/*===========================================================================
*
*                            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
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*/

/**
* Unit tests for NGS C interface, CSRA1 archives, ReferenceWindow-related functions
*/

#include "ngs_c_fixture.hpp"

#include <kdb/manager.h>

#include <vdb/manager.h>
#include <vdb/vdb-priv.h>

#include <klib/printf.h>

#include <limits.h>

using namespace std;
using namespace ncbi::NK;

TEST_SUITE(NgsCsra1RefWinTestSuite);

const char* CSRA1_PrimaryOnly   = "SRR1063272";
const char* CSRA1_WithSecondary = "SRR833251";
const char* CSRA1_WithCircularReference = "SRR821492";

class CSRA1_Fixture : public NGS_C_Fixture
{
public:
    CSRA1_Fixture()
    : m_align (0)
    {
    }
    ~CSRA1_Fixture()
    {
    }
    virtual void Release()
    {
        if (m_ctx != 0)
        {
            if (m_align != 0)
            {
                NGS_AlignmentRelease ( m_align, m_ctx );
            }
        }
        NGS_C_Fixture :: Release ();
    }

    void GetAlignment(uint64_t id)
    {
        stringstream str;
        str << id;
        m_align = NGS_ReadCollectionGetAlignment ( m_coll, m_ctx, str . str () . c_str () );
    }
    void SkipAlignments ( size_t num, bool print = false )
    {
        for (size_t i = 0; i < num; ++i)
        {
            if ( ! NGS_AlignmentIteratorNext ( m_align, m_ctx ) )
                throw logic_error ("premature end of iterator");
            if ( m_ctx -> rc != 0 )
                throw logic_error ("NGS_AlignmentIteratorNext failed");

            if (print)
                cout << toString ( NGS_AlignmentGetAlignmentId ( m_align, m_ctx ), m_ctx, true ) << endl;
        }
    }
    void PrintAlignment ()
    {
        cout << "id=" << toString ( NGS_AlignmentGetAlignmentId ( m_align, m_ctx ), m_ctx, true )
             << " pos=" << NGS_AlignmentGetAlignmentPosition ( m_align, m_ctx )
             << " len=" << NGS_AlignmentGetAlignmentLength ( m_align, m_ctx )
             << ( NGS_AlignmentIsPrimary ( m_align, m_ctx ) ? " PRI" : " SEC" )
             << " mapq=" << NGS_AlignmentGetMappingQuality( m_align, m_ctx )
             << endl;
    }

    bool NextId (const string& p_expected)
    {
        if ( ! NGS_AlignmentIteratorNext ( m_align, m_ctx ) || m_ctx -> rc != 0 )
        {
            cout << "NextId: NGS_AlignmentIteratorNext FAILED" << endl;
            return false;
        }
        string actual = toString ( NGS_AlignmentGetAlignmentId ( m_align, m_ctx ), m_ctx, true );
        if ( p_expected !=  actual )
        {
            cout << "NextId: expected '" << p_expected << "', actual '" << actual << "'" <<endl;
            return false;
        }
        return m_ctx -> rc == 0;
    }

    bool VerifyOrder()
    {
        uint64_t prevPos = 0;
        uint64_t prevLen = 0;
        bool     prevIsPrimary = true;
        int      prevMapq = 0;
        while ( NGS_AlignmentIteratorNext ( m_align, m_ctx ) )
        {
            uint64_t newPos = NGS_AlignmentGetAlignmentPosition ( m_align, m_ctx );
            uint64_t newLen = NGS_AlignmentGetAlignmentLength ( m_align, m_ctx );
            bool     newIsPrimary = NGS_AlignmentIsPrimary ( m_align, m_ctx );
            int      newMapq = NGS_AlignmentGetMappingQuality( m_align, m_ctx );
            if (prevPos > newPos)
            {
                PrintAlignment();
                return false;
            }
            if ( prevPos == newPos )
            {
                if ( prevLen < newLen )
                {
                    PrintAlignment();
                    return false;
                }
                if ( prevLen == newLen )
                {
                    if ( ! ( prevIsPrimary || ! newIsPrimary) )
                    {
                        PrintAlignment();
                        return false;
                    }
                    if ( prevIsPrimary == newIsPrimary )
                    {
                        if ( prevMapq < newMapq )
                        {
                            PrintAlignment();
                            return false;
                        }
                    }
                }
            }
            prevPos = newPos;
            prevLen = newLen;
            prevIsPrimary = newIsPrimary;
            prevMapq = newMapq;
        }
        return true;
    }

    NGS_Alignment*      m_align;
};

// ReferenceWindow as an Alignment
FIXTURE_TEST_CASE(CSRA1_NGS_ReferenceWindow_NoAccessBeforeNext, CSRA1_Fixture)
{
    ENTRY_GET_REF ( CSRA1_PrimaryOnly, "supercont2.1" );

    m_align = NGS_ReferenceGetAlignments ( m_ref, ctx, true, false );

