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comparison pyPRADA_1.2/tools/samtools-0.1.16/bgzip.c @ 0:acc2ca1a3ba4

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author siyuan
date Thu, 20 Feb 2014 00:44:58 -0500
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-1:000000000000 0:acc2ca1a3ba4
1 /* The MIT License
2
3 Copyright (c) 2008 Broad Institute / Massachusetts Institute of Technology
4
5 Permission is hereby granted, free of charge, to any person obtaining a copy
6 of this software and associated documentation files (the "Software"), to deal
7 in the Software without restriction, including without limitation the rights
8 to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
9 copies of the Software, and to permit persons to whom the Software is
10 furnished to do so, subject to the following conditions:
11
12 The above copyright notice and this permission notice shall be included in
13 all copies or substantial portions of the Software.
14
15 THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
16 IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
17 FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
18 AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
19 LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
20 OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
21 THE SOFTWARE.
22 */
23
24 #include <stdlib.h>
25 #include <string.h>
26 #include <stdio.h>
27 #include <fcntl.h>
28 #include <unistd.h>
29 #include <errno.h>
30 #include <sys/select.h>
31 #include <sys/stat.h>
32 #include "bgzf.h"
33
34 static const int WINDOW_SIZE = 64 * 1024;
35
36 static int bgzip_main_usage()
37 {
38 fprintf(stderr, "\n");
39 fprintf(stderr, "Usage: bgzip [options] [file] ...\n\n");
40 fprintf(stderr, "Options: -c write on standard output, keep original files unchanged\n");
41 fprintf(stderr, " -d decompress\n");
42 fprintf(stderr, " -f overwrite files without asking\n");
43 fprintf(stderr, " -b INT decompress at virtual file pointer INT\n");
44 fprintf(stderr, " -s INT decompress INT bytes in the uncompressed file\n");
45 fprintf(stderr, " -h give this help\n");
46 fprintf(stderr, "\n");
47 return 1;
48 }
49
50 static int write_open(const char *fn, int is_forced)
51 {
52 int fd = -1;
53 char c;
54 if (!is_forced) {
55 if ((fd = open(fn, O_WRONLY | O_CREAT | O_TRUNC | O_EXCL, 0666)) < 0 && errno == EEXIST) {
56 fprintf(stderr, "[bgzip] %s already exists; do you wish to overwrite (y or n)? ", fn);
57 scanf("%c", &c);
58 if (c != 'Y' && c != 'y') {
59 fprintf(stderr, "[bgzip] not overwritten\n");
60 exit(1);
61 }
62 }
63 }
64 if (fd < 0) {
65 if ((fd = open(fn, O_WRONLY | O_CREAT | O_TRUNC, 0666)) < 0) {
66 fprintf(stderr, "[bgzip] %s: Fail to write\n", fn);
67 exit(1);
68 }
69 }
70 return fd;
71 }
72
73 static void fail(BGZF* fp)
74 {
75 fprintf(stderr, "Error: %s\n", fp->error);
76 exit(1);
77 }
78
79 int main(int argc, char **argv)
80 {
81 int c, compress, pstdout, is_forced;
82 BGZF *fp;
83 void *buffer;
84 long start, end, size;
85
86 compress = 1; pstdout = 0; start = 0; size = -1; end = -1; is_forced = 0;
87 while((c = getopt(argc, argv, "cdhfb:s:")) >= 0){
