Fix behavior of --merge none

The option `--merge none` is expected to create no new multiallelic sites,
but it should allow to merge, say, A>C with A>C,AT

Fixes #2333

NEWS

@@ -29,6 +29,9 @@ Changes affecting specific commands:
 
     - Preserve phasing in half-missing genotypes (#2331)
 
+    - The option `--merge none` is expected to create no new multiallelic sites, but it should
+      allow to merge, say, A>C with A>C,AT (#2333)
+
 * bcftools query
 
     - The functions used in -i/-e filtering expressions (such as SUM, MEDIAN, etc) can be

test/test.pl

@@ -1,6 +1,6 @@
 #!/usr/bin/env perl
 #
-#   Copyright (C) 2012-2024 Genome Research Ltd.
+#   Copyright (C) 2012-2025 Genome Research Ltd.
 #
 #   Author: Petr Danecek <[email protected]>
 #
@@ -61,6 +61,8 @@
 run_test(\&test_vcf_isec,$opts,in=>['isec-miss.1.1','isec-miss.1.2','isec-miss.1.3'],out=>'isec-miss.1.1.out',args=>'-R {PATH}/isec-miss.1.regs.txt -n +1');
 run_test(\&test_vcf_isec,$opts,in=>['isec-miss.2.1','isec-miss.2.2','isec-miss.2.3'],out=>'isec-miss.2.1.out',args=>'-n +1 -r 20:100,20:140,12:55,20:140,20:100');
 run_test(\&test_vcf_isec,$opts,in=>['isec-miss.2.1','isec-miss.2.2','isec-miss.2.3'],out=>'isec-miss.2.1.out',args=>'-R {PATH}/isec-miss.1.regs.txt -n +1');
+run_test(\&test_vcf_merge,$opts,in=>['merge.12.a','merge.12.b'],out=>'merge.12.1.out',args=>'--merge none');
+run_test(\&test_vcf_merge,$opts,in=>['merge.12.a','merge.12.b'],out=>'merge.12.1.out',args=>'--merge both');
 run_test(\&test_vcf_merge,$opts,in=>['merge.phased.1.a','merge.phased.1.b'],out=>'merge.phased.1.1.out',args=>'');
 run_test(\&test_vcf_merge,$opts,in=>['merge.11.a','merge.11.b'],out=>'merge.11.1.out',args=>'');
 run_test(\&test_vcf_merge,$opts,in=>['merge.join.a','merge.join.b'],out=>'merge.join.1.out',args=>'-i AF:join');

vcfmerge.c

@@ -1,6 +1,6 @@
 /*  vcfmerge.c -- Merge multiple VCF/BCF files to create one multi-sample file.
 
-    Copyright (C) 2012-2024 Genome Research Ltd.
+    Copyright (C) 2012-2025 Genome Research Ltd.
 
     Author: Petr Danecek <[email protected]>
 
@@ -2968,10 +2968,10 @@ static inline int types_compatible(args_t *args, int selected_types, buffer_t *b
 
     // The -m none mode or exact matching requested
     // Simple test first: are the variants of the same type?
-    int x = selected_types >> 1;        // remove REF
-    int y = rec_types >> 1;             // remove REF
-    while ( x && y ) { x>>=1; y>>=1; }
-    if ( x || y ) return 0;             // the types differ
+    int x = selected_types;
+    int y = rec_types;
+    if ( !(x&y) ) return 0;                 // no matching type
+    if ( (x&y)!=x && (x&y)!=y ) return 0;   // not a subset
 
     if ( vcmp_set_ref(args->vcmp,maux->als[0],rec->d.allele[0]) < 0 ) return 0;   // refs are not compatible
     for (k=1; k<rec->n_allele; k++)