Fix a bug in genotype filtering

An empty genotype field (".") followed a non-empty field (e.g. "0/1") was
not fully reset on next site, causing the program to crash.

Resolves #2314

filter.c

@@ -1191,12 +1191,9 @@ static void filters_set_format_string(filter_t *flt, bcf1_t *line, token_t *tok)
 }
 static void _filters_set_genotype(filter_t *flt, bcf1_t *line, token_t *tok, int type)
 {
+    tok->nvalues = tok->str_value.l = 0;
     bcf_fmt_t *fmt = bcf_get_fmt(flt->hdr, line, "GT");
-    if ( !fmt )
-    {
-        tok->nvalues = tok->str_value.l = 0;
-        return;
-    }
+    if ( !fmt ) return;
 
     int i,j, nsmpl = bcf_hdr_nsamples(flt->hdr), nvals1 = type==2 ? 3 : 4;
     if ( tok->str_value.m <= nvals1*nsmpl )
@@ -1276,12 +1273,10 @@ static void filters_set_genotype4(filter_t *flt, bcf1_t *line, token_t *tok) { _
 
 static void filters_set_genotype_string(filter_t *flt, bcf1_t *line, token_t *tok)
 {
+    tok->nvalues = tok->str_value.l = 0;
     bcf_fmt_t *fmt = bcf_get_fmt(flt->hdr, line, "GT");
-    if ( !fmt )
-    {
-        tok->nvalues = 0;
-        return;
-    }
+    if ( !fmt ) return;
+
     int i, blen = 4, nsmpl = line->n_sample;
 
 gt_length_too_big:

test/query.filter.14.1.out

@@ -0,0 +1,2 @@
+chr1:1  SM 0|1
+chr1:2  SM .

test/query.filter.14.2.out

@@ -0,0 +1 @@
+chr1:2  SM .

test/query.filter.14.3.out

@@ -0,0 +1 @@
+chr1:1  SM 0|1

test/query.filter.14.vcf

@@ -0,0 +1,6 @@
+##fileformat=VCFv4.2
+##contig=<ID=chr1>
+##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
+#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	SM
+chr1	1	.	A	C	.	.	.	GT	0|1
+chr1	2	.	G	T	.	.	.	.	.

test/test.pl

@@ -112,6 +112,9 @@
 run_test(\&test_vcf_merge,$opts,in=>['merge.gvcf.5.a','merge.gvcf.5.b'],out=>'merge.gvcf.5.1.out',args=>'--gvcf - --merge none');
 run_test(\&test_vcf_merge,$opts,in=>['merge.gvcf.11.a','merge.gvcf.11.b','merge.gvcf.11.c'],out=>'merge.gvcf.11.1.out',args=>'--gvcf -');
 # run_test(\&test_vcf_merge_big,$opts,in=>'merge_big.1',out=>'merge_big.1.1',nsmpl=>79000,nfiles=>79,nalts=>486,args=>'');   # commented out for speed
+run_test(\&test_vcf_query,$opts,in=>'query.filter.14',out=>'query.filter.14.1.out',args=>q[-f '%CHROM:%POS [ %SAMPLE %GT]']);
+run_test(\&test_vcf_query,$opts,in=>'query.filter.14',out=>'query.filter.14.2.out',args=>q[-f '%CHROM:%POS [ %SAMPLE %GT]' -i'GT="."']);
+run_test(\&test_vcf_query,$opts,in=>'query.filter.14',out=>'query.filter.14.3.out',args=>q[-f '%CHROM:%POS [ %SAMPLE %GT]' -i'GT="0|1"']);
 run_test(\&test_vcf_query,$opts,in=>'query.func.1',out=>'query.func.1.1.out',args=>q[-f '%CHROM:%POS\\t%INFO/AD\\t%SUM(INFO/AD)']);
 run_test(\&test_vcf_query,$opts,in=>'query.func.1',out=>'query.func.1.2.out',args=>q[-f '%CHROM:%POS\\t[%AD ]\\t%SUM(FORMAT/AD)']);
 run_test(\&test_vcf_query,$opts,in=>'query.func.1',out=>'query.func.1.3.out',args=>q[-f '%CHROM:%POS\\t[%AD ]\\t[ %SUM(FORMAT/AD)]']);