X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=padding.c;h=4061f247589dc641771b8b8da0bcba81475b49f3;hb=ccb7838cb53bf0ca6917a77f7991d940057c12db;hp=d76cb31a3b5bb8ea957503eccb35d2c307ae79ca;hpb=df50415f5380510f5b44bee2361413fc39c8bbcf;p=samtools.git

diff --git a/padding.c b/padding.c
index d76cb31..4061f24 100644
--- a/padding.c
+++ b/padding.c
@@ -30,23 +30,39 @@ static void replace_cigar(bam1_t *b, int n, uint32_t *cigar)
 static void unpad_seq(bam1_t *b, kstring_t *s)
 {
 	int k, j, i;
+	int length;
 	uint32_t *cigar = bam1_cigar(b);
 	uint8_t *seq = bam1_seq(b);
-	ks_resize(s, b->core.l_qseq);
+	// b->core.l_qseq gives length of the SEQ entry (including soft clips, S)
+	// We need the padded length after alignment from the CIGAR (excluding
+	// soft clips S, but including pads from CIGAR D operations)
+	length = 0;
+	for (k = 0; k < b->core.n_cigar; ++k) {
+		int op, ol;
+		op= bam_cigar_op(cigar[k]);
+		ol = bam_cigar_oplen(cigar[k]);
+		if (op == BAM_CMATCH || op == BAM_CEQUAL || op == BAM_CDIFF || op == BAM_CDEL)
+			length += ol;
+	}
+	ks_resize(s, length);
 	for (k = 0, s->l = 0, j = 0; k < b->core.n_cigar; ++k) {
 		int op, ol;
 		op = bam_cigar_op(cigar[k]);
 		ol = bam_cigar_oplen(cigar[k]);
-		assert(op == BAM_CMATCH || op == BAM_CDEL || op == BAM_CSOFT_CLIP);
-		if (op == BAM_CMATCH) {
-			for (i = 0; i < ol; ++i) s->s[s->l++] = bam1_seqi(seq, j);
-			++j;
+		if (op == BAM_CMATCH || op == BAM_CEQUAL || op == BAM_CDIFF) {
+			for (i = 0; i < ol; ++i, ++j) s->s[s->l++] = bam1_seqi(seq, j);
 		} else if (op == BAM_CSOFT_CLIP) {
 			j += ol;
-		} else {
+		} else if (op == BAM_CHARD_CLIP) {
+			/* do nothing */
+		} else if (op == BAM_CDEL) {
 			for (i = 0; i < ol; ++i) s->s[s->l++] = 0;
+                } else {
+			fprintf(stderr, "[depad] ERROR: Didn't expect CIGAR op %c in read %s\n", BAM_CIGAR_STR[op], bam1_qname(b));
+                        assert(-1);
 		}
 	}
+	assert(length == s->l);
 }
 
 int bam_pad2unpad(bamFile in, bamFile out)
@@ -54,10 +70,12 @@ int bam_pad2unpad(bamFile in, bamFile out)
 	bam_header_t *h;
 	bam1_t *b;
 	kstring_t r, q;
+	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;
@@ -66,20 +84,49 @@ int bam_pad2unpad(bamFile in, bamFile out)
 		n2 = 0;
 		if (b->core.pos == 0 && b->core.tid >= 0 && strcmp(bam1_qname(b), h->target_name[b->core.tid]) == 0) {
 			int i, k;
+			/*
+			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) {
+				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 {
+		} else if (b->core.n_cigar > 0) {
 			int i, k, op;
+			if (b->core.tid < 0) {
+				fprintf(stderr, "[depad] ERROR: Read %s has CIGAR but no RNAME\n", bam1_qname(b));
+				return -1;
+			} else if (b->core.tid != r_tid) {
+				fprintf(stderr, "[depad] ERROR: Missing %s embedded reference sequence\n", h->target_name[b->core.tid]);
+				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));
@@ -87,10 +134,33 @@ 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;
@@ -108,13 +178,14 @@ int bam_pad2unpad(bamFile in, bamFile out)
 int main_pad2unpad(int argc, char *argv[])
 {
 	bamFile in, out;
+        int result=0;
 	if (argc == 1) {
-		fprintf(stderr, "Usage: samtools pad2unpad <in.bam>\n");
+		fprintf(stderr, "Usage: samtools depad <in.bam>\n");
 		return 1;
 	}
 	in = strcmp(argv[1], "-")? bam_open(argv[1], "r") : bam_dopen(fileno(stdin), "r");
 	out = bam_dopen(fileno(stdout), "w");
-	bam_pad2unpad(in, out);
+	result = bam_pad2unpad(in, out);
 	bam_close(in); bam_close(out);
-	return 0;
+	return result;
 }