Mercurial > repos > calkan > mrsfast
comparison mrsfast-2.3.0.2/Common.h @ 0:ec628ba33878 default tip
Uploaded source code for mrsFAST
author | calkan |
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date | Tue, 21 Feb 2012 10:39:28 -0500 |
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-1:000000000000 | 0:ec628ba33878 |
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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 |