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comparison mrfast-2.1.0.5/Common.c @ 1:d4054b05b015 default tip

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Version update to 2.1.0.5
author calkan
date Fri, 09 Mar 2012 07:35:51 -0500
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0:7b3dc85dc7fd 1:d4054b05b015
1 /*
2 * Copyright (c) <2008 - 2012>, University of Washington, Simon Fraser University
3 * All rights reserved.
4 *
5 * Redistribution and use in source and binary forms, with or without modification,
6 * are permitted provided that the following conditions are met:
7 *
8 * Redistributions of source code must retain the above copyright notice, this list
9 * of conditions and the following disclaimer.
10 * - Redistributions in binary form must reproduce the above copyright notice, this
11 * list of conditions and the following disclaimer in the documentation and/or other
12 * materials provided with the distribution.
13 * - Neither the names of the University of Washington, Simon Fraser University,
14 * nor the names of its contributors may be
15 * used to endorse or promote products derived from this software without specific
16 * prior written permission.
17 *
18 * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
19 * "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
20 * LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR
21 * A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR
22 * CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
23 * EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
24 * PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR
25 * PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF
26 * LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING
27 * NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
28 * SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
29 */
30
31 /*
32 Authors:
33 Farhad Hormozdiari
34 Faraz Hach
35 Can Alkan
36 Emails:
37 farhadh AT uw DOT edu
38 fhach AT cs DOT sfu DOT ca
39 calkan AT uw DOT edu
40 */
41
42
43
44 #include <stdio.h>
45 #include <stdlib.h>
46 #include <sys/time.h>
47 #include <zlib.h>
48 #include <string.h>
49 #include "Common.h"
50
51
52 unsigned short SEQ_LENGTH = 0;
53 long long memUsage = 0;
54 /**********************************************/
55 FILE *fileOpen(char *fileName, char *mode)
56 {
57 FILE *fp;
58 fp = fopen (fileName, mode);
59 if (fp == NULL)
60 {
61 fprintf(stdout, "Error: Cannot Open the file %s\n", fileName);
62 fflush(stdout);
63 exit(0);
64 }
65 return fp;
66 }
67 /**********************************************/
68 gzFile fileOpenGZ(char *fileName, char *mode)
69 {
70 gzFile gzfp;
71 gzfp = gzopen (fileName, mode);
72 if (gzfp == Z_NULL)
73 {
74 fprintf(stdout, "Error: Cannot Open the file %s\n", fileName);
75 fflush(stdout);
76 exit(0);
77 }
78 return gzfp;
79 }
80 /**********************************************/
81 double getTime(void)
82 {
83 struct timeval t;
84 gettimeofday(&t, NULL);
85 return t.tv_sec+t.tv_usec/1000000.0;
86 }
87
88 /**********************************************/
89 char reverseCompleteChar(char c)
90 {
91 char ret;
92 switch (c)
93 {
94 case 'A':
95 ret = 'T';
96 break;
97 case 'T':
98 ret = 'A';
99 break;
100 case 'C':
101 ret = 'G';
102 break;
103 case 'G':
104 ret = 'C';
105 break;
106 default:
107 ret = 'N';
108 break;
109 }
110 return ret;
111 }
112 /**********************************************/
113 void reverseComplete (char *seq, char *rcSeq , int length)
114 {
115 int i;
116 for (i=0; i<length; i++)
117 {
118 rcSeq[i]=reverseCompleteChar (seq[length-1-i]) ;
119 }
120 }
121 /**********************************************/
122 void * getMem(size_t size)
123 {
124 void *ret;
125 ret = malloc(size);
126 if (ret == NULL){
127 fprintf(stderr, "Cannot allocate memory. Currently addressed memory = %0.2f MB, requested memory = %0.2f MB.\nCheck the available main memory, and if you have user limits (ulimit -v).\n", getMemUsage(), (double)size);
128 exit(0);
129 }
130 memUsage+=size;
131 return ret;
132 }
133 /**********************************************/
134 void freeMem(void *ptr, size_t size)
135 {
136 memUsage-=size;
137 free(ptr);
138 }
139 /**********************************************/
140 double getMemUsage()
141 {
142 return memUsage/1048576.0;
143 }
144 /**********************************************/
145 void reverse (char *seq, char *rcSeq , int length)
146 {
147 int i;
148 int l = length;
149 if(l != strlen(seq))
150 l = strlen(seq);
151 for (i=0; i<l; i++)
152 {
153 rcSeq[i]=seq[l-1-i] ;
154 }
155 rcSeq[l] = '\0';
156 }
157 /**********************************************/
158 void stripPath(char *full, char **path, char **fileName)
159 {
160 int i;
161 int pos = -1;
162
163 for (i=strlen(full)-1; i>=0; i--)
164 {
165 if (full[i]=='/')
166 {
167 pos = i;
168 break;
169 }
170
171 }
172
173 if (pos != -1)
174 {
175 sprintf(*fileName, "%s%c", (full+pos+1), '\0');
176 full[pos+1]='\0';
177 sprintf(*path,"%s%c", full, '\0');
178 }
179 else
180 {
181 sprintf(*fileName, "%s%c", full, '\0');
182 sprintf(*path,"%c", '\0');
183 }
184 }