From fe98a6b54536246ce650ad5fde0b75e99bb22fa0 Mon Sep 17 00:00:00 2001
From: Petr Danecek <pd3@sanger.ac.uk>
Date: Fri, 24 Feb 2023 15:37:41 +0100
Subject: [PATCH] The `-m` function did not respect the `--min-overlap` option

Fixes #1869
---
 NEWS                     | 2 ++
 test/annotate.olap.2.out | 3 ++-
 test/test.pl             | 2 +-
 vcfannotate.c            | 3 ++-
 4 files changed, 7 insertions(+), 3 deletions(-)

diff --git a/NEWS b/NEWS
index 3609f0004..59a7efdd3 100644
--- a/NEWS
+++ b/NEWS
@@ -7,6 +7,8 @@ Changes affecting specific commands:
     - The `-m, --mark-sites` option can be now used to mark all sites without the
       need to provide the `-a` file (#1861)
 
+    - Fix a bug where the `-m` function did not respect the `--min-overlap` option (#1869)
+
 * bcftools stats
 
     - Collect new VAF (variant allele frequency) statistics from FORMAT/AD field
diff --git a/test/annotate.olap.2.out b/test/annotate.olap.2.out
index eab0ef4fc..8453306df 100644
--- a/test/annotate.olap.2.out
+++ b/test/annotate.olap.2.out
@@ -5,6 +5,7 @@
 ##ALT=<ID=CNV,Description="Copy Number Variation">
 ##INFO=<ID=END,Number=1,Type=Integer,Description="End position of the variant described in this record">
 ##INFO=<ID=DB,Number=1,Type=String,Description="CNV id from a database">
+##INFO=<ID=XXX,Number=0,Type=Flag,Description="Sites listed in XXX">
 #CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO
-1	10	.	C	<CNV>	.	.	END=19;DB=cnv10_15
+1	10	.	C	<CNV>	.	.	END=19;DB=cnv10_15;XXX
 1	20	.	C	<CNV>	.	.	END=30
diff --git a/test/test.pl b/test/test.pl
index 316a40be4..0d8490240 100755
--- a/test/test.pl
+++ b/test/test.pl
@@ -499,7 +499,7 @@
 run_test(\&test_vcf_annotate,$opts,in=>'annotate.missing',tab=>'annotate.missing',out=>'annotate.missing.5.out',args=>'-c CHROM,POS,REF,ALT,.=TSTR,.=TFLT,.=TINT');
 run_test(\&test_vcf_annotate,$opts,in=>'annotate.missing',tab=>'annotate.missing',out=>'annotate.missing.6.out',args=>'-c CHROM,POS,REF,ALT,=TSTR,=TFLT,=TINT');
 run_test(\&test_vcf_annotate,$opts,in=>'annotate.olap',tab=>'annots.olap',out=>'annotate.olap.1.out',args=>'-c CHROM,BEG,END,DB -l DB:unique');
-run_test(\&test_vcf_annotate,$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');
+run_test(\&test_vcf_annotate,$opts,in=>'annotate.olap',tab=>'annots.olap',out=>'annotate.olap.2.out',args=>'-c CHROM,BEG,END,DB -l DB:unique --min-overlap 0.4:0.5 -m XXX');
 run_test(\&test_vcf_annotate,$opts,in=>'annotate.id',vcf=>'annots.id',out=>'annotate.id.1.out',args=>'-c ALT');
 run_test(\&test_vcf_annotate,$opts,in=>'annotate.id',vcf=>'annots.id',out=>'annotate.id.2.out',args=>'-c +ALT');
 run_test(\&test_vcf_annotate,$opts,in=>'annotate.id.2',vcf=>'annots.id.2',out=>'annotate.id.2.1.out',args=>'--pair-logic some -c +ID');
diff --git a/vcfannotate.c b/vcfannotate.c
index e0122585f..0f2e86380 100644
--- a/vcfannotate.c
+++ b/vcfannotate.c
@@ -3103,9 +3103,9 @@ static void annotate(args_t *args, bcf1_t *line)
                         error("fixme: Could not set %s at %s:%"PRId64"\n", args->cols[j].hdr_key_src,bcf_seqname(args->hdr,line),(int64_t) line->pos+1);
                     if ( ret==0 )
                         args->cols[j].done = 1;
+                    has_overlap = 1;
                 }
             }
-            has_overlap = 1;
         }
         for (j=0; j<args->ncols; j++)
         {
@@ -3264,6 +3264,7 @@ static void annotate(args_t *args, bcf1_t *line)
             has_overlap = 1;
         }
     }
+fprintf(stderr,"has_overlap=%d  mark=%s\n",has_overlap,args->mark_sites);
     if ( args->set_ids )
     {
         args->tmpks.l = 0;