--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/pyPRADA_1.2/tools/samtools-0.1.16/knetfile.c	Thu Feb 20 00:44:58 2014 -0500
@@ -0,0 +1,632 @@
+/* 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 "knetfile.h"
+
+/* 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 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 (getaddrinfo(host, port, &hints, &res) != 0) __err_connect("getaddrinfo");
+	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?!)
+	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, 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 = 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
+	netwrite(ftp->ctrl_fd, cmd, strlen(cmd));
+	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 = 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 = calloc(l + 1, 1);
+	if (strchr(mode, 'c')) fp->no_reconnect = 1;
+	strncpy(fp->host, fn + 6, l);
+	fp->retr = calloc(strlen(p) + 8, 1);
+	sprintf(fp->retr, "RETR %s\r\n", p);
+    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);
+    kftp_send_cmd(fp, fp->size_cmd, 1);
+#ifndef _WIN32
+    if ( sscanf(fp->response,"%*d %lld", &file_size) != 1 )
+    {
+        fprintf(stderr,"[kftp_connect_file] %s\n", fp->response);
+        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 = 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 : "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 = 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");
+	netwrite(fp->fd, buf, l);
+	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
+		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) {
+		free(buf);
+		fprintf(stderr, "[khttp_connect_file] fail to open file (HTTP code: %d).\n", ret);
+		netclose(fp->fd);
+		fp->fd = -1;
+		return -1;
+	}
+	free(buf);
+	fp->is_ready = 1;
+	return 0;
+}
+
+/********************
+ * Generic routines *
+ ********************/
+
+knetFile *knet_open(const char *fn, const char *mode)
+{
+	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)
+{
+	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 = 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
+		off_t rest = len, curr;
+		while (rest) {
+			do {
+				curr = read(fp->fd, 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, int64_t off, int whence)
+{
+	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) {
+            // Be silent, it is OK for knet_seek to fail when the file is streamed
+            // fprintf(stderr,"[knet_seek] %s\n", strerror(errno));
+			return -1;
+		}
+		fp->offset = offset;
+		return 0;
+	}
+    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 0;
+	} 
+    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;
+		fp->is_ready = 0;
+		return 0;
+	}
+	errno = EINVAL;
+    fprintf(stderr,"[knet_seek] %s\n", strerror(errno));
+	return -1;
+}
+
+int knet_close(knetFile *fp)
+{
+	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