X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=padding.c;h=4061f247589dc641771b8b8da0bcba81475b49f3;hb=ccb7838cb53bf0ca6917a77f7991d940057c12db;hp=b80463fe80cd7222507b081f56990be97a21e32e;hpb=24d1a2d1200afd8b6c88cb22a3c9b76248e994b1;p=samtools.git

diff --git a/padding.c b/padding.c
index b80463f..4061f24 100644
--- a/padding.c
+++ b/padding.c
@@ -30,9 +30,21 @@ 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]);
@@ -43,13 +55,14 @@ static void unpad_seq(bam1_t *b, kstring_t *s)
 			j += ol;
 		} else if (op == BAM_CHARD_CLIP) {
 			/* do nothing */
-		} else if (op == BAM_CDEL || op == BAM_CPAD) {
+		} 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)
@@ -136,7 +149,7 @@ int bam_pad2unpad(bamFile in, bamFile out)
 					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_CDIFF) || (post_op == BAM_CMATCH || post_op == BAM_CDIFF)) {
+					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 */