--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/pyPRADA_1.2/tools/samtools-0.1.16/razip.c	Thu Feb 20 00:44:58 2014 -0500
@@ -0,0 +1,141 @@
+#include <stdio.h>
+#include <fcntl.h>
+#include <unistd.h>
+#include <errno.h>
+#include <stdlib.h>
+#include <string.h>
+#include "razf.h"
+
+#define WINDOW_SIZE 4096
+
+static int razf_main_usage()
+{
+	printf("\n");
+	printf("Usage:   razip [options] [file] ...\n\n");
+	printf("Options: -c      write on standard output, keep original files unchanged\n");
+	printf("         -d      decompress\n");
+	printf("         -l      list compressed file contents\n");
+	printf("         -b INT  decompress at INT position in the uncompressed file\n");
+	printf("         -s INT  decompress INT bytes in the uncompressed file\n");
+	printf("         -h      give this help\n");
+	printf("\n");
+	return 0;
+}
+
+static int write_open(const char *fn, int is_forced)
+{
+	int fd = -1;
+	char c;
+	if (!is_forced) {
+		if ((fd = open(fn, O_WRONLY | O_CREAT | O_TRUNC | O_EXCL, 0666)) < 0 && errno == EEXIST) {
+			printf("razip: %s already exists; do you wish to overwrite (y or n)? ", fn);
+			scanf("%c", &c);
+			if (c != 'Y' && c != 'y') {
+				printf("razip: not overwritten\n");
+				exit(1);
+			}
+		}
+	}
+	if (fd < 0) {
+		if ((fd = open(fn, O_WRONLY | O_CREAT | O_TRUNC, 0666)) < 0) {
+			fprintf(stderr, "razip: %s: Fail to write\n", fn);
+			exit(1);
+		}
+	}
+	return fd;
+}
+
+int main(int argc, char **argv)
+{
+	int c, compress, pstdout, is_forced;
+	RAZF *rz;
+	void *buffer;
+	long start, end, size;
+
+	compress = 1; pstdout = 0; start = 0; size = -1; end = -1; is_forced = 0;
+	while((c  = getopt(argc, argv, "cdlhfb:s:")) >= 0){
+		switch(c){
+		case 'h': return razf_main_usage();
+		case 'd': compress = 0; break;
+		case 'c': pstdout = 1; break;
+		case 'l': compress = 2; break;
+		case 'b': start = atol(optarg); break;
+		case 's': size = atol(optarg); break;
+		case 'f': is_forced = 1; break;
+		}
+	}
+	if (size >= 0) end = start + size;
+	if(end >= 0 && end < start){
+		fprintf(stderr, " -- Illegal region: [%ld, %ld] --\n", start, end);
+		return 1;
+	}
+	if(compress == 1){
+		int f_src, f_dst = -1;
+		if(argc > optind){
+			if((f_src = open(argv[optind], O_RDONLY)) < 0){
+				fprintf(stderr, " -- Cannot open file: %s --\n", argv[optind]);
+				return 1;
+			}
+			if(pstdout){
+				f_dst = fileno(stdout);
+			} else {
+				char *name = malloc(sizeof(strlen(argv[optind]) + 5));
+				strcpy(name, argv[optind]);
+				strcat(name, ".rz");
+				f_dst = write_open(name, is_forced);
+				if (f_dst < 0) return 1;
+				free(name);
+			}
+		} else if(pstdout){ 
+			f_src = fileno(stdin);
+			f_dst = fileno(stdout);
+		} else return razf_main_usage();
+		rz = razf_dopen(f_dst, "w");
+		buffer = malloc(WINDOW_SIZE);
+		while((c = read(f_src, buffer, WINDOW_SIZE)) > 0) razf_write(rz, buffer, c);
+		razf_close(rz); // f_dst will be closed here
+		if (argc > optind && !pstdout) unlink(argv[optind]);
+		free(buffer);
+		close(f_src);
+		return 0;
+	} else {
+		if(argc <= optind) return razf_main_usage();
+		if(compress == 2){
+			rz = razf_open(argv[optind], "r");
+			if(rz->file_type == FILE_TYPE_RZ) {
+							printf("%20s%20s%7s %s\n", "compressed", "uncompressed", "ratio", "name");
+				printf("%20lld%20lld%6.1f%% %s\n", (long long)rz->end, (long long)rz->src_end, rz->end * 100.0f / rz->src_end,
+					   argv[optind]);
+			} else fprintf(stdout, "%s is not a regular rz file\n", argv[optind]);
+		} else {
+			int f_dst;
+			if (argc > optind && !pstdout) {
+				char *name;
+				if (strstr(argv[optind], ".rz") - argv[optind] != strlen(argv[optind]) - 3) {
+					printf("razip: %s: unknown suffix -- ignored\n", argv[optind]);
+					return 1;
+				}
+				name = strdup(argv[optind]);
+				name[strlen(name) - 3] = '\0';
+				f_dst = write_open(name, is_forced);
+				free(name);
+			} else f_dst = fileno(stdout);
+			rz = razf_open(argv[optind], "r");
+			buffer = malloc(WINDOW_SIZE);
+			razf_seek(rz, start, SEEK_SET);
+			while(1){
+				if(end < 0) c = razf_read(rz, buffer, WINDOW_SIZE);
+				else c = razf_read(rz, buffer, (end - start > WINDOW_SIZE)? WINDOW_SIZE:(end - start));
+				if(c <= 0) break;
+				start += c;
+				write(f_dst, buffer, c);
+				if(end >= 0 && start >= end) break;
+			}
+			free(buffer);
+			if (!pstdout) unlink(argv[optind]);
+		}
+		razf_close(rz);
+		return 0;
+	}
+}
+