/*
 
 Copyright (C) 2010,2011 Timo Lassmann <timolassmann@gmail.com>
 
 This file is part of aln_filter.
 
 aln_filter 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.
 
 aln_filter 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 aln_filter.  If not, see <http://www.gnu.org/licenses/>.
 
 */

#include <stdio.h>
#include <getopt.h>
#include <stdlib.h>
#include <string.h>


struct parameters {
	FILE* foutfile;
	char** infile;
	char* outfile;
	char* outfile2;
	float id_cutoff;
	int infiles;
	int quiet_flag;
	int discard;
};


#define OPT_discard 1

struct parameters* interface(struct parameters* param,int argc, char *argv[]);
struct db* fix_sam_file(struct db* db,struct parameters* param);

void free_param(struct parameters* param);

void usage(void);