:0
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20 275 . A C,G 999 PASS INDEL;AN=2;AC=0,2 GT:PL:DP:FGF:FGI:FGS:FSTR 2:0,0,0:0:1e+06,2e+06,3e+06:1111,2222,3333:A,BB,CCC:WORD 2:0,0,0:0:1e+06,2e+06,3e+06:1111,2222,3333:A,BB,CCC:WORD
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20 278 . AAAAAAAAAAAAAAAAA AAAAAAAAAAAAAAAAAAA 999 PASS INDEL;AN=0;AC=0 GT:PL:DP ./.:0,0,0:0 ./.:0,0,0:0
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20 300 . A C,G 999 PASS INDEL;AN=0;AC=0,0 GT:PL:DP ./.:0,0,0,0,0,0:0 ./.:0,0,0,0,0,0:0
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20 300 . T C,G 999 PASS INDEL;AN=0;AC=0,0 GT:PL:DP ./.:0,0,0,0,0,0:0 ./.:0,0,0,0,0,0:0
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21 1 id TTTA TTTATTATTA,TTTATTATTATTATTATTATTA,T,TTATTATTA 999 PASS INDEL;AN=0;AC=0,0,0,0 GT:DP ./.:0 ./.:0

‎test/test.pl‎

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test_vcf_norm($opts,in=>'norm',out=>'norm.out',fai=>'norm');
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test_vcf_norm($opts,in=>'norm.split',out=>'norm.split.out',args=>'-m-');
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test_vcf_norm($opts,in=>'norm.merge',out=>'norm.merge.out',args=>'-m+');
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test_vcf_norm($opts,in=>'norm.merge.2',out=>'norm.merge.2.out',args=>'-m+');
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test_vcf_norm($opts,in=>'norm.merge',out=>'norm.merge.strict.out',args=>'-m+ -s');
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test_vcf_norm($opts,in=>'norm.setref',out=>'norm.setref.out',args=>'-Nc s',fai=>'norm');
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test_vcf_view($opts,in=>'view',out=>'view.1.out',args=>'-aUc1 -C1 -s NA00002 -v snps',reg=>'');

‎vcfcall.c‎

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@@ -191,6 +191,9 @@ static char **parse_ped_samples(call_t *call, char **vals, int _n)
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for (i=0; i<call->nfams; i++)
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assert( call->fams[i].sample[0]>=0 && call->fams[i].sample[1]>=0 && call->fams[i].sample[2]>=0 ); // multiple childs, not a trio
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// for (i=0; i<call->nfams; i++)
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// fprintf(stderr,"mother=%s, father=%s, child=%s\n", sam[call->fams[i].sample[MOTHER]],sam[call->fams[i].sample[FATHER]],sam[call->fams[i].sample[CHILD]]);
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return sam;
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}
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