88 switch(c){
89 case 'h': return bgzip_main_usage();
90 case 'd': compress = 0; break;
91 case 'c': pstdout = 1; break;
92 case 'b': start = atol(optarg); break;
93 case 's': size = atol(optarg); break;
94 case 'f': is_forced = 1; break;
95 }
96 }
97 if (size >= 0) end = start + size;
98 if (end >= 0 && end < start) {
99 fprintf(stderr, "[bgzip] Illegal region: [%ld, %ld]\n", start, end);
100 return 1;
101 }
102 if (compress == 1) {
103 struct stat sbuf;
104 int f_src = fileno(stdin);
105 int f_dst = fileno(stdout);
106
107 if ( argc>optind )
108 {
109 if ( stat(argv[optind],&sbuf)<0 )
110 {
111 fprintf(stderr, "[bgzip] %s: %s\n", strerror(errno), argv[optind]);
112 return 1;
113 }
114
115 if ((f_src = open(argv[optind], O_RDONLY)) < 0) {
116 fprintf(stderr, "[bgzip] %s: %s\n", strerror(errno), argv[optind]);
117 return 1;
118 }
119
120 if (pstdout)
121 f_dst = fileno(stdout);
122 else
123 {
124 char *name = malloc(strlen(argv[optind]) + 5);
125 strcpy(name, argv[optind]);
126 strcat(name, ".gz");
127 f_dst = write_open(name, is_forced);
128 if (f_dst < 0) return 1;
129 free(name);
130 }
131 }
132 else if (!pstdout && isatty(fileno((FILE *)stdout)) )
133 return bgzip_main_usage();
134
135 fp = bgzf_fdopen(f_dst, "w");
136 buffer = malloc(WINDOW_SIZE);
137 while ((c = read(f_src, buffer, WINDOW_SIZE)) > 0)
138 if (bgzf_write(fp, buffer, c) < 0) fail(fp);
139 // f_dst will be closed here
140 if (bgzf_close(fp) < 0) fail(fp);
141 if (argc > optind && !pstdout) unlink(argv[optind]);
142 free(buffer);
143 close(f_src);
144 return 0;
145 } else {
146 struct stat sbuf;
147 int f_dst;
148
149 if ( argc>optind )
150 {
151 if ( stat(argv[optind],&sbuf)<0 )
152 {
153 fprintf(stderr, "[bgzip] %s: %s\n", strerror(errno), argv[optind]);
154 return 1;
155 }
156 char *name;
157 int len = strlen(argv[optind]);
158 if ( strcmp(argv[optind]+len-3,".gz") )
159 {
160 fprintf(stderr, "[bgzip] %s: unknown suffix -- ignored\n", argv[optind]);
161 return 1;
162 }
163 fp = bgzf_open(argv[optind], "r");
164 if (fp == NULL) {
165 fprintf(stderr, "[bgzip] Could not open file: %s\n", argv[optind]);
166 return 1;
167 }
168
169 if (pstdout) {
170 f_dst = fileno(stdout);
171 }
172 else {
173 name = strdup(argv[optind]);
174 name[strlen(name) - 3] = '\0';
175 f_dst = write_open(name, is_forced);
176 free(name);
177 }
178 }
179 else if (!pstdout && isatty(fileno((FILE *)stdin)) )
180 return bgzip_main_usage();
181 else
182 {
183 f_dst = fileno(stdout);
184 fp = bgzf_fdopen(fileno(stdin), "r");
185 if (fp == NULL) {
186 fprintf(stderr, "[bgzip] Could not read from stdin: %s\n", strerror(errno));
187 return 1;
188 }
189 }
190 buffer = malloc(WINDOW_SIZE);
191 if (bgzf_seek(fp, start, SEEK_SET) < 0) fail(fp);
192 while (1) {
193 if (end < 0) c = bgzf_read(fp, buffer, WINDOW_SIZE);
194 else c = bgzf_read(fp, buffer, (end - start > WINDOW_SIZE)? WINDOW_SIZE:(end - start));
195 if (c == 0) break;
196 if (c < 0) fail(fp);
197 start += c;
198 write(f_dst, buffer, c);
199 if (end >= 0 && start >= end) break;
200 }
201 free(buffer);
202 if (bgzf_close(fp) < 0) fail(fp);
203 if (!pstdout) unlink(argv[optind]);
204 return 0;
205 }
206 }