Imported Upstream version 0.1.18

[samtools.git] / bam_pileup.c

diff --git a/bam_pileup.c b/bam_pileup.c
index 55e51e27804cfc58fc5576b40ae7ba10416a3e8f..57434e098e2398fc4a6eab32b0d507d7724aa96e 100644 (file)
--- a/bam_pileup.c
+++ b/bam_pileup.c
@@ -78,13 +78,13 @@ static inline int resolve_cigar2(bam_pileup1_t *p, uint32_t pos, cstate_t *s)
        if (s->k == -1) { // never processed
                is_head = 1;
                if (c->n_cigar == 1) { // just one operation, save a loop
-                       if (_cop(cigar[0]) == BAM_CMATCH) s->k = 0, s->x = c->pos, s->y = 0;
-               } else { // find the first match
+                 if (_cop(cigar[0]) == BAM_CMATCH || _cop(cigar[0]) == BAM_CEQUAL || _cop(cigar[0]) == BAM_CDIFF) s->k = 0, s->x = c->pos, s->y = 0;
+               } else { // find the first match or deletion
                        for (k = 0, s->x = c->pos, s->y = 0; k < c->n_cigar; ++k) {
                                int op = _cop(cigar[k]);
                                int l = _cln(cigar[k]);
-                               if (op == BAM_CMATCH) break;
-                               else if (op == BAM_CDEL || op == BAM_CREF_SKIP) s->x += l;
+                               if (op == BAM_CMATCH || op == BAM_CDEL || op == BAM_CEQUAL || op == BAM_CDIFF) break;
+                               else if (op == BAM_CREF_SKIP) s->x += l;
                                else if (op == BAM_CINS || op == BAM_CSOFT_CLIP) s->y += l;
                        }
                        assert(k < c->n_cigar);
@@ -95,16 +95,16 @@ static inline int resolve_cigar2(bam_pileup1_t *p, uint32_t pos, cstate_t *s)
                if (pos - s->x >= l) { // jump to the next operation
                        assert(s->k < c->n_cigar); // otherwise a bug: this function should not be called in this case
                        op = _cop(cigar[s->k+1]);
-                       if (op == BAM_CMATCH || op == BAM_CDEL || op == BAM_CREF_SKIP) { // jump to the next without a loop
-                               if (_cop(cigar[s->k]) == BAM_CMATCH) s->y += l;
+                       if (op == BAM_CMATCH || op == BAM_CDEL || op == BAM_CREF_SKIP || op == BAM_CEQUAL || op == BAM_CDIFF) { // jump to the next without a loop
+                         if (_cop(cigar[s->k]) == BAM_CMATCH|| _cop(cigar[s->k]) == BAM_CEQUAL || _cop(cigar[s->k]) == BAM_CDIFF) s->y += l;
                                s->x += l;
                                ++s->k;
-                       } else { // find the next M/D/N
-                               if (_cop(cigar[s->k]) == BAM_CMATCH) s->y += l;
+                       } else { // find the next M/D/N/=/X
+                         if (_cop(cigar[s->k]) == BAM_CMATCH|| _cop(cigar[s->k]) == BAM_CEQUAL || _cop(cigar[s->k]) == BAM_CDIFF) s->y += l;
                                s->x += l;
                                for (k = s->k + 1; k < c->n_cigar; ++k) {
                                        op = _cop(cigar[k]), l = _cln(cigar[k]);
-                                       if (op == BAM_CMATCH || op == BAM_CDEL || op == BAM_CREF_SKIP) break;
+                                       if (op == BAM_CMATCH || op == BAM_CDEL || op == BAM_CREF_SKIP || op == BAM_CEQUAL || op == BAM_CDIFF) break;
                                        else if (op == BAM_CINS || op == BAM_CSOFT_CLIP) s->y += l;
                                }
                                s->k = k;
@@ -126,12 +126,12 @@ static inline int resolve_cigar2(bam_pileup1_t *p, uint32_t pos, cstate_t *s)
                                for (k = s->k + 2; k < c->n_cigar; ++k) {
                                        op2 = _cop(cigar[k]); l2 = _cln(cigar[k]);
                                        if (op2 == BAM_CINS) l3 += l2;
-                                       else if (op2 == BAM_CDEL || op2 == BAM_CMATCH || op2 == BAM_CREF_SKIP) break;
+                                       else if (op2 == BAM_CDEL || op2 == BAM_CMATCH || op2 == BAM_CREF_SKIP || op2 == BAM_CEQUAL || op2 == BAM_CDIFF) break;
                                }
                                if (l3 > 0) p->indel = l3;
                        }
                }
-               if (op == BAM_CMATCH) {
+               if (op == BAM_CMATCH || op == BAM_CEQUAL || op == BAM_CDIFF) {
                        p->qpos = s->y + (pos - s->x);
                } else if (op == BAM_CDEL || op == BAM_CREF_SKIP) {
                        p->is_del = 1; p->qpos = s->y; // FIXME: distinguish D and N!!!!!