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Fix GT splitting in bcftools norm #344

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Fix GT splitting in bcftools norm #344

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22 changes: 11 additions & 11 deletions test/norm.split.and.norm.out
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Original file line number Diff line number Diff line change
Expand Up @@ -32,29 +32,29 @@
##FORMAT=<ID=FSTR,Number=1,Type=String,Description="Test String in FORMAT">
##INFO=<ID=ISTR,Number=1,Type=String,Description="Test String in INFO">
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT XY00001 XY00002
1 105 . TAAACCCTA T 999 PASS INDEL;AN=4;AC=2;DP=19;ISTR=SomeString;XRF=1e+06,2e+06;XRI=1111,2222;XRS=AAA,BBB;XAF=1e+06;XAI=1111;XAS=AAA;XGF=1e+06,2e+06,3e+06;XGI=1111,2222,3333;XGS=A,B,C GT:PL:DP:FRF:FRI:FRS:FAF:FAI:FAS:FGF:FGI:FGS 1/0:1,2,3:1:1e+06,2e+06:1111,2222:AAAA,BBB:1e+06:1111:A:1e+06,2e+06,3e+06:1111,2222,3333:A,BB,CCC 1/0:1,2,3:1:1e+06,2e+06:1111,2222:AAAA,BBB:1e+06:1111:A:1e+06,2e+06,3e+06:1111,2222,3333:A,BB,CCC
1 105 . TA T 999 PASS INDEL;AN=4;AC=2;DP=19;ISTR=SomeString;XRF=1e+06,500000;XRI=1111,5555;XRS=AAA,DDD;XAF=500000;XAI=5555;XAS=DDD;XGF=1e+06,500000,9e+09;XGI=1111,5555,9999;XGS=A,E,F GT:PL:DP:FRF:FRI:FRS:FAF:FAI:FAS:FGF:FGI:FGS 0/1:1,4,6:1:1e+06,500000:1111,5555:AAAA,CC:500000:5555:BB:1e+06,500000,9e+09:1111,5555,9999:A,EEEE,FFFFF 0/1:1,4,6:1:1e+06,500000:1111,5555:AAAA,CC:500000:5555:BB:1e+06,500000,9e+09:1111,5555,9999:A,EEEE,FFFFF
1 105 . TAAACCCTA T 999 PASS INDEL;AN=4;AC=2;DP=19;ISTR=SomeString;XRF=1e+06,2e+06;XRI=1111,2222;XRS=AAA,BBB;XAF=1e+06;XAI=1111;XAS=AAA;XGF=1e+06,2e+06,3e+06;XGI=1111,2222,3333;XGS=A,B,C GT:PL:DP:FRF:FRI:FRS:FAF:FAI:FAS:FGF:FGI:FGS 1/.:1,2,3:1:1e+06,2e+06:1111,2222:AAAA,BBB:1e+06:1111:A:1e+06,2e+06,3e+06:1111,2222,3333:A,BB,CCC 1/.:1,2,3:1:1e+06,2e+06:1111,2222:AAAA,BBB:1e+06:1111:A:1e+06,2e+06,3e+06:1111,2222,3333:A,BB,CCC
1 105 . TA T 999 PASS INDEL;AN=4;AC=2;DP=19;ISTR=SomeString;XRF=1e+06,500000;XRI=1111,5555;XRS=AAA,DDD;XAF=500000;XAI=5555;XAS=DDD;XGF=1e+06,500000,9e+09;XGI=1111,5555,9999;XGS=A,E,F GT:PL:DP:FRF:FRI:FRS:FAF:FAI:FAS:FGF:FGI:FGS ./1:1,4,6:1:1e+06,500000:1111,5555:AAAA,CC:500000:5555:BB:1e+06,500000,9e+09:1111,5555,9999:A,EEEE,FFFFF ./1:1,4,6:1:1e+06,500000:1111,5555:AAAA,CC:500000:5555:BB:1e+06,500000,9e+09:1111,5555,9999:A,EEEE,FFFFF
2 1 . GGGCGTCTCATAGCTGGAGCAATGGCGAGCGCCTGGACAAGGGAGGGGAAGGGGTTCTTATTACTGACGCGGGTAGCCCCTACTGCTGTGTGGTTCCCCTATTTTTTTTTTTTTCTTTTTGAGACGGAGTCTCGCTCTGTCACCCAGGCTGGAGTGCAGTGGCACAATCTCGGCTCACTGCAAGCTCCACC ACG 999 PASS INDEL;AN=4;AC=2 GT:DP 1/0:1 1/0:1
