Correct my error message; assed some comments

diff --git a/padding.c b/padding.c
index 8d0df07a838b849cfb2ad8d09672f856dfdb81b9..6c8b31ff3de5d01afa79bb94428bd4e711078116 100644 (file)
--- a/padding.c
+++ b/padding.c
@@ -45,7 +45,7 @@ static void unpad_seq(bam1_t *b, kstring_t *s)
                } 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 embedded reference %s\n", BAM_CIGAR_STR[op], bam1_qname(b));
+                       fprintf(stderr, "[depad] ERROR: Didn't expect CIGAR op %c in read %s\n", BAM_CIGAR_STR[op], bam1_qname(b));
                         assert(-1);
                }
        }
@@ -79,7 +79,7 @@ int bam_pad2unpad(bamFile in, bamFile out)
                        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 if (b->core.n_cigar > 0) {
@@ -93,8 +93,10 @@ int bam_pad2unpad(bamFile in, bamFile out)
                        }
                        unpad_seq(b, &q);
                        if (bam_cigar_op(cigar[0]) == BAM_CSOFT_CLIP) write_cigar(cigar2, n2, m2, cigar[0]);
+                       /* 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);
+                       /* 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));
@@ -103,6 +105,7 @@ int bam_pad2unpad(bamFile in, bamFile out)
                        }
                        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]);
+                       /* Remove redundant P operators between M operators, e.g. 5M2P10M -> 15M */
                        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;