//
//  aln_filter.h
//  aln_filter
//
//  Created by timo on 06/04/2011.
//  Copyright 2011 RIKEN Yokohama Institute, Genome Exploration Research Group. All rights reserved.
//


#include <stdio.h>

#include <stdlib.h>
#include <unistd.h>
#include <ctype.h>

#define VERSION "aln_filter 1.1"

#define MAX_LINE 1000




struct db_seq_info{
	unsigned char** names;
	unsigned int* len;
	float* nuc_counts;
	int* sn_len;
	int num_seq;
	unsigned int total_len;
};

struct db{
	struct db_seq_info* seq_info;
	char* dbname;
	unsigned int* bfa; 
};

FILE* outfile;

void free_db(struct db* db);

int byg_end(const char* pattern,const char*text);
int get_aln_length(char* cigar);
unsigned int get_chr_offset(struct db_seq_info* si, char* chr);
unsigned char* get_chr_name(struct db_seq_info* si, unsigned int pos);
unsigned int  get_chr_pos(struct db_seq_info* si, unsigned int pos);