2 101 . A ATT 999 PASS INDEL;AN=4;AC=4 GT:DP 1/1:1 1/1:1
2 101 . A AT 999 PASS INDEL;AN=4;AC=2 GT:DP 0/1:1 0/1:1
2 114 . T TTC 999 PASS INDEL;AN=4;AC=2 GT:DP 1/0:1 1/0:1
2 101 . A AT 999 PASS INDEL;AN=4;AC=2 GT:DP ./1:1 ./1:1
2 114 . T TTC 999 PASS INDEL;AN=4;AC=2 GT:DP 1/.:1 1/.:1
2 115 . C T 999 PASS INDEL;AN=4;AC=4 GT:DP 1/1:1 1/1:1
20 3 . G CT 999 PASS INDEL;AN=4;AC=2 GT 0/1 0/1
20 5 . TG CT 999 PASS INDEL;AN=4;AC=2 GT 1/0 1/0
20 5 . TGG T . PASS INDEL;AN=4;AC=2 GT:PL:DP 0/1:1,4,6:1 0/1:1,4,6:1
20 5 . T TG . PASS INDEL;AN=4;AC=0 GT:PL:DP 0/0:1,7,10:1 0/0:1,7,10:1
20 5 . TGGG AC . PASS INDEL;AN=4;AC=0 GT:PL:DP 0/0:1,11,15:1 0/0:1,11,15:1
20 6 . GGG AC . PASS INDEL;AN=4;AC=2 GT:PL:DP 1/0:1,2,3:1 1/0:1,2,3:1
20 5 . TGG T . PASS INDEL;AN=4;AC=2 GT:PL:DP ./1:1,4,6:1 ./1:1,4,6:1
20 5 . T TG . PASS INDEL;AN=4;AC=0 GT:PL:DP ./.:1,7,10:1 ./.:1,7,10:1
20 5 . TGGG AC . PASS INDEL;AN=4;AC=0 GT:PL:DP ./.:1,11,15:1 ./.:1,11,15:1
20 6 . GGG AC . PASS INDEL;AN=4;AC=2 GT:PL:DP 1/.:1,2,3:1 1/.:1,2,3:1
20 59 . AG . 999 PASS AN=4 GT:PL:DP 0/0:0:4 0/0:0:4
20 81 . A C 999 PASS AN=4;AC=2 GT:PL:DP 0/1:255,0,255:13 0/1:255,0,255:13
20 84 . G T 999 PASS AN=4;AC=2 GT:PL:DP 0/1:255,0,255:13 0/1:255,0,255:13
20 95 . T A 999 PASS AN=4;AC=2 GT:PL:DP 0/1:255,0,255:13 0/1:255,0,255:13
20 95 . TCACCG AAAAAA 999 PASS AN=4;AC=2 GT:PL:DP 0/1:255,0,255:13 0/1:255,0,255:13
20 273 . C CAA 999 PASS INDEL;AN=4;AC=2 GT:PL:DP 1/0:0,3,5:1 1/0:0,3,5:1
20 273 . C CAAA 999 PASS INDEL;AN=4;AC=2 GT:PL:DP 0/1:0,3,5:1 0/1:0,3,5:1
20 273 . C CAA 999 PASS INDEL;AN=4;AC=2 GT:PL:DP 1/.:0,3,5:1 1/.:0,3,5:1
20 273 . C CAAA 999 PASS INDEL;AN=4;AC=2 GT:PL:DP ./1:0,3,5:1 ./1:0,3,5:1
20 273 . C CAAAAAAAAAA 999 PASS INDEL;AN=0;AC=0 GT:PL:DP ./.:0,0,0:0 ./.:0,0,0:0
20 273 . C CAA 999 PASS INDEL;AN=0;AC=0 GT:PL:DP ./.:0,0,0:0 ./.:0,0,0:0
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
20 275 . A C 999 PASS INDEL;AN=2;AC=0 GT:PL:DP:FGF:FGI:FGS:FSTR .:0,0:0:1e+06,2e+06:1111,2222:A,BB:WORD .:0,0:0:1e+06,2e+06:1111,2222:A,BB:WORD
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
20 300 . T C 999 PASS INDEL;AN=0;AC=0 GT:PL:DP ./.:0,0,0:0 ./.:0,0,0:0
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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22 changes: 11 additions & 11 deletions test/norm.split.out
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Original file line number Diff line number Diff line change
Expand Up @@ -32,28 +32,28 @@
##FORMAT=<ID=FSTR,Number=1,Type=String,Description="Test String in FORMAT">
