# Install the manual page of bcftools.

[samtools.git] / bam_index.c

diff --git a/bam_index.c b/bam_index.c
index 1ad2e93e5051972b084513d5d7391c45c6cf7bf2..328f011c16ccf4a9a558702317ecdecfbcc5212a 100644 (file)
--- a/bam_index.c
+++ b/bam_index.c
@@ -212,7 +212,7 @@ bam_index_t *bam_index_core(bamFile fp)
        }
        if (save_tid >= 0) {
                insert_offset(idx->index[save_tid], save_bin, save_off, bam_tell(fp));
-               insert_offset(idx->index[save_tid], BAM_MAX_BIN, off_beg, off_end);
+               insert_offset(idx->index[save_tid], BAM_MAX_BIN, off_beg, bam_tell(fp));
                insert_offset(idx->index[save_tid], BAM_MAX_BIN, n_mapped, n_unmapped);
        }
        merge_chunks(idx);
@@ -608,6 +608,9 @@ bam_iter_t bam_iter_query(const bam_index_t *idx, int tid, int beg, int end)
                }
        }
        free(bins);
+       if (n_off == 0) {
+               free(off); return iter;
+       }
        {
                bam1_t *b = (bam1_t*)calloc(1, sizeof(bam1_t));
                int l;
@@ -695,6 +698,7 @@ int bam_fetch(bamFile fp, const bam_index_t *idx, int tid, int beg, int end, voi
        b = bam_init1();
        iter = bam_iter_query(idx, tid, beg, end);
        while ((ret = bam_iter_read(fp, iter, b)) >= 0) func(b, data);
+       bam_iter_destroy(iter);
        bam_destroy1(b);
        return (ret == -1)? 0 : ret;
 }