diff SNV/SNVMix2_source/SNVMix2-v0.12.1-rc1/samtools-0.1.6/bgzip.c @ 0:74f5ea818cea

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/SNV/SNVMix2_source/SNVMix2-v0.12.1-rc1/samtools-0.1.6/bgzip.c	Wed Oct 12 19:50:38 2011 -0400
@@ -0,0 +1,179 @@
+/* The MIT License
+
+   Copyright (c) 2008 Broad Institute / Massachusetts Institute of Technology
+
+   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.
+*/
+
+#include <stdlib.h>
+#include <string.h>
+#include <stdio.h>
+#include <fcntl.h>
+#include <unistd.h>
+#include <errno.h>
+#include "bgzf.h"
+
+static const int WINDOW_SIZE = 64 * 1024;
+
+static int bgzip_main_usage()
+{
+	printf("\n");
+	printf("Usage:   bgzip [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 virtual file pointer INT\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, 0644)) < 0 && errno == EEXIST) {
+			printf("bgzip: %s already exists; do you wish to overwrite (y or n)? ", fn);
+			scanf("%c", &c);
+			if (c != 'Y' && c != 'y') {
+				printf("bgzip: not overwritten\n");
+				exit(1);
+			}
+		}
+	}
+	if (fd < 0) {
+		if ((fd = open(fn, O_WRONLY | O_CREAT | O_TRUNC, 0644)) < 0) {
+			fprintf(stderr, "bgzip: %s: Fail to write\n", fn);
+			exit(1);
+		}
+	}
+	return fd;
+}
+
+static
+void
+fail(BGZF* fp)
+{
+    printf("Error: %s\n", fp->error);
+    exit(1);
+}
+
+int main(int argc, char **argv)
+{
+	int c, compress, pstdout, is_forced;
+	BGZF *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 bgzip_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, ".gz");
+				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 bgzip_main_usage();
+		rz = bgzf_fdopen(f_dst, "w");
+		buffer = malloc(WINDOW_SIZE);
+		while((c = read(f_src, buffer, WINDOW_SIZE)) > 0) {
+                  if (bgzf_write(rz, buffer, c) < 0) {
+                    fail(rz);
+                  }
+                }
+                // f_dst will be closed here
+		if (bgzf_close(rz) < 0) {
+                  fail(rz);
+                }
+		if (argc > optind) unlink(argv[optind]);
+		free(buffer);
+		close(f_src);
+		return 0;
+	} else {
+		if(argc <= optind) return bgzip_main_usage();
+                int f_dst;
+                if (argc > optind && !pstdout) {
+                  char *name;
+                  if (strstr(argv[optind], ".gz") - argv[optind] != strlen(argv[optind]) - 3) {
+                    printf("bgzip: %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 = bgzf_open(argv[optind], "r");
+                if (rz == NULL) {
+                  printf("Could not open file: %s\n", argv[optind]);
+                  return 1;
+                }
+                buffer = malloc(WINDOW_SIZE);
+                if (bgzf_seek(rz, start, SEEK_SET) < 0) {
+                  fail(rz);
+                }
+                while(1){
+                  if(end < 0) c = bgzf_read(rz, buffer, WINDOW_SIZE);
+                  else c = bgzf_read(rz, buffer, (end - start > WINDOW_SIZE)? WINDOW_SIZE:(end - start));
+                  if(c == 0) break;
+                  if (c < 0) fail(rz);
+                  start += c;
+                  write(f_dst, buffer, c);
+                  if(end >= 0 && start >= end) break;
+                }
+                free(buffer);
+		if (bgzf_close(rz) < 0) {
+                  fail(rz);
+                }
+                if (!pstdout) unlink(argv[optind]);
+		return 0;
+	}
+}
+