    REQUIRE_NULL ( NGS_AlignmentGetAlignmentId ( m_align, ctx ) );
    REQUIRE_FAILED ();
    REQUIRE_NULL ( NGS_AlignmentGetReferenceSpec ( m_align, ctx ) );
    REQUIRE_FAILED ();
    NGS_AlignmentGetMappingQuality ( m_align, ctx );
    REQUIRE_FAILED ();
    REQUIRE_NULL ( NGS_AlignmentGetReadGroup ( m_align, ctx ) );
    REQUIRE_FAILED ();
    REQUIRE_NULL ( NGS_AlignmentGetReadId ( m_align, ctx ) );
    REQUIRE_FAILED ();
    REQUIRE_NULL ( NGS_AlignmentGetClippedFragmentBases ( m_align, ctx ) );
    REQUIRE_FAILED ();
    REQUIRE_NULL ( NGS_AlignmentGetClippedFragmentQualities ( m_align, ctx ) );
    REQUIRE_FAILED ();
    NGS_AlignmentIsPrimary ( m_align, ctx );
    REQUIRE_FAILED ();
    NGS_AlignmentGetAlignmentPosition ( m_align, ctx );
    REQUIRE_FAILED ();
    NGS_AlignmentGetAlignmentLength ( m_align, ctx );
    REQUIRE_FAILED ();
    NGS_AlignmentGetIsReversedOrientation ( m_align, ctx );
    REQUIRE_FAILED ();
    NGS_AlignmentGetSoftClip ( m_align, ctx, true );
    REQUIRE_FAILED ();
    NGS_AlignmentGetTemplateLength ( m_align, ctx );
    REQUIRE_FAILED ();
    REQUIRE_NULL ( NGS_AlignmentGetShortCigar ( m_align, ctx, true ) );
    REQUIRE_FAILED ();
    REQUIRE_NULL ( NGS_AlignmentGetLongCigar ( m_align, ctx, true ) );
    REQUIRE_FAILED ();
    NGS_AlignmentIsFirst ( m_align, ctx );
    REQUIRE_FAILED ();

    REQUIRE ( ! NGS_AlignmentHasMate ( m_align, ctx ) );
    REQUIRE ( ! FAILED () ); /* HasMate does not throw */

    REQUIRE_NULL ( NGS_AlignmentGetMateAlignmentId ( m_align, ctx ) );
    REQUIRE_FAILED ();
    REQUIRE_NULL ( NGS_AlignmentGetMateAlignment ( m_align, ctx ) );
    REQUIRE_FAILED ();
    REQUIRE_NULL ( NGS_AlignmentGetMateReferenceSpec ( m_align, ctx ) );
    REQUIRE_FAILED ();
    NGS_AlignmentGetMateIsReversedOrientation ( m_align, ctx );
    REQUIRE_FAILED ();

    // fragment functions
    REQUIRE_NULL ( NGS_FragmentGetId ( (NGS_Fragment*)m_align, ctx ) );
    REQUIRE_FAILED ();
    REQUIRE_NULL ( NGS_FragmentGetSequence ( (NGS_Fragment*)m_align, ctx, 2, 5 ) );
    REQUIRE_FAILED ();
    REQUIRE_NULL ( NGS_FragmentGetQualities ( (NGS_Fragment*)m_align, ctx, 2, 5 ) );
    REQUIRE_FAILED ();

    EXIT;
}

FIXTURE_TEST_CASE(CSRA1_NGS_ReferenceWindow_AccessAfterNext, CSRA1_Fixture)
{
    ENTRY_GET_REF ( CSRA1_PrimaryOnly, "supercont2.1" );

    m_align = NGS_ReferenceGetAlignments ( m_ref, ctx, true, false );
    REQUIRE ( NGS_AlignmentIteratorNext ( m_align, ctx ) );
    REQUIRE ( ! FAILED () );

    REQUIRE_STRING ( string ( CSRA1_PrimaryOnly ) + ".PA.1", NGS_AlignmentGetAlignmentId ( m_align, ctx ) );
    REQUIRE ( ! FAILED () );

    REQUIRE_STRING ( "supercont2.1", NGS_AlignmentGetReferenceSpec ( m_align, ctx ) );
    REQUIRE ( ! FAILED () );

    REQUIRE_EQ ( 60, NGS_AlignmentGetMappingQuality ( m_align, ctx ) );
    REQUIRE ( ! FAILED () );

    REQUIRE_STRING ( "C1ELY.6", NGS_AlignmentGetReadGroup ( m_align, ctx ) );
    REQUIRE ( ! FAILED () );

    REQUIRE_STRING ( string ( CSRA1_PrimaryOnly ) + ".R.1", NGS_AlignmentGetReadId ( m_align, ctx ) );
    REQUIRE ( ! FAILED () );

    REQUIRE_STRING ( "ACTCGACATTCTGCCTTCGACCTATCTTTCTCCTCTCCCAGTCATCGCCCAGTAGAATTACCAGGCAATGAACCAGGGCCTTCCATCCCAACGGCACAGCA",
                     NGS_AlignmentGetClippedFragmentBases ( m_align, ctx ) );
    REQUIRE ( ! FAILED () );

