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Add support for matching VCF lines by ID
See #1739
1 parent a79ca97 commit 3d994d3

12 files changed

+105
-8
lines changed

‎test/annotate35.1.out

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##fileformat=VCFv4.2
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##FILTER=<ID=PASS,Description="All filters passed">
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##INFO=<ID=src,Number=1,Type=String,Description="">
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##INFO=<ID=dst,Number=1,Type=String,Description="">
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##contig=<ID=chr1,length=248956422>
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#CHROM POS ID REF ALT QUAL FILTER INFO
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chr1 902 ID6 N <INS> . PASS src=ID6
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chr1 902 ID5 N <INS> . PASS src=ID5
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chr1 902 ID4 N <INS> . PASS src=ID4
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chr1 902 ID3 N <INS> . PASS src=ID3
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chr1 902 ID2 N <INS> . PASS src=ID2
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chr1 902 ID1 N <INS> . PASS src=ID1

‎test/annotate35.2.out

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##fileformat=VCFv4.2
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##FILTER=<ID=PASS,Description="All filters passed">
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##INFO=<ID=src,Number=1,Type=String,Description="">
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##INFO=<ID=dst,Number=1,Type=String,Description="">
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##contig=<ID=chr1,length=248956422>
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#CHROM POS ID REF ALT QUAL FILTER INFO
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chr1 902 ID6 N <INS> . PASS src=ID6;dst=ID6
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chr1 902 ID5 N <INS> . PASS src=ID5;dst=ID5
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chr1 902 ID4 N <INS> . PASS src=ID4;dst=ID4
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chr1 902 ID3 N <INS> . PASS src=ID3;dst=ID3
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chr1 902 ID2 N <INS> . PASS src=ID2;dst=ID2
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chr1 902 ID1 N <INS> . PASS src=ID1;dst=ID1

‎test/annotate35.vcf

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##fileformat=VCFv4.2
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##INFO=<ID=src,Number=1,Type=String,Description="">
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##INFO=<ID=dst,Number=1,Type=String,Description="">
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##contig=<ID=chr1,length=248956422>
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#CHROM POS ID REF ALT QUAL FILTER INFO
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chr1 902 ID6 N <INS> . PASS src=ID6
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chr1 902 ID5 N <INS> . PASS src=ID5
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chr1 902 ID4 N <INS> . PASS src=ID4
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chr1 902 ID3 N <INS> . PASS src=ID3
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chr1 902 ID2 N <INS> . PASS src=ID2
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chr1 902 ID1 N <INS> . PASS src=ID1

‎test/annots35.tab

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chr1 902 ID4 N <INS> ID4
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chr1 902 ID2 N <INS> ID2
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chr1 902 ID6 N <INS> ID6
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chr1 902 ID1 N <INS> ID1
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chr1 902 ID3 N <INS> ID3
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chr1 902 ID5 N <INS> ID5

‎test/annots35.vcf

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##fileformat=VCFv4.2
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##INFO=<ID=src,Number=1,Type=String,Description="">
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##INFO=<ID=dst,Number=1,Type=String,Description="">
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##contig=<ID=chr1,length=248956422>
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#CHROM POS ID REF ALT QUAL FILTER INFO
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chr1 902 ID4 N <INS> . PASS src=ID4
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chr1 902 ID2 N <INS> . PASS src=ID2
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chr1 902 ID6 N <INS> . PASS src=ID6
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chr1 902 ID3 N <INS> . PASS src=ID3
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chr1 902 ID1 N <INS> . PASS src=ID1
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chr1 902 ID5 N <INS> . PASS src=ID5

‎test/isec.match-id.1.1.vcf

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##fileformat=VCFv4.2
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##INFO=<ID=src,Number=1,Type=String,Description="">
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##contig=<ID=chr1,length=248956422>
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#CHROM POS ID REF ALT QUAL FILTER INFO
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chr1 902 ID1 A C . . .
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chr1 902 ID2 A C . . .
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chr1 902 ID3 A C . . .

‎test/isec.match-id.1.2.vcf

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##fileformat=VCFv4.2
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##INFO=<ID=src,Number=1,Type=String,Description="">
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##contig=<ID=chr1,length=248956422>
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#CHROM POS ID REF ALT QUAL FILTER INFO
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chr1 902 ID3 A C . . .
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chr1 902 ID2 A C . . .
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chr1 902 ID1 A C . . .

