7df6e18265341f87a69fba808aa1f92f8ebca841
markd
  Wed Apr 15 13:39:42 2026 -0700
move copy of htslib

diff --git src/htslib/knetfile.c src/htslib/knetfile.c
deleted file mode 100644
index ebd1cf78bbb..00000000000
--- src/htslib/knetfile.c
+++ /dev/null
@@ -1,684 +0,0 @@
-/* The MIT License
-
-   Copyright (c) 2008 by Genome Research Ltd (GRL).
-                 2010 by Attractive Chaos <attractor@live.co.uk>
-
-   Permission is hereby granted, free of charge, to any person obtaining
-   a copy of this software and associated documentation files (the
-   "Software"), to deal in the Software without restriction, including
-   without limitation the rights to use, copy, modify, merge, publish,
-   distribute, sublicense, and/or sell copies of the Software, and to
-   permit persons to whom the Software is furnished to do so, subject to
-   the following conditions:
-
-   The above copyright notice and this permission notice shall be
-   included in all copies or substantial portions of the Software.
-
-   THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
-   EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
-   MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
-   NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS
-   BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN
-   ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN
-   CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
-   SOFTWARE.
-*/
-
-/* Probably I will not do socket programming in the next few years and
-   therefore I decide to heavily annotate this file, for Linux and
-   Windows as well.  -ac */
-
-#include <time.h>
-#include <stdio.h>
-#include <ctype.h>
-#include <stdlib.h>
-#include <string.h>
-#include <errno.h>
-#include <unistd.h>
-#include <sys/types.h>
-
-#ifndef _WIN32
-#include <netdb.h>
-#include <arpa/inet.h>
-#include <sys/socket.h>
-#endif
-
-#include "htslib/knetfile.h"
-#ifdef KNETFILE_HOOKS
-// Static global function pointers that may be set by knet_init_alt()
-// to replace the usual knet functionality with alternate I/O implementation.
-static knet_alt_open_f alt_open = NULL;
-static knet_alt_dopen_f alt_dopen = NULL;
-static knet_alt_read_f alt_read = NULL;
-static knet_alt_seek_f alt_seek = NULL;
-static knet_alt_tell_f alt_tell = NULL;
-static knet_alt_close_f alt_close = NULL;
-
-void knet_init_alt(knet_alt_open_f open, knet_alt_dopen_f dopen, knet_alt_read_f read,
-                                   knet_alt_seek_f seek, knet_alt_tell_f tell, knet_alt_close_f close)
-
-{
-       alt_open = open;
-       alt_dopen = dopen;
-       alt_read = read;
-       alt_seek = seek;
-       alt_tell = tell;
-       alt_close = close;
-}      
-#endif 
-
-
-/* In winsock.h, the type of a socket is SOCKET, which is: "typedef
- * u_int SOCKET". An invalid SOCKET is: "(SOCKET)(~0)", or signed
- * integer -1. In knetfile.c, I use "int" for socket type
- * throughout. This should be improved to avoid confusion.
- *
- * In Linux/Mac, recv() and read() do almost the same thing. You can see
- * in the header file that netread() is simply an alias of read(). In
- * Windows, however, they are different and using recv() is mandatory.
