X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=padding.c;h=a093d45ff8cf78891ed4d78a741229270481d21d;hb=62254fe022c4c69988c2a71dabf93f90d93e0014;hp=b33032639151453a750e2e9cfe69f2c7282d8349;hpb=fe8fbc9eae570d7afc3e0e91df735e6b6fdc329d;p=samtools.git

diff --git a/padding.c b/padding.c
index b330326..a093d45 100644
--- a/padding.c
+++ b/padding.c
@@ -38,14 +38,15 @@ static void unpad_seq(bam1_t *b, kstring_t *s)
 		op = bam_cigar_op(cigar[k]);
 		ol = bam_cigar_oplen(cigar[k]);
 		if (op == BAM_CMATCH || op == BAM_CEQUAL || op == BAM_CDIFF) {
-			for (i = 0; i < ol; ++i) s->s[s->l++] = bam1_seqi(seq, j);
-			++j;
+			for (i = 0; i < ol; ++i, ++j) s->s[s->l++] = bam1_seqi(seq, j);
 		} else if (op == BAM_CSOFT_CLIP) {
 			j += ol;
+		} else if (op == BAM_CHARD_CLIP) {
+			/* do nothing */
 		} else if (op == BAM_CDEL || op == BAM_CPAD) {
 			for (i = 0; i < ol; ++i) s->s[s->l++] = 0;
                 } else {
-			fprintf(stderr, "[depad] ERROR: Didn't expect CIGAR op %c in embedded reference %s\n", BAM_CIGAR_STR[op], bam1_qname(b));
+			fprintf(stderr, "[depad] ERROR: Didn't expect CIGAR op %c in read %s\n", BAM_CIGAR_STR[op], bam1_qname(b));
                         assert(-1);
 		}
 	}
@@ -56,11 +57,12 @@ int bam_pad2unpad(bamFile in, bamFile out)
 	bam_header_t *h;
 	bam1_t *b;
 	kstring_t r, q;
-        int r_tid = -1;
+	int r_tid = -1;
 	uint32_t *cigar2 = 0;
 	int n2 = 0, m2 = 0, *posmap = 0;
 
 	h = bam_header_read(in);
+	/* TODO - The reference sequence lengths in the BAM + SAM headers should be updated */
 	bam_header_write(out, h);
 	b = bam_init1();
 	r.l = r.m = q.l = q.m = 0; r.s = q.s = 0;
@@ -74,11 +76,15 @@ int bam_pad2unpad(bamFile in, bamFile out)
 			*/
 			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);
+				return -1;
+			}
 			write_cigar(cigar2, n2, m2, bam_cigar_gen(b->core.l_qseq, BAM_CMATCH));
 			replace_cigar(b, n2, cigar2);
 			posmap = realloc(posmap, r.m * sizeof(int));
 			for (i = k = 0; i < r.l; ++i) {
-				posmap[i] = k; // note that a read should NOT start at a padding
+				posmap[i] = k;
 				if (r.s[i]) ++k;
 			}
 		} else if (b->core.n_cigar > 0) {
@@ -91,9 +97,23 @@ int bam_pad2unpad(bamFile in, bamFile out)
 				return -1;
 			}
 			unpad_seq(b, &q);
-			if (bam_cigar_op(cigar[0]) == BAM_CSOFT_CLIP) write_cigar(cigar2, n2, m2, cigar[0]);
+			if (bam_cigar_op(cigar[0]) == BAM_CSOFT_CLIP) {
+				write_cigar(cigar2, n2, m2, cigar[0]);
+			} else if (bam_cigar_op(cigar[0]) == BAM_CHARD_CLIP) {
+				write_cigar(cigar2, n2, m2, cigar[0]);
+				if (b->core.n_cigar > 2 && bam_cigar_op(cigar[1]) == BAM_CSOFT_CLIP) {
+					write_cigar(cigar2, n2, m2, cigar[1]);
+				}
+			}
+			/* Determine CIGAR operator for each base in the aligned read */
 			for (i = 0, k = b->core.pos; i < q.l; ++i, ++k)
 				q.s[i] = q.s[i]? (r.s[k]? BAM_CMATCH : BAM_CINS) : (r.s[k]? BAM_CDEL : BAM_CPAD);
+			/* Include any pads if starts with an insert */
+			if (q.s[0] == BAM_CINS) {
+				for (k = 0; k+1 < b->core.pos && !r.s[b->core.pos - k - 1]; ++k);
+				if (k) write_cigar(cigar2, n2, m2, bam_cigar_gen(k, BAM_CPAD));
+			}
+			/* Count consecutive CIGAR operators to turn into a CIGAR string */
 			for (i = k = 1, op = q.s[0]; i < q.l; ++i) {
 				if (op != q.s[i]) {
 					write_cigar(cigar2, n2, m2, bam_cigar_gen(k, op));
@@ -101,10 +121,33 @@ int bam_pad2unpad(bamFile in, bamFile out)
 				} else ++k;
 			}
 			write_cigar(cigar2, n2, m2, bam_cigar_gen(k, op));
-			if (bam_cigar_op(cigar[b->core.n_cigar-1]) == BAM_CSOFT_CLIP) write_cigar(cigar2, n2, m2, cigar[b->core.n_cigar-1]);
+			if (bam_cigar_op(cigar[b->core.n_cigar-1]) == BAM_CSOFT_CLIP) {
+				write_cigar(cigar2, n2, m2, cigar[b->core.n_cigar-1]);
+                        } else if (bam_cigar_op(cigar[b->core.n_cigar-1]) == BAM_CHARD_CLIP) {
+				if (b->core.n_cigar > 2 && bam_cigar_op(cigar[b->core.n_cigar-2]) == BAM_CSOFT_CLIP) {
+					write_cigar(cigar2, n2, m2, cigar[b->core.n_cigar-2]);
+			  	}
+				write_cigar(cigar2, n2, m2, cigar[b->core.n_cigar-1]);
+			}
+			/* Remove redundant P operators between M/X/=/D operators, e.g. 5M2P10M -> 15M */
+			int pre_op, post_op;
 			for (i = 2; i < n2; ++i)
-				if (bam_cigar_op(cigar2[i]) == BAM_CMATCH && bam_cigar_op(cigar2[i-1]) == BAM_CPAD && bam_cigar_op(cigar2[i-2]) == BAM_CMATCH)
-					cigar2[i] += cigar2[i-2], cigar2[i-2] = cigar2[i-1] = 0;
+				if (bam_cigar_op(cigar2[i-1]) == BAM_CPAD) {
+					pre_op = bam_cigar_op(cigar2[i-2]);
+					post_op = bam_cigar_op(cigar2[i]);
+					/* Note don't need to check for X/= as code above will use M only */
+					if ((pre_op == BAM_CMATCH || pre_op == BAM_CDEL) && (post_op == BAM_CMATCH || post_op == BAM_CDEL)) {
+						/* This is a redundant P operator */
+						cigar2[i-1] = 0; // i.e. 0M
+						/* If had same operator either side, combine them in post_op */
+						if (pre_op == post_op) {
+							/* If CIGAR M, could treat as simple integers since BAM_CMATCH is zero*/
+							cigar2[i] = bam_cigar_gen(bam_cigar_oplen(cigar2[i-2]) + bam_cigar_oplen(cigar2[i]), post_op);
+							cigar2[i-2] = 0; // i.e. 0M
+						}
+					}
+				}
+			/* Remove the zero'd operators (0M) */
 			for (i = k = 0; i < n2; ++i)
 				if (cigar2[i]) cigar2[k++] = cigar2[i];
 			n2 = k;