‎test/isec.match-id.1.out

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##fileformat=VCFv4.2
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##FILTER=<ID=PASS,Description="All filters passed">
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##INFO=<ID=src,Number=1,Type=String,Description="">
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##contig=<ID=chr1,length=248956422>
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#CHROM POS ID REF ALT QUAL FILTER INFO
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chr1 902 ID3 A C . . .
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chr1 902 ID2 A C . . .
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chr1 902 ID1 A C . . .

‎test/isec.match-id.2.out

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##fileformat=VCFv4.2
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##FILTER=<ID=PASS,Description="All filters passed">
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##INFO=<ID=src,Number=1,Type=String,Description="">
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##contig=<ID=chr1,length=248956422>
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#CHROM POS ID REF ALT QUAL FILTER INFO
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chr1 902 ID1 A C . . .
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chr1 902 ID2 A C . . .
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chr1 902 ID3 A C . . .

‎test/test.pl

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@@ -49,6 +49,8 @@
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run_test(\&test_vcf_stats,$opts,in=>['stats.counts'],out=>'stats.counts.chk',args=>'-s -');
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run_test(\&test_vcf_stats,$opts,in=>['stats.counts'],out=>'stats.counts.2.chk',args=>q[-s - -i 'type="snp"']);
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run_test(\&test_vcf_stats,$opts,in=>['stats.vaf'],out=>'stats.vaf.1.chk',args=>q[-s -]);
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run_test(\&test_vcf_isec,$opts,in=>['isec.match-id.1.1','isec.match-id.1.2'],out=>'isec.match-id.1.out',args=>'-n =2 -w 2 --no-version');
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run_test(\&test_vcf_isec,$opts,in=>['isec.match-id.1.1','isec.match-id.1.2'],out=>'isec.match-id.2.out',args=>'-n =2 -w 2 -c id --no-version');
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run_test(\&test_vcf_isec,$opts,in=>['isec.a','isec.b'],out=>'isec.ab.out',args=>'-n =2');
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run_test(\&test_vcf_isec,$opts,in=>['isec.a','isec.b'],out=>'isec.ab.flt.out',args=>'-n =2 -i"STRLEN(REF)==2"');
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run_test(\&test_vcf_isec,$opts,in=>['isec.a','isec.b'],out=>'isec.ab.both.out',args=>'-n =2 -c both');
@@ -524,6 +526,8 @@
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run_test(\&test_vcf_sort,$opts,in=>'sort',out=>'sort.out',args=>q[-m 0],fmt=>'%CHROM\\t%POS\\t%REF,%ALT\\n');
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run_test(\&test_vcf_sort,$opts,in=>'sort',out=>'sort.out',args=>q[-m 1000],fmt=>'%CHROM\\t%POS\\t%REF,%ALT\\n');
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run_test(\&test_vcf_regions,$opts,in=>'regions');
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run_test(\&test_vcf_annotate,$opts,in=>'annotate35',vcf=>'annots35',out=>'annotate35.1.out',args=>q[-c CHROM,POS,~ID,REF,ALT,INFO/src]);
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run_test(\&test_vcf_annotate,$opts,in=>'annotate35',tab=>'annots35',out=>'annotate35.2.out',args=>q[-c CHROM,POS,~ID,REF,ALT,dst:=src]);
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run_test(\&test_vcf_annotate,$opts,in=>'annotate.escape.1',tab=>'annotate.escape.1',out=>'annotate.escape.1.1.out',args=>q[-c CHROM,POS,ISTR,FMT/FSTR]);
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run_test(\&test_vcf_annotate,$opts,in=>'annotate.match.1',tab=>'annotate.match.1',out=>'annotate.match.1.1.out',args=>q[-c CHROM,POS,-,-,SCORE,~X,-,- -i'STR={X}']);
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run_test(\&test_vcf_annotate,$opts,in=>'annotate.match.1',tab=>'annotate.match.1',out=>'annotate.match.1.2.out',args=>q[-c CHROM,POS,REF,ALT,SCORE,-,~X,- -i'INT={X}']);
@@ -1477,7 +1481,9 @@ sub test_vcf_isec
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my $files = join(' ',@files);
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$args{args} =~ s/{PATH}/$$opts{path}/g;
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test_cmd($opts,%args,cmd=>"$$opts{bin}/bcftools isec $args{args} $files");
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test_cmd($opts,%args,cmd=>"$$opts{bin}/bcftools isec -Ob $args{args} $files");
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# Either improve or disable completely: the output type does not make sense in all modes
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# test_cmd($opts,%args,cmd=>"$$opts{bin}/bcftools isec -Ob $args{args} $files");
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}
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sub test_vcf_isec2
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{

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