- */
-
-/* This function tests if the file handler is ready for reading (or
- * writing if is_read==0). */
-static int socket_wait(int fd, int is_read)
-{
-	fd_set fds, *fdr = 0, *fdw = 0;
-	struct timeval tv;
-	int ret;
-	tv.tv_sec = 5; tv.tv_usec = 0; // 5 seconds time out
-	FD_ZERO(&fds);
-	FD_SET(fd, &fds);
-	if (is_read) fdr = &fds;
-	else fdw = &fds;
-	ret = select(fd+1, fdr, fdw, 0, &tv);
-#ifndef _WIN32
-	if (ret == -1) perror("select");
-#else
-	if (ret == 0)
-		fprintf(stderr, "select time-out\n");
-	else if (ret == SOCKET_ERROR)
-		fprintf(stderr, "select: %d\n", WSAGetLastError());
-#endif
-	return ret;
-}
-
-#ifndef _WIN32
-/* This function does not work with Windows due to the lack of
- * getaddrinfo() in winsock. It is addapted from an example in "Beej's
- * Guide to Network Programming" (http://beej.us/guide/bgnet/). */
-static int socket_connect(const char *host, const char *port)
-{
-#define __err_connect(func) do { perror(func); freeaddrinfo(res); return -1; } while (0)
-
-	int ai_err, on = 1, fd;
-	struct linger lng = { 0, 0 };
-	struct addrinfo hints, *res = 0;
-	memset(&hints, 0, sizeof(struct addrinfo));
-	hints.ai_family = AF_UNSPEC;
-	hints.ai_socktype = SOCK_STREAM;
-	/* In Unix/Mac, getaddrinfo() is the most convenient way to get
-	 * server information. */
-	if ((ai_err = getaddrinfo(host, port, &hints, &res)) != 0) { fprintf(stderr, "can't resolve %s:%s: %s\n", host, port, gai_strerror(ai_err)); return -1; }
-	if ((fd = socket(res->ai_family, res->ai_socktype, res->ai_protocol)) == -1) __err_connect("socket");
-	/* The following two setsockopt() are used by ftplib
-	 * (http://nbpfaus.net/~pfau/ftplib/). I am not sure if they
-	 * necessary. */
-	if (setsockopt(fd, SOL_SOCKET, SO_REUSEADDR, &on, sizeof(on)) == -1) __err_connect("setsockopt");
-	if (setsockopt(fd, SOL_SOCKET, SO_LINGER, &lng, sizeof(lng)) == -1) __err_connect("setsockopt");
-	if (connect(fd, res->ai_addr, res->ai_addrlen) != 0) __err_connect("connect");
-	freeaddrinfo(res);
-	return fd;
-}
-#else
-/* MinGW's printf has problem with "%lld" */
-char *int64tostr(char *buf, int64_t x)
-{
-	int cnt;
-	int i = 0;
-	do {
-		buf[i++] = '0' + x % 10;
-		x /= 10;
-	} while (x);
-	buf[i] = 0;
-	for (cnt = i, i = 0; i < cnt/2; ++i) {
-		int c = buf[i]; buf[i] = buf[cnt-i-1]; buf[cnt-i-1] = c;
-	}
-	return buf;
-}
-
-int64_t strtoint64(const char *buf)
-{
-	int64_t x;
-	for (x = 0; *buf != '\0'; ++buf)
-		x = x * 10 + ((int64_t) *buf - 48);
-	return x;
-}
-/* In windows, the first thing is to establish the TCP connection. */
-int knet_win32_init()
-{
-	WSADATA wsaData;
-	return WSAStartup(MAKEWORD(2, 2), &wsaData);
-}
-void knet_win32_destroy()
-{
-	WSACleanup();
-}
-/* A slightly modfied version of the following function also works on
- * Mac (and presummably Linux). However, this function is not stable on
- * my Mac. It sometimes works fine but sometimes does not. Therefore for
- * non-Windows OS, I do not use this one. */
-static SOCKET socket_connect(const char *host, const char *port)
-{
-#define __err_connect(func)										\
-	do {														\
-		fprintf(stderr, "%s: %d\n", func, WSAGetLastError());	\
-		return -1;												\
-	} while (0)
-
-	int on = 1;
-	SOCKET fd;
-	struct linger lng = { 0, 0 };
-	struct sockaddr_in server;
-	struct hostent *hp = 0;
-	// open socket
-	if ((fd = socket(AF_INET, SOCK_STREAM, IPPROTO_TCP)) == INVALID_SOCKET) __err_connect("socket");
-	if (setsockopt(fd, SOL_SOCKET, SO_REUSEADDR, (char*)&on, sizeof(on)) == -1) __err_connect("setsockopt");
-	if (setsockopt(fd, SOL_SOCKET, SO_LINGER, (char*)&lng, sizeof(lng)) == -1) __err_connect("setsockopt");
-	// get host info
-	if (isalpha(host[0])) hp = gethostbyname(host);
-	else {
-		struct in_addr addr;
-		addr.s_addr = inet_addr(host);
-		hp = gethostbyaddr((char*)&addr, 4, AF_INET);
-	}
-	if (hp == 0) __err_connect("gethost");
-	// connect
-	server.sin_addr.s_addr = *((unsigned long*)hp->h_addr);
-	server.sin_family= AF_INET;
-	server.sin_port = htons(atoi(port));
-	if (connect(fd, (struct sockaddr*)&server, sizeof(server)) != 0) __err_connect("connect");
-	// freehostent(hp); // strangely in MSDN, hp is NOT freed (memory leak?!)
