Revert one of my earlier changes - Heng was right, CIGAR P not sensible in a padded...

diff --git a/padding.c b/padding.c
index b544aab20bcb25fe5700543ada6cf83371d253c6..4061f247589dc641771b8b8da0bcba81475b49f3 100644 (file)
--- 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));