Support wildcards in read file names.

#include "chromap_driver.h"

#include <glob.h>

#include <cassert>

#include <iomanip>

#include <string>

      cxxopts::value<int>(), "INT");

}

// Return all file paths that match the input pattern.

std::vector<std::string> GetMatchedFilePaths(const std::string &pattern) {

  glob_t glob_result;

  memset(&glob_result, 0, sizeof(glob_result));

  const int return_value =

      glob(pattern.c_str(), GLOB_TILDE, NULL, &glob_result);

  if (return_value != 0) {

    globfree(&glob_result);

    chromap::ExitWithMessage("glob() failed with return value " +

                             std::to_string(return_value) + "\n");

  }

  std::vector<std::string> matched_file_paths;

  matched_file_paths.reserve(glob_result.gl_pathc);

  for (size_t i = 0; i < glob_result.gl_pathc; ++i) {

    matched_file_paths.push_back(std::string(glob_result.gl_pathv[i]));

    std::cerr << matched_file_paths.back() << "\n";

  }

  globfree(&glob_result);

  return matched_file_paths;

}

// Return all file paths that match the input patterns.

std::vector<std::string> GetMatchedFilePaths(

    const std::vector<std::string> &patterns) {

  std::vector<std::string> all_matched_file_paths;

  for (const auto &pattern : patterns) {

    std::vector<std::string> matched_file_paths = GetMatchedFilePaths(pattern);

    all_matched_file_paths.reserve(all_matched_file_paths.size() +

                                   matched_file_paths.size());

    all_matched_file_paths.insert(

        std::end(all_matched_file_paths),

        std::make_move_iterator(std::begin(matched_file_paths)),

        std::make_move_iterator(std::end(matched_file_paths)));

  }

  return all_matched_file_paths;

}

}  // namespace

void ChromapDriver::ParseArgsAndRun(int argc, char *argv[]) {

    }

    if (result.count("1")) {

      mapping_parameters.read_file1_paths =

          result["read1"].as<std::vector<std::string>>();

          GetMatchedFilePaths(result["read1"].as<std::vector<std::string>>());

    } else {

      chromap::ExitWithMessage("No read file specified!");

    }

    if (result.count("2")) {

      mapping_parameters.read_file2_paths =

          result["read2"].as<std::vector<std::string>>();

          GetMatchedFilePaths(result["read2"].as<std::vector<std::string>>());

    }

    if (result.count("b")) {

      mapping_parameters.is_bulk_data = false;

      mapping_parameters.barcode_file_paths =

          result["barcode"].as<std::vector<std::string>>();

          GetMatchedFilePaths(result["barcode"].as<std::vector<std::string>>());

      if (result.count("barcode-whitelist") == 0) {

        std::cerr << "WARNING: there are input barcode files but a barcode "

                     "whitelist file is missing!\n";