X-Git-Url: http://woldlab.caltech.edu/gitweb/?p=samtools.git;a=blobdiff_plain;f=bam_index.c;h=51c27014da0f9f010b563db92112f71d7ad6bdd6;hp=f60a6f874b106f03c655d1207dddf21c4df7fc48;hb=9f4bebab2e0917c676ae739b2d05cb22ad6c4ed5;hpb=6a0c6f060a60789b48e10a72b1381f6e54599302

diff --git a/bam_index.c b/bam_index.c
index f60a6f8..51c2701 100644
--- a/bam_index.c
+++ b/bam_index.c
@@ -212,13 +212,20 @@ 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);
 	fill_missing(idx);
-	if (ret >= 0)
-		while ((ret = bam_read1(fp, b)) >= 0) ++n_no_coor;
+	if (ret >= 0) {
+		while ((ret = bam_read1(fp, b)) >= 0) {
+			++n_no_coor;
+			if (c->tid >= 0 && n_no_coor) {
+				fprintf(stderr, "[bam_index_core] the alignment is not sorted: reads without coordinates prior to reads with coordinates.\n");
+				exit(1);
+			}
+		}
+	}
 	if (ret < -1) fprintf(stderr, "[bam_index_core] truncated file? Continue anyway. (%d)\n", ret);
 	free(b->data); free(b);
 	idx->n_no_coor = n_no_coor;
@@ -698,6 +705,7 @@ 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;
 }