* samtools-0.1.4-19 (r364)

 * knetfile: report error when the file is not present on FTP

diff --git a/bamtk.c b/bamtk.c
index a64a929458306fcd40a4d0136a28f6f2edfc3f70..db428738bff71284e29b5faa2346696ffab183db 100644 (file)
--- a/bamtk.c
+++ b/bamtk.c
@@ -3,7 +3,7 @@
 #include "bam.h"
 
 #ifndef PACKAGE_VERSION
-#define PACKAGE_VERSION "0.1.4-18 (r363)"
+#define PACKAGE_VERSION "0.1.4-19 (r364)"
 #endif
 
 int bam_taf2baf(int argc, char *argv[]);

diff --git a/knetfile.c b/knetfile.c
index 9a6878d24da19f0675566b63612d713d6acc035e..45c921f7b2fa11a7f76e79325f352c8526f9bba8 100644 (file)
--- a/knetfile.c
+++ b/knetfile.c
@@ -15,7 +15,7 @@ static int kftp_get_response(knetFile *ftp)
        int n = 0;
        char *p;
        while (read(ftp->ctrl_fd, &c, 1)) { // FIXME: this is *VERY BAD* for unbuffered I/O
-//             fputc(c, stderr);
+               //fputc(c, stderr);
                if (n >= ftp->max_response) {
                        ftp->max_response = ftp->max_response? ftp->max_response<<1 : 256;
                        ftp->response = realloc(ftp->response, ftp->max_response);
@@ -138,6 +138,7 @@ knetFile *kftp_prep(const char *fn, const char *mode)
 // place ->fd at offset off
 int kftp_connect_file(knetFile *fp)
 {
+       int ret;
        if (fp->fd) {
                close(fp->fd);
                if (fp->no_reconnect) kftp_get_response(fp);
@@ -150,7 +151,12 @@ int kftp_connect_file(knetFile *fp)
        }
        kftp_send_cmd(fp, fp->retr, 0);
        kftp_pasv_connect(fp);
-       kftp_get_response(fp);
+       ret = kftp_get_response(fp);
+       if (ret != 150) {
+               fprintf(stderr, "[kftp_connect_file] %s\n", fp->response);
+               close(fp->fd);
+               fp->fd = -1;
+       }
        fp->is_ready = 1;
        return 0;
 }
@@ -170,6 +176,10 @@ knetFile *knet_open(const char *fn, const char *mode)
                        return 0;
                }
                kftp_connect_file(fp);
+               if (fp->fd == -1) {
+                       knet_close(fp);
+                       return 0;
+               }
        } else {
                int fd = open(fn, O_RDONLY);
                if (fd == -1) {
@@ -194,6 +204,7 @@ knetFile *knet_dopen(int fd, const char *mode)
 off_t knet_read(knetFile *fp, void *buf, off_t len)
 {
        off_t l = 0;
+       if (fp->fd < 0) return 0;
        if (fp->type == KNF_TYPE_LOCAL) {
                l = read(fp->fd, buf, len);
                fp->offset += l;