    REQUIRE_STRING ( "@@CDDBDFFBFHFIEEFGIGGHIEHIGIGGFGEGAFDHIIIIIGGGDFHII;=BF@FEHGIEEH?AHHFHFFFFDC5'5=?CC?ADCD@AC??9BDDCDB<",
                     NGS_AlignmentGetClippedFragmentQualities ( m_align, ctx ) );
    REQUIRE ( ! FAILED () );

    REQUIRE ( NGS_AlignmentIsPrimary ( m_align, ctx ) );
    REQUIRE ( ! FAILED () );

    REQUIRE_EQ ( (int64_t)85, NGS_AlignmentGetAlignmentPosition ( m_align, ctx ) );
    REQUIRE ( ! FAILED () );

    REQUIRE_EQ ( (uint64_t)101, NGS_AlignmentGetAlignmentLength ( m_align, ctx ) );
    REQUIRE ( ! FAILED () );

    REQUIRE ( ! NGS_AlignmentGetIsReversedOrientation ( m_align, ctx ) );
    REQUIRE ( ! FAILED () );

    REQUIRE_EQ ( (int)0, NGS_AlignmentGetSoftClip ( m_align, ctx, true ) );
    REQUIRE ( ! FAILED () );

    REQUIRE_EQ ( (uint64_t)201, NGS_AlignmentGetTemplateLength ( m_align, ctx ) );
    REQUIRE ( ! FAILED () );

    REQUIRE_STRING ( "101M", NGS_AlignmentGetShortCigar ( m_align, ctx, true ) );
    REQUIRE ( ! FAILED () );

    REQUIRE_STRING ( "13=1X61=1X6=1X18=", NGS_AlignmentGetLongCigar ( m_align, ctx, true ) );
    REQUIRE ( ! FAILED () );

    REQUIRE ( NGS_AlignmentHasMate ( m_align, ctx ) );
    REQUIRE ( ! FAILED () );

    REQUIRE_STRING ( string ( CSRA1_PrimaryOnly ) + ".PA.2", NGS_AlignmentGetMateAlignmentId ( m_align, ctx ) );
    REQUIRE ( ! FAILED () );

    NGS_Alignment * mate = NGS_AlignmentGetMateAlignment ( m_align, ctx );
    REQUIRE_NOT_NULL ( mate );
    REQUIRE ( ! FAILED () );
    NGS_RefcountRelease ( NGS_AlignmentToRefcount ( mate ) , ctx );
    REQUIRE ( ! FAILED () );

    REQUIRE_STRING ( "supercont2.1", NGS_AlignmentGetMateReferenceSpec ( m_align, ctx ) );
    REQUIRE ( ! FAILED () );

    REQUIRE ( NGS_AlignmentGetMateIsReversedOrientation ( m_align, ctx ) );
    REQUIRE ( ! FAILED () );

    NGS_AlignmentIsFirst ( m_align, ctx );
    REQUIRE ( ! FAILED () );

    // fragment functions
    REQUIRE_STRING ( string ( CSRA1_PrimaryOnly ) + ".FA0.1", NGS_FragmentGetId ( (NGS_Fragment*)m_align, ctx ) );
    REQUIRE ( ! FAILED () );

    REQUIRE_STRING (  "ACTCG",  NGS_FragmentGetSequence ( (NGS_Fragment*)m_align, ctx, 0, 5 ) );
    REQUIRE ( ! FAILED () );

    REQUIRE_STRING ( "@@CDD",  NGS_FragmentGetQualities ( (NGS_Fragment*)m_align, ctx, 0, 5 ) );
    REQUIRE ( ! FAILED () );

    REQUIRE ( ! NGS_FragmentIteratorNext ( (NGS_Fragment*)m_align, ctx ) );
    REQUIRE_FAILED ();

    EXIT;
}

// Iteration over a ReferenceWindow

FIXTURE_TEST_CASE(CSRA1_NGS_ReferenceWindow_Primary, CSRA1_Fixture)
{
    ENTRY_GET_REF ( CSRA1_WithSecondary, "gi|169794206|ref|NC_010410.1|" );

    m_align = NGS_ReferenceGetAlignments ( m_ref, ctx, true, false );

    REQUIRE ( NextId ( string ( CSRA1_WithSecondary ) + ".PA.1") );
    REQUIRE ( NextId ( string ( CSRA1_WithSecondary ) + ".PA.2") );
    // etc

    EXIT;
}

FIXTURE_TEST_CASE(CSRA1_NGS_ReferenceWindow_Primary_Only, CSRA1_Fixture)
{
    ENTRY_GET_REF ( CSRA1_WithSecondary, "gi|169794206|ref|NC_010410.1|" );

    m_align = NGS_ReferenceGetAlignments ( m_ref, ctx, true, false );

    // skip to where a secondary alignment which would show up, between primary alignments 34 and 35
    SkipAlignments( 33 );

    REQUIRE ( NextId ( string ( CSRA1_WithSecondary ) + ".PA.34") );
    REQUIRE ( NextId ( string ( CSRA1_WithSecondary ) + ".PA.35") );

