/*

* Copyright (c) 2012-2013 Cristina Yenyxe Gonzalez Garcia (ICM-CIPF)

* Copyright (c) 2012 Ignacio Medina (ICM-CIPF)

*

* This file is part of hpg-variant.

*

* hpg-variant 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 2 of the License, or

* (at your option) any later version.

*

* hpg-variant 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 hpg-variant. If not, see <http://www.gnu.org/licenses/>.

*/

#ifndef HPG_VARIANT_UTIL_H

#define HPG_VARIANT_UTIL_H

#include <math.h>

#include <stdlib.h>

#include <sys/stat.h>

#include <bioformats/family/family.h>

#include <bioformats/ped/ped_file.h>

#include <bioformats/vcf/vcf_file.h>

#include <commons/file_utils.h>

#include <commons/log.h>

#include <containers/khash.h>

#include <containers/list.h>

#include "shared_options.h"

#define HPG_VARIANT_VERSION "2.0"

#define MIN(X,Y) ((X) < (Y) ? (X) : (Y))

/* ***********************

* Initialization *

* ***********************/

char *find_configuration_file(int argc, char *argv[]);

array_list_t *get_configuration_search_paths(int argc, char *argv[]);

char *get_config_path_from_args(int argc, char *argv[]);

char *get_config_home_folder(char *config_dirpaths[], int num_dirpaths);

array_list_t *sort_config_paths_by_priority(char *config_arg_path, char *home_path);

/* **********************

* Config files *

* **********************/

char *retrieve_config_file(char *filename, array_list_t *paths_to_search);

/* **********************

* Job management *

* **********************/

FILE *new_job_status_file(char *path);

void update_job_status_file(int percentage, FILE *file);

void close_job_status_file(FILE *file);

/* ***********************

* Filtering *

* ***********************/

/**

* @brief Creates files that will contain the output of filtering tools, using the VCF input filename as prefix.

* @param shared_options Options for deciding the destination of the filter output

* @param passed_file File containing entries that pass filters tests

* @param failed_file File containing entries that don't pass filters tests

* @return 0 if no errors occurred, 1 otherwise

*/

int get_filtering_output_files(shared_options_data_t *shared_options, FILE **passed_file, FILE **failed_file);

int write_filtering_output_files(array_list_t *passed_records, array_list_t *failed_records, FILE* passed_file, FILE* failed_file);

array_list_t *filter_records(filter_t** filters, int num_filters, individual_t **individuals, khash_t(ids) *sample_ids, int num_variables,

array_list_t *input_records, array_list_t **failed_records);

void free_filtered_records(array_list_t *passed_records, array_list_t *failed_records, array_list_t *input_records);

/* ***********************

* Output *

* ***********************/

FILE *get_output_file(shared_options_data_t *shared_options_data, char *default_name, char **path);

/* ***********************

* Miscellaneous *

* ***********************/

void show_usage(char *tool, void **argtable);

void show_version(char *tool);

/**

* @brief Given a list of records, distributes them in chunks of similar size

* @param records list of records to separate in chunks

* @param max_chunk_size maximum size of a chunk

* @param[out] num_chunks number of chunks created

* @param[out] chunk_sizes size of each chunk

* @return The indices of the beginning of each chunk

*

* Given a list of records, defines another list of chunks whose elements point to records separated

* by a maximum distance of max_chunk_size. These records will mark the beginning of each chunk.

*/

int *create_chunks(int length, int max_chunk_size, int *num_chunks, int **chunk_sizes);

int compare_int(const void *a, const void *b);

#endif