Calculate unpadded reference length, update BAM header (SAM header pending)

diff --git a/padding.c b/padding.c
index 27bbd4b6cd982864262dc909cb068df8f9355f3c..23d1b23c9ac68dd8dd6a5d1c7847d714e3e837ed 100644 (file)
--- 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);