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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 FILEIO_H
#define FILEIO_H
/*
* fileio.h
* declarations for file io
*
* @author Steve Hoffmann
* @date Sat 25 Nov 2006
*
* SVN
* Revision of last commit: $Rev: 19 $
* Author: $Author: steve $
* Date: $Date: 2008-05-14 15:43:29 +0200 (Wed, 14 May 2008) $
*
* Id: $Id: fileio.h 19 2008-05-14 13:43:29Z steve $
* Url: $URL: file:///homes/bierdepot/steve/svn/segemehl/trunk/libs/fileio.h $
*/
#ifndef ALLOCMEMORY
#include "memory.h"
#endif
#include <math.h>
#include <sys/types.h>
#include <pthread.h>
#include "stringutils.h"
char * bl_getTempFile(char *path, char *tmp);
int bl_UnixSort(void *space, char *filename, const char *fieldstring, const char delim);
char* readfile(void *, char *, size_t*);
stringset_t **readcsv(void *, char *, char*, Uint *);
void writeY(char *, double *, Uint, Uint, Uint);
void writeXYUint(char *filename, Uint *X, Uint *Y, Uint len);
int bl_fgets(void *space, FILE *fp, char **str);
char * bl_basename (const char *name);
char* bl_replacealphanum(char *s, Uint len);
char* bl_replacenonalphanum(char *s, Uint len);
int bl_fileprefixlen(char *filename);
int bl_UnixSortMerge(void *space, char **filenames, Uint nooffiles, const char *fieldstring, const char delim, char *outfile);
void bl_writeFileHeader(char *filename, char *header) ;
void bl_freplace(char *filename, char oldchar, char newchar, char stop);
void bl_freplacearr(char *filename, char* oldchars, char *newchars, Uint len, char stop);
void bl_freplacestr(char *filename, char* str, Uint len, char stop);
void writeXYZ(char *filename, double *X, double *Y, double *Z, Uint len);
int bl_rm(void *space, char *filename);
void writeYUint(char *filename, Uint *Y, Uint len, Uint xoff, Uint yoff);
void writeYUintNorm(char *filename, Uint *Y, Uint len, Uint yoff);
double* readX(void *space, char *filename, Uint *nvals);
char *bl_changefilesuffix(char *base, char *suffix);
char* bl_dirname(char *origpath);
const char *bl_fsuffix(char *fn);
#endif
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