* samtools-0.1.5-4 (r394)

 * http_proxy support in knetfile library (check http_proxy ENV)

diff --git a/bamtk.c b/bamtk.c
index 5f22a30ded0eab96e7e3157ad3576ecf3bd3e6ac..0846a70ef5585ead7d773fb1a807d27841059749 100644 (file)
--- a/bamtk.c
+++ b/bamtk.c
@@ -4,7 +4,7 @@
 #include "bam.h"
 
 #ifndef PACKAGE_VERSION
 #include "bam.h"
 
 #ifndef PACKAGE_VERSION

-#define PACKAGE_VERSION "0.1.5-3 (r393)"
+#define PACKAGE_VERSION "0.1.5-4 (r394)"

 #endif
 
 int bam_taf2baf(int argc, char *argv[]);
 #endif
 
 int bam_taf2baf(int argc, char *argv[]);

diff --git a/knetfile.c b/knetfile.c
index e5f8501a7fa5994be68f37a24acbf70a31744bec..bcf74a89024b5533941cf322ccc6e83c6d28210d 100644 (file)
--- a/knetfile.c
+++ b/knetfile.c
@@ -123,7 +123,7 @@ static int kftp_pasv_connect(knetFile *ftp)
 
 int kftp_connect(knetFile *ftp)
 {
 
 int kftp_connect(knetFile *ftp)
 {

-       ftp->ctrl_fd = socket_connect(ftp->host, "ftp");
+       ftp->ctrl_fd = socket_connect(ftp->host, ftp->port);

        if (ftp->ctrl_fd == -1) return -1;
        kftp_get_response(ftp);
        kftp_send_cmd(ftp, "USER anonymous\r\n", 1);
        if (ftp->ctrl_fd == -1) return -1;
        kftp_get_response(ftp);
        kftp_send_cmd(ftp, "USER anonymous\r\n", 1);


@@ -155,6 +155,7 @@ knetFile *kftp_parse_url(const char *fn, const char *mode)
        fp = calloc(1, sizeof(knetFile));
        fp->type = KNF_TYPE_FTP;
        fp->fd = -1;
        fp = calloc(1, sizeof(knetFile));
        fp->type = KNF_TYPE_FTP;
        fp->fd = -1;

+       fp->port = strdup("ftp");

        fp->host = calloc(l + 1, 1);
        if (strchr(mode, 'c')) fp->no_reconnect = 1;
        strncpy(fp->host, fn + 6, l);
        fp->host = calloc(l + 1, 1);
        if (strchr(mode, 'c')) fp->no_reconnect = 1;
        strncpy(fp->host, fn + 6, l);


@@ -197,20 +198,34 @@ int kftp_connect_file(knetFile *fp)
 knetFile *khttp_parse_url(const char *fn, const char *mode)
 {
        knetFile *fp;
 knetFile *khttp_parse_url(const char *fn, const char *mode)
 {
        knetFile *fp;

-       char *p;
+       char *p, *proxy, *q;

        int l;
        if (strstr(fn, "http://") != fn) return 0;
        int l;
        if (strstr(fn, "http://") != fn) return 0;

+       // set ->http_host

        for (p = (char*)fn + 7; *p && *p != '/'; ++p);
        l = p - fn - 7;
        fp = calloc(1, sizeof(knetFile));
        for (p = (char*)fn + 7; *p && *p != '/'; ++p);
        l = p - fn - 7;
        fp = calloc(1, sizeof(knetFile));

