# Uploaded samtools version 0.1.14-1.

[samtools.git] / bam_index.c

diff --git a/bam_index.c b/bam_index.c
index f60a6f874b106f03c655d1207dddf21c4df7fc48..51c27014da0f9f010b563db92112f71d7ad6bdd6 100644 (file)
--- 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;
 }