    EXIT;
}

FIXTURE_TEST_CASE(CSRA1_NGS_ReferenceWindow_Secondary, CSRA1_Fixture)
{
    ENTRY_GET_REF ( CSRA1_WithSecondary, "gi|169794206|ref|NC_010410.1|" );

    m_align = NGS_ReferenceGetAlignments ( m_ref, ctx, false, true );


    REQUIRE ( NextId ( string ( CSRA1_WithSecondary ) + ".SA.169") );
    REQUIRE ( NextId ( string ( CSRA1_WithSecondary ) + ".SA.170") );
    REQUIRE ( NextId ( string ( CSRA1_WithSecondary ) + ".SA.171") );
    REQUIRE ( NextId ( string ( CSRA1_WithSecondary ) + ".SA.172") );
    REQUIRE ( NextId ( string ( CSRA1_WithSecondary ) + ".SA.173") );
    REQUIRE ( NextId ( string ( CSRA1_WithSecondary ) + ".SA.174") );
    REQUIRE ( NextId ( string ( CSRA1_WithSecondary ) + ".SA.175") );
    REQUIRE ( NextId ( string ( CSRA1_WithSecondary ) + ".SA.176") );
    REQUIRE ( NextId ( string ( CSRA1_WithSecondary ) + ".SA.177") );
    REQUIRE ( NextId ( string ( CSRA1_WithSecondary ) + ".SA.178") );

    REQUIRE ( ! NGS_AlignmentIteratorNext ( m_align, ctx ) );

    EXIT;
}

FIXTURE_TEST_CASE(CSRA1_NGS_ReferenceWindow_PrimaryAndSecondary, CSRA1_Fixture)
{
    ENTRY_GET_REF ( CSRA1_WithSecondary, "gi|169794206|ref|NC_010410.1|" );

    m_align = NGS_ReferenceGetAlignments ( m_ref, ctx, true, true );

    // skip to where a secondary alignment is expected, between primary alignments 34 and 35
    SkipAlignments( 33 );
    REQUIRE ( NextId ( string ( CSRA1_WithSecondary ) + ".PA.34") );
    REQUIRE ( NextId ( string ( CSRA1_WithSecondary ) + ".SA.169") );
    REQUIRE ( NextId ( string ( CSRA1_WithSecondary ) + ".PA.35") );

    EXIT;
}

FIXTURE_TEST_CASE(CSRA1_NGS_ReferenceWindow_Sort, CSRA1_Fixture)
{
    ENTRY_GET_REF ( CSRA1_WithSecondary, "gi|169794206|ref|NC_010410.1|" );

    m_align = NGS_ReferenceGetAlignments ( m_ref, ctx, true, true );

    // secondary 170 should go before primary 62
    SkipAlignments( 61 ); /*skip over 60 primary and 1 secondary */
    REQUIRE ( NextId ( string ( CSRA1_WithSecondary ) + ".PA.61") );
    REQUIRE ( NextId ( string ( CSRA1_WithSecondary ) + ".SA.170") );
    REQUIRE ( NextId ( string ( CSRA1_WithSecondary ) + ".PA.62") );

    EXIT;
}

FIXTURE_TEST_CASE(CSRA1_NGS_ReferenceWindow_FullPrimary_Order, CSRA1_Fixture)
{
    ENTRY_GET_REF ( CSRA1_WithSecondary, "gi|169794206|ref|NC_010410.1|" );
    m_align = NGS_ReferenceGetAlignments ( m_ref, ctx, true, false );
    REQUIRE ( VerifyOrder() );
    EXIT;
}
FIXTURE_TEST_CASE(CSRA1_NGS_ReferenceWindow_FullSecondary_Order, CSRA1_Fixture)
{
    ENTRY_GET_REF ( CSRA1_WithSecondary, "gi|169794206|ref|NC_010410.1|" );
    m_align = NGS_ReferenceGetAlignments ( m_ref, ctx, false, true );
    REQUIRE ( VerifyOrder() );
    EXIT;
}
FIXTURE_TEST_CASE(CSRA1_NGS_ReferenceWindow_FullAll_Order, CSRA1_Fixture)
{
    ENTRY_GET_REF ( CSRA1_WithSecondary, "gi|169794206|ref|NC_010410.1|" );
    m_align = NGS_ReferenceGetAlignments ( m_ref, ctx, true, true );
    REQUIRE ( VerifyOrder() );
    EXIT;
}

FIXTURE_TEST_CASE(CSRA1_NGS_ReferenceWindow_Slice_Empty, CSRA1_Fixture)
{
    ENTRY_GET_REF( "SRR960954", "gi|296100371|ref|NC_014121.1|" );

    m_align = NGS_ReferenceGetAlignmentSlice ( m_ref, ctx, 0, 20000, false, false );
    REQUIRE ( ! FAILED () );

    REQUIRE ( ! NGS_AlignmentIteratorNext ( m_align, ctx ) );

