comparison mrsfast-2.3.0.2/Common.h @ 0:ec628ba33878 default tip

Uploaded source code for mrsFAST
author calkan
date Tue, 21 Feb 2012 10:39:28 -0500
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-1:000000000000 0:ec628ba33878
1 /*
2 * Copyright (c) <2008 - 2009>, 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 name of the <ORGANIZATION> nor the names of its contributors may be
14 * used to endorse or promote products derived from this software without specific
15 * prior written permission.
16 *
17 * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
18 * "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
19 * LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR
20 * A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR
21 * CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
22 * EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
23 * PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR
24 * PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF
25 * LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING
26 * NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
27 * SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
28 */
29
30 /*
31 * Author : Faraz Hach
32 * Email : fhach AT cs DOT sfu
33 * Last Update : 2009-12-08
34 */
35
36
37 #ifndef __COMMON__
38 #define __COMMON__
39
40 #include <zlib.h>
41
42 #define SEQ_MAX_LENGTH 200 // Seq Max Length
43 #define CONTIG_OVERLAP 200 // No. of characters overlapped between contings
44 #define CONTIG_NAME_SIZE 200 // Contig name max size
45 #define FILE_NAME_LENGTH 400 // Filename Max Length
46 #define DISCORDANT_CUT_OFF 800
47
48 extern unsigned int CONTIG_SIZE;
49 extern unsigned int CONTIG_MAX_SIZE;
50
51
52 extern unsigned char WINDOW_SIZE ; // WINDOW SIZE for indexing/searching
53 extern unsigned short SEQ_LENGTH; // Sequence(read) length
54 extern unsigned short QUAL_LENGTH;
55
56 extern char *versionNumber;
57 extern char *versionNumberF;
58 extern unsigned char mrFAST;
59
60
61 extern int uniqueMode;
62 extern int indexingMode;
63 extern int searchingMode;
64 extern int bisulfiteMode;
65 extern int pairedEndMode;
66 extern int pairedEndDiscordantMode;
67 extern int pairedEndProfilingMode;
68 extern int seqCompressed;
69 extern int outCompressed;
70 extern int cropSize;
71 extern int progressRep;
72 extern char *seqFile1;
73 extern char *seqFile2;
74 extern char *seqUnmapped;
75 extern char *mappingOutput;
76 extern char *mappingOutputPath;
77 extern char *unmappedOutput;
78 extern unsigned char seqFastq;
79 extern unsigned char errThreshold;
80 extern unsigned char maxHits;
81 extern int minPairEndedDiscordantDistance;
82 extern int maxPairEndedDiscordantDistance;
83 extern int minPairEndedDistance;
84 extern int maxPairEndedDistance;
85 extern char fileName[1000][2][FILE_NAME_LENGTH];
86 extern int fileCnt;
87 extern long long memUsage;
88
89 FILE * fileOpen(char *fileName, char *mode);
90 gzFile fileOpenGZ(char *fileName, char *mode);
91 double getTime(void);
92 void reverseComplete (char *seq, char *rcSeq , int length);
93 void * getMem(size_t size);
94 void freeMem(void * ptr, size_t size);
95 double getMemUsage();
96 void reverse (char *seq, char *rcSeq , int length);
97 void stripPath(char *full, char **path, char **fileName);
98 #endif