X-Git-Url: http://woldlab.caltech.edu/gitweb/?p=samtools.git;a=blobdiff_plain;f=bam_index.c;h=328f011c16ccf4a9a558702317ecdecfbcc5212a;hp=1ad2e93e5051972b084513d5d7391c45c6cf7bf2;hb=a8ea86b6acaafbfa2108c4cc047ae3fdd6385488;hpb=62781a2daa24d74a3c590e2669fad1fa7cabf933

diff --git a/bam_index.c b/bam_index.c
index 1ad2e93..328f011 100644
--- 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;
 }