-
-	/* FOR CODE TO CONNECT SUPPORTING IPV6 and IPV4 using our net.c:
-	fd = netConnect(host, port);
-	*/
-
-	return fd;
-}
-#endif
-
-static off_t my_netread(int fd, void *buf, off_t len)
-{
-	off_t rest = len, curr, l = 0;
-	/* recv() and read() may not read the required length of data with
-	 * one call. They have to be called repeatedly. */
-	while (rest) {
-		if (socket_wait(fd, 1) <= 0) break; // socket is not ready for reading
-		curr = netread(fd, (void*)((char*)buf + l), rest);
-		/* According to the glibc manual, section 13.2, a zero returned
-		 * value indicates end-of-file (EOF), which should mean that
-		 * read() will not return zero if EOF has not been met but data
-		 * are not immediately available. */
-		if (curr == 0) break;
-		l += curr; rest -= curr;
-	}
-	return l;
-}
-
-/*************************
- * FTP specific routines *
- *************************/
-
-static int kftp_get_response(knetFile *ftp)
-{
-#ifndef _WIN32
-	unsigned char c;
-#else
-	char c;
-#endif
-	int n = 0;
-	char *p;
-	if (socket_wait(ftp->ctrl_fd, 1) <= 0) return 0;
-	while (netread(ftp->ctrl_fd, &c, 1)) { // FIXME: this is *VERY BAD* for unbuffered I/O
-		//fputc(c, stderr);
-		if (n >= ftp->max_response) {
-			ftp->max_response = ftp->max_response? ftp->max_response<<1 : 256;
-			ftp->response = (char*)realloc(ftp->response, ftp->max_response);
-		}
-		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;
-			n = 0;
-			continue;
-		}
-	}
-	if (n < 2) return -1;
-	ftp->response[n-2] = 0;
-	return strtol(ftp->response, &p, 0);
-}
-
-static int kftp_send_cmd(knetFile *ftp, const char *cmd, int is_get)
-{
-	if (socket_wait(ftp->ctrl_fd, 0) <= 0) return -1; // socket is not ready for writing
-    int len = strlen(cmd);
-	if ( netwrite(ftp->ctrl_fd, cmd, len) != len ) return -1;
-	return is_get? kftp_get_response(ftp) : 0;
-}
-
-static int kftp_pasv_prep(knetFile *ftp)
-{
-	char *p;
-	int v[6];
-	kftp_send_cmd(ftp, "PASV\r\n", 1);
-	for (p = ftp->response; *p && *p != '('; ++p);
-	if (*p != '(') return -1;
-	++p;
-	sscanf(p, "%d,%d,%d,%d,%d,%d", &v[0], &v[1], &v[2], &v[3], &v[4], &v[5]);
-	memcpy(ftp->pasv_ip, v, 4 * sizeof(int));
-	ftp->pasv_port = (v[4]<<8&0xff00) + v[5];
-	return 0;
-}
-
-
-static int kftp_pasv_connect(knetFile *ftp)
-{
-	char host[80], port[10];
-	if (ftp->pasv_port == 0) {
-		fprintf(stderr, "[kftp_pasv_connect] kftp_pasv_prep() is not called before hand.\n");
-		return -1;
-	}
-	sprintf(host, "%d.%d.%d.%d", ftp->pasv_ip[0], ftp->pasv_ip[1], ftp->pasv_ip[2], ftp->pasv_ip[3]);
-	sprintf(port, "%d", ftp->pasv_port);
-	ftp->fd = socket_connect(host, port);
-	if (ftp->fd == -1) return -1;
-	return 0;
-}
-
-int kftp_connect(knetFile *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);
-	kftp_send_cmd(ftp, "PASS kftp@\r\n", 1);
-	kftp_send_cmd(ftp, "TYPE I\r\n", 1);
-	return 0;
-}
-
-int kftp_reconnect(knetFile *ftp)
-{
-	if (ftp->ctrl_fd != -1) {
-		netclose(ftp->ctrl_fd);
-		ftp->ctrl_fd = -1;
-	}
-	netclose(ftp->fd);
