/*===========================================================================
*
*                            PUBLIC DOMAIN NOTICE
*               National Center for Biotechnology Information
*
*  This software/database is a "United States Government Work" under the
*  terms of the United States Copyright Act.  It was written as part of
*  the author's official duties as a United States Government employee and
*  thus cannot be copyrighted.  This software/database is freely available
*  to the public for use. The National Library of Medicine and the U.S.
*  Government have not placed any restriction on its use or reproduction.
*
*  Although all reasonable efforts have been taken to ensure the accuracy
*  and reliability of the software and data, the NLM and the U.S.
*  Government do not and cannot warrant the performance or results that
*  may be obtained by using this software or data. The NLM and the U.S.
*  Government disclaim all warranties, express or implied, including
*  warranties of performance, merchantability or fitness for any particular
*  purpose.
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*  Please cite the author in any work or product based on this material.
*
* ===========================================================================
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*/

#include <ncbi-vdb/NGS.hpp>
#include <ngs-bam/ngs-bam.hpp>
#include <ngs/ErrorMsg.hpp>
#include <ngs/ReadCollection.hpp>
#include <ngs/Reference.hpp>
#include <ngs/AlignmentIterator.hpp>
#include <ngs/Alignment.hpp>

#include <math.h>
#include <iostream>

using namespace ngs;
using namespace std;

class AlignSliceTest
{
public:

    static void run_common ( ReadCollection & run, String refname, int start, int stop )
    {

        String run_name = run.getName ();

        // get requested reference
        Reference ref = run.getReference ( refname );

        // start iterator on requested range
        long count = stop - start + 1;
        AlignmentIterator it = ref.getAlignmentSlice ( start, count, Alignment::primaryAlignment );

        long i;
        for ( i = 0; it . nextAlignment (); ++ i )
        {
            cout         << it.getReadId ()
                 << '\t' << it.getReferenceSpec ()
                 << '\t' << it.getAlignmentPosition ()
                 << '\t' << it.getLongCigar ( false )         // unclipped
                 << '\t' << it.getAlignedFragmentBases ()
                 << '\n';
        }

        cerr << "Read " <<  i <<  " alignments for " <<  run_name << '\n';
    }

    static void run_csra ( String acc, String refname, int start, int stop )
    {
        // open requested accession using SRA implementation of the API
        ReadCollection run = ncbi::NGS::openReadCollection ( acc );
        run_common ( run, refname, start, stop );
    }

    static void run_bam ( String acc, String refname, int start, int stop )
    {
        // open requested accession using example BAM implementation of the API
        ReadCollection run = NGS_BAM::openReadCollection ( acc );
        run_common ( run, refname, start, stop );
    }

    static void run ( String acc, String refname, int start, int stop )
    {
        size_t dot = acc . find_last_of ( '.' );
        if ( dot != string :: npos )
        {
            String extension = acc . substr ( dot );
            if ( extension == ".bam" || extension == ".BAM" )
            {
                run_bam ( acc, refname, start, stop );
                return;
            }
        }

        run_csra ( acc, refname, start, stop );
    }


};

int main ( int argc, char const *argv[] )
{
    if ( argc != 5 )
    {
        cerr << "Usage: AlignSliceTest accession reference start stop\n";
    }
    else try
    {
        ncbi::NGS::setAppVersionString ( "AlignSliceTest.1.1.0" );
        AlignSliceTest::run ( argv[1], argv[2], atoi ( argv[3] ), atoi ( argv[4] ) );
        return 0;
    }
    catch ( ErrorMsg & x )
    {
        cerr <<  x.toString () << '\n';
    }
    catch ( exception & x )
    {
        cerr <<  x.what () << '\n';
    }
    catch ( ... )
    {
        cerr <<  "unknown exception\n";
    }

    return 10;
}
