* samtools-0.1.4-16 (r360)

[samtools.git] / knetfile.c

diff --git a/knetfile.c b/knetfile.c
index d30fcbbb0617f0e86d255ed2261f1891c8426b0f..322885a379642d19b638a9b0164b153cdcf5ed0b 100644 (file)
--- a/knetfile.c
+++ b/knetfile.c
@@ -22,7 +22,8 @@ static int kftp_get_response(knetFile *ftp)
                }
                ftp->response[n++] = c;
                if (c == '\n') {
-                       if (n >= 4 && isdigit(ftp->response[0]) && isdigit(ftp->response[1]) && isdigit(ftp->response[2]) && ftp->response[3] != '-') break;
+                       if (n >= 4 && isdigit(ftp->response[0]) && isdigit(ftp->response[1]) && isdigit(ftp->response[2])
+                               && ftp->response[3] != '-') break;
                        n = 0;
                        continue;
                }
@@ -58,7 +59,7 @@ static int kftp_pasv_connect(knetFile *ftp)
 
        struct addrinfo hints, *res;
        struct linger lng = { 0, 0 };
-       int on;
+       int on = 1;
        char host[80], port[10];
 
        if (ftp->pasv_port == 0) {
@@ -83,7 +84,7 @@ int kftp_connect(knetFile *ftp)
 {
 #define __err_connect(func) do { perror(func); return -1; } while (0)
 
-       int on;
+       int on = 1;
        { // open socket
                struct addrinfo hints, *res;
                memset(&hints, 0, sizeof(struct addrinfo));
@@ -129,7 +130,7 @@ knetFile *kftp_prep(const char *fn, const char *mode)
        fp->host = calloc(l + 1, 1);
        if (strchr(mode, 'c')) fp->no_reconnect = 1;
        strncpy(fp->host, fn + 6, l);
-       fp->retr = calloc(strlen(p) + 7, 1);
+       fp->retr = calloc(strlen(p) + 8, 1);
        sprintf(fp->retr, "RETR %s\r\n", p);
        return fp;
 }
@@ -181,29 +182,52 @@ knetFile *knet_open(const char *fn, const char *mode)
        return fp;
 }
 
+knetFile *knet_dopen(int fd, const char *mode)
+{
+       knetFile *fp = (knetFile*)calloc(1, sizeof(knetFile));
+       fp->type = KNF_TYPE_LOCAL;
+       fp->fd = fd;
+       return fp;
+}
+
 off_t knet_read(knetFile *fp, void *buf, off_t len)
 {
-       off_t l = read(fp->fd, buf, len);
-       fp->offset += l;
+       off_t l = 0;
+       if (fp->type == KNF_TYPE_LOCAL) {
+               l = read(fp->fd, buf, len);
+               fp->offset += l;
+       } else {
+               off_t rest = len, curr;
+               while (rest) {
+                       curr = read(fp->fd, buf + l, rest);
+                       if (curr == 0) break; // FIXME: end of file or bad network? I do not know...
+                       l += curr; rest -= curr;
+               }
+               fp->offset += l;
+       }
        return l;
 }
 
-off_t knet_seek(knetFile *fp, off_t off, int whence)
+int knet_seek(knetFile *fp, off_t off, int whence)
 {
        if (fp->type == KNF_TYPE_LOCAL) {
-               fp->offset = lseek(fp->fd, off, whence);
-               return fp->offset;
+               if (lseek(fp->fd, off, whence) == -1) {
+                       perror("lseek");
+                       return -1;
+               }
+               fp->offset = off;
+               return 0;
        }
        if (fp->type == KNF_TYPE_FTP) {
-               if (whence != SEEK_SET) {
+               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. Offset is unchanged.\n");
                        return -1;
                }
                if (!fp->no_reconnect) kftp_reconnect(fp);
                kftp_connect_file(fp, off);
-               return fp->offset;
+               return 0;
        }
-       return 0;
+       return -1;
 }
 
 int knet_close(knetFile *fp)
@@ -222,8 +246,8 @@ int main(void)
        char buf[256];
        knetFile *fp;
 //     fp = knet_open("ftp://ftp.ncbi.nih.gov/1000genomes/ftp/data/NA12878/alignment/NA12878.chrom6.SLX.SRP000032.2009_06.bam", "r"); knet_seek(fp, 2500000000ll, SEEK_SET);
-//     fp = knet_open("ftp://ftp.sanger.ac.uk/pub4/treefam/tmp/index.shtml", "r"); knet_seek(fp, 2000, SEEK_SET);
-       fp = knet_open("knetfile.c", "r"); knet_seek(fp, 2000, SEEK_SET);
+       fp = knet_open("ftp://ftp.sanger.ac.uk/pub4/treefam/tmp/index.shtml", "r"); knet_seek(fp, 2000, SEEK_SET);
+//     fp = knet_open("knetfile.c", "r"); knet_seek(fp, 2000, SEEK_SET);
        knet_read(fp, buf, 255);
        buf[255] = 0;
        printf("%s\n", buf);