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Better support of duplicate removal of symbolic alleles
For example, these variants should not be removed with `-d exact` POS=1 ALT=<DEL> SVLEN=-1000 POS=1 ALT=<DEL> SVLEN=-2000 POS=1 ALT=<DEL> SVLEN=-3000 Resolves #2182
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Original file line number | Diff line number | Diff line change |
---|---|---|
@@ -0,0 +1,9 @@ | ||
##fileformat=VCFv4.1 | ||
##FILTER=<ID=PASS,Description="All filters passed"> | ||
##INFO=<ID=SVLEN,Number=.,Type=Integer,Description="Difference in length between REF and ALT alleles"> | ||
##contig=<ID=1> | ||
#CHROM POS ID REF ALT QUAL FILTER INFO | ||
1 1 . A <DEL> . . SVLEN=-1000 | ||
1 1 . A <DEL> . . SVLEN=-2000 | ||
1 1 . A <DEL> . . SVLEN=-3000 | ||
1 18 . AC A . . . |
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Original file line number | Diff line number | Diff line change |
---|---|---|
@@ -0,0 +1,7 @@ | ||
##fileformat=VCFv4.1 | ||
##FILTER=<ID=PASS,Description="All filters passed"> | ||
##INFO=<ID=SVLEN,Number=.,Type=Integer,Description="Difference in length between REF and ALT alleles"> | ||
##contig=<ID=1> | ||
#CHROM POS ID REF ALT QUAL FILTER INFO | ||
1 1 . A <DEL> . . SVLEN=-1000 | ||
1 18 . AC A . . . |
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Original file line number | Diff line number | Diff line change |
---|---|---|
@@ -0,0 +1,2 @@ | ||
>1 | ||
ACGTACGTCCCGTACGTACCCCCGT |
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Original file line number | Diff line number | Diff line change |
---|---|---|
@@ -0,0 +1,15 @@ | ||
##fileformat=VCFv4.1 | ||
##INFO=<ID=SVLEN,Number=.,Type=Integer,Description="Difference in length between REF and ALT alleles"> | ||
##contig=<ID=1> | ||
#CHROM POS ID REF ALT QUAL FILTER INFO | ||
1 10 . C <DEL> . . SVLEN=-1000 | ||
1 10 . C <DEL> . . SVLEN=-1000 | ||
1 10 . C <DEL> . . SVLEN=-2000 | ||
1 10 . C <DEL> . . SVLEN=-1000 | ||
1 10 . C <DEL> . . SVLEN=-3000 | ||
1 10 . C <DEL> . . SVLEN=-2000 | ||
1 10 . C <DEL> . . SVLEN=-1000 | ||
1 10 . C <DEL> . . SVLEN=-3000 | ||
1 10 . C <DEL> . . SVLEN=-2000 | ||
1 20 . CCC CC . . . | ||
1 20 . CC C . . . |
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