-	ftp->fd = -1;
-	return kftp_connect(ftp);
-}
-
-// initialize ->type, ->host, ->retr and ->size
-knetFile *kftp_parse_url(const char *fn, const char *mode)
-{
-	knetFile *fp;
-	char *p;
-	int l;
-	if (strstr(fn, "ftp://") != fn) return 0;
-	for (p = (char*)fn + 6; *p && *p != '/'; ++p);
-	if (*p != '/') return 0;
-	l = p - fn - 6;
-	fp = (knetFile*)calloc(1, sizeof(knetFile));
-	fp->type = KNF_TYPE_FTP;
-	fp->fd = -1;
-	/* the Linux/Mac version of socket_connect() also recognizes a port
-	 * like "ftp", but the Windows version does not. */
-	fp->port = strdup("21");
-	fp->host = (char*)calloc(l + 1, 1);
-	if (strchr(mode, 'c')) fp->no_reconnect = 1;
-	strncpy(fp->host, fn + 6, l);
-	fp->retr = (char*)calloc(strlen(p) + 8, 1);
-	sprintf(fp->retr, "RETR %s\r\n", p);
-    fp->size_cmd = (char*)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);
-    kftp_send_cmd(fp, fp->size_cmd, 1);
-#ifndef _WIN32
-    // If the file does not exist, the response will be "550 Could not get file
-    // size". Be silent on failure, hts_idx_load can be trying the existence of .csi or .tbi.
-    if ( sscanf(fp->response,"%*d %lld", &file_size) != 1 ) return -1;
-#else
-	const char *p = fp->response;
-	while (*p != ' ') ++p;
-	while (*p < '0' || *p > '9') ++p;
-	file_size = strtoint64(p);
-#endif
-	fp->file_size = file_size;
-	if (fp->offset>=0) {
-		char tmp[32];
-#ifndef _WIN32
-		sprintf(tmp, "REST %lld\r\n", (long long)fp->offset);
-#else
-		strcpy(tmp, "REST ");
-		int64tostr(tmp + 5, fp->offset);
-		strcat(tmp, "\r\n");
-#endif
-		kftp_send_cmd(fp, tmp, 1);
-	}
-	kftp_send_cmd(fp, fp->retr, 0);
-	kftp_pasv_connect(fp);
-	ret = kftp_get_response(fp);
-	if (ret != 150) {
-		fprintf(stderr, "[kftp_connect_file] %s\n", fp->response);
-		netclose(fp->fd);
-		fp->fd = -1;
-		return -1;
-	}
-	fp->is_ready = 1;
-	return 0;
-}
-
-
-/**************************
- * HTTP specific routines *
- **************************/
-
-knetFile *khttp_parse_url(const char *fn, const char *mode)
-{
-	knetFile *fp;
-	char *p, *proxy, *q;
-	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 = (knetFile*)calloc(1, sizeof(knetFile));
-	fp->http_host = (char*)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 : "80");
-		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 : "80");
-		fp->path = strdup(fn);
-	}
-	fp->type = KNF_TYPE_HTTP;
-	fp->ctrl_fd = fp->fd = -1;
-	fp->seek_offset = 0;
-	return fp;
-}
-
-int khttp_connect_file(knetFile *fp)
-{
-	int ret, l = 0;
-	char *buf, *p;
-	if (fp->fd != -1) netclose(fp->fd);
-	fp->fd = socket_connect(fp->host, fp->port);
-	buf = (char*)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);
-	l += sprintf(buf + l, "Range: bytes=%lld-\r\n", (long long)fp->offset);
-	l += sprintf(buf + l, "\r\n");
-	if ( netwrite(fp->fd, buf, l) != l ) { free(buf); return -1; }
-	l = 0;
-	while (netread(fp->fd, buf + l, 1)) { // read HTTP header; FIXME: bad efficiency
-		if (buf[l] == '\n' && l >= 3)
-			if (strncmp(buf + l - 3, "\r\n\r\n", 4) == 0) break;
