main.cpp

#include <ctime>
#include <string>
#include <sys/stat.h>

#include <spdlog/sinks/stdout_color_sinks.h>
#include <spdlog/spdlog.h>

#include "caller.hpp"
#include "config.hpp"
#include "ping_pong.hpp"
#include "smoother.hpp"

using namespace std;

const string version = "v2.0.0";

int main(int argc, char **argv) {
  time_t t;
  time(&t);
  spdlog::set_default_logger(spdlog::stderr_color_st("stderr"));

  auto c = Configuration::getInstance();

  if (argc == 1) {
    c->print_help("");
    exit(EXIT_FAILURE);
  }

  c->parse(argc, argv);
  if (c->verbose)
    spdlog::set_level(spdlog::level::debug);

  if (c->version) {
    cout << "SVDSS, " << version << endl;
    exit(EXIT_SUCCESS);
  }

  if (c->help) {
    c->print_help(argv[1]);
    exit(EXIT_SUCCESS);
  }

  if (strcmp(argv[1], "call") == 0) {
    if (c->reference == "" || c->bam == "" || c->sfs == "") {
      c->print_help(argv[1]);
      exit(EXIT_FAILURE);
    }
    auto caller = new Caller();
    caller->run();
  } else if (strcmp(argv[1], "index") == 0) {
    if (c->reference == "" || c->index == "") {
      c->print_help(argv[1]);
      exit(EXIT_FAILURE);
    }
    auto pingpong = new PingPong();
    pingpong->index();
  } else if (strcmp(argv[1], "search") == 0) {
    if (c->index == "" || (c->fastq == "" && c->bam == "")) {
      c->print_help(argv[1]);
      exit(EXIT_FAILURE);
    }
    auto pingpong = new PingPong();
    pingpong->search();
    // } else if (strcmp(argv[1], "assemble") == 0) {
    //   auto assembler = new Assembler();
    //   assembler->run();
  } else if (strcmp(argv[1], "smooth") == 0) {
    if (c->reference == "" || c->bam == "") {
      c->print_help(argv[1]);
      exit(EXIT_FAILURE);
    }
    auto smoother = new Smoother();
    smoother->run();
  } else {
    c->print_help("");
    exit(EXIT_FAILURE);
  }
  time_t s;
  time(&s);
  spdlog::info("All done! Runtime: {} seconds", s - t);

  return 0;
}