+       fp->http_host = calloc(l + 1, 1);
+       strncpy(fp->http_host, fn + 7, l);
+       fp->http_host[l] = 0;
+       for (q = fp->http_host; *q && *q != ':'; ++q);
+       if (*q == ':') *q++ = 0;
+       // get http_proxy
+       proxy = getenv("http_proxy");
+       // set ->host, ->port and ->path
+       if (proxy == 0) {
+               fp->host = strdup(fp->http_host); // when there is no proxy, server name is identical to http_host name.
+               fp->port = strdup(*q? q : "http");
+               fp->path = strdup(*p? p : "/");
+       } else {
+               fp->host = (strstr(proxy, "http://") == proxy)? strdup(proxy + 7) : strdup(proxy);
+               for (q = fp->host; *q && *q != ':'; ++q);
+               if (*q == ':') *q++ = 0; 
+               fp->port = strdup(*q? q : "http");
+               fp->path = strdup(fn);
+       }

        fp->type = KNF_TYPE_HTTP;
        fp->type = KNF_TYPE_HTTP;

-       fp->fd = fp->ctrl_fd = -1;
-       fp->host = calloc(l + 1, 1);
-       if (strchr(mode, 'c')) fp->no_reconnect = 1;
-       strncpy(fp->host, fn + 7, l);
-       l = strlen(fn);
-       fp->path = calloc(strlen(p) + 2, 1);
-       strcpy(fp->path, *p? p : "/");
+       fp->ctrl_fd = fp->fd = -1;

        fp->seek_offset = -1;
        return fp;
 }
        fp->seek_offset = -1;
        return fp;
 }


@@ -220,9 +235,9 @@ int khttp_connect_file(knetFile *fp)
        int ret, l = 0;
        char *buf, *p;
        if (fp->fd >= 0) close(fp->fd);
        int ret, l = 0;
        char *buf, *p;
        if (fp->fd >= 0) close(fp->fd);

-       fp->fd = socket_connect(fp->host, "http");
+       fp->fd = socket_connect(fp->host, fp->port);

        buf = calloc(0x10000, 1); // FIXME: I am lazy... But in principle, 64KB should be large enough.
        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->host);
+       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, "\r\n");
        if (fp->offset)
                l += sprintf(buf + l, "Range: bytes=%lld-\r\n", (long long)fp->offset);
        l += sprintf(buf + l, "\r\n");


@@ -350,9 +365,11 @@ int knet_seek(knetFile *fp, off_t off, int whence)
 int knet_close(knetFile *fp)
 {
        if (fp == 0) return 0;
 int knet_close(knetFile *fp)
 {
        if (fp == 0) return 0;

-       if (fp->ctrl_fd >= 0) close(fp->ctrl_fd);
+       if (fp->ctrl_fd >= 0) close(fp->ctrl_fd); // FTP specific

        if (fp->fd >= 0) close(fp->fd);
        if (fp->fd >= 0) close(fp->fd);

-       free(fp->response); free(fp->retr); free(fp->host); free(fp->path);
+       free(fp->host); free(fp->port);
+       free(fp->response); free(fp->retr); // FTP specific
+       free(fp->path); free(fp->http_host); // HTTP specific

        free(fp);
        return 0;
 }
        free(fp);
        return 0;
 }

diff --git a/knetfile.h b/knetfile.h
index 1692b3a2b606bb60f6a81eae6dacab292b447f19..2c55c802a508d2e81266320053af249861bab8d6 100644 (file)
--- a/knetfile.h
+++ b/knetfile.h
@@ -13,7 +13,7 @@
 typedef struct knetFile_s {
        int type, fd;
        int64_t offset;
 typedef struct knetFile_s {
        int type, fd;
        int64_t offset;

-       char *host;
+       char *host, *port;

 
        // the following are for FTP only
        int ctrl_fd, pasv_ip[4], pasv_port, max_response, no_reconnect, is_ready;
 
        // the following are for FTP only
        int ctrl_fd, pasv_ip[4], pasv_port, max_response, no_reconnect, is_ready;


@@ -21,7 +21,7 @@ typedef struct knetFile_s {
        int64_t seek_offset; // for lazy seek
 
        // the following are for HTTP only
        int64_t seek_offset; // for lazy seek
 
        // the following are for HTTP only

-       char *path;
+       char *path, *http_host;

 } knetFile;
 
 #define knet_tell(fp) ((fp)->offset)
 } knetFile;
 
 #define knet_tell(fp) ((fp)->offset)