ngs_server 0.4 → 0.5

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
data/ext/tabix/bgzf.h ADDED
@@ -0,0 +1,157 @@
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
+ #ifndef __BGZF_H
25
+ #define __BGZF_H
26
+
27
+ #include <stdint.h>
28
+ #include <stdio.h>
29
+ #include <zlib.h>
30
+ #ifdef _USE_KNETFILE
31
+ #include "knetfile.h"
32
+ #endif
33
+
34
+ //typedef int8_t bool;
35
+
36
+ typedef struct {
37
+ int file_descriptor;
38
+ char open_mode; // 'r' or 'w'
39
+ int16_t owned_file, compress_level;
40
+ #ifdef _USE_KNETFILE
41
+ union {
42
+ knetFile *fpr;
43
+ FILE *fpw;
44
+ } x;
45
+ #else
46
+ FILE* file;
47
+ #endif
48
+ int uncompressed_block_size;
49
+ int compressed_block_size;
50
+ void* uncompressed_block;
51
+ void* compressed_block;
52
+ int64_t block_address;
53
+ int block_length;
54
+ int block_offset;
55
+ int cache_size;
56
+ const char* error;
57
+ void *cache; // a pointer to a hash table
58
+ } BGZF;
59
+
60
+ #ifdef __cplusplus
61
+ extern "C" {
62
+ #endif
63
+
64
+ /*
65
+ * Open an existing file descriptor for reading or writing.
66
+ * Mode must be either "r" or "w".
67
+ * A subsequent bgzf_close will not close the file descriptor.
68
+ * Returns null on error.
69
+ */
70
+ BGZF* bgzf_fdopen(int fd, const char* __restrict mode);
71
+
72
+ /*
73
+ * Open the specified file for reading or writing.
74
+ * Mode must be either "r" or "w".
75
+ * Returns null on error.
76
+ */
77
+ BGZF* bgzf_open(const char* path, const char* __restrict mode);
78
+
79
+ /*
80
+ * Close the BGZ file and free all associated resources.
81
+ * Does not close the underlying file descriptor if created with bgzf_fdopen.
82
+ * Returns zero on success, -1 on error.
83
+ */
84
+ int bgzf_close(BGZF* fp);
85
+
86
+ /*
87
+ * Read up to length bytes from the file storing into data.
88
+ * Returns the number of bytes actually read.
89
+ * Returns zero on end of file.
90
+ * Returns -1 on error.
91
+ */
92
+ int bgzf_read(BGZF* fp, void* data, int length);
93
+
94
+ /*
95
+ * Write length bytes from data to the file.
96
+ * Returns the number of bytes written.
97
+ * Returns -1 on error.
98
+ */
99
+ int bgzf_write(BGZF* fp, const void* data, int length);
100
+
101
+ /*
102
+ * Return a virtual file pointer to the current location in the file.
103
+ * No interpetation of the value should be made, other than a subsequent
104
+ * call to bgzf_seek can be used to position the file at the same point.
105
+ * Return value is non-negative on success.
106
+ * Returns -1 on error.
107
+ */
108
+ #define bgzf_tell(fp) ((fp->block_address << 16) | (fp->block_offset & 0xFFFF))
109
+
110
+ /*
111
+ * Set the file to read from the location specified by pos, which must
112
+ * be a value previously returned by bgzf_tell for this file (but not
113
+ * necessarily one returned by this file handle).
114
+ * The where argument must be SEEK_SET.
115
+ * Seeking on a file opened for write is not supported.
116
+ * Returns zero on success, -1 on error.
117
+ */
118
+ int64_t bgzf_seek(BGZF* fp, int64_t pos, int where);
119
+
120
+ /*
121
+ * Set the cache size. Zero to disable. By default, caching is
122
+ * disabled. The recommended cache size for frequent random access is
123
+ * about 8M bytes.
124
+ */
125
+ void bgzf_set_cache_size(BGZF *fp, int cache_size);
126
+
127
+ int bgzf_check_EOF(BGZF *fp);
128
+ int bgzf_read_block(BGZF* fp);
129
+ int bgzf_flush(BGZF* fp);
130
+ int bgzf_flush_try(BGZF *fp, int size);
131
+ int bgzf_check_bgzf(const char *fn);
132
+
133
+ #ifdef __cplusplus
134
+ }
135
+ #endif
136
+
137
+ static inline int bgzf_getc(BGZF *fp)
138
+ {
139
+ int c;
140
+ if (fp->block_offset >= fp->block_length) {
141
+ if (bgzf_read_block(fp) != 0) return -2; /* error */
142
+ if (fp->block_length == 0) return -1; /* end-of-file */
143
+ }
144
+ c = ((unsigned char*)fp->uncompressed_block)[fp->block_offset++];
145
+ if (fp->block_offset == fp->block_length) {
146
+ #ifdef _USE_KNETFILE
147
+ fp->block_address = knet_tell(fp->x.fpr);
148
+ #else
149
+ fp->block_address = ftello(fp->file);
150
+ #endif
151
+ fp->block_offset = 0;
152
+ fp->block_length = 0;
153
+ }
154
+ return c;
155
+ }
156
+
157
+ #endif
data/ext/tabix/bgzip.c ADDED
@@ -0,0 +1,206 @@
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
+ }
Binary file
Binary file
@@ -0,0 +1 @@
1
+ puts "nothing to do"