Improve the recent consensus fixes.

Resolves samtools#938

consensus.c

@@ -538,7 +538,11 @@ static void apply_variant(args_t *args, bcf1_t *rec)
         // Can be still OK iff this is an insertion (and which does not follow another insertion, see #888).
         // This still may not be enough for more complicated cases with multiple duplicate positions
         // and other types in between. In such case let the user normalize the VCF and remove duplicates.
-        if ( !(bcf_get_variant_type(rec,ialt) & VCF_INDEL) || rec->d.var[ialt].n <= 0 || args->prev_is_insert )
+        int overlap = 0;
+        if ( rec->pos < args->fa_frz_pos || !(bcf_get_variant_type(rec,ialt) & VCF_INDEL) ) overlap = 1;
+        else if ( rec->d.var[ialt].n <= 0 || args->prev_is_insert ) overlap = 1;
+
+        if ( overlap )
         {
             fprintf(stderr,"The site %s:%d overlaps with another variant, skipping...\n", bcf_seqname(args->hdr,rec),rec->pos+1);
             return;

test/consensus6.fa

@@ -0,0 +1,5 @@
+>NW_019171628.1:64330-64531
+GAGAAAGAGAGAGAGAGCATGCTTCCAAACCCTTTGTTCTTTTTCTTCTGAAGAGAAGGT
+GACCTGGTTTTGAAACACTGGCTACAGCAAATCACTCAGAACACACACACACACAACACA
+CACACACACACACACACACACACACACACTCTCAGAACACACACACACACACGCACTTAC
+ATTTAGCCTTGGTGTTACTAT

test/consensus6.out

@@ -0,0 +1,5 @@
+>NW_019171628.1:64330-64531
+GAGAAAGAGAGAGAGAGAGCATGCTTCCAAACCCTTTGTTCTTTTTCTTCTGAAGAGAAG
+GTGACCTGGTTTTGAAACACTGGCTACAGCAAATCACTCAGAACACACACACACACACAC
+ACACACACACACACACACACACTCTCAGAACACACACACACACACGCACTTACATTTAGC
+CTTGGTGTTACTAT

test/consensus6.vcf

@@ -0,0 +1,8 @@
+##fileformat=VCFv4.2
+##reference=consensus6.fa
+##contig=<ID=NW_019171628.1,length=354362>
+##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
+#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	sample
+NW_019171628.1	64334	.	A	AAG	159	.	.	GT	1/1
+NW_019171628.1	64435	.	CACACACACA	C	170	.	.	GT	1/1
+NW_019171628.1	64443	.	C	CACTCAG	72	.	.	GT	1/1

test/test.pl

@@ -394,6 +394,7 @@
 test_vcf_consensus($opts,in=>'consensus3',out=>'consensus3.2.out',fa=>'consensus2.fa',args=>'-H 2 -M "?" -p xx_');
 test_vcf_consensus($opts,in=>'consensus4',out=>'consensus4.out',fa=>'consensus2.fa',args=>'');
 test_vcf_consensus($opts,in=>'consensus5',out=>'consensus5.out',fa=>'consensus5.fa',args=>'--haplotype LA');
+test_vcf_consensus($opts,in=>'consensus6',out=>'consensus6.out',fa=>'consensus6.fa',args=>'');
 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