https://github.com/sfu-compbio/mrsfast
Tip revision: 47fe86a0ea0072838e53cc01d81640bb784ed3c2 authored by Faraz Hach on 30 August 2016, 18:00:51 UTC
Changing the version number to 3.3.11
Changing the version number to 3.3.11
Tip revision: 47fe86a
Reads.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 __READ__
#define __READ__
typedef struct
{
int32_t hv;
CheckSumType checksum;
int32_t seqInfo;
} Pair;
typedef struct
{
uint16_t *hits;
char *seq;
char *qual;
char *rseq;
CompressedSeq *cseq;
CompressedSeq *crseq;
char *name;
unsigned char *alphCnt;
} Read;
int readChunk(Read **seqList, unsigned int *seqListSize);
void finalizeReads();
void getSamplingLocsInfo(int **samplingLocs, int **samplingLocsSeg, int **samplingLocsOffset, int **samplingLocsLen, int **samplingLocsLenFull, int *samplingLocsSize);
int initRead(char *seqFile1, char *seqFile2);
void getReadIndex(ReadIndexTable ***rIndex, int **rIndexSize);
void releaseChunk();
#endif