annotate ezBAMQC/src/htslib/cram/misc.h @ 20:9de3bbec2479 draft default tip

Uploaded
author youngkim
date Thu, 31 Mar 2016 10:10:37 -0400
parents dfa3745e5fd8
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
dfa3745e5fd8 Uploaded
youngkim
parents:
diff changeset
1 /*
dfa3745e5fd8 Uploaded
youngkim
parents:
diff changeset
2 Copyright (c) 1994-1997, 2001-2002 MEDICAL RESEARCH COUNCIL
dfa3745e5fd8 Uploaded
youngkim
parents:
diff changeset
3 All rights reserved
dfa3745e5fd8 Uploaded
youngkim
parents:
diff changeset
4
dfa3745e5fd8 Uploaded
youngkim
parents:
diff changeset
5 Redistribution and use in source and binary forms, with or without
dfa3745e5fd8 Uploaded
youngkim
parents:
diff changeset
6 modification, are permitted provided that the following conditions are met:
dfa3745e5fd8 Uploaded
youngkim
parents:
diff changeset
7
dfa3745e5fd8 Uploaded
youngkim
parents:
diff changeset
8 1 Redistributions of source code must retain the above copyright notice,
dfa3745e5fd8 Uploaded
youngkim
parents:
diff changeset
9 this list of conditions and the following disclaimer.
dfa3745e5fd8 Uploaded
youngkim
parents:
diff changeset
10
dfa3745e5fd8 Uploaded
youngkim
parents:
diff changeset
11 2 Redistributions in binary form must reproduce the above copyright notice,
dfa3745e5fd8 Uploaded
youngkim
parents:
diff changeset
12 this list of conditions and the following disclaimer in the documentation
dfa3745e5fd8 Uploaded
youngkim
parents:
diff changeset
13 and/or other materials provided with the distribution.
dfa3745e5fd8 Uploaded
youngkim
parents:
diff changeset
14
dfa3745e5fd8 Uploaded
youngkim
parents:
diff changeset
15 3 Neither the name of the MEDICAL RESEARCH COUNCIL, THE LABORATORY OF
dfa3745e5fd8 Uploaded
youngkim
parents:
diff changeset
16 MOLECULAR BIOLOGY nor the names of its contributors may be used to endorse or
dfa3745e5fd8 Uploaded
youngkim
parents:
diff changeset
17 promote products derived from this software without specific prior written
dfa3745e5fd8 Uploaded
youngkim
parents:
diff changeset
18 permission.
dfa3745e5fd8 Uploaded
youngkim
parents:
diff changeset
19
dfa3745e5fd8 Uploaded
youngkim
parents:
diff changeset
20 THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND
dfa3745e5fd8 Uploaded
youngkim
parents:
diff changeset
21 ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
dfa3745e5fd8 Uploaded
youngkim
parents:
diff changeset
22 WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
dfa3745e5fd8 Uploaded
youngkim
parents:
diff changeset
23 DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR
dfa3745e5fd8 Uploaded
youngkim
parents:
diff changeset
24 ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES
dfa3745e5fd8 Uploaded
youngkim
parents:
diff changeset
25 (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
dfa3745e5fd8 Uploaded
youngkim
parents:
diff changeset
26 LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON
dfa3745e5fd8 Uploaded
youngkim
parents:
diff changeset
27 ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
dfa3745e5fd8 Uploaded
youngkim
parents:
diff changeset
28 (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
dfa3745e5fd8 Uploaded
youngkim
parents:
diff changeset
29 SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
dfa3745e5fd8 Uploaded
youngkim
parents:
diff changeset
30 */
dfa3745e5fd8 Uploaded
youngkim
parents:
diff changeset
31
dfa3745e5fd8 Uploaded
youngkim
parents:
diff changeset
32 /*
dfa3745e5fd8 Uploaded
youngkim
parents:
diff changeset
33 Copyright (c) 2003-2013 Genome Research Ltd.
dfa3745e5fd8 Uploaded
youngkim
parents:
diff changeset
34
dfa3745e5fd8 Uploaded
youngkim
parents:
diff changeset
35 Author: James Bonfield <jkb@sanger.ac.uk>
dfa3745e5fd8 Uploaded
youngkim
parents:
diff changeset
36
dfa3745e5fd8 Uploaded
youngkim
parents:
diff changeset
37 Redistribution and use in source and binary forms, with or without
dfa3745e5fd8 Uploaded
youngkim
parents:
diff changeset
38 modification, are permitted provided that the following conditions are met:
dfa3745e5fd8 Uploaded
youngkim
parents:
diff changeset
39
dfa3745e5fd8 Uploaded
youngkim
parents:
diff changeset
40 1. Redistributions of source code must retain the above copyright notice,
dfa3745e5fd8 Uploaded
youngkim
parents:
diff changeset
41 this list of conditions and the following disclaimer.
