* samtools-0.1.4-21 (r368)

[samtools.git] / bam_index.c

diff --git a/bam_index.c b/bam_index.c
index 329df323851f7bd61ecbbc345790f122b4303b6f..72ef270f9c7afd143759e1f98d681ce69147bb13 100644 (file)
--- a/bam_index.c
+++ b/bam_index.c
@@ -1,4 +1,5 @@
 #include <ctype.h>
+#include <assert.h>
 #include "bam.h"
 #include "khash.h"
 #include "ksort.h"
@@ -324,7 +325,6 @@ static bam_index_t *bam_index_load_core(FILE *fp)
 
 bam_index_t *bam_index_load_local(const char *_fn)
 {
-       bam_index_t *idx;
        FILE *fp;
        char *fnidx, *fn;
 
@@ -347,9 +347,11 @@ bam_index_t *bam_index_load_local(const char *_fn)
                }
        }
        free(fnidx); free(fn);
-       idx = bam_index_load_core(fp);
-       fclose(fp);
-       return idx;
+       if (fp) {
+               bam_index_t *idx = bam_index_load_core(fp);
+               fclose(fp);
+               return idx;
+       } else return 0;
 }
 
 static void download_from_remote(const char *url)
@@ -394,6 +396,7 @@ bam_index_t *bam_index_load(const char *fn)
                download_from_remote(fnidx);
                idx = bam_index_load_local(fn);
        }
+       if (idx == 0) fprintf(stderr, "[bam_index_load] fail to load BAM index.\n");
        return idx;
 }
 
@@ -403,7 +406,10 @@ int bam_index_build2(const char *fn, const char *_fnidx)
        FILE *fpidx;
        bamFile fp;
        bam_index_t *idx;
-       assert(fp = bam_open(fn, "r"));
+       if ((fp = bam_open(fn, "r")) == 0) {
+               fprintf(stderr, "[bam_index_build2] fail to open the BAM file.\n");
+               return -1;
+       }
        idx = bam_index_core(fp);
        bam_close(fp);
        if (_fnidx == 0) {
@@ -414,7 +420,7 @@ 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);
-               return 1;
+               return -1;
        }
        bam_index_save(idx, fpidx);
        bam_index_destroy(idx);