From: peterjc
Date: Wed, 4 Apr 2012 09:54:16 +0000 (+0100)
Subject: Check embedded reference against FASTA if given in 'samtools depad'
X-Git-Url: https://git.donarmstrong.com/?a=commitdiff_plain;h=ed708a64a1fdf9216d022a60e164c669fe2c5828;hp=685647d11f95cc490f13ad6ce708811439c1f867;p=samtools.git
Check embedded reference against FASTA if given in 'samtools depad'
---
diff --git a/padding.c b/padding.c
index d03e598..19b95a9 100644
--- a/padding.c
+++ b/padding.c
@@ -89,14 +89,13 @@ int load_unpadded_ref(faidx_t *fai, char *ref_name, int ref_len, kstring_t *seq)
// Map gaps to null to match unpad_seq function
seq->s[seq->l++] = 0;
} else {
- // Want to map IUPAC bases to upper case, and reject other chars
int i = bam_nt16_table[(int)base];
if (i == 0 || i==16) { // Equals maps to 0, anything unexpected to 16
fprintf(stderr, "[depad] ERROR: Invalid character %c (ASCII %i) in FASTA sequence %s\n", base, (int)base, ref_name);
free(fai_ref);
return -1;
}
- seq->s[seq->l++] = bam_nt16_rev_table[i];
+ seq->s[seq->l++] = i;
}
}
assert(ref_len == seq->l);
@@ -133,23 +132,31 @@ int bam_pad2unpad(samfile_t *in, samfile_t *out, faidx_t *fai)
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));
- // TODO - Check this embedded reference matches the FASTA file (if given)
r_tid = b->core.tid;
unpad_seq(b, &r);
if (h->target_len[r_tid] != r.l) {
fprintf(stderr, "[depad] ERROR: (Padded) length of %s is %i in BAM header, but %ld in embedded reference\n", bam1_qname(b), h->target_len[r_tid], r.l);
return -1;
}
+ if (fai) {
+ // Check the embedded reference matches the FASTA file
+ if (load_unpadded_ref(fai, h->target_name[b->core.tid], h->target_len[b->core.tid], &q)) return -1;
+ assert(r.l == q.l);
+ int i;
+ for (i = 0; i < r.l; ++i) {
+ if (r.s[i] != q.s[i]) {
+ // Show gaps as ASCII 45
+ fprintf(stderr, "[depad] ERROR: Embedded sequence and reference FASTA don't match for %s base %i, '%c' vs '%c'\n",
+ h->target_name[b->core.tid], i+1,
+ r.s[i] ? bam_nt16_rev_table[r.s[i]] : 45,
+ q.s[i] ? bam_nt16_rev_table[q.s[i]] : 45);
+ return -1;
+ }
+ }
+ }
write_cigar(cigar2, n2, m2, bam_cigar_gen(b->core.l_qseq, BAM_CMATCH));
replace_cigar(b, n2, cigar2);
posmap = update_posmap(posmap, r);
- /*
- posmap = realloc(posmap, r.m * sizeof(int));
- for (i = k = 0; i < r.l; ++i) {
- posmap[i] = k;
- if (r.s[i]) ++k;
- }
- */
} else if (b->core.n_cigar > 0) {
int i, k, op;
if (b->core.tid < 0) {