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/*
* segemehl - a read aligner
* Copyright (C) 2008-2017 Steve Hoffmann and Christian Otto
*
* This program is free software: you can redistribute it and/or modify
* it under the terms of the GNU General Public License as published by
* the Free Software Foundation, either version 3 of the License, or
* (at your option) any later version.
*
* This program is distributed in the hope that it will be useful,
* but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
* GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License
* along with this program. If not, see <http://www.gnu.org/licenses/>.
*/
#ifndef MATCHFILESFIELDS_H
#define MATCHFILESFIELDS_H
/*
*
* matchfilesfields.h
*
*
* @author Steve Hoffmann, steve@bioinf.uni-leipzig.de
* @company Bioinformatics, University of Leipzig
* @date 01.03.2011 17:40:56 CET
*
*/
#include "matchfiles.h"
Uint bl_matchfileGetPNext (stringset_t *fields, unsigned char fmt);
char* bl_matchfileGetRNext ( stringset_t *fields, unsigned char fmt);
char* bl_matchfileGetQname(stringset_t *fields, unsigned char fmt);
Uint bl_matchfileGetFlag(stringset_t *fields, unsigned char fmt);
unsigned char bl_matchfileIsHeader(char *buffer, Uint len, unsigned char fmt);
Uint bl_matchfileGetStartPos(stringset_t *fields, unsigned char fmt);
Uint bl_matchfileGetEndPos(stringset_t *fields, unsigned char fmt);
char* bl_matchfileGetRead(stringset_t *fields, unsigned char fmt);
char* bl_matchfileGetQual(stringset_t *fields, unsigned char fmt);
char bl_matchfileGetStrand(stringset_t *fields, unsigned fmt);
char* bl_matchfileGetChrom(stringset_t *fields, unsigned fmt);
Uint bl_matchfileGetMatchCnt(stringset_t *fields, unsigned char fmt);
Uint bl_matchfileGetEdist(stringset_t *fields, unsigned char fmt);
Uint bl_matchfileGetBisulfite(stringset_t *fields, unsigned char fmt);
char* bl_matchfileGetAln(stringset_t *fields, unsigned char fmt);
char* bl_matchfileGetDiffString(stringset_t *fields, unsigned char fmt);
Uint bl_matchfileGetPrevPos(stringset_t *fields, unsigned char fmt);
Uint bl_matchfileGetNextPos(stringset_t *fields, unsigned char fmt);
char* bl_matchfileGetNextChr(stringset_t *fields, unsigned char fmt);
char* bl_matchfileGetPrevChr(stringset_t *fields, unsigned char fmt);
Uint bl_matchfileGetSplitStart(stringset_t *fields, unsigned char fmt);
Uint bl_matchfileGetSplitEnd(stringset_t *fields, unsigned char fmt);
Uint bl_matchfileGetSplitNumber(stringset_t *fields, unsigned char fmt);
Uint bl_matchfileGetPrevFlag(stringset_t *fields, unsigned char fmt);
Uint bl_matchfileGetNextFlag(stringset_t *fields, unsigned char fmt);
Uint bl_matchfileGetMappingID(stringset_t *fields, unsigned char fmt);
matchfileRec_t * bl_matchfileGetMatchFileRec(matchfileRec_t *rec, Uint fields, stringset_t *token, Uint fmt);
#endif
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