https://github.com/sfu-compbio/mrsfast
Tip revision: 43923aacceec957252da43f440ed8cce87f4a7b7 authored by Faraz Hach on 23 July 2013, 22:57:58 UTC
Changelog for 2.6.0.4 is update.
Changelog for 2.6.0.4 is update.
Tip revision: 43923aa
Output.h
/*
* Copyright (c) <2008 - 2009>, 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
* Email : fhach AT cs DOT sfu
*/
#ifndef __OUTPUT__
#define __OUTPUT__
#define FORWARD 0
#define REVERSE 1
typedef struct
{
char *tag;
char type;
char cVal;
int iVal;
float fVal;
char *sVal;
} OPT_FIELDS;
typedef struct
{
char *QNAME;
short FLAG;
char *RNAME;
int POS;
unsigned char MAPQ;
char *CIGAR;
char *MRNAME;
int MPOS;
int ISIZE;
char *SEQ;
char *QUAL;
int optSize;
OPT_FIELDS *optFields;
} SAM;
int initOutput(char *fileName, int compressed);
void (*finalizeOutput)();
void (*output)(SAM map);
#endif