X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=padding.c;h=476e393166983b0d00434789ad8596f0403a8f34;hb=8e3b3f229a04cb81b680987ce06ae1507c9d8b69;hp=fbbb204421f16dfcb6434053d6ef85e729086272;hpb=4f0d8b980118cb40591bc689bcbe9ff1ad7b72ae;p=samtools.git

diff --git a/padding.c b/padding.c
index fbbb204..476e393 100644
--- 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;