* samtools-0.1.5-8 (r404)

[samtools.git] / bam_index.c

diff --git a/bam_index.c b/bam_index.c
index 329df323851f7bd61ecbbc345790f122b4303b6f..5126f00c8d8da0c41e0ba2179ca23cc8d436e53f 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"
@@ -324,11 +325,10 @@ 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;
 
-       if (strstr(_fn, "ftp://") == _fn) {
+       if (strstr(_fn, "ftp://") == _fn || strstr(_fn, "http://") == _fn) {
                const char *p;
                int l = strlen(_fn);
                for (p = _fn + l - 1; p >= _fn; --p)
@@ -347,11 +347,14 @@ 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;
 }
 
+#ifdef _USE_KNETFILE
 static void download_from_remote(const char *url)
 {
        const int buf_size = 1 * 1024 * 1024;
@@ -360,7 +363,7 @@ static void download_from_remote(const char *url)
        uint8_t *buf;
        knetFile *fp_remote;
        int l;
-       if (strstr(url, "ftp://") != url) return;
+       if (strstr(url, "ftp://") != url && strstr(url, "http://") != url) return;
        l = strlen(url);
        for (fn = (char*)url + l - 1; fn >= url; --fn)
                if (*fn == '/') break;
@@ -382,18 +385,25 @@ static void download_from_remote(const char *url)
        fclose(fp);
        knet_close(fp_remote);
 }
+#else
+static void download_from_remote(const char *url)
+{
+       return;
+}
+#endif
 
 bam_index_t *bam_index_load(const char *fn)
 {
        bam_index_t *idx;
        idx = bam_index_load_local(fn);
-       if (idx == 0 && strstr(fn, "ftp://") == fn) {
+       if (idx == 0 && (strstr(fn, "ftp://") == fn || strstr(fn, "http://") == fn)) {
                char *fnidx = calloc(strlen(fn) + 5, 1);
                strcat(strcpy(fnidx, fn), ".bai");
                fprintf(stderr, "[bam_index_load] attempting to download the remote index file.\n");
                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 +413,10 @@ 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 +427,7 @@ 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);