* samtools-0.1.6-5 (r462)

[samtools.git] / knetfile.c

diff --git a/knetfile.c b/knetfile.c
index e110aa720f6577e7f8dee34fddc32cb6220d7154..ac51a6bf39b4e702bbe24cc4afdb118bf5524911 100644 (file)
--- a/knetfile.c
+++ b/knetfile.c
@@ -262,7 +262,7 @@ int kftp_reconnect(knetFile *ftp)
        return kftp_connect(ftp);
 }
 
-// initialize ->type, ->host and ->retr
+// initialize ->type, ->host, ->retr and ->size
 knetFile *kftp_parse_url(const char *fn, const char *mode)
 {
        knetFile *fp;
@@ -283,19 +283,28 @@ knetFile *kftp_parse_url(const char *fn, const char *mode)
        strncpy(fp->host, fn + 6, l);
        fp->retr = calloc(strlen(p) + 8, 1);
        sprintf(fp->retr, "RETR %s\r\n", p);
-       fp->seek_offset = -1;
+    fp->size_cmd = calloc(strlen(p) + 8, 1);
+    sprintf(fp->size_cmd, "SIZE %s\r\n", p);
+       fp->seek_offset = 0;
        return fp;
 }
 // place ->fd at offset off
 int kftp_connect_file(knetFile *fp)
 {
        int ret;
+       long long file_size;
        if (fp->fd != -1) {
                netclose(fp->fd);
                if (fp->no_reconnect) kftp_get_response(fp);
        }
        kftp_pasv_prep(fp);
-       if (fp->offset) {
+    kftp_send_cmd(fp, fp->size_cmd, 1);
+    if ( sscanf(fp->response,"%*d %lld", &file_size) != 1 )
+    {
+        fprintf(stderr,"[kftp_connect_file] %s\n", fp->response);
+        return -1;
+    } else fp->file_size = file_size;
+       if (fp->offset>=0) {
                char tmp[32];
 #ifndef _WIN32
                sprintf(tmp, "REST %lld\r\n", (long long)fp->offset);
@@ -319,6 +328,7 @@ int kftp_connect_file(knetFile *fp)
        return 0;
 }
 
+
 /**************************
  * HTTP specific routines *
  **************************/
@@ -354,7 +364,7 @@ knetFile *khttp_parse_url(const char *fn, const char *mode)
        }
        fp->type = KNF_TYPE_HTTP;
        fp->ctrl_fd = fp->fd = -1;
-       fp->seek_offset = -1;
+       fp->seek_offset = 0;
        return fp;
 }
 
@@ -366,8 +376,7 @@ int khttp_connect_file(knetFile *fp)
        fp->fd = socket_connect(fp->host, fp->port);
        buf = calloc(0x10000, 1); // FIXME: I am lazy... But in principle, 64KB should be large enough.
        l += sprintf(buf + l, "GET %s HTTP/1.0\r\nHost: %s\r\n", fp->path, fp->http_host);
-       if (fp->offset)
-               l += sprintf(buf + l, "Range: bytes=%lld-\r\n", (long long)fp->offset);
+    l += sprintf(buf + l, "Range: bytes=%lld-\r\n", (long long)fp->offset);
        l += sprintf(buf + l, "\r\n");
        netwrite(fp->fd, buf, l);
        l = 0;
@@ -383,7 +392,7 @@ int khttp_connect_file(knetFile *fp)
                return -1;
        }
        ret = strtol(buf + 8, &p, 0); // HTTP return code
-       if (ret == 200 && fp->offset) { // 200 (complete result); then skip beginning of the file
+       if (ret == 200 && fp->offset>0) { // 200 (complete result); then skip beginning of the file
                off_t rest = fp->offset;
                while (rest) {
                        off_t l = rest < 0x10000? rest : 0x10000;
@@ -482,7 +491,7 @@ off_t knet_read(knetFile *fp, void *buf, off_t len)
        return l;
 }
 
-int knet_seek(knetFile *fp, off_t off, int whence)
+off_t knet_seek(knetFile *fp, off_t off, int whence)
 {
        if (whence == SEEK_SET && off == fp->offset) return 0;
        if (fp->type == KNF_TYPE_LOCAL) {
@@ -494,15 +503,31 @@ int knet_seek(knetFile *fp, off_t off, int whence)
                        return -1;
                }
                fp->offset = offset;
-               return 0;
-       } else if (fp->type == KNF_TYPE_FTP || fp->type == KNF_TYPE_HTTP) {
-               if (whence != SEEK_SET) { // FIXME: we can surely allow SEEK_CUR and SEEK_END in future
-                       fprintf(stderr, "[knet_seek] only SEEK_SET is supported for FTP/HTTP. Offset is unchanged.\n");
+               return fp->offset;
+       }
+    else if (fp->type == KNF_TYPE_FTP) 
+    {
+        if (whence==SEEK_CUR)
+            fp->offset += off;
+        else if (whence==SEEK_SET)
+            fp->offset = off;
+        else if ( whence==SEEK_END)
+            fp->offset = fp->file_size+off;
+               fp->is_ready = 0;
+               return fp->offset;
+       } 
+    else if (fp->type == KNF_TYPE_HTTP) 
+    {
+               if (whence == SEEK_END) { // FIXME: we can surely allow SEEK_CUR and SEEK_END in future
+                       fprintf(stderr, "[knet_seek] SEEK_END is supported for HTTP. Offset is unchanged.\n");
                        return -1;
                }
-               fp->offset = off;
+        if (whence==SEEK_CUR)
+            fp->offset += off;
+        else if (whence==SEEK_SET)
+            fp->offset = off;
                fp->is_ready = 0;
-               return 0;
+               return fp->offset;
        }
        return -1;
 }