X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=padding.c;h=3ee8087d4d054768f0f7d317e24acd208ac18683;hb=698a60f0225ea0d46364522db77a559d64b3052a;hp=fbbb204421f16dfcb6434053d6ef85e729086272;hpb=4f0d8b980118cb40591bc689bcbe9ff1ad7b72ae;p=samtools.git

diff --git a/padding.c b/padding.c
index fbbb204..3ee8087 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) {
@@ -202,6 +202,7 @@ 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]);
@@ -270,33 +271,43 @@ int bam_pad2unpad(samfile_t *in, samfile_t *out, faidx_t *fai)
 				if (cigar2[i]) cigar2[k++] = cigar2[i];
 			n2 = k;
 			replace_cigar(b, n2, cigar2);
-			b->core.pos = posmap[b->core.pos];
-			if (b->core.mpos < 0) {
-				/* Nice case, no mate to worry about*/
-			} else if (b->core.mtid == b->core.tid) {
-				/* Nice case, same reference */
-				b->core.mpos = posmap[b->core.mpos];
-			} else {
-				/* Nasty case, Must load alternative posmap */
-				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);
+		}
+		/* Even unmapped reads can have a POS value, e.g. if their mate was mapped */
+		if (b->core.pos != -1) b->core.pos = posmap[b->core.pos];
+		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);
 		}
+		/* Most reads will have been moved so safest to always recalculate the BIN value */
+		b->core.bin = bam_reg2bin(b->core.pos, bam_calend(&b->core, bam1_cigar(b)));
 		samwrite(out, b);
 	}
 	if (read_ret < -1) {
@@ -455,7 +466,7 @@ 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");
@@ -463,7 +474,7 @@ 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");