##INFO=<ID=ISTR,Number=1,Type=String,Description="Test String in INFO">
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT XY00001 XY00002
1 105 . TAAACCCTAAA TAA 999 PASS INDEL;AN=4;AC=2;DP=19;ISTR=SomeString;XRF=1e+06,2e+06;XRI=1111,2222;XRS=AAA,BBB;XAF=1e+06;XAI=1111;XAS=AAA;XGF=1e+06,2e+06,3e+06;XGI=1111,2222,3333;XGS=A,B,C GT:PL:DP:FRF:FRI:FRS:FAF:FAI:FAS:FGF:FGI:FGS 1/0:1,2,3:1:1e+06,2e+06:1111,2222:AAAA,BBB:1e+06:1111:A:1e+06,2e+06,3e+06:1111,2222,3333:A,BB,CCC 1/0:1,2,3:1:1e+06,2e+06:1111,2222:AAAA,BBB:1e+06:1111:A:1e+06,2e+06,3e+06:1111,2222,3333:A,BB,CCC
1 105 . TAAACCCTAAA TAACCCTAAA 999 PASS INDEL;AN=4;AC=2;DP=19;ISTR=SomeString;XRF=1e+06,500000;XRI=1111,5555;XRS=AAA,DDD;XAF=500000;XAI=5555;XAS=DDD;XGF=1e+06,500000,9e+09;XGI=1111,5555,9999;XGS=A,E,F GT:PL:DP:FRF:FRI:FRS:FAF:FAI:FAS:FGF:FGI:FGS 0/1:1,4,6:1:1e+06,500000:1111,5555:AAAA,CC:500000:5555:BB:1e+06,500000,9e+09:1111,5555,9999:A,EEEE,FFFFF 0/1:1,4,6:1:1e+06,500000:1111,5555:AAAA,CC:500000:5555:BB:1e+06,500000,9e+09:1111,5555,9999:A,EEEE,FFFFF
1 105 . TAAACCCTAAA TAA 999 PASS INDEL;AN=4;AC=2;DP=19;ISTR=SomeString;XRF=1e+06,2e+06;XRI=1111,2222;XRS=AAA,BBB;XAF=1e+06;XAI=1111;XAS=AAA;XGF=1e+06,2e+06,3e+06;XGI=1111,2222,3333;XGS=A,B,C GT:PL:DP:FRF:FRI:FRS:FAF:FAI:FAS:FGF:FGI:FGS 1/.:1,2,3:1:1e+06,2e+06:1111,2222:AAAA,BBB:1e+06:1111:A:1e+06,2e+06,3e+06:1111,2222,3333:A,BB,CCC 1/.:1,2,3:1:1e+06,2e+06:1111,2222:AAAA,BBB:1e+06:1111:A:1e+06,2e+06,3e+06:1111,2222,3333:A,BB,CCC
1 105 . TAAACCCTAAA TAACCCTAAA 999 PASS INDEL;AN=4;AC=2;DP=19;ISTR=SomeString;XRF=1e+06,500000;XRI=1111,5555;XRS=AAA,DDD;XAF=500000;XAI=5555;XAS=DDD;XGF=1e+06,500000,9e+09;XGI=1111,5555,9999;XGS=A,E,F GT:PL:DP:FRF:FRI:FRS:FAF:FAI:FAS:FGF:FGI:FGS ./1:1,4,6:1:1e+06,500000:1111,5555:AAAA,CC:500000:5555:BB:1e+06,500000,9e+09:1111,5555,9999:A,EEEE,FFFFF ./1:1,4,6:1:1e+06,500000:1111,5555:AAAA,CC:500000:5555:BB:1e+06,500000,9e+09:1111,5555,9999:A,EEEE,FFFFF
2 1 . GGGCGTCTCATAGCTGGAGCAATGGCGAGCGCCTGGACAAGGGAGGGGAAGGGGTTCTTATTACTGACGCGGGTAGCCCCTACTGCTGTGTGGTTCCCCTATTTTTTTTTTTTTCTTTTTGAGACGGAGTCTCGCTCTGTCACCCAGGCTGGAGTGCAGTGGCACAATCTCGGCTCACTGCAAGCTCCACCT ACGT 999 PASS INDEL;AN=4;AC=2 GT:DP 1/0:1 1/0:1
2 101 . ATTTTTTTTTTTTT ATTTTTTTTTTTTTTT 999 PASS INDEL;AN=4;AC=4 GT:DP 1/1:1 1/1:1
2 114 . TC TTCC 999 PASS INDEL;AN=4;AC=2 GT:DP 1/0:1 1/0:1
2 114 . TC TTC 999 PASS INDEL;AN=4;AC=2 GT:DP 0/1:1 0/1:1
2 114 . TC TTCC 999 PASS INDEL;AN=4;AC=2 GT:DP 1/.:1 1/.:1
2 114 . TC TTC 999 PASS INDEL;AN=4;AC=2 GT:DP ./1:1 ./1:1
2 115 . C T 999 PASS INDEL;AN=4;AC=4 GT:DP 1/1:1 1/1:1
20 3 . G CT 999 PASS INDEL;AN=4;AC=2 GT 0/1 0/1
20 3 . GATG GACT 999 PASS INDEL;AN=4;AC=2 GT 1/0 1/0
