* samtools-0.1.4-20 (r365)

 * download the BAM index file if it is not found in the current working directory.

diff --git a/bam_index.c b/bam_index.c
index 1c0b29b09c9e6b063549b08d56cf5941d6ffccac..329df323851f7bd61ecbbc345790f122b4303b6f 100644 (file)
--- a/bam_index.c
+++ b/bam_index.c
@@ -3,6 +3,7 @@
 #include "khash.h"
 #include "ksort.h"
 #include "bam_endian.h"
+#include "knetfile.h"
 
 /*!
   @header
@@ -321,16 +322,7 @@ 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;
@@ -360,6 +352,51 @@ bam_index_t *bam_index_load(const char *_fn)
        return idx;
 }
 
+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) 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);
+}
+
+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) {
+               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);
+       }
+       return idx;
+}
+
 int bam_index_build2(const char *fn, const char *_fnidx)
 {
        char *fnidx;

diff --git a/bamtk.c b/bamtk.c
index db428738bff71284e29b5faa2346696ffab183db..61ead1058c818b5ee6b00df27fad2864db3f664f 100644 (file)
--- a/bamtk.c
+++ b/bamtk.c
@@ -3,7 +3,7 @@
 #include "bam.h"
 
 #ifndef PACKAGE_VERSION
-#define PACKAGE_VERSION "0.1.4-19 (r364)"
+#define PACKAGE_VERSION "0.1.4-20 (r365)"
 #endif
 
 int bam_taf2baf(int argc, char *argv[]);

diff --git a/knetfile.c b/knetfile.c
index 45c921f7b2fa11a7f76e79325f352c8526f9bba8..8dd7e86b896c54ffcbb6f48eca0e0991eed9ca1b 100644 (file)
--- a/knetfile.c
+++ b/knetfile.c
@@ -116,7 +116,7 @@ int kftp_reconnect(knetFile *ftp)
 }
 
 // initialize ->type, ->host and ->retr
-knetFile *kftp_prep(const char *fn, const char *mode)
+knetFile *kftp_parse_url(const char *fn, const char *mode)
 {
        knetFile *fp;
        char *p;
@@ -156,6 +156,7 @@ int kftp_connect_file(knetFile *fp)
                fprintf(stderr, "[kftp_connect_file] %s\n", fp->response);
                close(fp->fd);
                fp->fd = -1;
+               return -1;
        }
        fp->is_ready = 1;
        return 0;
@@ -169,7 +170,7 @@ knetFile *knet_open(const char *fn, const char *mode)
                return 0;
        }
        if (strstr(fn, "ftp://") == fn) {
-               fp = kftp_prep(fn, mode);
+               fp = kftp_parse_url(fn, mode);
                if (fp == 0) return 0;
                if (kftp_connect(fp) == -1) {
                        knet_close(fp);

diff --git a/knetfile.h b/knetfile.h
index 85f348c5886910df7b61633080c64064d549800b..bf45f3df809b8f3ebd54b17c711dd188ab3dbb36 100644 (file)
--- a/knetfile.h
+++ b/knetfile.h
@@ -29,8 +29,22 @@ extern "C" {
 #endif
 
        knetFile *knet_open(const char *fn, const char *mode);
+
+       /* 
+          This only works with local files.
+        */
        knetFile *knet_dopen(int fd, const char *mode);
+
+       /*
+         If ->is_ready==0, this routine updates ->fd; otherwise, it simply
+         reads from ->fd.
+        */
        off_t knet_read(knetFile *fp, void *buf, off_t len);
+
+       /*
+         This routine only sets ->offset and ->is_ready=0. It does not
+         communicate with the FTP server.
+        */
        int knet_seek(knetFile *fp, off_t off, int whence);
        int knet_close(knetFile *fp);