From 2b4d9b14c3cdd96b9b1df2e9f2c83ceef4a76593 Mon Sep 17 00:00:00 2001
From: peterjc
Date: Tue, 12 Jun 2012 15:33:03 +0100
Subject: [PATCH] Calculate unpadded reference length, update BAM header (SAM
header pending)
---
padding.c | 88 ++++++++++++++++++++++++++++++++++++++++++++++++++-----
1 file changed, 80 insertions(+), 8 deletions(-)
diff --git a/padding.c b/padding.c
index 27bbd4b..23d1b23 100644
--- a/padding.c
+++ b/padding.c
@@ -7,6 +7,8 @@
#include "bam.h"
#include "faidx.h"
+bam_header_t *bam_header_dup(const bam_header_t *h0); /*in sam.c*/
+
static void replace_cigar(bam1_t *b, int n, uint32_t *cigar)
{
if (n != b->core.n_cigar) {
@@ -103,6 +105,39 @@ int load_unpadded_ref(faidx_t *fai, char *ref_name, int ref_len, kstring_t *seq)
return 0;
}
+int get_unpadded_len(faidx_t *fai, char *ref_name, int padded_len)
+{
+ char base;
+ char *fai_ref = 0;
+ int fai_ref_len = 0, k;
+ int bases=0, gaps=0;
+
+ fai_ref = fai_fetch(fai, ref_name, &fai_ref_len);
+ if (fai_ref_len != padded_len) {
+ fprintf(stderr, "[depad] ERROR: FASTA sequence '%s' length %i, expected %i\n", ref_name, fai_ref_len, padded_len);
+ free(fai_ref);
+ return -1;
+ }
+ for (k = 0; k < padded_len; ++k) {
+ //fprintf(stderr, "[depad] checking base %i of %i or %i\n", k+1, ref_len, strlen(fai_ref));
+ base = fai_ref[k];
+ if (base == '-' || base == '*') {
+ gaps += 1;
+ } else {
+ 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;
+ }
+ bases += 1;
+ }
+ }
+ free(fai_ref);
+ assert (padded_len == bases + gaps);
+ return bases;
+}
+
inline int * update_posmap(int *posmap, kstring_t ref)
{
int i, k;
@@ -116,8 +151,8 @@ inline int * update_posmap(int *posmap, kstring_t ref)
int bam_pad2unpad(samfile_t *in, samfile_t *out, faidx_t *fai)
{
- bam_header_t *h;
- bam1_t *b;
+ bam_header_t *h = 0;
+ bam1_t *b = 0;
kstring_t r, q;
int r_tid = -1;
uint32_t *cigar2 = 0;
@@ -135,12 +170,15 @@ int bam_pad2unpad(samfile_t *in, samfile_t *out, faidx_t *fai)
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);
+ fprintf(stderr, "[depad] ERROR: (Padded) length of '%s' is %i in BAM header, but %id 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;
+ if (load_unpadded_ref(fai, h->target_name[b->core.tid], h->target_len[b->core.tid], &q)) {
+ fprintf(stderr, "[depad] ERROR: Failed to load embedded reference '%s' from FASTA\n", h->target_name[b->core.tid]);
+ return -1;
+ }
assert(r.l == q.l);
int i;
for (i = 0; i < r.l; ++i) {
@@ -160,12 +198,15 @@ int bam_pad2unpad(samfile_t *in, samfile_t *out, faidx_t *fai)
} 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));
+ fprintf(stderr, "[depad] ERROR: Read '%s' has CIGAR but no RNAME\n", bam1_qname(b));
return -1;
} 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;
+ 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);
r_tid = b->core.tid;
// fprintf(stderr, "[depad] Loaded %s from FASTA file\n", h->target_name[b->core.tid]);
@@ -242,11 +283,31 @@ int bam_pad2unpad(samfile_t *in, samfile_t *out, faidx_t *fai)
return ret;
}
+bam_header_t * fix_header(bam_header_t *old, faidx_t *fai)
+{
+ int i = 0, unpadded_len = 0;
+ bam_header_t *header = 0 ;
+
+ header = bam_header_dup(old);
+ for (i = 0; i < old->n_targets; ++i) {
+ unpadded_len = get_unpadded_len(fai, old->target_name[i], old->target_len[i]);
+ if (unpadded_len < 0) {
+ fprintf(stderr, "[depad] ERROR getting unpadded length of '%s', padded length %i\n", old->target_name[i], old->target_len[i]);
+ } else {
+ header->target_len[i] = unpadded_len;
+ fprintf(stderr, "[depad] Recalculating '%s' length %i -> %i\n", old->target_name[i], old->target_len[i], header->target_len[i]);
+ }
+ }
+ /* TODO - Correct the @SQ reference lengths from padded to unpadded */
+ return header;
+}
+
static int usage(int is_long_help);
int main_pad2unpad(int argc, char *argv[])
{
samfile_t *in = 0, *out = 0;
+ bam_header_t *h = 0;
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;
@@ -293,8 +354,18 @@ int main_pad2unpad(int argc, char *argv[])
ret = 1;
goto depad_end;
}
- /* TODO - The reference sequence lengths in the BAM + SAM headers should be updated */
- if ((out = samopen(fn_out? fn_out : "-", out_mode, in->header)) == 0) {
+ if (in->header->text == 0 || in->header->l_text == 0) {
+ fprintf(stderr, "[depad] Warning - failed to read any header text from \"%s\".\n", argv[optind]);
+ assert (0 == in->header->l_text);
+ assert (0 == in->header->text);
+ }
+ if (fn_ref) {
+ h = fix_header(in->header, fai);
+ } else {
+ fprintf(stderr, "[depad] Warning - reference lengths will not be corrected without FASTA reference\n");
+ h = in->header;
+ }
+ if ((out = samopen(fn_out? fn_out : "-", out_mode, h)) == 0) {
fprintf(stderr, "[depad] failed to open \"%s\" for writing.\n", fn_out? fn_out : "standard output");
ret = 1;
goto depad_end;
@@ -306,6 +377,7 @@ int main_pad2unpad(int argc, char *argv[])
depad_end:
// close files, free and return
free(fn_list); free(fn_out);
+ if (h != in->header) bam_header_destroy(h);
samclose(in);
samclose(out);
fai_destroy(fai);
--
2.39.2