-		++l;
-	}
-	buf[l] = 0;
-	if (l < 14) { // prematured header
-		free(buf);
-		netclose(fp->fd);
-		fp->fd = -1;
-		return -1;
-	}
-	ret = strtol(buf + 8, &p, 0); // HTTP return code
-	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;
-			rest -= my_netread(fp->fd, buf, l);
-		}
-	} else if (ret != 206 && ret != 200) {
-		// failed to open file
-		free(buf);
-		netclose(fp->fd);
-		switch (ret) {
-		case 401: errno = EPERM; break;
-		case 403: errno = EACCES; break;
-		case 404: errno = ENOENT; break;
-		case 407: errno = EPERM; break;
-		case 408: errno = ETIMEDOUT; break;
-		case 410: errno = ENOENT; break;
-		case 503: errno = EAGAIN; break;
-		case 504: errno = ETIMEDOUT; break;
-		default:  errno = (ret >= 400 && ret < 500)? EINVAL : EIO; break;
-		}
-		fp->fd = -1;
-		return -1;
-	}
-	free(buf);
-	fp->is_ready = 1;
-	return 0;
-}
-
-/********************
- * Generic routines *
- ********************/
-
-knetFile *knet_open(const char *fn, const char *mode)
-{
-#ifdef KNETFILE_HOOKS
-    if (alt_open)
-        return alt_open(fn, mode);
-#endif
-	knetFile *fp = 0;
-	if (mode[0] != 'r') {
-		fprintf(stderr, "[kftp_open] only mode \"r\" is supported.\n");
-		return 0;
-	}
-	if (strstr(fn, "ftp://") == fn) {
-		fp = kftp_parse_url(fn, mode);
-		if (fp == 0) return 0;
-		if (kftp_connect(fp) == -1) {
-			knet_close(fp);
-			return 0;
-		}
-		kftp_connect_file(fp);
-	} else if (strstr(fn, "http://") == fn) {
-		fp = khttp_parse_url(fn, mode);
-		if (fp == 0) return 0;
-		khttp_connect_file(fp);
-	} else { // local file
-#ifdef _WIN32
-		/* In windows, O_BINARY is necessary. In Linux/Mac, O_BINARY may
-		 * be undefined on some systems, although it is defined on my
-		 * Mac and the Linux I have tested on. */
-		int fd = open(fn, O_RDONLY | O_BINARY);
-#else		
-		int fd = open(fn, O_RDONLY);
-#endif
-		if (fd == -1) {
-			perror("open");
-			return 0;
-		}
-		fp = (knetFile*)calloc(1, sizeof(knetFile));
-		fp->type = KNF_TYPE_LOCAL;
-		fp->fd = fd;
-		fp->ctrl_fd = -1;
-	}
-	if (fp && fp->fd == -1) {
-		knet_close(fp);
-		return 0;
-	}
-	return fp;
-}
-
-knetFile *knet_dopen(int fd, const char *mode)
-{
-#ifdef KNETFILE_HOOKS
-       if (alt_dopen)
-               return alt_dopen(fd, mode);
-#endif
-
-	knetFile *fp = (knetFile*)calloc(1, sizeof(knetFile));
-	fp->type = KNF_TYPE_LOCAL;
-	fp->fd = fd;
-	return fp;
-}
-
-ssize_t knet_read(knetFile *fp, void *buf, size_t len)
-{
-#ifdef KNETFILE_HOOKS
-       if (alt_read)  
-               return alt_read(fp, buf, len);
-#endif  
-
-	off_t l = 0;
-	if (fp->fd == -1) return 0;
-	if (fp->type == KNF_TYPE_FTP) {
-		if (fp->is_ready == 0) {
-			if (!fp->no_reconnect) kftp_reconnect(fp);
-			kftp_connect_file(fp);
-		}
-	} else if (fp->type == KNF_TYPE_HTTP) {
-		if (fp->is_ready == 0)
-			khttp_connect_file(fp);
-	}
-	if (fp->type == KNF_TYPE_LOCAL) { // on Windows, the following block is necessary; not on UNIX
-		size_t rest = len;
-		ssize_t curr;
