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comparison pyPRADA_1.2/tools/bwa-0.5.7-mh/utils.c @ 0:acc2ca1a3ba4

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author siyuan
date Thu, 20 Feb 2014 00:44:58 -0500
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1 /* The MIT License
2
3 Copyright (c) 2008 Genome Research Ltd (GRL).
4
5 Permission is hereby granted, free of charge, to any person obtaining
6 a copy of this software and associated documentation files (the
7 "Software"), to deal in the Software without restriction, including
8 without limitation the rights to use, copy, modify, merge, publish,
9 distribute, sublicense, and/or sell copies of the Software, and to
10 permit persons to whom the Software is furnished to do so, subject to
11 the following conditions:
12
13 The above copyright notice and this permission notice shall be
14 included in all copies or substantial portions of the Software.
15
16 THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
17 EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
18 MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
19 NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS
20 BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN
21 ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN
22 CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
23 SOFTWARE.
24 */
25
26 /* Contact: Heng Li <lh3@sanger.ac.uk> */
27
28 #include <stdio.h>
29 #include <stdarg.h>
30 #include <stdlib.h>
31 #include <string.h>
32 #include <zlib.h>
33 #include "utils.h"
34
35 FILE *err_xopen_core(const char *func, const char *fn, const char *mode)
36 {
37 FILE *fp = 0;
38 if (strcmp(fn, "-") == 0)
39 return (strstr(mode, "r"))? stdin : stdout;
40 if ((fp = fopen(fn, mode)) == 0) {
41 fprintf(stderr, "[%s] fail to open file '%s'. Abort!\n", func, fn);
42 abort();
43 }
44 return fp;
45 }
46 gzFile err_xzopen_core(const char *func, const char *fn, const char *mode)
47 {
48 gzFile fp;
49 if (strcmp(fn, "-") == 0)
50 return gzdopen(fileno((strstr(mode, "r"))? stdin : stdout), mode);
51 if ((fp = gzopen(fn, mode)) == 0) {
52 fprintf(stderr, "[%s] fail to open file '%s'. Abort!\n", func, fn);
53 abort();
54 }
55 return fp;
56 }
57 void err_fatal(const char *header, const char *fmt, ...)
58 {
59 va_list args;
60 va_start(args, fmt);
61 fprintf(stderr, "[%s] ", header);
62 vfprintf(stderr, fmt, args);
63 fprintf(stderr, " Abort!\n");
64 va_end(args);
65 abort();
66 }
67
68 void err_fatal_simple_core(const char *func, const char *msg)
69 {
70 fprintf(stderr, "[%s] %s Abort!\n", func, msg);
71 abort();
72 }