|
0
|
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
|
