Updated samtools to 0.1.19

[rsem.git] / sam / bam_index.c

diff --git a/sam/bam_index.c b/sam/bam_index.c
index 9610a2656031657b796abc68bf32c1b6f1564745..f916e0461dca145499303db8edb011e6db86f793 100644 (file)
--- a/sam/bam_index.c
+++ b/sam/bam_index.c
@@ -159,9 +159,14 @@ bam_index_t *bam_index_core(bamFile fp)
        bam1_core_t *c;
        uint64_t save_off, last_off, n_mapped, n_unmapped, off_beg, off_end, n_no_coor;
 
+       h = bam_header_read(fp);
+       if(h == 0) {
+           fprintf(stderr, "[bam_index_core] Invalid BAM header.");
+           return NULL;
+       }
+
        idx = (bam_index_t*)calloc(1, sizeof(bam_index_t));
        b = (bam1_t*)calloc(1, sizeof(bam1_t));
-       h = bam_header_read(fp);
        c = &b->core;
 
        idx->n = h->n_targets;
@@ -459,6 +464,7 @@ bam_index_t *bam_index_load(const char *fn)
                strcat(strcpy(fnidx, fn), ".bai");
                fprintf(stderr, "[bam_index_load] attempting to download the remote index file.\n");
                download_from_remote(fnidx);
+        free(fnidx);
                idx = bam_index_load_local(fn);
        }
        if (idx == 0) fprintf(stderr, "[bam_index_load] fail to load BAM index.\n");
@@ -489,6 +495,7 @@ int bam_index_build2(const char *fn, const char *_fnidx)
        if (fpidx == 0) {
                fprintf(stderr, "[bam_index_build2] fail to create the index file.\n");
                free(fnidx);
+        bam_index_destroy(idx);
                return -1;
        }
        bam_index_save(idx, fpidx);