    EXIT;
}
FIXTURE_TEST_CASE(CSRA1_NGS_ReferenceWindow_Slice_OutOfBounds, CSRA1_Fixture)
{
    ENTRY_GET_REF( "SRR960954", "gi|296100371|ref|NC_014121.1|" );

    m_align = NGS_ReferenceGetAlignmentSlice ( m_ref, ctx, NGS_ReferenceGetLength ( m_ref, ctx ), 1, true, true );
    REQUIRE ( ! FAILED () );

    REQUIRE ( ! NGS_AlignmentIteratorNext ( m_align, ctx ) );

    EXIT;
}

FIXTURE_TEST_CASE(CSRA1_NGS_ReferenceWindow_Slice, CSRA1_Fixture)
{
    ENTRY_GET_REF ( CSRA1_WithSecondary, "gi|169794206|ref|NC_010410.1|" );

    m_align = NGS_ReferenceGetAlignmentSlice ( m_ref, ctx, 517000, 100000, true, true );
    REQUIRE ( ! FAILED () );

    REQUIRE ( NextId ( string ( CSRA1_WithSecondary ) + ".PA.34") );
    REQUIRE ( NextId ( string ( CSRA1_WithSecondary ) + ".SA.169") );
    REQUIRE ( NextId ( string ( CSRA1_WithSecondary ) + ".PA.35") );

    EXIT;
}
FIXTURE_TEST_CASE(CSRA1_NGS_ReferenceWindow_Slice_Order, CSRA1_Fixture)
{
    ENTRY_GET_REF ( CSRA1_WithSecondary, "gi|169794206|ref|NC_010410.1|" );
    m_align = NGS_ReferenceGetAlignmentSlice ( m_ref, ctx, 517000, 100000, true, true );
    REQUIRE ( VerifyOrder() );
    EXIT;
}

FIXTURE_TEST_CASE(CSRA1_NGS_ReferenceWindow_Slice_NoSecondary, CSRA1_Fixture)
{   // VDB-2658: exception when there is no REFERENCE.SECONDARY_ALIGNMENT_IDS column
    const char* accesssion = "SRR644545";
    ENTRY_GET_REF ( accesssion, "NC_000004.11" );

    m_align = NGS_ReferenceGetAlignmentSlice ( m_ref, ctx, 0, 100000, true, true );
    REQUIRE ( ! FAILED () );

    REQUIRE ( NextId ( string ( accesssion ) + ".PA.1") );

    EXIT;
}

FIXTURE_TEST_CASE(CSRA1_NGS_ReferenceWindow_Slice_Overlap_Primary, CSRA1_Fixture)
{
    ENTRY_GET_REF ( CSRA1_PrimaryOnly, "supercont2.1" );

    m_align = NGS_ReferenceGetAlignmentSlice ( m_ref, ctx, 10000, 100, true, true );
    REQUIRE ( ! FAILED () );

    // 2 primary alignments start in the previous chunk and overlap with the chunk starting at 10000
    REQUIRE ( NextId ( string ( CSRA1_PrimaryOnly ) + ".PA.96") );
    REQUIRE ( NextId ( string ( CSRA1_PrimaryOnly ) + ".PA.97") );

    EXIT;
}
FIXTURE_TEST_CASE(CSRA1_NGS_ReferenceWindow_Slice_Overlap_Primary_Order, CSRA1_Fixture)
{
    ENTRY_GET_REF ( CSRA1_PrimaryOnly, "supercont2.1" );
    m_align = NGS_ReferenceGetAlignmentSlice ( m_ref, ctx, 10000, 100, true, true );
    REQUIRE ( VerifyOrder() );
    EXIT;
}

FIXTURE_TEST_CASE(CSRA1_NGS_ReferenceWindow_Slice_Overlap_Secondary, CSRA1_Fixture)
{
    ENTRY_GET_REF ( "SRR960954", "gi|296100371|ref|NC_014121.1|" );

    m_align = NGS_ReferenceGetAlignmentSlice ( m_ref, ctx, 4020000, 100, true, true );
    REQUIRE ( ! FAILED () );

    // a secondary alignment starts in the previous chunk and overlaps with the chunk starting at 4020000
    REQUIRE ( NextId ( string ( "SRR960954.SA.1384") ) );

    EXIT;
}

FIXTURE_TEST_CASE(CSRA1_NGS_ReferenceWindow_Slice_Overlap_PrimaryAndSecondary, CSRA1_Fixture)
{
    ENTRY_GET_REF ( "ERR225922", "2" );

    m_align = NGS_ReferenceGetAlignmentSlice ( m_ref, ctx, 203895000, 100, true, true );
    REQUIRE ( ! FAILED () );

