Fix a bug introduced in 1.14

The bug caused that records with INFO/END annotation would incorrectly
trigger `-c ~INFO/END` mode of comparison even when not explicitly requested,
which would result in not transferring the annotation from a tab-delimited file.

Resolves #1733

NEWS

@@ -14,6 +14,13 @@ Changes affecting the whole of bcftools, or multiple commands:
 
 Changes affecting specific commands:
 
+* bcftools annotate
+
+    - A bug introduced in 1.14 caused that records with INFO/END annotation would
+      incorrectly trigger `-c ~INFO/END` mode of comparison even when not explicitly
+      requested, which would result in not transferring the annotation from a tab-delimited
+      file (#1733)
+
 * bcftools mpileup
 
     - New NMBZ annotation for Mann-Whitney U-z test on number of mismatches within

test/annotate.32.out

@@ -0,0 +1,12 @@
+##fileformat=VCFv4.2
+##FILTER=<ID=PASS,Description="All filters passed">
+##ALT=<ID=DEL,Description="Deletion">
+##ALT=<ID=INS,Description="Duplication">
+##INFO=<ID=END,Number=1,Type=Integer,Description="End position of the structural variant">
+##INFO=<ID=EVIDENCE,Number=.,Type=String,Description="Classes of random forest support.">
+##contig=<ID=chr1,length=248956422>
+#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO
+chr1	54713	.	N	<INS>	.	PASS	END=54714;EVIDENCE=RD,PE,SR
+chr1	66224	.	N	<DEL>	.	PASS	END=66275;EVIDENCE=RD,PE,SR
+chr1	66242	.	N	<DEL>	.	PASS	END=66520;EVIDENCE=RD,PE,SR
+chr1	998763	.	N	<INS>	.	PASS	END=998764;EVIDENCE=RD,PE,SR

test/annotate27.tab

@@ -0,0 +1,4 @@
+chr1	54713	N	<INS>	RD,PE,SR
+chr1	66224	N	<DEL>	RD,PE,SR
+chr1	66242	N	<DEL>	RD,PE,SR
+chr1	998763	N	<INS>	RD,PE,SR

test/annotate27.vcf

@@ -0,0 +1,12 @@
+##fileformat=VCFv4.2
+##FILTER=<ID=PASS,Description="All filters passed">
+##ALT=<ID=DEL,Description="Deletion">
+##ALT=<ID=INS,Description="Duplication">
+##INFO=<ID=END,Number=1,Type=Integer,Description="End position of the structural variant">
+##INFO=<ID=EVIDENCE,Number=.,Type=String,Description="Classes of random forest support.">
+##contig=<ID=chr1,length=248956422>
+#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO
+chr1	54713	.	N	<INS>	.	PASS	END=54714
+chr1	66224	.	N	<DEL>	.	PASS	END=66275
+chr1	66242	.	N	<DEL>	.	PASS	END=66520
+chr1	998763	.	N	<INS>	.	PASS	END=998764

test/test.pl

@@ -489,6 +489,7 @@
 test_vcf_annotate($opts,in=>'annotate.olap',tab=>'annots.olap',out=>'annotate.olap.2.out',args=>'-c CHROM,BEG,END,DB -l DB:unique --min-overlap 0.4:0.5');
 test_vcf_annotate($opts,in=>'annotate.id',vcf=>'annots.id',out=>'annotate.id.1.out',args=>'-c ALT');
 test_vcf_annotate($opts,in=>'annotate.id',vcf=>'annots.id',out=>'annotate.id.2.out',args=>'-c +ALT');
+test_vcf_annotate($opts,in=>'annotate27',tab=>'annotate27',out=>'annotate.32.out',args=>'-c CHROM,POS,REF,ALT,EVIDENCE');
 test_vcf_plugin($opts,in=>'checkploidy',out=>'checkploidy.out',cmd=>'+check-ploidy --no-version');
 test_vcf_plugin($opts,in=>'checkploidy.2',out=>'checkploidy.2.out',cmd=>'+check-ploidy --no-version');
 test_vcf_plugin($opts,in=>'checkploidy.2',out=>'checkploidy.3.out',cmd=>'+check-ploidy --no-version',args=>'-- -m');

vcfannotate.c

@@ -140,8 +140,8 @@ typedef struct _args_t
     int ref_idx, alt_idx, chr_idx, beg_idx, end_idx;   // -1 if not present
     annot_col_t *cols;      // column indexes and setters
     int ncols;
-    int match_id;           // set iff `-c ~ID` given
-    int match_end;          // set iff `-c ~INFO/END` is given
+    int match_id;           // set iff `-c ~ID` given, -1 otherwise
+    int match_end;          // set iff `-c ~INFO/END` is given, -1 otherwise
 
     char *set_ids_fmt;
     convert_t *set_ids;
@@ -3145,7 +3145,7 @@ static void annotate(args_t *args, bcf1_t *line)
                         ialt++;
                     }
                     if ( args->match_id>=0 && !strstr_match(line->d.id,args->alines[i].cols[args->match_id]) ) continue;
-                    if ( match_end.l && strcmp(match_end.s,args->alines[i].cols[args->match_end]) ) continue;
+                    if ( args->match_end>=0 && match_end.l && strcmp(match_end.s,args->alines[i].cols[args->match_end]) ) continue;
                     args->srt_alines[args->nsrt_alines++] = (ialt<<16) | i;
                     has_overlap = 1;
                     break;
@@ -3335,6 +3335,7 @@ int main_vcfannotate(int argc, char *argv[])
     args->ref_idx = args->alt_idx = args->chr_idx = args->beg_idx = args->end_idx = -1;
     args->set_ids_replace = 1;
     args->match_id = -1;
+    args->match_end = -1;
     args->clevel = -1;
     args->pair_logic = -1;
     int regions_is_file = 0;