/*
 * sideRETRO - A pipeline for detecting Somatic Insertion of DE novo RETROcopies
 * Copyright (C) 2019-2020 Thiago L. A. Miller <tmiller@mochsl.org.br
 *
 * 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 VCF_H
#define VCF_H

#include "db.h"

struct _VCFOption
{
	long        near_gene_dist;
	float       orientation_error;
	const char *fasta_file;
};

typedef struct _VCFOption VCFOption;

void vcf (sqlite3 *db, const char *output_file, VCFOption *opt);

#endif /* vcf.h */