    // several primary and secondary alignments start in the previous chunk and overlap with the chunk starting at 203895000
                                    // pos, len, mapq
    REQUIRE ( NextId ( string ( "ERR225922.PA.7023")    ) );
    REQUIRE ( NextId ( string ( "ERR225922.PA.7024")    ) );
    REQUIRE ( NextId ( string ( "ERR225922.PA.7025")    ) );
    REQUIRE ( NextId ( string ( "ERR225922.PA.7026")    ) );
    REQUIRE ( NextId ( string ( "ERR225922.PA.7028")    ) );    // 203894959, 76, 60 (higher MAPQ than 7027, same pos/len)
    REQUIRE ( NextId ( string ( "ERR225922.PA.7027")    ) );    // 203894959, 76, 60
    REQUIRE ( NextId ( string ( "ERR225922.PA.7029")    ) );    // 203894961, 76, 60 (same as 45681 but primary)
    REQUIRE ( NextId ( string ( "ERR225922.SA.45681")   ) );   // 203894961, 76, 60 (same as 7029 but secondary; id=45521+160 )
    REQUIRE ( NextId ( string ( "ERR225922.PA.7030")    ) );
    REQUIRE ( NextId ( string ( "ERR225922.PA.7031")    ) );
    REQUIRE ( NextId ( string ( "ERR225922.PA.7032")    ) );
    REQUIRE ( NextId ( string ( "ERR225922.PA.7033")    ) );
    REQUIRE ( NextId ( string ( "ERR225922.SA.45682")   ) );   // (id=45,521+161)
    REQUIRE ( ! NGS_AlignmentIteratorNext ( m_align, m_ctx ) );

    EXIT;
}
FIXTURE_TEST_CASE(CSRA1_NGS_ReferenceWindow_Slice_Overlap_PrimaryAndSecondary_Cutoff, CSRA1_Fixture)
{
    ENTRY_GET_REF ( "ERR225922", "2" );

    m_align = NGS_ReferenceGetAlignmentSlice ( m_ref, ctx, 203895050, 100, true, true ); // increase offset by 50 bases
    REQUIRE ( ! FAILED () );

    // compared to the test above, alignments that do not reach 50+ bases into the chunk are excluded
    REQUIRE ( NextId ( string ( "ERR225922.PA.7032")  ) );
    REQUIRE ( NextId ( string ( "ERR225922.PA.7033")  ) );
    REQUIRE ( NextId ( string ( "ERR225922.SA.45682") ) ); // 45,521+161
    REQUIRE ( ! NGS_AlignmentIteratorNext ( m_align, m_ctx ) );

    EXIT;
}
FIXTURE_TEST_CASE(CSRA1_NGS_ReferenceWindow_Slice_Overlap_PrimaryAndSecondary_FullCutoff, CSRA1_Fixture)
{
    ENTRY_GET_REF ( "ERR225922", "2" );

    m_align = NGS_ReferenceGetAlignmentSlice ( m_ref, ctx, 203895150, 100, true, true ); // increase offset to exclude all overlaps
    REQUIRE ( ! FAILED () );

    // none of the alignments reach 150+ bases into the chunk
    REQUIRE ( ! NGS_AlignmentIteratorNext ( m_align, m_ctx ) );

    EXIT;
}
FIXTURE_TEST_CASE(CSRA1_NGS_ReferenceWindow_Slice_Filtered, CSRA1_Fixture)
{
    ENTRY_GET_REF ( "ERR225922", "2" );

    const bool wants_primary = true;
    const bool wants_secondary = true;
#pragma message ( "filtering did not work prior to today's changes. I have set filter bits to allow this test to pass. the test should be fixed so that filters are set to the two desired flags." )
    const uint32_t filters = NGS_AlignmentFilterBits_pass_bad | NGS_AlignmentFilterBits_pass_dups |
        NGS_AlignmentFilterBits_no_wraparound | NGS_AlignmentFilterBits_start_within_window;
    const int32_t no_map_qual = 0;

    m_align = NGS_ReferenceGetFilteredAlignmentSlice ( m_ref, ctx, 203894961, 100, wants_primary, wants_secondary, filters, no_map_qual ); // only the ones that start within the window
    REQUIRE ( ! FAILED () );

    // only the alignments starting inside the slice (203894961)
    REQUIRE ( NextId ( string ( "ERR225922.PA.7029")    ) );    // 203894961, 76, 60 (same as 45681 but primary)
    REQUIRE ( NextId ( string ( "ERR225922.SA.45681")   ) );   // 203894961, 76, 60 (same as 7029 but secondary; id=45521+160 )
    REQUIRE ( NextId ( string ( "ERR225922.PA.7030")    ) );
    REQUIRE ( NextId ( string ( "ERR225922.PA.7031")    ) );
    REQUIRE ( NextId ( string ( "ERR225922.PA.7032")    ) );
    REQUIRE ( NextId ( string ( "ERR225922.PA.7033")    ) );
    REQUIRE ( NextId ( string ( "ERR225922.SA.45682")   ) );   // (id=45,521+161)
    REQUIRE ( ! NGS_AlignmentIteratorNext ( m_align, m_ctx ) );

    EXIT;
}

// FIXTURE_TEST_CASE(CSRA1_NGS_ReferenceWindow_Slice_Overlap_LookbackMoreThanOneChunk, CSRA1_Fixture)
// FIXTURE_TEST_CASE(CSRA1_NGS_ReferenceWindow_Slice_Overlap_LookbackDiffersForPrimaryAndSecondary, CSRA1_Fixture)
// FIXTURE_TEST_CASE(CSRA1_NGS_ReferenceWindow_Slice_Overlap_DefaultLookback, CSRA1_Fixture)

