More elegant solution to avoid superfluous leading P ops

diff --git a/padding.c b/padding.c
index fe11da29e3bd285066fc3cb41cf80717c7b0cfc1..b80463fe80cd7222507b081f56990be97a21e32e 100644 (file)
--- a/padding.c
+++ b/padding.c
@@ -104,16 +104,15 @@ int bam_pad2unpad(bamFile in, bamFile out)
                                if (b->core.n_cigar > 2 && bam_cigar_op(cigar[1]) == BAM_CSOFT_CLIP) {
                                        write_cigar(cigar2, n2, m2, cigar[1]);
                                }
-                       } else {
-                               /* Insert a dummy 0M entry to let use remove superfluous leading P ops */
-                               write_cigar(cigar2, n2, m2, 0);
                        }
-                       /* Include any pads if starts with an insert */
-                       for (k = 0; k+1 < b->core.pos && !r.s[b->core.pos - k - 1]; ++k);
-                       if (k) write_cigar(cigar2, n2, m2, bam_cigar_gen(k, BAM_CPAD));
                        /* 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);
+                       /* Include any pads if starts with an insert */
+                       if (q.s[0] == BAM_CINS) {
+                               for (k = 0; k+1 < b->core.pos && !r.s[b->core.pos - k - 1]; ++k);
+                               if (k) write_cigar(cigar2, n2, m2, bam_cigar_gen(k, 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]) {
@@ -131,14 +130,13 @@ int bam_pad2unpad(bamFile in, bamFile out)
                                write_cigar(cigar2, n2, m2, cigar[b->core.n_cigar-1]);
                        }
                        /* Remove redundant P operators between M/X/=/D operators, e.g. 5M2P10M -> 15M */
-                       /* or right at the start before M/X/=/D */
                        int pre_op, post_op;
                        for (i = 2; i < n2; ++i)
                                if (bam_cigar_op(cigar2[i-1]) == BAM_CPAD) {
                                        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 || pre_op == BAM_CSOFT_CLIP || pre_op == BAM_CHARD_CLIP) || (post_op == BAM_CMATCH || post_op == BAM_CDIFF)) {
+                                       if ((pre_op == BAM_CMATCH || pre_op == BAM_CDIFF) || (post_op == BAM_CMATCH || post_op == BAM_CDIFF)) {
                                                /* This is a redundant P operator */
                                                cigar2[i-1] = 0; // i.e. 0M
                                                /* If had same operator either side, combine them in post_op */