From 70c84f409b060067e70087e51b29700215cbddbb Mon Sep 17 00:00:00 2001 From: peterjc Date: Thu, 22 Mar 2012 17:49:40 +0000 Subject: [PATCH] Check current reference sequence matches RNAME in samtools depad --- padding.c | 21 +++++++++++++++++---- 1 file changed, 17 insertions(+), 4 deletions(-) diff --git a/padding.c b/padding.c index 4290485..ad68728 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) { for (i = 0; i < ol; ++i) s->s[s->l++] = 0; } else { - fprintf(stderr, "[unpad_seq] Didn't expect CIGAR op %c in %s\n", BAM_CIGAR_STR[op], bam1_qname(b)); + fprintf(stderr, "[depad] ERROR: Didn't expect CIGAR op %c in %s\n", BAM_CIGAR_STR[op], bam1_qname(b)); assert(-1); } } @@ -56,6 +56,7 @@ int bam_pad2unpad(bamFile in, bamFile out) bam_header_t *h; bam1_t *b; kstring_t r, q; + int r_tid = -1; uint32_t *cigar2 = 0; int n2 = 0, m2 = 0, *posmap = 0; @@ -68,6 +69,10 @@ int bam_pad2unpad(bamFile in, bamFile out) n2 = 0; if (b->core.pos == 0 && b->core.tid >= 0 && strcmp(bam1_qname(b), h->target_name[b->core.tid]) == 0) { int i, k; + /* + fprintf(stderr, "[depad] Found embedded reference %s\n", bam1_qname(b)); + */ + r_tid = b->core.tid; unpad_seq(b, &r); write_cigar(cigar2, n2, m2, bam_cigar_gen(b->core.l_qseq, BAM_CMATCH)); replace_cigar(b, n2, cigar2); @@ -76,8 +81,15 @@ int bam_pad2unpad(bamFile in, bamFile out) posmap[i] = k; // note that a read should NOT start at a padding if (r.s[i]) ++k; } - } else { + } else if (b->core.n_cigar > 0) { int i, k, op; + if (b->core.tid < 0) { + fprintf(stderr, "[depad] ERROR: Read %s has CIGAR but no RNAME\n", bam1_qname(b)); + return -1; + } else if (b->core.tid != r_tid) { + fprintf(stderr, "[depad] ERROR: Missing %s embedded reference sequence\n", h->target_name[b->core.tid]); + return -1; + } unpad_seq(b, &q); if (bam_cigar_op(cigar[0]) == BAM_CSOFT_CLIP) write_cigar(cigar2, n2, m2, cigar[0]); for (i = 0, k = b->core.pos; i < q.l; ++i, ++k) @@ -110,13 +122,14 @@ int bam_pad2unpad(bamFile in, bamFile out) int main_pad2unpad(int argc, char *argv[]) { bamFile in, out; + int result=0; if (argc == 1) { fprintf(stderr, "Usage: samtools depad \n"); return 1; } in = strcmp(argv[1], "-")? bam_open(argv[1], "r") : bam_dopen(fileno(stdin), "r"); out = bam_dopen(fileno(stdout), "w"); - bam_pad2unpad(in, out); + result = bam_pad2unpad(in, out); bam_close(in); bam_close(out); - return 0; + return result; } -- 2.39.2