From 19657fe4e35bf36016fd2137cff46ba15959d76d Mon Sep 17 00:00:00 2001
From: peterjc
Date: Fri, 23 Mar 2012 16:59:53 +0000
Subject: [PATCH] Correct my error message; assed some comments
---
padding.c | 7 +++++--
1 file changed, 5 insertions(+), 2 deletions(-)
diff --git a/padding.c b/padding.c
index 8d0df07..6c8b31f 100644
--- a/padding.c
+++ b/padding.c
@@ -45,7 +45,7 @@ static void unpad_seq(bam1_t *b, kstring_t *s)
} else if (op == BAM_CDEL || op == BAM_CPAD) {
for (i = 0; i < ol; ++i) s->s[s->l++] = 0;
} else {
- fprintf(stderr, "[depad] ERROR: Didn't expect CIGAR op %c in embedded reference %s\n", BAM_CIGAR_STR[op], bam1_qname(b));
+ fprintf(stderr, "[depad] ERROR: Didn't expect CIGAR op %c in read %s\n", BAM_CIGAR_STR[op], bam1_qname(b));
assert(-1);
}
}
@@ -79,7 +79,7 @@ int bam_pad2unpad(bamFile in, bamFile out)
replace_cigar(b, n2, cigar2);
posmap = realloc(posmap, r.m * sizeof(int));
for (i = k = 0; i < r.l; ++i) {
- posmap[i] = k; // note that a read should NOT start at a padding
+ posmap[i] = k;
if (r.s[i]) ++k;
}
} else if (b->core.n_cigar > 0) {
@@ -93,8 +93,10 @@ int bam_pad2unpad(bamFile in, bamFile out)
}
unpad_seq(b, &q);
if (bam_cigar_op(cigar[0]) == BAM_CSOFT_CLIP) write_cigar(cigar2, n2, m2, cigar[0]);
+ /* Determine CIGAR operator for each base in the aligned read */
for (i = 0, k = b->core.pos; i < q.l; ++i, ++k)
q.s[i] = q.s[i]? (r.s[k]? BAM_CMATCH : BAM_CINS) : (r.s[k]? BAM_CDEL : BAM_CPAD);
+ /* Count consecutive CIGAR operators to turn into a CIGAR string */
for (i = k = 1, op = q.s[0]; i < q.l; ++i) {
if (op != q.s[i]) {
write_cigar(cigar2, n2, m2, bam_cigar_gen(k, op));
@@ -103,6 +105,7 @@ int bam_pad2unpad(bamFile in, bamFile out)
}
write_cigar(cigar2, n2, m2, bam_cigar_gen(k, op));
if (bam_cigar_op(cigar[b->core.n_cigar-1]) == BAM_CSOFT_CLIP) write_cigar(cigar2, n2, m2, cigar[b->core.n_cigar-1]);
+ /* Remove redundant P operators between M operators, e.g. 5M2P10M -> 15M */
for (i = 2; i < n2; ++i)
if (bam_cigar_op(cigar2[i]) == BAM_CMATCH && bam_cigar_op(cigar2[i-1]) == BAM_CPAD && bam_cigar_op(cigar2[i-2]) == BAM_CMATCH)
cigar2[i] += cigar2[i-2], cigar2[i-2] = cigar2[i-1] = 0;
--
2.39.2