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