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
MrsFAST.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 __MRS_FAST__
#define __MRS_FAST__
#include "Reads.h"
#define MAP_CHUNKS 15
enum BestMappingStatus { unset = 0, first_mate, second_mate, trans_loc, improper, proper };
typedef struct mn
{
int loc;
char dir;
char err;
char mderr;
float score;
int hits;
int secondBestHits;
int secondBestErrors;
char md[40];
char chr[40];
} FullMappingInfo;
typedef struct mnp
{
int loc1;
char dir1;
char err1;
char mderr1;
char md1[40];
char chr1[40];
int loc2;
char dir2;
char err2;
char mderr2;
char md2[40];
char chr2[40];
enum BestMappingStatus status;
} BestMappingInfoPE;
typedef struct lc
{
int loc[MAP_CHUNKS];
char err[MAP_CHUNKS];
struct lc *next;
} MappingLocations;
typedef struct inf
{
int size;
MappingLocations *next;
} MappingInfo;
typedef struct
{
FILE * fp;
char name[400];
} FILE_STRUCT;
extern long long verificationCnt;
extern long long mappingCnt;
extern long long mappedSeqCnt;
extern long long completedSeqCnt;
void initializeFAST(int seqListSize);
void initFASTChunk(Read *seqList, int seqListSize);
void initFASTContig();
void finalizeFAST();
void mapSeq(unsigned char contigFlag);
#endif
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