-		while (rest) {
-			do {
-				curr = read(fp->fd, (void*)((char*)buf + l), rest);
-			} while (curr < 0 && EINTR == errno);
-			if (curr < 0) return -1;
-			if (curr == 0) break;
-			l += curr; rest -= curr;
-		}
-	} else l = my_netread(fp->fd, buf, len);
-	fp->offset += l;
-	return l;
-}
-
-off_t knet_seek(knetFile *fp, off_t off, int whence)
-{
-#ifdef KNETFILE_HOOKS
-       if (alt_seek)
-               return alt_seek(fp, off, whence);
-#endif
-
-	if (whence == SEEK_SET && off == fp->offset) return 0;
-	if (fp->type == KNF_TYPE_LOCAL) {
-		/* Be aware that lseek() returns the offset after seeking, while fseek() returns zero on success. */
-		off_t offset = lseek(fp->fd, off, whence);
-		if (offset == -1) return -1;
-		fp->offset = offset;
-		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;
-		else return -1;
-		fp->is_ready = 0;
-		return fp->offset;
-	} else if (fp->type == KNF_TYPE_HTTP) {
-		if (whence == SEEK_END) { // FIXME: can we allow SEEK_END in future?
-			fprintf(stderr, "[knet_seek] SEEK_END is not supported for HTTP. Offset is unchanged.\n");
-			errno = ESPIPE;
-			return -1;
-		}
-		if (whence == SEEK_CUR) fp->offset += off;
-		else if (whence == SEEK_SET) fp->offset = off;
-		else return -1;
-		fp->is_ready = 0;
-		return fp->offset;
-	}
-	errno = EINVAL;
-	fprintf(stderr,"[knet_seek] %s\n", strerror(errno));
-	return -1;
-}
-
-int knet_close(knetFile *fp)
-{
-#ifdef KNETFILE_HOOKS
-       if (alt_close)
-               return alt_close(fp);
-#endif    
-
-	if (fp == 0) return 0;
-	if (fp->ctrl_fd != -1) netclose(fp->ctrl_fd); // FTP specific
-	if (fp->fd != -1) {
-		/* On Linux/Mac, netclose() is an alias of close(), but on
-		 * Windows, it is an alias of closesocket(). */
-		if (fp->type == KNF_TYPE_LOCAL) close(fp->fd);
-		else netclose(fp->fd);
-	}
-	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;
-}
-
-#ifdef KNETFILE_MAIN
-int main(void)
-{
-	char *buf;
-	knetFile *fp;
-	int type = 4, l;
-#ifdef _WIN32
-	knet_win32_init();
-#endif
-	buf = calloc(0x100000, 1);
-	if (type == 0) {
-		fp = knet_open("knetfile.c", "r");
-		knet_seek(fp, 1000, SEEK_SET);
-	} else if (type == 1) { // NCBI FTP, large file
-		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);
-		l = knet_read(fp, buf, 255);
-	} else if (type == 2) {
-		fp = knet_open("ftp://ftp.sanger.ac.uk/pub4/treefam/tmp/index.shtml", "r");
-		knet_seek(fp, 1000, SEEK_SET);
-	} else if (type == 3) {
-		fp = knet_open("http://www.sanger.ac.uk/Users/lh3/index.shtml", "r");
-		knet_seek(fp, 1000, SEEK_SET);
-	} else if (type == 4) {
-		fp = knet_open("http://www.sanger.ac.uk/Users/lh3/ex1.bam", "r");
-		knet_read(fp, buf, 10000);
-		knet_seek(fp, 20000, SEEK_SET);
-		knet_seek(fp, 10000, SEEK_SET);
-		l = knet_read(fp, buf+10000, 10000000) + 10000;
-	}
-	if (type != 4 && type != 1) {
-		knet_read(fp, buf, 255);
-		buf[255] = 0;
-		printf("%s\n", buf);
-	} else write(fileno(stdout), buf, l);
-	knet_close(fp);
-	free(buf);
-	return 0;
-}
-#endif