FastBQSR/src/main.cpp

#include <spdlog/cfg/env.h>
#include <spdlog/sinks/stdout_color_sinks.h>
#include <spdlog/spdlog.h>
#include <time.h>

#include <argparse/argparse.hpp>
#include <iostream>
#include <map>
#include <set>
#include <string>

#include "fastbqsr_version.h"
#include "bqsr/bqsr_args.h"
#include "util/profiling.h"

namespace nsgv {
extern BQSRArg gBqsrArg;
};

int BaseRecalibrator();
int ApplyBQSR();

string get_current_time_str() {
    time_t time_val;
    struct tm *at;
    char now[80];
    time(&time_val);
    at = localtime(&time_val);
    strftime(now, 79, "%B %d, %Y at %I:%M:%S %p %Z", at);
    return string(now);
}

int main_BaseRecalibrator(int argc, char *argv[]) {
    // init arg parser
    argparse::ArgumentParser program(nsgv::gBqsrArg.PROGRAM_RECORD_ID, FASTBQSR_VERSION, argparse::default_arguments::none);
    program.add_description(
        "First pass of the Base Quality Score Recalibration (BQSR) -- Generates recalibration table based on various\n"
        "user-specified covariates (such as read group, reported quality score, machine cycle, and nucleotide context.)");

    program.add_argument("--input")
        .help("BAM/SAM/CRAM file containing reads  This argument must be specified at least once.")
        .metavar("<INPUT>")
        .required();

    program.add_argument("--output")
        .help("The output recalibration table file to create.")
        .metavar("<OUTPUT>")
        .required();

    program.add_argument("--reference")
        .help("Reference sequence file.")
        .metavar("<Reference>")
        .required();

    program.add_argument("--num-threads")
        .help("Number of threads to use.")
        .scan<'i', int>()
        .default_value(1)
        .nargs(1)
        .metavar("<NUM_THREADS>");

    program.add_argument("--known-sites")
        .help(
            "One or more databases of known polymorphic sites used to exclude regions around known polymorphisms from "
            "analysis.  This argument must be specified at least once.")
        .metavar("<KnownSites>")
        .nargs(argparse::nargs_pattern::any);

    program.add_argument("--create-index")
        .help("Whether to create an index when writing coordinate sorted BAM output.")
        .default_value(false)
        .implicit_value(true);

    program.add_argument("--index-format")
        .help("Format for bam index file. Possible values: {BAI, CSI}")
        .default_value(std::string("BAI"))
        .choices("BAI", "CSI")
        .nargs(1)
        .metavar("<IndexFormat>");

    program.add_argument("--enable-baq")
        .help("Whether to do BAQ correction.")
        .default_value(false)
        .implicit_value(true)
        .hidden();

    // add help and version args
    program.add_argument("-h", "--help")
        .action([&](const auto & /*unused*/) {
            std::cout << program.help().str();
            std::exit(0);
        })
        .default_value(false)
        .help("shows help message and exits")
        .implicit_value(true)
        .nargs(0);

    program.add_argument("-v", "--version")
        .action([&](const auto & /*unused*/) {
            std::cout << FASTBQSR_VERSION << std::endl;
            std::exit(0);
        })
        .default_value(false)
        .help("prints version information and exits")
        .implicit_value(true)
        .nargs(0);

    // std::cout << program << std::endl;

    nsgv::gBqsrArg.START_TIME = get_current_time_str();
    nsgv::gBqsrArg.CLI_STR = argv[0];
    for (int i = 1; i < argc; ++i) {
        nsgv::gBqsrArg.CLI_STR += " " + std::string(argv[i]);
    }

    try {
        program.parse_args(argc, argv);
        nsgv::gBqsrArg.INPUT_FILE = program.get("--input");
        nsgv::gBqsrArg.OUTPUT_FILE = program.get("--output");
        nsgv::gBqsrArg.NUM_THREADS = program.get<int>("--num-threads");
        nsgv::gBqsrArg.CREATE_INDEX = program.get<bool>("--create-index");
        nsgv::gBqsrArg.REFERENCE_FILE = program.get<string>("--reference");
        nsgv::gBqsrArg.KNOWN_SITES_VCFS = program.get<std::vector<string>>("--known-sites");
        nsgv::gBqsrArg.enableBAQ = program.get<bool>("--enable-baq");
        // spdlog::info("known sites vcf files:");
        // for (const auto& ks : nsgv::gBqsrArg.KNOWN_SITES_VCFS) {
        //     spdlog::info("  {}", ks);
        // }

        nsgv::gBqsrArg.INDEX_FORMAT =
            program.get("--index-format") == "BAI" ? nsbqsr::IndexFormat::BAI : nsbqsr::IndexFormat::CSI;

    } catch (const std::exception &err) {
        spdlog::error(err.what());
        return 1;
    }

    spdlog::info("fast base recalibration phase-1 start");
    BaseRecalibrator();
    spdlog::info("fast base recalibration phase-1 end");

    DisplayProfiling(1);

    return 0;
}

int main_ApplyBQSR(int argc, char* argv[]) { return 0; }

int main(int argc, char *argv[]) {
    // init log
    spdlog::set_default_logger(spdlog::stderr_color_st("fastbqsr"));
    spdlog::cfg::load_env_levels();

    string bqsr_prog = argv[1];
    if (bqsr_prog == "BaseRecalibrator") {
        return main_BaseRecalibrator(argc - 1, argv + 1);
    } else if (bqsr_prog == "ApplyBQSR") {
        return main_ApplyBQSR(argc - 1, argv + 1);
    } else {
        spdlog::error("unknown program name: {}, should be BaseRecalibrator or ApplyBQSR", bqsr_prog);
    }

    return -1;
}