Make it possible to test for VCF_REF as declared in the documentation

pd3 · daviesrob · commit c6c1d19c3956 · 2025-01-27T16:35:07.000Z
Currently bcf_has_variant_types always returns 0 when testing for
the presence of VCF_REF, regardless of the actual type
diff --git a/vcf.c b/vcf.c
@@ -5161,6 +5161,7 @@ int bcf_has_variant_types(bcf1_t *rec, uint32_t bitmask,
         else return bitmask & type;
     }
     // mode == bcf_match_exact
+    if ( bitmask==VCF_REF ) return type==bitmask ? 1 : 0;
     return type==bitmask ? type : 0;
 }
 

Original file line number	Diff line number	Diff line change
`@@ -5161,6 +5161,7 @@ int bcf_has_variant_types(bcf1_t *rec, uint32_t bitmask,`
`5161`	`5161`	`else return bitmask & type;`
`5162`	`5162`	`}`
`5163`	`5163`	`// mode == bcf_match_exact`
	`5164`	`+ if ( bitmask==VCF_REF ) return type==bitmask ? 1 : 0;`
`5164`	`5165`	`return type==bitmask ? type : 0;`
`5165`	`5166`	`}`
`5166`	`5167`