smithlab_os.hpp

/* Part of SMITHLAB software
 *
 * Copyright (C) 2008-2018 University of Southern California and
 *                         Andrew D. Smith
 *
 * Authors: Andrew D. Smith
 *
 * 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.
 */

#ifndef SMITHLAB_OS_HPP
#define SMITHLAB_OS_HPP

#include <string>
#include <unordered_map>
#include <vector>

bool isdir(const char *filename);

bool is_fastq(const std::string &filename);

bool is_valid_filename(const std::string &name,
                       const std::string &filename_suffix);

std::string path_join(const std::string &a, const std::string &b);

void identify_chromosomes(
    const std::string &chrom_file,
    const std::string fasta_suffix, // could be const char*
    std::unordered_map<std::string, std::string> &chrom_files);

void identify_and_read_chromosomes(
    const std::string &chrom_file, const std::string fasta_suffix,
    std::unordered_map<std::string, std::string> &chrom_files);

void read_dir(const std::string &dirname,
              std::string filename_suffix, // could be const char*
              std::vector<std::string> &filenames);

void read_fasta_file(const std::string &filename,
                     std::vector<std::string> &names,
                     std::vector<std::string> &sequences);
void read_fasta_file_short_names(const std::string &filename,
                                 std::vector<std::string> &names,
                                 std::vector<std::string> &sequences);

// This verstion looks for the sequence matching a particular name
void read_fasta_file(const std::string &filename, const std::string &target,
                     std::string &sequence);

void read_fastq_file(const char *filename, std::vector<std::string> &names,
                     std::vector<std::string> &sequences,
                     std::vector<std::vector<double>> &scores);

void read_fastq_file(const char *filename, std::vector<std::string> &names,
                     std::vector<std::string> &sequences,
                     std::vector<std::string> &scores);

void read_filename_file(const char *filename,
                        std::vector<std::string> &filenames);

size_t get_filesize(std::string filename);

std::string basename(std::string filename);

void parse_dir_basename_suffix(const std::string &full_path,
                               std::string &dirname, std::string &base_name,
                               std::string &suffix);

void format_dir_basename_suffix(const std::string &directory_name,
                                const std::string &file_base_name,
                                const std::string &file_name_suffix,
                                std::string &full_path);

std::string strip_path(std::string full_path);

std::string strip_path_and_suffix(std::string full_path);

void read_dir(const std::string &dirname, std::vector<std::string> &filenames);

bool is_valid_output_file(const std::string &filename);

bool has_gz_ext(const std::string &filename);

#endif