Mercurial > repos > calkan > mrsfast
view mrsfast-2.3.0.2/Output.h @ 0:ec628ba33878 default tip
Uploaded source code for mrsFAST
author | calkan |
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date | Tue, 21 Feb 2012 10:39:28 -0500 |
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/* * 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 * Last Update : 2009-12-08 */ #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