Apply mask even if the VCF has no notion about the chromosome

When `contig` lines are not present in the VCF and the file does not contain
any variants, the mask region was not applied.

Fixes #1592

Author: pd3

NEWS

@@ -56,6 +56,13 @@ Changes affecting specific commands:
       `--ligate-warn` option (previously this was the default). To keep such
       sites, use the new `--ligate-force` option (#1567).
 
+* bcftools consensus:
+
+    - Apply mask even when the VCF has no notion about the chromosome. It
+      was possible to encounter this problem when `contig` lines were not
+      present in the VCF header and no variants were called on that chromosome
+      (#1592)
+
 * bcftools +contrast:
 
     - support for chunking within map/reduce framework allowing to collect

consensus.c

@@ -975,7 +975,7 @@ static void consensus(args_t *args)
         // determine if uppercase or lowercase is used in this fasta file
         if ( args->fa_case==-1 ) args->fa_case = toupper(str.s[0])==str.s[0] ? 1 : 0;
 
-        if ( args->mask && args->rid>=0) mask_region(args, str.s, str.l);
+        if ( args->mask ) mask_region(args, str.s, str.l);
         kputs(str.s, &args->fa_buf);
 
         bcf1_t **rec_ptr = NULL;

test/consensus.17.bed

@@ -0,0 +1,4 @@
+1	0	59
+2	0	60
+3	0	30
+4	31	62

test/consensus.17.vcf

@@ -0,0 +1,5 @@
+##fileformat=VCFv4.2
+##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
+##reference=file://some/path/human_g1k_v37.fasta
+##contig=<ID=1,assembly=b37,length=249250621>
+#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	NA001

test/consensus17.1.out

@@ -0,0 +1,10 @@
+>1
+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
+>2
+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
+>3
+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNATAACCTACGTATCAACTAAAGTGGTTGTT
+C
+>4
+CCCCTACCATATGTGACATATAAAAAAGAACNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
+NN

test/test.pl

@@ -693,6 +693,7 @@
 test_vcf_consensus($opts,in=>'consensus.15',out=>'consensus.17.out',fa=>'consensus.15.fa',args=>'-H I --mark-ins lc --mark-snv lc');
 test_vcf_consensus($opts,in=>'consensus.16',out=>'consensus.18.out',fa=>'consensus.fa',args=>'-I');
 test_vcf_consensus($opts,in=>'consensus.16',out=>'consensus.18.out',fa=>'consensus.fa',args=>'-H I');
+test_vcf_consensus($opts,in=>'consensus.17',out=>'consensus17.1.out',fa=>'consensus2.fa',mask=>'consensus.17.bed',args=>'-M N');
 test_mpileup($opts,in=>[qw(mpileup.1 mpileup.2 mpileup.3)],out=>'mpileup/mpileup.1.out',args=>q[-r17:100-150],test_list=>1);
 test_mpileup($opts,in=>[qw(mpileup.1 mpileup.2 mpileup.3)],out=>'mpileup/mpileup.2.out',args=>q[-a DP,DV -r17:100-600]); # test files from samtools mpileup test suite
 test_mpileup($opts,in=>[qw(mpileup.1)],out=>'mpileup/mpileup.3.out',args=>q[-B --ff 0x14 -r17:1050-1060]); # test file converted to vcf from samtools mpileup test suite