* aggressive gapped aligner is implemented in calmd.

[samtools.git] / bam_pileup.c

diff --git a/bam_pileup.c b/bam_pileup.c
index 8a75829cf6e92889ed72e2b23f08056abedb516d..db170e8f15114e21c63cd11849b2d78a05996ea6 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
@@ -71,32 +73,45 @@ 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
-                                       if (k < c->n_cigar - 1) { // there are additional operation(s)
+                                       int has_next_match = 0;
+                                       unsigned i;
+                                       for (i = k + 1; i < c->n_cigar; ++i) {
+                                               uint32_t cigar = bam1_cigar(b)[i];
+                                               int opi = cigar&BAM_CIGAR_MASK;
+                                               if (opi == BAM_CMATCH) {
+                                                       has_next_match = 1;
+                                                       break;
+                                               } else if (opi == BAM_CSOFT_CLIP || opi == BAM_CREF_SKIP || opi == BAM_CHARD_CLIP) break;
+                                       }
+                                       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
                                                if (op_next == BAM_CDEL) p->indel = -(int32_t)(cigar>>BAM_CIGAR_SHIFT); // del
                                                else if (op_next == BAM_CINS) p->indel = cigar>>BAM_CIGAR_SHIFT; // ins
-                                               if (op_next == BAM_CDEL || op_next == BAM_CINS) {
-                                                       if (k + 2 < c->n_cigar) op_next = bam1_cigar(b)[k+2]&BAM_CIGAR_MASK;
-                                                       else p->is_tail = 1;
+                                               else if (op_next == BAM_CPAD && k + 2 < c->n_cigar) { // no working for adjacent padding
+                                                       cigar = bam1_cigar(b)[k+2]; op_next = cigar&BAM_CIGAR_MASK;
+                                                       if (op_next == BAM_CDEL) p->indel = -(int32_t)(cigar>>BAM_CIGAR_SHIFT); // del
+                                                       else if (op_next == BAM_CINS) p->indel = cigar>>BAM_CIGAR_SHIFT; // ins
                                                }
-                                               if (op_next == BAM_CSOFT_CLIP || op_next == BAM_CREF_SKIP || op_next == BAM_CHARD_CLIP)
-                                                       p->is_tail = 1; // tail
-                                       } else p->is_tail = 1; // this is the last operation; set tail
+                                       }
                                }
                        }
                        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;
                else if (op == BAM_CINS || op == BAM_CSOFT_CLIP) y += l;
-               is_restart = (op == BAM_CREF_SKIP || op == BAM_CSOFT_CLIP || op == BAM_CHARD_CLIP);
+               if (is_restart) is_restart ^= (op == BAM_CMATCH);
+               else is_restart ^= (op == BAM_CREF_SKIP || op == BAM_CSOFT_CLIP || op == BAM_CHARD_CLIP);
                if (x > pos) {
                        if (op == BAM_CREF_SKIP) ret = 0; // then do not put it into pileup at all
                        break;
@@ -232,6 +247,7 @@ const bam_pileup1_t *bam_plp_auto(bam_plp_t iter, int *_tid, int *_pos, int *_n_
        if ((plp = bam_plp_next(iter, _tid, _pos, _n_plp)) != 0) return plp;
        else {
                *_n_plp = 0;
+               if (iter->is_eof) return 0;
                while (iter->func(iter->data, iter->b) >= 0) {
                        if (bam_plp_push(iter, iter->b) < 0) {
                                *_n_plp = -1;
@@ -239,6 +255,8 @@ const bam_pileup1_t *bam_plp_auto(bam_plp_t iter, int *_tid, int *_pos, int *_n_
                        }
                        if ((plp = bam_plp_next(iter, _tid, _pos, _n_plp)) != 0) return plp;
                }
+               bam_plp_push(iter, 0);
+               if ((plp = bam_plp_next(iter, _tid, _pos, _n_plp)) != 0) return plp;
                return 0;
        }
 }
@@ -353,7 +371,7 @@ void bam_mplp_destroy(bam_mplp_t iter)
 {
        int i;
        for (i = 0; i < iter->n; ++i) bam_plp_destroy(iter->iter[i]);
-       free(iter->pos); free(iter->n_plp); free(iter->plp);
+       free(iter->iter); free(iter->pos); free(iter->n_plp); free(iter->plp);
        free(iter);
 }
 
@@ -367,7 +385,7 @@ int bam_mplp_auto(bam_mplp_t iter, int *_tid, int *_pos, int *n_plp, const bam_p
                        iter->plp[i] = bam_plp_auto(iter->iter[i], &tid, &pos, &iter->n_plp[i]);
                        iter->pos[i] = (uint64_t)tid<<32 | pos;
                }
-               if (iter->pos[i] < new_min) new_min = iter->pos[i];
+               if (iter->plp[i] && iter->pos[i] < new_min) new_min = iter->pos[i];
        }
        iter->min = new_min;
        if (new_min == (uint64_t)-1) return 0;