https://github.com/sfu-compbio/mrsfast
Tip revision: e2fe564aef6a8091d6f6ec21c9ab46b027b259b0 authored by Faraz Hach on 13 June 2012, 07:43:50 UTC
Version 2.0.0.0
Version 2.0.0.0
Tip revision: e2fe564
Common.h
/*
* Copyright (c) <2008 - 2009>, University of Washington, Simon Fraser University
* All rights reserved.
*
* Redistribution and use in source and binary forms, with or without modification,
* are permitted provided that the following conditions are met:
*
* Redistributions of source code must retain the above copyright notice, this list
* of conditions and the following disclaimer.
* - Redistributions in binary form must reproduce the above copyright notice, this
* list of conditions and the following disclaimer in the documentation and/or other
* materials provided with the distribution.
* - Neither the name of the <ORGANIZATION> nor the names of its contributors may be
* used to endorse or promote products derived from this software without specific
* prior written permission.
*
* THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
* "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
* LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR
* A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR
* CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
* EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
* PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR
* PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF
* LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING
* NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
* SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
*/
#ifndef __COMMON__
#define __COMMON__
#include <zlib.h>
#define SEQ_MAX_LENGTH 200 // Seq Max Length
#define CONTIG_OVERLAP 200 // No. of characters overlapped between contings
#define CONTIG_NAME_SIZE 200 // Contig name max size
#define FILE_NAME_LENGTH 400 // Filename Max Length
#define DISCORDANT_CUT_OFF 800
extern unsigned int CONTIG_SIZE;
extern unsigned int CONTIG_MAX_SIZE;
extern unsigned char WINDOW_SIZE ; // WINDOW SIZE for indexing/searching
extern unsigned short SEQ_LENGTH; // Sequence(read) length
extern char *versionNumber;
extern char *versionNumberF;
extern unsigned char mrFAST;
extern int indexingMode;
extern int searchingMode;
extern int bisulfiteMode;
extern int pairedEndMode;
extern int pairedEndDiscordantMode;
extern int pairedEndProfilingMode;
extern int seqCompressed;
extern int outCompressed;
extern int cropSize;
extern int progressRep;
extern char *seqFile1;
extern char *seqFile2;
extern char *seqUnmapped;
extern char *mappingOutput;
extern char *unmappedOutput;
extern unsigned char seqFastq;
extern unsigned char errThreshold;
extern unsigned char maxHits;
extern int minPairEndedDiscordantDistance;
extern int maxPairEndedDiscordantDistance;
extern int minPairEndedDistance;
extern int maxPairEndedDistance;
extern char fileName[1000][2][FILE_NAME_LENGTH];
extern int fileCnt;
extern long long memUsage;
FILE * fileOpen(char *fileName, char *mode);
gzFile fileOpenGZ(char *fileName, char *mode);
double getTime(void);
void reverseComplete (char *seq, char *rcSeq , int length);
void * getMem(size_t size);
void freeMem(void * ptr, size_t size);
double getMemUsage();
void reverse (char *seq, char *rcSeq , int length);
#endif