From 685647d11f95cc490f13ad6ce708811439c1f867 Mon Sep 17 00:00:00 2001
From: peterjc
Date: Wed, 4 Apr 2012 10:53:35 +0100
Subject: [PATCH] Use FASTA file when no embedded reference in 'samtools depad'
---
padding.c | 68 +++++++++++++++++++++++++++++++++++++++++++++++++------
1 file changed, 61 insertions(+), 7 deletions(-)
diff --git a/padding.c b/padding.c
index 9f8bca7..d03e598 100644
--- a/padding.c
+++ b/padding.c
@@ -69,6 +69,52 @@ static void unpad_seq(bam1_t *b, kstring_t *s)
assert(length == s->l);
}
+int load_unpadded_ref(faidx_t *fai, char *ref_name, int ref_len, kstring_t *seq)
+{
+ char base;
+ char *fai_ref = 0;
+ int fai_ref_len = 0, k;
+
+ fai_ref = fai_fetch(fai, ref_name, &fai_ref_len);
+ if (fai_ref_len != ref_len) {
+ fprintf(stderr, "[depad] ERROR: FASTA sequence %s length %i, expected %i\n", ref_name, fai_ref_len, ref_len);
+ free(fai_ref);
+ return -1;
+ }
+ ks_resize(seq, ref_len);
+ seq->l = 0;
+ for (k = 0; k < ref_len; ++k) {
+ base = fai_ref[k];
+ if (base == '-' || base == '*') {
+ // 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];
+ }
+ }
+ assert(ref_len == seq->l);
+ free(fai_ref);
+ return 0;
+}
+
+inline int * update_posmap(int *posmap, kstring_t ref)
+{
+ int i, k;
+ posmap = realloc(posmap, ref.m * sizeof(int));
+ for (i = k = 0; i < ref.l; ++i) {
+ posmap[i] = k;
+ if (ref.s[i]) ++k;
+ }
+ return posmap;
+}
+
int bam_pad2unpad(samfile_t *in, samfile_t *out, faidx_t *fai)
{
bam_header_t *h;
@@ -86,10 +132,8 @@ 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) {
- int i, k;
- /*
- fprintf(stderr, "[depad] Found embedded reference %s\n", bam1_qname(b));
- */
+ // 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) {
@@ -98,18 +142,28 @@ int bam_pad2unpad(samfile_t *in, samfile_t *out, faidx_t *fai)
}
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) {
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]);
+ } else if (b->core.tid == r_tid) {
+ ; // good case, reference available
+ } else if (fai) {
+ if (load_unpadded_ref(fai, h->target_name[b->core.tid], h->target_len[b->core.tid], &r)) return -1;
+ posmap = update_posmap(posmap, r);
+ r_tid = b->core.tid;
+ // fprintf(stderr, "[depad] Loaded %s from FASTA file\n", h->target_name[b->core.tid]);
+ } else {
+ fprintf(stderr, "[depad] ERROR: Missing %s embedded reference sequence (and no FASTA file)\n", h->target_name[b->core.tid]);
return -1;
}
unpad_seq(b, &q);
@@ -186,7 +240,7 @@ static int usage(int is_long_help);
int main_pad2unpad(int argc, char *argv[])
{
samfile_t *in = 0, *out = 0;
- faidx_t *fai;
+ faidx_t *fai = 0;
int c, is_bamin = 1, compress_level = -1, is_bamout = 1, is_long_help = 0;
char in_mode[5], out_mode[5], *fn_out = 0, *fn_list = 0, *fn_ref = 0;
int ret=0;
--
2.39.2