Remove unnecessary assert in text output, only with no csq. Fixes #2446

Author: pd3

csq.c

@@ -2108,6 +2108,7 @@ fprintf(stderr,"csq_push: pos=%d .. type=%d  ial=%d\n",(int)rec->pos+1,csq->type
 #define node2rend(i) (hap->stack[i].node->sbeg + hap->stack[i].node->rlen)
 #define node2rpos(i) (hap->stack[i].node->rec->pos)
 
+// Format variant consequence into a string like "inframe_deletion|XYZ|ENST01|+|5TY>5I|121ACG>A+124TA>T"
 void kput_vcsq(args_t *args, vcsq_t *csq, kstring_t *str)
 {
     // Remove start/stop from incomplete CDS, but only if there is another
@@ -2143,7 +2144,6 @@ void kput_vcsq(args_t *args, vcsq_t *csq, kstring_t *str)
     if ( csq->gene ) kputs(csq->gene , str);
 
     kputc_('|', str);
-//    if ( csq->type & CSQ_PRN_TSCRIPT ) kputs(args->tscript_ids.str[csq->trid], str);
     if ( csq->type & CSQ_PRN_TSCRIPT ) kputs(gff_id2string(args->gff,transcript,csq->trid), str);
 
     kputc_('|', str);
@@ -2561,7 +2561,7 @@ static inline void csq_print_text(args_t *args, csq_t *csq, int ismpl, int ihap)
         fprintf(args->out,"-");
 
     args->str.l = 0;
-    kput_vcsq(args, &csq->type, &args->str);
+    kput_vcsq(args, &csq->type, &args->str);    // format the csq string
     fprintf(args->out,"\t%s\t%d\t%s\n",chr,csq->pos+1,args->str.s);
 }
 static inline void hap_print_text(args_t *args, gf_tscript_t *tr, int ismpl, int ihap, hap_node_t *node)
@@ -2576,7 +2576,7 @@ static inline void hap_print_text(args_t *args, gf_tscript_t *tr, int ismpl, int
     {
         csq_t *csq = node->csq_list + i;
         if ( csq->type.type & CSQ_PRINTED_UPSTREAM ) continue;
-        assert( csq->type.vstr.l );
+        if ( !csq->type.vstr.l ) continue;  // not sure why this happens, see test/csq/ENST00000000001
 
         fprintf(args->out,"CSQ\t%s\t", smpl);
         if ( ihap>0 )
@@ -2585,7 +2585,7 @@ static inline void hap_print_text(args_t *args, gf_tscript_t *tr, int ismpl, int
             fprintf(args->out,"-");
 
         args->str.l = 0;
-        kput_vcsq(args, &csq->type, &args->str);
+        kput_vcsq(args, &csq->type, &args->str);    // format the csq string
         fprintf(args->out,"\t%s\t%d\t%s\n",chr,csq->pos+1,args->str.s);
     }
 }
@@ -2636,7 +2636,9 @@ void hap_flush(args_t *args, uint32_t pos)
             if ( args->output_type==FT_TAB_TEXT )   // plain text output, not a vcf
             {
                 if ( args->phase==PHASE_DROP_GT )
+                {
                     hap_print_text(args, tr, -1,0, TSCRIPT_AUX(tr)->hap[0]);
+                }
                 else
                 {
                     for (i=0; i<args->smpl->n; i++)
@@ -2743,11 +2745,11 @@ void vbuf_flush(args_t *args, uint32_t pos)
             }
 
             args->str.l = 0;
-            kput_vcsq(args, &vrec->vcsq[0], &args->str);
+            kput_vcsq(args, &vrec->vcsq[0], &args->str);    // format the csq string
             for (j=1; j<vrec->nvcsq; j++)
             {
                 kputc_(',', &args->str);
-                kput_vcsq(args, &vrec->vcsq[j], &args->str);
+                kput_vcsq(args, &vrec->vcsq[j], &args->str);    // format the csq string
             }
             bcf_update_info_string(args->hdr, vrec->line, args->bcsq_tag, args->str.s);
             if ( args->hdr_nsmpl )

test/csq/ENST00000000001/ENST00000000001.fa

@@ -0,0 +1,2 @@
+>example
+ATGGCCGTCA

test/csq/ENST00000000001/ENST00000000001.fa.fai

@@ -0,0 +1 @@
+example	10	9	10	11

test/csq/ENST00000000001/ENST00000000001.gff

@@ -0,0 +1,4 @@
+##gff-version 3
+example	custom	gene	1	10	.	+	.	ID=gene00000000001;biotype=protein_coding
+example	custom	transcript	1	10	.	+	.	ID=transcript00000000001;Parent=gene00000000001;biotype=protein_coding
+example	custom	CDS	1	10	.	+	0	Parent=transcript00000000001

test/csq/ENST00000000001/test.1.cmd

@@ -0,0 +1 @@
+{bin}/bcftools csq -f ENST00000000001.fa -g ENST00000000001.gff test.vcf -p a | ../sort-csq | {bin}/bcftools query -f'%POS\t%REF\t%ALT\t%BCSQ\n'

test/csq/ENST00000000001/test.1.cmd.out

@@ -0,0 +1,2 @@
+1	A	T	start_lost|gene00000000001|transcript00000000001|protein_coding|+
+3	GGC	G	.

test/csq/ENST00000000001/test.2.cmd

@@ -0,0 +1 @@
+{bin}/bcftools csq -f ENST00000000001.fa -g ENST00000000001.gff test.vcf -p a -Ot | grep -v ^#

test/csq/ENST00000000001/test.2.cmd.out

@@ -0,0 +1 @@
+CSQ	T	2	example	1	start_lost|gene00000000001|transcript00000000001|protein_coding|+

test/csq/ENST00000000001/test.vcf

@@ -0,0 +1,6 @@
+##fileformat=VCFv4.2
+##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
+##contig=<ID=example,length=10>
+#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	T
+example	1	.	A	T	.	.	.	GT	0/1
+example	3	.	GGC	G	.	.	.	GT	0/1