Add TODO note about reference lengths

[samtools.git] / padding.c

diff --git a/padding.c b/padding.c
index ad68728b28761d114c99ef0ebcbad339102d99b9..8d0df07a838b849cfb2ad8d09672f856dfdb81b9 100644 (file)
--- a/padding.c
+++ b/padding.c
@@ -42,10 +42,10 @@ static void unpad_seq(bam1_t *b, kstring_t *s)
                        ++j;
                } else if (op == BAM_CSOFT_CLIP) {
                        j += ol;
-               } else if (op == BAM_CDEL) {
+               } 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 %s\n", BAM_CIGAR_STR[op], bam1_qname(b));
+                       fprintf(stderr, "[depad] ERROR: Didn't expect CIGAR op %c in embedded reference %s\n", BAM_CIGAR_STR[op], bam1_qname(b));
                         assert(-1);
                }
        }
@@ -61,6 +61,7 @@ int bam_pad2unpad(bamFile in, bamFile out)
        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;