// circular reference

FIXTURE_TEST_CASE(CSRA1_NGS_ReferenceWindow_Circular, CSRA1_Fixture)
{
    ENTRY_GET_REF ( CSRA1_WithCircularReference, "chrM" );

    m_align = NGS_ReferenceGetAlignments ( m_ref, ctx, true, true );
    REQUIRE ( ! FAILED () );

    // chrM is 16569 bases long          // pos, len, mapq
    REQUIRE ( NextId ( string ( CSRA1_WithCircularReference ) + ".PA.4511855081") );   // 16528, 42, 0   // last base 16528+42-1 = 16569 (mod 16569 = #0 in 0-based coord)
    REQUIRE ( NextId ( string ( CSRA1_WithCircularReference ) + ".PA.4511855600") );   // 16529, 41, 66
    REQUIRE ( NextId ( string ( CSRA1_WithCircularReference ) + ".PA.4511855598") );   // 16529, 41, 35
    REQUIRE ( NextId ( string ( CSRA1_WithCircularReference ) + ".PA.4511855595") );   // 16529, 41, 28
    REQUIRE ( NextId ( string ( CSRA1_WithCircularReference ) + ".PA.4511855597") );   // 16529, 41, 4
    REQUIRE ( NextId ( string ( CSRA1_WithCircularReference ) + ".PA.4511855596") );   // 16529, 41, 0
    REQUIRE ( NextId ( string ( CSRA1_WithCircularReference ) + ".PA.4511855599") );   // 16529, 41, 0

    // ...

    // TODO: make sure alignments do not reappear at the end of iteration!
    EXIT;
}

FIXTURE_TEST_CASE(CSRA1_NGS_ReferenceWindow_Circular_Slice, CSRA1_Fixture)
{
    ENTRY_GET_REF ( CSRA1_WithCircularReference, "chrM" );

    m_align = NGS_ReferenceGetAlignmentSlice ( m_ref, ctx, 1, 100, true, true );
    REQUIRE ( ! FAILED () );
                                         // pos, len, mapq
    REQUIRE ( NextId ( string ( CSRA1_WithCircularReference ) + ".PA.4511856243") );   // -39, 41, 56
    REQUIRE ( NextId ( string ( CSRA1_WithCircularReference ) + ".PA.4511856241") );   // -39, 41, 0
    REQUIRE ( NextId ( string ( CSRA1_WithCircularReference ) + ".PA.4511856242") );   // -39, 41, 0
    REQUIRE ( NextId ( string ( CSRA1_WithCircularReference ) + ".PA.4511857002") );   // -38, 40, 74
    REQUIRE ( NextId ( string ( CSRA1_WithCircularReference ) + ".PA.4511857001") );   // -38, 40, 70

    // ...

    EXIT;
}

// NGS_ReferenceGetFilteredAlignmentSlice

uint64_t SliceOffset = 5;
uint64_t SliceLength = 100;

FIXTURE_TEST_CASE(CSRA1_NGS_ReferenceGetFilteredAlignmentSlice_Wraparound, CSRA1_Fixture )
{   // wraparound alignments overlapping with a slice
    ENTRY_GET_REF( CSRA1_WithCircularReference, "chrM" );

    const bool wants_primary = true;
    const bool wants_secondary = true;
#pragma message ( "filtering did not work prior to today's changes. I have set filter bits to allow this test to pass. the test should be fixed so that filters are set to the two desired flags." )
    const uint32_t no_filters = NGS_AlignmentFilterBits_pass_bad | NGS_AlignmentFilterBits_pass_dups;
    const int32_t no_map_qual = 0;

    m_align = NGS_ReferenceGetFilteredAlignmentSlice ( m_ref, ctx, SliceOffset, SliceLength, wants_primary, wants_secondary, no_filters, no_map_qual );
    REQUIRE ( ! FAILED () && m_align );
    REQUIRE ( NGS_AlignmentIteratorNext ( m_align, ctx ) );

    // the first returned alignment starts before the start of the circular reference, overlaps with slice
    int64_t pos = NGS_AlignmentGetAlignmentPosition ( m_align, ctx );
    REQUIRE_LT ( ( int64_t ) ( SliceOffset + SliceLength ), pos );

    // check for overlap with the slice
    uint64_t refLen = NGS_ReferenceGetLength ( m_ref, ctx );
    pos -= ( int64_t ) refLen;
    REQUIRE_GT ( ( int64_t ) 0, pos );
    REQUIRE_GE ( pos + NGS_AlignmentGetAlignmentLength( m_align, ctx ), SliceOffset );