dfa3745e5fd8 Uploaded
youngkim
parents:
diff changeset
42
dfa3745e5fd8 Uploaded
youngkim
parents:
diff changeset
43 2. Redistributions in binary form must reproduce the above copyright notice,
dfa3745e5fd8 Uploaded
youngkim
parents:
diff changeset
44 this list of conditions and the following disclaimer in the documentation
dfa3745e5fd8 Uploaded
youngkim
parents:
diff changeset
45 and/or other materials provided with the distribution.
dfa3745e5fd8 Uploaded
youngkim
parents:
diff changeset
46
dfa3745e5fd8 Uploaded
youngkim
parents:
diff changeset
47 3. Neither the names Genome Research Ltd and Wellcome Trust Sanger
dfa3745e5fd8 Uploaded
youngkim
parents:
diff changeset
48 Institute nor the names of its contributors may be used to endorse or promote
dfa3745e5fd8 Uploaded
youngkim
parents:
diff changeset
49 products derived from this software without specific prior written permission.
dfa3745e5fd8 Uploaded
youngkim
parents:
diff changeset
50
dfa3745e5fd8 Uploaded
youngkim
parents:
diff changeset
51 THIS SOFTWARE IS PROVIDED BY GENOME RESEARCH LTD AND CONTRIBUTORS "AS IS" AND
dfa3745e5fd8 Uploaded
youngkim
parents:
diff changeset
52 ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
dfa3745e5fd8 Uploaded
youngkim
parents:
diff changeset
53 WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
dfa3745e5fd8 Uploaded
youngkim
parents:
diff changeset
54 DISCLAIMED. IN NO EVENT SHALL GENOME RESEARCH LTD OR CONTRIBUTORS BE LIABLE
dfa3745e5fd8 Uploaded
youngkim
parents:
diff changeset
55 FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
dfa3745e5fd8 Uploaded
youngkim
parents:
diff changeset
56 DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
dfa3745e5fd8 Uploaded
youngkim
parents:
diff changeset
57 SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
dfa3745e5fd8 Uploaded
youngkim
parents:
diff changeset
58 CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
dfa3745e5fd8 Uploaded
youngkim
parents:
diff changeset
59 OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
dfa3745e5fd8 Uploaded
youngkim
parents:
diff changeset
60 OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
dfa3745e5fd8 Uploaded
youngkim
parents:
diff changeset
61 */
dfa3745e5fd8 Uploaded
youngkim
parents:
diff changeset
62
dfa3745e5fd8 Uploaded
youngkim
parents:
diff changeset
63 #ifndef _misc_h
dfa3745e5fd8 Uploaded
youngkim
parents:
diff changeset
64 #define _misc_h
dfa3745e5fd8 Uploaded
youngkim
parents:
diff changeset
65
dfa3745e5fd8 Uploaded
youngkim
parents:
diff changeset
66 #include "cram/os.h"
dfa3745e5fd8 Uploaded
youngkim
parents:
diff changeset
67
dfa3745e5fd8 Uploaded
youngkim
parents:
diff changeset
68 #include <stdio.h>
dfa3745e5fd8 Uploaded
youngkim
parents:
diff changeset
69 #include <stdarg.h> /* varargs needed for v*printf() prototypes */
dfa3745e5fd8 Uploaded
youngkim
parents:
diff changeset
70 #include <sys/types.h>
dfa3745e5fd8 Uploaded
youngkim
parents:
diff changeset
71
dfa3745e5fd8 Uploaded
youngkim
parents:
diff changeset
72 #ifdef __cplusplus
dfa3745e5fd8 Uploaded
youngkim
parents:
diff changeset
73 extern "C" {
dfa3745e5fd8 Uploaded
youngkim
parents:
diff changeset
74 #endif
dfa3745e5fd8 Uploaded
youngkim
parents:
diff changeset
75
dfa3745e5fd8 Uploaded
youngkim
parents:
diff changeset
76 /*
dfa3745e5fd8 Uploaded
youngkim
parents:
diff changeset
77 * This informs gcc that crash() doesn't return, so it doesn't need to
dfa3745e5fd8 Uploaded
youngkim
parents:
diff changeset
78 * concern itself that code paths going via crash could mean some variables
dfa3745e5fd8 Uploaded
youngkim
parents:
diff changeset
79 * being undefined and then issuing uninitialised variable warnings.
