Overlapping deletions must not be forgotten in subsequent records wit…

…h -a N. Fixes samtools#1155
EEGKit · Feb 18, 2020 · f3203e3 · f3203e3
1 parent 3f96f33
commit f3203e3
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Showing 5 changed files with 14 additions and 0 deletions.
diff --git a/consensus.c b/consensus.c
@@ -391,6 +391,7 @@ static void apply_absent(args_t *args, hts_pos_t pos)
 }
 static void freeze_ref(args_t *args, bcf1_t *rec)
 {
+    if ( args->fa_frz_pos >= rec->pos + rec->rlen - 1 ) return;
     args->fa_frz_pos = rec->pos + rec->rlen - 1;
     args->fa_frz_mod = rec->pos - args->fa_ori_pos + args->fa_mod_off + rec->rlen;
 }

diff --git a/test/consensus.11.1.out b/test/consensus.11.1.out
@@ -0,0 +1,2 @@
+>1
+CGCGCACCCACGTATACGCGTA
diff --git a/test/consensus.11.2.out b/test/consensus.11.2.out
@@ -0,0 +1,2 @@
+>1
+NNNNNNNNNNNNNNTNNNNNNN
diff --git a/test/consensus.11.fa b/test/consensus.11.fa
@@ -0,0 +1,2 @@
+>1
+CGCGCACCCACGTATACGTGTACACGCGTA
diff --git a/test/consensus.11.vcf b/test/consensus.11.vcf
@@ -0,0 +1,7 @@
+##fileformat=VCFv4.2
+##contig=<ID=1,length=249250621>
+##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
+#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	smpl
+1	15	.	TACGTGTAC	T	.	.	.	GT	0/1
+1	18	.	G	A	.	.	.	GT	0/0
+1	19	.	T	C	.	.	.	GT	1/1