Verify old BIN value of reads during 'samtools index'.

[samtools.git] / padding.c

diff --git a/padding.c b/padding.c
index fbbb204421f16dfcb6434053d6ef85e729086272..476e393166983b0d00434789ad8596f0403a8f34 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]);
@@ -271,13 +273,21 @@ 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];
-                       if (b->core.mpos < 0) {
+                       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;