// Copyright (c) 2015, Pacific Biosciences of California, Inc.
//
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// modification, are permitted (subject to the limitations in the
// disclaimer below) provided that the following conditions are met:
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//    notice, this list of conditions and the following disclaimer.
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//    copyright notice, this list of conditions and the following
//    disclaimer in the documentation and/or other materials provided
//    with the distribution.
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//    from this software without specific prior written permission.
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// GRANTED BY THIS LICENSE. THIS SOFTWARE IS PROVIDED BY PACIFIC
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// Author: Derek Barnett

#include "OptionParser.h"
#include "PbIndex.h"
#include "PbIndexVersion.h"
#include <cassert>
#include <iostream>
using namespace std;

static
pbindex::Settings fromCommandLine(optparse::OptionParser& parser,
                                  int argc, char* argv[])
{
    const optparse::Values options = parser.parse_args(argc, argv);
    (void)options;

    pbindex::Settings settings;

    // get input filename
    const vector<string> positionalArgs = parser.args();
    const size_t numPositionalArgs = positionalArgs.size();
    if (numPositionalArgs == 0)
        settings.errors_.push_back("pbindex requires an input BAM filename");
    else if (numPositionalArgs == 1)
        settings.inputBamFilename_ = parser.args().front();
    else {
        assert(numPositionalArgs > 1);
        settings.errors_.push_back("pbindex does not support more than one input file per run");
    }

    return settings;
}

int main(int argc, char* argv[])
{
    // setup help & options
    optparse::OptionParser parser;
    parser.description("pbindex creates a index file that enables random-access to PacBio-specific data in BAM files. "
                       "Generated index filename will be the same as input BAM plus .pbi suffix."
                       );
    parser.prog("pbindex");
    parser.usage("pbindex <input>");
    parser.version(pbindex::Version);
    parser.add_version_option(true);
    parser.add_help_option(true);

    auto ioGroup = optparse::OptionGroup(parser, "Input/Output");
    ioGroup.add_option("")
           .dest("input")
           .metavar("input")
           .help("Input BAM file");
    parser.add_option_group(ioGroup);

    // parse command line for settings
    const pbindex::Settings settings = fromCommandLine(parser, argc, argv);
    if (!settings.errors_.empty()) {
        cerr << endl;
        for (const auto e : settings.errors_)
            cerr << "ERROR: " << e << endl;
        cerr << endl;
        parser.print_help();
        return EXIT_FAILURE;
    }

    // run tool
    return pbindex::PbIndex::Run(settings);
}
