From f5c347706ae6ecce3e1794cb3141981a3c45397e Mon Sep 17 00:00:00 2001
From: peterjc
Date: Fri, 17 Aug 2012 11:28:27 +0100
Subject: [PATCH] Fix 'samtools depad' seg-fault when MPOS/PNEXT given but
MRNM/RNEXT is not
---
padding.c | 12 ++++++++++--
1 file changed, 10 insertions(+), 2 deletions(-)
diff --git a/padding.c b/padding.c
index fbbb204..a8da562 100644
--- a/padding.c
+++ b/padding.c
@@ -166,7 +166,7 @@ int bam_pad2unpad(samfile_t *in, samfile_t *out, faidx_t *fai)
uint32_t *cigar = bam1_cigar(b);
n2 = 0;
if (b->core.pos == 0 && b->core.tid >= 0 && strcmp(bam1_qname(b), h->target_name[b->core.tid]) == 0) {
- // fprintf(stderr, "[depad] Found embedded reference %s\n", bam1_qname(b));
+ // fprintf(stderr, "[depad] Found embedded reference '%s'\n", bam1_qname(b));
r_tid = b->core.tid;
unpad_seq(b, &r);
if (h->target_len[r_tid] != r.l) {
@@ -202,6 +202,7 @@ int bam_pad2unpad(samfile_t *in, samfile_t *out, faidx_t *fai)
return -1;
} else if (b->core.tid == r_tid) {
; // good case, reference available
+ //fprintf(stderr, "[depad] Have ref '%s' for read '%s'\n", h->target_name[b->core.tid], bam1_qname(b));
} else if (fai) {
if (load_unpadded_ref(fai, h->target_name[b->core.tid], h->target_len[b->core.tid], &r)) {
fprintf(stderr, "[depad] ERROR: Failed to load '%s' from reference FASTA\n", h->target_name[b->core.tid]);
@@ -271,13 +272,20 @@ int bam_pad2unpad(samfile_t *in, samfile_t *out, faidx_t *fai)
n2 = k;
replace_cigar(b, n2, cigar2);
b->core.pos = posmap[b->core.pos];
- if (b->core.mpos < 0) {
+ if (b->core.mtid < 0 || b->core.mpos < 0) {
/* Nice case, no mate to worry about*/
+ // fprintf(stderr, "[depad] Read '%s' mate not mapped\n", bam1_qname(b));
+ /* TODO - Warning if FLAG says mate should be mapped? */
+ /* Clean up funny input where mate position is given but mate reference is missing: */
+ b->core.mtid = -1;
+ b->core.mpos = -1;
} else if (b->core.mtid == b->core.tid) {
/* Nice case, same reference */
+ // fprintf(stderr, "[depad] Read '%s' mate mapped to same ref\n", bam1_qname(b));
b->core.mpos = posmap[b->core.mpos];
} else {
/* Nasty case, Must load alternative posmap */
+ // fprintf(stderr, "[depad] Loading reference '%s' temporarily\n", h->target_name[b->core.mtid]);
if (!fai) {
fprintf(stderr, "[depad] ERROR: Needed reference %s sequence for mate (and no FASTA file)\n", h->target_name[b->core.mtid]);
return -1;
--
2.39.2