Fix error introduced by e412f74, the precedence of smpl_count function was not set

Author: pd3

filter.c

@@ -170,9 +170,9 @@ struct _filter_t
 #define TOK_FISHER  42
 #define TOK_sCOUNT  43
 
-//                      0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41
+//                      0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43
 //                        ( ) [ < = > ] ! | &  +  -  *  /  M  m  a  A  O  ~  ^  S  .  l  f  c  p  b  P  i  s                          %
-static int op_prec[] = {0,1,1,5,5,5,5,5,5,2,3, 6, 6, 7, 7, 8, 8, 8, 3, 2, 5, 5, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 7, 0};
+static int op_prec[] = {0,1,1,5,5,5,5,5,5,2,3, 6, 6, 7, 7, 8, 8, 8, 3, 2, 5, 5, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 7, 0, 8, 8};
 #define TOKEN_STRING "x()[<=>]!|&+-*/MmaAO~^S.lfcpis"       // this is only for debugging, not maintained diligently
 
 static void cmp_vector_strings(token_t *atok, token_t *btok, token_t *rtok);
@@ -2007,8 +2007,7 @@ static int func_smpl_count(filter_t *flt, bcf1_t *line, token_t *rtok, token_t *
     if ( !rtok->usmpl ) rtok->usmpl = (uint8_t*) malloc(tok->nsamples);
     memcpy(rtok->usmpl, tok->usmpl, tok->nsamples);
     int i,j;
-    assert( tok->tag && tok->nsamples );
-    if ( tok->tag && tok->nsamples )
+    if ( tok->nsamples )
     {
         // raw number of values in a FMT tag, e.g. COUNT(FMT/TAG)
         if ( tok->is_str ) error("todo: Type=String for COUNT on FORMAT fields?\n");

test/smpl-count.1.out

@@ -0,0 +1,6 @@
+chr	1	0/0	.	0
+chr	1	0/1	1	1
+
+chr	2	1/1	1	1
+chr	2	1/2	1,2	2
+

test/smpl-count.2.out

@@ -0,0 +1,4 @@
+chr	1	0/1	1	1
+
+chr	2	1/1	1	1
+

test/smpl-count.3.out

@@ -0,0 +1,2 @@
+chr	2	1/1	1	1
+

test/smpl-count.vcf

@@ -0,0 +1,7 @@
+##fileformat=VCFv4.2
+##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
+##FORMAT=<ID=LAA,Number=.,Type=Integer,Description="">
+##contig=<ID=chr,length=123456>
+#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	smpl1	smpl2
+chr	1	.	A	C	.	.	.	GT:LAA	0/0:.	0/1:1
+chr	2	.	A	C,T	.	.	.	GT:LAA	1/1:1	1/2:1,2

test/test.pl

@@ -61,6 +61,7 @@
 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.broken-phase.a','merge.broken-phase.b'],out=>'merge.broken-phase.1.out',args=>'');
 run_test(\&test_vcf_merge,$opts,in=>['merge.broken-gvcf.a','merge.broken-gvcf.b'],out=>'merge.broken-gvcf.1.out',args=>'');
 run_test(\&test_vcf_merge,$opts,in=>['merge.symbolic.1.a','merge.symbolic.1.b'],out=>'merge.symbolic.1.1.out',args=>'');
 run_test(\&test_vcf_merge,$opts,in=>['merge.multiallelics.1.a','merge.multiallelics.1.b'],out=>'merge.multiallelics.1.1.out',args=>'--merge none');
@@ -119,6 +120,10 @@
 run_test(\&test_vcf_merge,$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,$opts,in=>'smpl-count',out=>'smpl-count.1.out',args=>q[-f '[%CHROM\\t%POS\\t%GT\\t%LAA\\t%smpl_count(FMT/LAA)\\n]\\n']);
+run_test(\&test_vcf_query,$opts,in=>'smpl-count',out=>'smpl-count.2.out',args=>q[-f '[%CHROM\\t%POS\\t%GT\\t%LAA\\t%smpl_count(FMT/LAA)\\n]\\n' -i'smpl_count(LAA)==1']);
+run_test(\&test_vcf_query,$opts,in=>'smpl-count',out=>'smpl-count.3.out',args=>q[-f '[%CHROM\\t%POS\\t%GT\\t%LAA\\t%smpl_count(FMT/LAA)\\n]\\n' -i'smpl_count(LAA)==1 & GT="hom"']);
+run_test(\&test_vcf_query,$opts,in=>'smpl-count',out=>'smpl-count.3.out',args=>q[-f '[%CHROM\\t%POS\\t%GT\\t%LAA\\t%smpl_count(FMT/LAA)\\n]\\n' -i'GT="hom" & smpl_count(LAA)==1']);
 run_test(\&test_vcf_query,$opts,in=>'query.filter.15',out=>'query.filter.15.1.out',args=>q[-f '%TAG' -i 'TAG[*]="."']);
 run_test(\&test_vcf_query,$opts,in=>'query.filter.15',out=>'query.filter.15.1.out',args=>q[-f '%TAG' -i 'TAG[*]~"\."']);
 run_test(\&test_vcf_query,$opts,in=>'query.filter.15',out=>'query.filter.15.2.out',args=>q[-f '%TAG' -i 'TAG[*]!="."']);