https://github.com/sfu-compbio/mrsfast
Revision 1caa3302ec8ed82bad744c34a71c3781873dfc59 authored by Iman Sarrafi on 12 September 2014, 18:05:58 UTC, committed by Iman Sarrafi on 12 September 2014, 18:05:58 UTC
1 parent 2c637a0
Tip revision: 1caa3302ec8ed82bad744c34a71c3781873dfc59 authored by Iman Sarrafi on 12 September 2014, 18:05:58 UTC
Bug fix: snp_indexer crashed when path did not exist. New version 3.3.3
Bug fix: snp_indexer crashed when path did not exist. New version 3.3.3
Tip revision: 1caa330
Common.h
/*
* Copyright (c) <2008 - 2020>, 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.
*/
/*
* Author:
* Faraz Hach (fhach AT cs DOT sfu DOT ca)
* Iman Sarrafi (isarrafi AT cs DOT sfu DOT ca)
*/
#ifndef __COMMON__
#define __COMMON__
#if SSE4==1
#define MRSFAST_SSE4
#endif
#include <zlib.h>
#include <stdint.h>
#define SEQ_MAX_LENGTH 500 // Seq Max Length
#define CMP_SEQ_MAX_LENGTH 10 // Compressed Seq Max Length
#define CONTIG_OVERLAP 1050 // No. of characters overlapped between contings -- equals 50 blocks of length 21
#define CONTIG_NAME_SIZE 200 // Contig name max size
#define FILE_NAME_LENGTH 500 // Filename Max Length
typedef uint64_t CompressedSeq;
typedef uint16_t CheckSumType;
extern unsigned int CONTIG_SIZE;
extern unsigned int CONTIG_MAX_SIZE;
extern unsigned int THREAD_COUNT;
extern double MAX_MEMORY;
extern int THREAD_ID[255];
extern unsigned char WINDOW_SIZE; // WINDOW SIZE for indexing/searching
extern unsigned short SEQ_LENGTH; // Sequence(read) length
extern unsigned short QUAL_LENGTH;
extern unsigned short CMP_SEQ_LENGTH;
extern unsigned short DISCORDANT_CUT_OFF;
extern int SNP_QUAL_THRESHOLD;
extern int indexingMode;
extern int searchingMode;
extern int pairedEndMode;
extern int pairedEndDiscordantMode;
extern int pairedEndProfilingMode;
extern int bestMappingMode;
extern int SNPMode;
extern int seqCompressed;
extern int outCompressed;
extern int cropSize;
extern int progressRep;
extern int nohitDisabled;
extern int noSamHeader;
extern char *seqFile1;
extern char *seqFile2;
extern char *seqUnmapped;
extern char *mappingOutput;
extern char *mappingOutputPath;
extern char *unmappedOutput;
extern unsigned char seqFastq;
extern int errThreshold;
extern short maxHits;
extern int minPairEndedDiscordantDistance;
extern int maxPairEndedDiscordantDistance;
extern int minPairEndedDistance;
extern int maxPairEndedDistance;
extern char fileName[3][FILE_NAME_LENGTH];
extern int fileCnt;
extern long long memUsage;
extern char *alphabet;
extern char checkSumLength;
#pragma pack(push, 1)
typedef struct
{
CheckSumType checksum;
uint32_t info; // ReadIndex => seqInfo | GenomeIndex ==> Loc
} GeneralIndex;
#pragma pack(pop)
typedef struct
{
int hv;
GeneralIndex *list;
} ReadIndexTable;
typedef struct
{
int loc;
char alt;
} SNPLoc;
FILE * fileOpen(char *fileName, char *mode);
gzFile fileOpenGZ(char *fileName, char *mode);
double getTime(void);
void reverseComplete (char *seq, char *rcSeq , int length);
char reverseCompleteChar(char);
void * getMem(size_t size);
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);
void compressSequence(char *seq, int seqLen, CompressedSeq *cseq);
int calculateCompressedLen(int normalLen);
int hashVal(char *seq);
int checkSumVal(char *seq);
void initCommon();
#endif
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