Numerical functions, such as SUM(INFO/DP), in formatting expressions of query

would previously return the value 0 when executed on missing values. This was incorrect, newly a missing value
is printed.

Author: pd3

NEWS

@@ -53,6 +53,11 @@ Changes affecting specific commands:
     - Make the -i/-e filtering option work for all options, such as line merging and
       duplication removal (#2415)
 
+* bcftools query
+
+    - Numerical functions, such as SUM(INFO/DP), would previously return the value 0 when
+      executed on missing values. This was incorrect, newly a missing value is printed.
+
 * bcftools reheader
 
     - Add options `--samples-list` and `--samples-file` to allow renaming samples from a list of

convert.c

@@ -1183,7 +1183,7 @@ static void process_filter_expr(convert_t *convert, bcf1_t *line, fmt_t *fmt, in
             val = filter_get_doubles(dat->filter,&nval,&nval1);
             if ( fmt->is_gt_field )
             {
-                if ( !dat->nval )
+                if ( nval && !dat->nval )
                 {
                     dat->nval = nval;
                     dat->val = malloc(nval*sizeof(double));
@@ -1204,7 +1204,8 @@ static void process_filter_expr(convert_t *convert, bcf1_t *line, fmt_t *fmt, in
     }
     if ( isample<0 ) isample = 0;
     if ( isample>=nval ) isample = 0;
-    kputd(val[isample], str);
+    if ( nval ) kputd(val[isample], str);
+    else kputc('.', str);
 }
 static void destroy_filter_expr(void *usr)
 {

filter.c

@@ -4379,15 +4379,10 @@ const double *filter_get_doubles(filter_t *filter, int *nval, int *nval1)
     {
         *nval  = tok->nvalues;
         *nval1 = tok->nval1;
+        return tok->values;
     }
-    else
-    {
-        if ( !tok->values ) error("fixme in filter_get_doubles(): %s\n", filter->str);
-        *nval  = 1;
-        *nval1 = 1;
-        tok->values[0] = filter->flt_stack[0]->pass_site;
-    }
-    return tok->values;
+    *nval = *nval1 = 0;
+    return NULL;
 }
 
 void filter_set_samples(filter_t *filter, const uint8_t *samples)

test/fill-tags.5.out

@@ -33,7 +33,7 @@
 ##INFO=<ID=DP_BC,Number=1,Type=Integer,Description="Added by +fill-tags expression DP:1=int(sum(FORMAT/DP)) in BC">
 #CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	NA00001	NA00002	NA00003
 11	2343543	.	A	.	999	PASS	DP=586;DP_AB=404;DP_BC=393	GT:PL:DP:GQ	0/0:0:193:99	0/0:0:211:99	0/0:0:182:99
-11	5464562	.	C	T	999	PASS	DP=0;DP_AB=0;DP_BC=0	GT:PL:DP:GQ	./.:0,0,0:.:.	./.:0,0,0:.:.	./.:0,0,0:.:.
+11	5464562	.	C	T	999	PASS	DP=.;DP_AB=.;DP_BC=.	GT:PL:DP:GQ	./.:0,0,0:.:.	./.:0,0,0:.:.	./.:0,0,0:.:.
 20	76962	rs6111385	T	C	999	PASS	DP4=110138,70822,421911,262673;DP=586;Dels=0;FS=21.447;HWE=0.491006;ICF=-0.01062;MQ0=1;MQ=46;PV4=2.5e-09,0,0,1;QD=22.31;DP_AB=404;DP_BC=393	GT:PL:DP:GQ	0/1:255,0,255:193:99	1/1:255,255,0:211:99	1/1:255,255,0:182:99
 20	126310	.	ACC	A	999	StrandBias;EndDistBias	DP4=125718,95950,113812,80890;DP=306;HWE=0.24036;ICF=0.01738;INDEL;IS=374,0.937343;MQ=49;PV4=9e-30,1,0,3.8e-13;QD=0.0172;AN=6;AC=4;DP_AB=228;DP_BC=189	GT:DP:GQ:PL	0/1:117:99:255,0,132	0/1:111:99:255,0,139	1/1:78:99:255,213,0
 20	138125	rs2298108	G	T	999	PASS	DP4=174391,20849,82080,4950;DP=203;Dels=0;FS=3200;HWE=0.199462;ICF=0.01858;MQ0=0;MQ=46;PV4=0,0,0,1;QD=17.22;AN=6;AC=4;DP_AB=137;DP_BC=137	GT:PL:DP:GQ	0/1:135,0,163:66:99	0/1:140,0,255:71:99	1/1:255,199,0:66:99

test/query.func.1.2.out

@@ -1,4 +1,4 @@
-1:150	. . 	0
+1:150	. . 	.
 1:153	.,.,. 0,0,210 	210
 1:154	30,13,0 300,13,0 	356
 1:155	20,0,10 200,0,10 	240

test/query.func.1.3.out

@@ -1,4 +1,4 @@
-1:150	. . 	 0 0
+1:150	. . 	 . .
 1:153	.,.,. 0,0,210 	 210 210
 1:154	30,13,0 300,13,0 	 356 356
 1:155	20,0,10 200,0,10 	 240 240