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Test case for htslib/1620 and htslib/1630
samtools/htslib#1620 samtools/htslib#1630
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‎test/test.pl‎

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run_test(\&test_vcf_norm,$opts,in=>'norm.phased-split',out=>'norm.phased-split.1.out',args=>'-m -any');
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run_test(\&test_vcf_norm,$opts,in=>'norm.phased-join',out=>'norm.phased-join.1.out',args=>'-m +any');
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run_test(\&test_vcf_norm,$opts,in=>'norm.symbolic',fai=>'norm.symbolic',out=>'norm.symbolic.1.out',args=>'--old-rec-tag ORI');
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run_test(\&test_vcf_view,$opts,in=>'weird-chr-names',out=>'weird-chr-names.1.out',args=>'',reg=>'-r 1');
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run_test(\&test_vcf_view,$opts,in=>'weird-chr-names',out=>'weird-chr-names.1.out',args=>'',reg=>'-r 1:1-2');
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run_test(\&test_vcf_view,$opts,in=>'weird-chr-names',out=>'weird-chr-names.1.out',args=>'',reg=>'-r 1:1,1:2');
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run_test(\&test_vcf_view,$opts,in=>'weird-chr-names',out=>'weird-chr-names.2.out',args=>'',reg=>'-r 1:1-1');
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run_test(\&test_vcf_view,$opts,in=>'weird-chr-names',out=>'weird-chr-names.3.out',args=>'',reg=>'-r {1:1}');
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run_test(\&test_vcf_view,$opts,in=>'weird-chr-names',out=>'weird-chr-names.3.out',args=>'',reg=>'-r {1:1}:1-2');
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run_test(\&test_vcf_view,$opts,in=>'weird-chr-names',out=>'weird-chr-names.3.out',args=>'',reg=>'-r {1:1}:1,{1:1}:2');
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run_test(\&test_vcf_view,$opts,in=>'weird-chr-names',out=>'weird-chr-names.4.out',args=>'',reg=>'-r {1:1}:1-1');
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run_test(\&test_vcf_view,$opts,in=>'weird-chr-names',out=>'weird-chr-names.5.out',args=>'',reg=>'-r {1:1-1}');
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run_test(\&test_vcf_view,$opts,in=>'weird-chr-names',out=>'weird-chr-names.5.out',args=>'',reg=>'-r {1:1-1}:1-2');
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run_test(\&test_vcf_view,$opts,in=>'weird-chr-names',out=>'weird-chr-names.5.out',args=>'',reg=>'-r {1:1-1}:1,{1:1-1}:2');
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run_test(\&test_vcf_view,$opts,in=>'weird-chr-names',out=>'weird-chr-names.6.out',args=>'',reg=>'-r {1:1-1}:1-1');
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run_test(\&test_vcf_view,$opts,in=>'view',out=>'view.1.out',args=>'-aUc1 -C1 -s NA00002 -v snps',reg=>'');
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run_test(\&test_vcf_view,$opts,in=>'view',out=>'view.2.out',args=>'-f PASS -Xks NA00003',reg=>'-r20,Y');
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run_test(\&test_vcf_view,$opts,in=>'view',out=>'view.3.out',args=>'-xs NA00003',reg=>'');

‎test/weird-chr-names.1.out‎

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##fileformat=VCFv4.3
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##FILTER=<ID=PASS,Description="All filters passed">
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##reference=ref.fa
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##contig=<ID=1>
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##contig=<ID=1:1>
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##contig=<ID=1:1-1>
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#CHROM POS ID REF ALT QUAL FILTER INFO
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1 1 . C T . . .
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1 2 . C T . . .

‎test/weird-chr-names.2.out‎

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##fileformat=VCFv4.3
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##FILTER=<ID=PASS,Description="All filters passed">
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##reference=ref.fa
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##contig=<ID=1>
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##contig=<ID=1:1>
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##contig=<ID=1:1-1>
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#CHROM POS ID REF ALT QUAL FILTER INFO
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1 1 . C T . . .

‎test/weird-chr-names.3.out‎

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##fileformat=VCFv4.3
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##FILTER=<ID=PASS,Description="All filters passed">
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##reference=ref.fa
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##contig=<ID=1>
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##contig=<ID=1:1>
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##contig=<ID=1:1-1>
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#CHROM POS ID REF ALT QUAL FILTER INFO
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1:1 1 . C T . . .
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1:1 2 . C T . . .

‎test/weird-chr-names.4.out‎

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##fileformat=VCFv4.3
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##FILTER=<ID=PASS,Description="All filters passed">
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##reference=ref.fa
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##contig=<ID=1>
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##contig=<ID=1:1>
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##contig=<ID=1:1-1>
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#CHROM POS ID REF ALT QUAL FILTER INFO
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1:1 1 . C T . . .

‎test/weird-chr-names.5.out‎

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##fileformat=VCFv4.3
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##FILTER=<ID=PASS,Description="All filters passed">
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##reference=ref.fa
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##contig=<ID=1>
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##contig=<ID=1:1>
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##contig=<ID=1:1-1>
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#CHROM POS ID REF ALT QUAL FILTER INFO
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1:1-1 1 . C T . . .
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1:1-1 2 . C T . . .

‎test/weird-chr-names.6.out‎

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##fileformat=VCFv4.3
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##FILTER=<ID=PASS,Description="All filters passed">
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##reference=ref.fa
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##contig=<ID=1>
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##contig=<ID=1:1>
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##contig=<ID=1:1-1>
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#CHROM POS ID REF ALT QUAL FILTER INFO
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1:1-1 1 . C T . . .

‎test/weird-chr-names.vcf‎

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##fileformat=VCFv4.3
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##reference=ref.fa
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##contig=<ID=1>
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##contig=<ID=1:1>
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##contig=<ID=1:1-1>
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#CHROM POS ID REF ALT QUAL FILTER INFO
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1 1 . C T . . .
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1 2 . C T . . .
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1:1 1 . C T . . .
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1:1 2 . C T . . .
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1:1-1 1 . C T . . .
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1:1-1 2 . C T . . .

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