* vcfutils.pl qstats: calculate marginal ts/tv

[samtools.git] / bam_pileup.c

diff --git a/bam_pileup.c b/bam_pileup.c
index 3c41a169127fcc5d3977df3e8febd944b7ced77e..266b96673713e3800001624bbf0f0a3baed78637 100644 (file)
--- a/bam_pileup.c
+++ b/bam_pileup.c
@@ -59,11 +59,13 @@ static inline int resolve_cigar(bam_pileup1_t *p, uint32_t pos)
        bam1_t *b = p->b;
        bam1_core_t *c = &b->core;
        uint32_t x = c->pos, y = 0;
-       int ret = 1, is_restart = 1;
+       int ret = 1, is_restart = 1, first_op, last_op;
 
        if (c->flag&BAM_FUNMAP) return 0; // unmapped read
        assert(x <= pos); // otherwise a bug
        p->qpos = -1; p->indel = 0; p->is_del = p->is_head = p->is_tail = 0;
+       first_op = bam1_cigar(b)[0] & BAM_CIGAR_MASK;
+       last_op = bam1_cigar(b)[c->n_cigar-1] & BAM_CIGAR_MASK;
        for (k = 0; k < c->n_cigar; ++k) {
                int op = bam1_cigar(b)[k] & BAM_CIGAR_MASK; // operation
                int l = bam1_cigar(b)[k] >> BAM_CIGAR_SHIFT; // length
@@ -71,7 +73,7 @@ static inline int resolve_cigar(bam_pileup1_t *p, uint32_t pos)
                        if (x + l > pos) { // overlap with pos
                                p->indel = p->is_del = 0;
                                p->qpos = y + (pos - x);
-                               if (x == pos && is_restart) p->is_head = 1;
+                               if (x == pos && is_restart && first_op != BAM_CDEL) p->is_head = 1;
                                if (x + l - 1 == pos) { // come to the end of a match
                                        int has_next_match = 0;
                                        unsigned i;
@@ -83,7 +85,7 @@ static inline int resolve_cigar(bam_pileup1_t *p, uint32_t pos)
                                                        break;
                                                } else if (opi == BAM_CSOFT_CLIP || opi == BAM_CREF_SKIP || opi == BAM_CHARD_CLIP) break;
                                        }
-                                       if (!has_next_match) p->is_tail = 1;
+                                       if (!has_next_match && last_op != BAM_CDEL) p->is_tail = 1;
                                        if (k < c->n_cigar - 1 && has_next_match) { // there are additional operation(s)
                                                uint32_t cigar = bam1_cigar(b)[k+1]; // next CIGAR
                                                int op_next = cigar&BAM_CIGAR_MASK; // next CIGAR operation
@@ -99,9 +101,11 @@ static inline int resolve_cigar(bam_pileup1_t *p, uint32_t pos)
                        }
                        x += l; y += l;
                } else if (op == BAM_CDEL) { // then set ->is_del
+                       if (k == 0 && x == pos) p->is_head = 1;
+                       else if (x + l - 1 == pos && k == c->n_cigar - 1) p->is_tail = 1;
                        if (x + l > pos) {
                                p->indel = 0; p->is_del = 1;
-                               p->qpos = y + (pos - x);
+                               p->qpos = y;
                        }
                        x += l;
                } else if (op == BAM_CREF_SKIP) x += l;
@@ -387,7 +391,7 @@ int bam_mplp_auto(bam_mplp_t iter, int *_tid, int *_pos, int *n_plp, const bam_p
        if (new_min == (uint64_t)-1) return 0;
        *_tid = new_min>>32; *_pos = (uint32_t)new_min;
        for (i = 0; i < iter->n; ++i) {
-               if (iter->pos[i] == iter->min) {
+               if (iter->pos[i] == iter->min) { // FIXME: valgrind reports "uninitialised value(s) at this line"
                        n_plp[i] = iter->n_plp[i], plp[i] = iter->plp[i];
                        ++ret;
                } else n_plp[i] = 0, plp[i] = 0;