Update 'samtools depad' help text regarding FASTA reference file

[samtools.git] / padding.c

diff --git a/padding.c b/padding.c
index 88945e2ca5c54c1a592a45899358996ddd810ece..71dfc25957bf38214e899cbd92b653bd729f3373 100644 (file)
--- a/padding.c
+++ b/padding.c
@@ -166,7 +166,7 @@ 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) {
-                       // fprintf(stderr, "[depad] Found embedded reference %s\n", bam1_qname(b));
+                       // fprintf(stderr, "[depad] Found embedded reference '%s'\n", bam1_qname(b));
                        r_tid = b->core.tid;
                        unpad_seq(b, &r);
                        if (h->target_len[r_tid] != r.l) {
@@ -195,6 +195,7 @@ 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);
+                       b->core.bin = bam_reg2bin(0, bam_calend(&b->core, bam1_cigar(b)));
                } else if (b->core.n_cigar > 0) {
                        int i, k, op;
                        if (b->core.tid < 0) {
@@ -202,6 +203,7 @@ int bam_pad2unpad(samfile_t *in, samfile_t *out, faidx_t *fai)
                                return -1;
                        } else if (b->core.tid == r_tid) {
                                ; // good case, reference available
+                               //fprintf(stderr, "[depad] Have ref '%s' for read '%s'\n", h->target_name[b->core.tid], bam1_qname(b));
                        } else if (fai) {
                                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]);
@@ -271,6 +273,39 @@ int bam_pad2unpad(samfile_t *in, samfile_t *out, faidx_t *fai)
                        n2 = k;
                        replace_cigar(b, n2, cigar2);
                        b->core.pos = posmap[b->core.pos];
+                       b->core.bin = bam_reg2bin(b->core.pos, bam_calend(&b->core.pos, bam1_cigar(b)));
+                       if (b->core.mtid < 0 || b->core.mpos < 0) {
+                               /* Nice case, no mate to worry about*/
+                               // fprintf(stderr, "[depad] Read '%s' mate not mapped\n", bam1_qname(b));
+                               /* TODO - Warning if FLAG says mate should be mapped? */
+                               /* Clean up funny input where mate position is given but mate reference is missing: */
+                               b->core.mtid = -1;
+                               b->core.mpos = -1;
+                       } else if (b->core.mtid == b->core.tid) {
+                               /* Nice case, same reference */
+                               // fprintf(stderr, "[depad] Read '%s' mate mapped to same ref\n", bam1_qname(b));
+                               b->core.mpos = posmap[b->core.mpos];
+                       } else {
+                               /* Nasty case, Must load alternative posmap */
+                               // fprintf(stderr, "[depad] Loading reference '%s' temporarily\n", h->target_name[b->core.mtid]);
+                               if (!fai) {
+                                       fprintf(stderr, "[depad] ERROR: Needed reference %s sequence for mate (and no FASTA file)\n", h->target_name[b->core.mtid]);
+                                       return -1;
+                               }
+                               /* Temporarily load the other reference sequence */
+                               if (load_unpadded_ref(fai, h->target_name[b->core.mtid], h->target_len[b->core.mtid], &r)) {
+                                       fprintf(stderr, "[depad] ERROR: Failed to load '%s' from reference FASTA\n", h->target_name[b->core.mtid]);
+                                       return -1;
+                               }
+                               posmap = update_posmap(posmap, r);
+                               b->core.mpos = posmap[b->core.mpos];
+                               /* Restore the reference and posmap*/
+                               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);
+                       }
                }
                samwrite(out, b);
        }
@@ -330,7 +365,7 @@ bam_header_t * fix_header(bam_header_t *old, faidx_t *fai)
        if (strlen(header->text) < header->l_text) {
                //fprintf(stderr, "[depad] Reallocating header buffer\n");
                assert (newtext == header->text);
-               newtext = calloc(strlen(header->text) + 1, 1);
+               newtext = malloc(strlen(header->text) + 1);
                strcpy(newtext, header->text);
                free(header->text);
                header->text = newtext;
@@ -414,11 +449,11 @@ 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);
+       if (fai) fai_destroy(fai);
+       if (h != in->header) bam_header_destroy(h);
        samclose(in);
        samclose(out);
-       fai_destroy(fai);
+       free(fn_list); free(fn_out);
        return ret;
 }
 
@@ -430,7 +465,7 @@ static int usage(int is_long_help)
        fprintf(stderr, "         -S       input is SAM (default is BAM)\n");
        fprintf(stderr, "         -u       uncompressed BAM output (can't use with -s)\n");
        fprintf(stderr, "         -1       fast compression BAM output (can't use with -s)\n");
-       fprintf(stderr, "         -T FILE  reference sequence file [null]\n");
+       fprintf(stderr, "         -T FILE  padded reference sequence file [null]\n");
        fprintf(stderr, "         -o FILE  output file name [stdout]\n");
        fprintf(stderr, "         -?       longer help\n");
        fprintf(stderr, "\n");
@@ -438,7 +473,7 @@ static int usage(int is_long_help)
                fprintf(stderr, "Notes:\n\
 \n\
   1. Requires embedded reference sequences (before the reads for that reference),\n\
-     with the future aim to also support a FASTA padded reference sequence file.\n\
+     or ideally a FASTA file of the padded reference sequences (via the -T argument).\n\
 \n\
   2. The input padded alignment read's CIGAR strings must not use P or I operators.\n\
 \n");