Fix missed VCF regions

Awaits the merge of samtools/htslib#1624

Resolves #1918

Author: pd3

consensus.c

@@ -324,7 +324,7 @@ static void init_region(args_t *args, char *line)
 {
     char *ss, *se = line;
     while ( *se && !isspace(*se) && *se!=':' ) se++;
-    int from = 0, to = 0;
+    hts_pos_t from = 0, to = 0;
     char tmp = 0, *tmp_ptr = NULL;
     if ( *se )
     {
@@ -356,7 +356,14 @@ static void init_region(args_t *args, char *line)
     args->fa_frz_mod = -1;
     args->fa_case    = -1;
     args->vcf_rbuf.n = 0;
-    bcf_sr_seek(args->files,line,args->fa_ori_pos);
+
+    kstring_t str = {0,0,0};
+    if ( from==0 ) from = 1;
+    if ( to==0 ) to = HTS_POS_MAX;
+    ksprintf(&str,"%s:%"PRIhts_pos"-%"PRIhts_pos,line,from,to);
+    bcf_sr_set_regions(args->files,line,0);
+    free(str.s);
+
     if ( tmp_ptr ) *tmp_ptr = tmp;
     fprintf(args->fp_out,">%s%s\n",args->chr_prefix?args->chr_prefix:"",line);
     if ( args->chain_fname )

test/consensus.21.fa

@@ -0,0 +1,6 @@
+>17
+ACGTACGT
+>18
+ACGTACGT
+>19
+ACGTACGT

test/consensus.21.vcf

@@ -0,0 +1,11 @@
+##fileformat=VCFv4.2
+##reference=file://some/path/human_g1k_v37.fasta
+##contig=<ID=17>
+##contig=<ID=18>
+##contig=<ID=19>
+##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
+#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	a
+19	2	.	C	A	.	.	.	GT	0/0
+19	3	.	G	C	.	.	.	GT	0/0
+19	4	.	T	C	.	.	.	GT	0/1
+19	5	.	A	C	.	.	.	GT	1/1

test/consensus21.1.out

@@ -0,0 +1,6 @@
+>17
+ACGTACGT
+>18
+ACGTACGT
+>19
+ACGYCCGT

test/test.pl

@@ -811,6 +811,7 @@
 run_test(\&test_vcf_consensus,$opts,in=>'consensus.20',out=>'consensus20.2.out',fa=>'consensus.20.fa',args=>'');
 run_test(\&test_vcf_consensus,$opts,in=>'consensus.20',out=>'consensus20.3.out',fa=>'consensus.20.fa',args=>'-M . -s b');
 run_test(\&test_vcf_consensus,$opts,in=>'consensus.20',out=>'consensus20.4.out',fa=>'consensus.20.fa',args=>'-M . -s a');
+run_test(\&test_vcf_consensus,$opts,in=>'consensus.21',out=>'consensus21.1.out',fa=>'consensus.21.fa',args=>'');
 run_test(\&test_mpileup,$opts,in=>[qw(mpileup.1 mpileup.2 mpileup.3)],out=>'mpileup/mpileup.1.out',args=>q[-r17:100-150],test_list=>1);
 run_test(\&test_mpileup,$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
 run_test(\&test_mpileup,$opts,in=>[qw(mpileup.1)],out=>'mpileup/mpileup.3.out',args=>q[-B --ff 0x14 -r17:1050-1060]); # test file converted to vcf from samtools mpileup test suite
@@ -1174,6 +1175,18 @@ sub bgzip_tabix_vcf
     my ($opts,$file) = @_;
     bgzip_tabix($opts,file=>$file,suffix=>'vcf',args=>'-p vcf');
 }
+sub bgzip_index_bcf
+{
+    my ($opts,$file) = @_;
+    if ( !-e "$$opts{tmp}/$file.bcf" or is_file_newer("$$opts{path}/$file.vcf","$$opts{tmp}/$file.bcf") )
+    {
+        cmd("$$opts{bin}/bcftools view -Ob $$opts{path}/$file.vcf -o $$opts{tmp}/$file.bcf");
+    }
+    if ( !-e "$$opts{tmp}/$file.bcf.csi" or is_file_newer("$$opts{tmp}/$file.bcf","$$opts{tmp}/$file.bcf.csi") )
+    {
+        cmd("$$opts{bin}/bcftools index -f $$opts{tmp}/$file.bcf");
+    }
+}
 
 
 # The tests --------------------------
@@ -1755,10 +1768,12 @@ sub test_vcf_consensus
 {
     my ($opts,%args) = @_;
     bgzip_tabix_vcf($opts,$args{in});
+    bgzip_index_bcf($opts,$args{in});
     $args{args} =~ s/{PATH}/$$opts{path}/g;
     my $mask = $args{mask} ? "-m $$opts{path}/$args{mask}" : '';
     my $chain = $args{chain} ? "-c $$opts{tmp}/$args{chain}" : '';
     test_cmd($opts,%args,cmd=>"$$opts{bin}/bcftools consensus $$opts{tmp}/$args{in}.vcf.gz -f $$opts{path}/$args{fa} $args{args} $mask $chain");
+    test_cmd($opts,%args,cmd=>"$$opts{bin}/bcftools consensus $$opts{tmp}/$args{in}.bcf    -f $$opts{path}/$args{fa} $args{args} $mask $chain");
 }
 sub test_vcf_consensus_chain
 {