From 545789370ce9f41f8b0e752d45f68006c3655e84 Mon Sep 17 00:00:00 2001
From: peterjc
Date: Wed, 20 Jun 2012 16:16:54 +0100
Subject: [PATCH] First attempt at updating MPOS in 'samtools depad'
---
padding.c | 25 +++++++++++++++++++++++++
1 file changed, 25 insertions(+)
diff --git a/padding.c b/padding.c
index 88945e2..ad8bf5c 100644
--- a/padding.c
+++ b/padding.c
@@ -271,6 +271,31 @@ 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) {
+ /* Nice case, no mate to worry about*/
+ } else if (b->core.mtid == b->core.tid) {
+ /* Nice case, same reference */
+ b->core.mpos = posmap[b->core.mpos];
+ } else {
+ /* Nasty case, Must load alternative posmap */
+ 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;
+ }
+ /* Temporarily load the other reference sequence */
+ if (load_unpadded_ref(fai, h->target_name[b->core.mtid], h->target_len[b->core.mtid], &r)) {
+ fprintf(stderr, "[depad] ERROR: Failed to load '%s' from reference FASTA\n", h->target_name[b->core.mtid]);
+ return -1;
+ }
+ posmap = update_posmap(posmap, r);
+ b->core.mpos = posmap[b->core.mpos];
+ /* Restore the reference and posmap*/
+ 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]);
+ return -1;
+ }
+ posmap = update_posmap(posmap, r);
+ }
}
samwrite(out, b);
}
--
2.39.2