/*
 * inc/Glf.h
 * 
 * Copyright (c) 2011-2013 BGI-Shenzhen <soap at genomics dot org dot cn>. 
 *
 * This file is part of SOAPdenovo-Trans.
 *
 * SOAPdenovo-Trans 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.
 *
 * SOAPdenovo-Trans 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 SOAPdenovo-Trans.  If not, see <http://www.gnu.org/licenses/>.
 *
 */
#ifndef GLF_H_
#define GLF_H_

typedef struct {
	unsigned char ref_base:4, dummy:4; /** "XACMGRSVTWYHKDBN"[ref_base] gives the reference base */
	unsigned char max_mapQ; /** maximum mapping quality */
	unsigned char lk[10];   /** log likelihood ratio, capped at 255 */
	unsigned min_lk:8, depth:24; /** minimum lk capped at 255, and the number of mapped reads */
} glf1_t;

#include <stdint.h>
#include "bgzf.h"
typedef BGZF *glfFile;

#define GLF3_RTYPE_END   0
#define GLF3_RTYPE_SUB   1
#define GLF3_RTYPE_INDEL 2

typedef struct {
	uint8_t ref_base:4, rtype:4; /** "XACMGRSVTWYHKDBN"[ref_base] gives the reference base */
	uint8_t rms_mapQ; /** RMS mapping quality */
	uint8_t lk[10];   /** log likelihood ratio, capped at 255 */
	uint32_t min_lk:8, depth:24; /** minimum lk capped at 255, and the number of mapped reads */
	int32_t offset; /** the first base in a chromosome has offset zero. */
	// for indel (lkHom1, lkHom2 and lkHet are the first three elements in lk[10])
	int16_t indel_len[2];
	int32_t max_len; // maximum indel len; will be modified by glf3_read1()
	char *indel_seq[2];
} glf3_t;

typedef struct {
	int32_t l_text;
	uint8_t *text;
} glf3_header_t;

#ifdef __cplusplus
extern "C" {
#endif

#define glf3_init1() ((glf3_t*)calloc(1, sizeof(glf3_t)))
#define glf3_destroy1(g3) do { free((g3)->indel_seq[0]); free((g3)->indel_seq[1]); free(g3); } while (0)

	glf3_header_t *glf3_header_init();
	glf3_header_t *glf3_header_read(glfFile fp);
	void glf3_header_write(glfFile fp, const glf3_header_t *h);
	void glf3_header_destroy(glf3_header_t *h);
	char *glf3_ref_read(glfFile fp, int *len);
	void glf3_ref_write(glfFile fp, const char *name, int len);
	int glf3_write1(glfFile fp, const glf3_t *g3);
	int glf3_read1(glfFile fp, glf3_t *g3);

#ifdef __cplusplus
}
#endif

#endif