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
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 * 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