X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=padding.c;h=4061f247589dc641771b8b8da0bcba81475b49f3;hb=ccb7838cb53bf0ca6917a77f7991d940057c12db;hp=b544aab20bcb25fe5700543ada6cf83371d253c6;hpb=6b9aa77bb5c4d990271917cdd6bba50f4503dd3b;p=samtools.git

diff --git a/padding.c b/padding.c
index b544aab..4061f24 100644
--- a/padding.c
+++ b/padding.c
@@ -35,13 +35,13 @@ static void unpad_seq(bam1_t *b, kstring_t *s)
 	uint8_t *seq = bam1_seq(b);
 	// 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)
+	// 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 || op == BAM_CPAD)
+		if (op == BAM_CMATCH || op == BAM_CEQUAL || op == BAM_CDIFF || op == BAM_CDEL)
 			length += ol;
 	}
 	ks_resize(s, length);
@@ -55,7 +55,7 @@ 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));