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Fix a bug in breakend detection #1858

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merged 1 commit into from
Nov 19, 2024
Merged

Fix a bug in breakend detection #1858

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13 changes: 13 additions & 0 deletions test/test-bcf_set_variant_type.c
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Original file line number Diff line number Diff line change
Expand Up @@ -91,6 +91,19 @@ static void test_bcf_set_variant_type(void)
{
error("[16:33625444[N was not detected as a breakend");
}

bcf_set_variant_type("T", "]chrB:123]AGTNNNNNCAT", &var3d);
if ( var3d.type != VCF_BND)
{
error("]chrB:123]AGTNNNNNCAT was not detected as a breakend");
}
bcf_set_variant_type("C", "CAGTNNNNNCA[chrA:321[", &var3d);
if ( var3d.type != VCF_BND)
{
error("CAGTNNNNNCA[chrA:321[ was not detected as a breakend");
}


// Test special reference alleles
bcf_variant_t var4a;
bcf_set_variant_type("A", "<NON_REF>", &var4a);
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2 changes: 1 addition & 1 deletion vcf.c
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Original file line number Diff line number Diff line change
Expand Up @@ -5025,8 +5025,8 @@ static void bcf_set_variant_type(const char *ref, const char *alt, bcf_variant_t

if ( *a && !*r )
{
if ( *a==']' || *a=='[' ) { var->type = VCF_BND; return; } // "joined after" breakend
while ( *a ) a++;
if ( *(a-1)==']' || *(a-1)=='[' ) { var->type = VCF_BND; return; } // "joined after" breakend
var->n = (a-alt)-(r-ref); var->type = VCF_INDEL | VCF_INS; return;
}
else if ( *r && !*a )
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