dfa3745e5fd8 Uploaded
youngkim
parents:
diff changeset
80 * This particularly affected convert.
dfa3745e5fd8 Uploaded
youngkim
parents:
diff changeset
81 */
dfa3745e5fd8 Uploaded
youngkim
parents:
diff changeset
82 #ifdef __GNUC__
dfa3745e5fd8 Uploaded
youngkim
parents:
diff changeset
83 # define __NORETURN__ __attribute__ ((__noreturn__))
dfa3745e5fd8 Uploaded
youngkim
parents:
diff changeset
84 #else
dfa3745e5fd8 Uploaded
youngkim
parents:
diff changeset
85 # define __NORETURN__
dfa3745e5fd8 Uploaded
youngkim
parents:
diff changeset
86 #endif
dfa3745e5fd8 Uploaded
youngkim
parents:
diff changeset
87
dfa3745e5fd8 Uploaded
youngkim
parents:
diff changeset
88 /*
dfa3745e5fd8 Uploaded
youngkim
parents:
diff changeset
89 * Used for printf style argument checking. We can request a function such
dfa3745e5fd8 Uploaded
youngkim
parents:
diff changeset
90 * as vTcl_SetResult does argument checking, avoiding bugs with using
dfa3745e5fd8 Uploaded
youngkim
parents:
diff changeset
91 * %d and passing in a 64-bit record.
dfa3745e5fd8 Uploaded
youngkim
parents:
diff changeset
92 */
dfa3745e5fd8 Uploaded
youngkim
parents:
diff changeset
93 #ifdef __GNUC__
dfa3745e5fd8 Uploaded
youngkim
parents:
diff changeset
94 # define __PRINTF_FORMAT__(a,b) __attribute__ ((format (printf, a, b)))
dfa3745e5fd8 Uploaded
youngkim
parents:
diff changeset
95 #else
dfa3745e5fd8 Uploaded
youngkim
parents:
diff changeset
96 # define __PRINTF_FORMAT__(a,b)
dfa3745e5fd8 Uploaded
youngkim
parents:
diff changeset
97 #endif
dfa3745e5fd8 Uploaded
youngkim
parents:
diff changeset
98
dfa3745e5fd8 Uploaded
youngkim
parents:
diff changeset
99 extern int is_directory(char * fn);
dfa3745e5fd8 Uploaded
youngkim
parents:
diff changeset
100 extern int is_file(char * fn);
dfa3745e5fd8 Uploaded
youngkim
parents:
diff changeset
101 extern int file_size(char * fn);
dfa3745e5fd8 Uploaded
youngkim
parents:
diff changeset
102
dfa3745e5fd8 Uploaded
youngkim
parents:
diff changeset
103 #define MIN(A,B) ( ( (A) < (B) ) ? (A) : (B) )
dfa3745e5fd8 Uploaded
youngkim
parents:
diff changeset
104 #define MAX(A,B) ( ( (A) > (B) ) ? (A) : (B) )
dfa3745e5fd8 Uploaded
youngkim
parents:
diff changeset
105
dfa3745e5fd8 Uploaded
youngkim
parents:
diff changeset
106 #ifdef __cplusplus
dfa3745e5fd8 Uploaded
youngkim
parents:
diff changeset
107 }
dfa3745e5fd8 Uploaded
youngkim
parents:
diff changeset
108 #endif
dfa3745e5fd8 Uploaded
youngkim
parents:
diff changeset
109
dfa3745e5fd8 Uploaded
youngkim
parents:
diff changeset
110 #endif /*_misc_h*/