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Common.h
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Common.h
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/*
* Copyright (c) <2008 - 2020>, University of Washington, Simon Fraser University, Bilkent 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 names of the University of Washington, Simon Fraser University,
* 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.
*/
/*
Authors:
Farhad Hormozdiari
Faraz Hach
Can Alkan
Emails:
farhadh AT uw DOT edu
fhach AT cs DOT sfu DOT ca
calkan AT cs DOT bilkent DOT edu DOT tr
*/
#ifndef __COMMON__
#define __COMMON__
#include <zlib.h>
#define SEQ_NAME_MAX_LENGTH 20 // Seq Name Max Length
#define SEQ_MAX_LENGTH 1000 // Seq Max Length
#define CONTIG_OVERLAP 2000 // 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
#define MAX_OPEN_FILE 600
#define MAX_TRANS_CHROMOSAL_OUTPUT 50
#define MAX_OEA_OUT 500
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 int maxOEAOutput;
extern int maxDiscordantOutput;
extern int uniqueMode;
extern int indexingMode;
extern int searchingMode;
extern int pairedEndModeMP;
extern int pairedEndModePE;
extern int pairedEndMode;
extern int pairedEndDiscordantMode;
extern int transChromosomal;
extern int pairedEndProfilingMode;
extern int bestMode;
extern int nosamMode;
extern int debugMode;
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 *mappingOutputPath;
extern char *unmappedOutput;
extern char readGroup[FILE_NAME_LENGTH];
extern char sampleName[FILE_NAME_LENGTH];
extern char libName[FILE_NAME_LENGTH];
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[2][FILE_NAME_LENGTH];
extern int fileCnt;
extern long long memUsage;
extern unsigned int maxInputRead;
extern int readFormat;
FILE * fileOpen(char *fileName, char *mode);
gzFile fileOpenGZ(char *fileName, char *mode);
double getTime(void);
void reverseComplement (char *seq, char *rcSeq , int length);
void * getMem(size_t size);
void reMem(void *, size_t, size_t);
void freeMem(void * ptr, size_t size);
double getMemUsage();
void reverse (char *seq, char *rcSeq , int length);
void stripPath(char *full, char **path, char **fileName);
#endif