A bug fix, "samtools view" is now working again.

[samtools.git] / bam_index.c

diff --git a/bam_index.c b/bam_index.c
index 1c0b29b09c9e6b063549b08d56cf5941d6ffccac..4ff6bd482505172741c5a48ab413f141342e93bc 100644 (file)
--- a/bam_index.c
+++ b/bam_index.c
@@ -1,8 +1,12 @@
 #include <ctype.h>
+#include <assert.h>
 #include "bam.h"
 #include "khash.h"
 #include "ksort.h"
 #include "bam_endian.h"
+#ifdef _USE_KNETFILE
+#include "knetfile.h"
+#endif
 
 /*!
   @header
@@ -321,22 +325,12 @@ static bam_index_t *bam_index_load_core(FILE *fp)
        return idx;
 }
 
-bam_index_t *bam_index_load2(const char *fnidx)
-{
-       bam_index_t *idx;
-       FILE *fp = fopen(fnidx, "r");
-       idx = bam_index_load_core(fp);
-       fclose(fp);
-       return idx;
-}
-
-bam_index_t *bam_index_load(const char *_fn)
+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)
@@ -355,8 +349,63 @@ bam_index_t *bam_index_load(const char *_fn)
                }
        }
        free(fnidx); free(fn);
-       idx = bam_index_load_core(fp);
+       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;
+       char *fn;
+       FILE *fp;
+       uint8_t *buf;
+       knetFile *fp_remote;
+       int l;
+       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;
+       ++fn; // fn now points to the file name
+       fp_remote = knet_open(url, "r");
+       if (fp_remote == 0) {
+               fprintf(stderr, "[download_from_remote] fail to open remote file.\n");
+               return;
+       }
+       if ((fp = fopen(fn, "w")) == 0) {
+               fprintf(stderr, "[download_from_remote] fail to create file in the working directory.\n");
+               knet_close(fp_remote);
+               return;
+       }
+       buf = (uint8_t*)calloc(buf_size, 1);
+       while ((l = knet_read(fp_remote, buf, buf_size)) != 0)
+               fwrite(buf, 1, l, fp);
+       free(buf);
        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 || 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;
 }
 
@@ -366,7 +415,10 @@ 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) {
@@ -377,7 +429,7 @@ 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);