20 5 . TGGG TAC . PASS INDEL;AN=4;AC=2 GT:PL:DP 1/0:1,2,3:1 1/0:1,2,3:1
20 5 . TGGG TG . PASS INDEL;AN=4;AC=2 GT:PL:DP 0/1:1,4,6:1 0/1:1,4,6:1
20 5 . TGGG TGGGG . PASS INDEL;AN=4;AC=0 GT:PL:DP 0/0:1,7,10:1 0/0:1,7,10:1
20 5 . TGGG AC . PASS INDEL;AN=4;AC=0 GT:PL:DP 0/0:1,11,15:1 0/0:1,11,15:1
20 5 . TGGG TAC . PASS INDEL;AN=4;AC=2 GT:PL:DP 1/.:1,2,3:1 1/.:1,2,3:1
20 5 . TGGG TG . PASS INDEL;AN=4;AC=2 GT:PL:DP ./1:1,4,6:1 ./1:1,4,6:1
20 5 . TGGG TGGGG . PASS INDEL;AN=4;AC=0 GT:PL:DP ./.:1,7,10:1 ./.:1,7,10:1
20 5 . TGGG AC . PASS INDEL;AN=4;AC=0 GT:PL:DP ./.:1,11,15:1 ./.:1,11,15:1
20 59 . AG . 999 PASS AN=4 GT:PL:DP 0/0:0:4 0/0:0:4
20 80 . CACAG CACAT 999 PASS AN=4;AC=2 GT:PL:DP 0/1:255,0,255:13 0/1:255,0,255:13
20 81 . A C 999 PASS AN=4;AC=2 GT:PL:DP 0/1:255,0,255:13 0/1:255,0,255:13
20 95 . TCACCG ACACCG 999 PASS AN=4;AC=2 GT:PL:DP 0/1:255,0,255:13 0/1:255,0,255:13
20 95 . TCACCG AAAAAA 999 PASS AN=4;AC=2 GT:PL:DP 0/1:255,0,255:13 0/1:255,0,255:13
20 273 . CAAAAAAAAAAAAAAAAAAAAA CAAAAAAAAAAAAAAAAAAAAAAA 999 PASS INDEL;AN=4;AC=2 GT:PL:DP 1/0:0,3,5:1 1/0:0,3,5:1
20 273 . CAAAAAAAAAAAAAAAAAAAAA CAAAAAAAAAAAAAAAAAAAAAAAA 999 PASS INDEL;AN=4;AC=2 GT:PL:DP 0/1:0,3,5:1 0/1:0,3,5:1
20 273 . CAAAAAAAAAAAAAAAAAAAAA CAAAAAAAAAAAAAAAAAAAAAAA 999 PASS INDEL;AN=4;AC=2 GT:PL:DP 1/.:0,3,5:1 1/.:0,3,5:1
20 273 . CAAAAAAAAAAAAAAAAAAAAA CAAAAAAAAAAAAAAAAAAAAAAAA 999 PASS INDEL;AN=4;AC=2 GT:PL:DP ./1:0,3,5:1 ./1:0,3,5:1
20 274 . AAAAAAAAA AAAAAAAAAAAAAAAAAAA 999 PASS INDEL;AN=0;AC=0 GT:PL:DP ./.:0,0,0:0 ./.:0,0,0:0
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
20 275 . A C 999 PASS INDEL;AN=2;AC=0 GT:PL:DP:FGF:FGI:FGS:FSTR .:0,0:0:1e+06,2e+06:1111,2222:A,BB:WORD .:0,0:0:1e+06,2e+06:1111,2222:A,BB:WORD
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
20 278 . AAAAAAAAAAAAAAAAA AAAAAAAAAAAAAAAAAAA 999 PASS INDEL;AN=0;AC=0 GT:PL:DP ./.:0,0,0:0 ./.:0,0,0:0
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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2 changes: 1 addition & 1 deletion vcfnorm.c
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Original file line number Diff line number Diff line change
Expand Up @@ -517,7 +517,7 @@ static void split_format_genotype(args_t *args, bcf1_t *src, bcf_fmt_t *fmt, int
if ( bcf_gt_allele(gt[j])==ialt+1 )
gt[j] = bcf_gt_unphased(1) | bcf_gt_is_phased(gt[j]); // set to first ALT
else
gt[j] = bcf_gt_unphased(0) | bcf_gt_is_phased(gt[j]); // set to REF
gt[j] = bcf_gt_missing | bcf_gt_is_phased(gt[j]); // set to REF
}
gt += ngts;
}
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