* samtools-0.1.7-15 (r592)

[samtools.git] / bam_pileup.c

diff --git a/bam_pileup.c b/bam_pileup.c
index 8a75829cf6e92889ed72e2b23f08056abedb516d..d9a75da013eecf772336bf5a03ef9baa4851b41d 100644 (file)
--- a/bam_pileup.c
+++ b/bam_pileup.c
@@ -232,6 +232,7 @@ 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 +240,8 @@ 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 +356,7 @@ 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 +370,7 @@ 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;