    EXIT;
}

FIXTURE_TEST_CASE(CSRA1_NGS_ReferenceGetFilteredAlignmentSlice_Wraparound_StartInWindow, CSRA1_Fixture )
{   // when StartInWindow filter is specified, it removes wraparound alignments as well
    ENTRY_GET_REF( CSRA1_WithCircularReference, "chrM" );

    const bool wants_primary = true;
    const bool wants_secondary = true;
#pragma message ( "filtering did not work prior to today's changes. I have set filter bits to allow this test to pass. the test should be fixed so that filters are set to the two desired flags." )
    const uint32_t filters = NGS_AlignmentFilterBits_pass_bad | NGS_AlignmentFilterBits_pass_dups |
        NGS_AlignmentFilterBits_start_within_window;
    const int32_t no_map_qual = 0;

    m_align = NGS_ReferenceGetFilteredAlignmentSlice ( m_ref, ctx, SliceOffset, SliceLength, wants_primary, wants_secondary, filters, no_map_qual );
    REQUIRE ( ! FAILED () && m_align );
    REQUIRE ( NGS_AlignmentIteratorNext ( m_align, ctx ) );

    // the first returned alignment starts inside the slice
    int64_t pos = NGS_AlignmentGetAlignmentPosition ( m_align, ctx );
    REQUIRE_LE ( ( int64_t ) SliceOffset, pos );
    REQUIRE_LT ( pos, ( int64_t ) ( SliceOffset + SliceLength ) );

    EXIT;
}

FIXTURE_TEST_CASE(CSRA1_NGS_ReferenceGetFilteredAlignmentSlice_NoWraparound, CSRA1_Fixture )
{   // only removes wraparound alignments, not the ones starting before the slice
    ENTRY_GET_REF( CSRA1_WithCircularReference, "chrM" );

    const bool wants_primary = true;
    const bool wants_secondary = true;
#pragma message ( "filtering did not work prior to today's changes. I have set filter bits to allow this test to pass. the test should be fixed so that filters are set to the two desired flags." )
    const uint32_t filters = NGS_AlignmentFilterBits_pass_bad | NGS_AlignmentFilterBits_pass_dups |
        NGS_AlignmentFilterBits_no_wraparound;
    const int32_t no_map_qual = 0;

    m_align = NGS_ReferenceGetFilteredAlignmentSlice ( m_ref, ctx, SliceOffset, SliceLength, wants_primary, wants_secondary, filters, no_map_qual );
    REQUIRE ( ! FAILED () && m_align );
    REQUIRE ( NGS_AlignmentIteratorNext ( m_align, ctx ) );

    // the first returned alignment starts outside the slice but does not wrap around
    REQUIRE_GT ( ( int64_t ) SliceOffset, NGS_AlignmentGetAlignmentPosition ( m_align, ctx ) );

    EXIT;
}

FIXTURE_TEST_CASE(CSRA1_NGS_ReferenceGetFilteredAlignmentSlice_NoWraparound_StartInWindow, CSRA1_Fixture )
{   // when StartInWindow filter is specified, it removes wraparound alignments as well
    ENTRY_GET_REF( CSRA1_WithCircularReference, "chrM" );

    const bool wants_primary = true;
    const bool wants_secondary = true;
#pragma message ( "filtering did not work prior to today's changes. I have set filter bits to allow this test to pass. the test should be fixed so that filters are set to the two desired flags." )
    const uint32_t filters = NGS_AlignmentFilterBits_pass_bad | NGS_AlignmentFilterBits_pass_dups |
        NGS_AlignmentFilterBits_no_wraparound | NGS_AlignmentFilterBits_start_within_window;
    const int32_t no_map_qual = 0;

    m_align = NGS_ReferenceGetFilteredAlignmentSlice ( m_ref, ctx, SliceOffset, SliceLength, wants_primary, wants_secondary, filters, no_map_qual );
    REQUIRE ( ! FAILED () && m_align );
    REQUIRE ( NGS_AlignmentIteratorNext ( m_align, ctx ) );

    // the first returned alignment starts inside the slice
    int64_t pos = NGS_AlignmentGetAlignmentPosition ( m_align, ctx );
    REQUIRE_LE ( ( int64_t ) SliceOffset, pos );
    REQUIRE_LT ( pos, ( int64_t ) ( SliceOffset + SliceLength ) );

    EXIT;
}



#if 0
FIXTURE_TEST_CASE(CSRA1_NGS_ReferenceWindow_PrintEmAll_1, CSRA1_Fixture)
{
//    ENTRY_GET_REF ( "SRR960954" , "gi|296100371|ref|NC_014121.1|" );
//    ENTRY_GET_REF ( "SRR822962" , "chr2" );
//    ENTRY_GET_REF ( CSRA1_WithSecondary, "gi|169794206|ref|NC_010410.1|" );
//    ENTRY_GET_REF ( CSRA1_PrimaryOnly, "supercont2.1" );
    ENTRY_GET_REF ( CSRA1_WithCircularReference, "chrM" );

    m_align = NGS_ReferenceGetAlignments ( m_ref, ctx, true, true );

    uint64_t prevPos = 0;
    uint64_t prevLen = 0;
    bool     prevIsPrimary = true;
    int      prevMapq = 0;
    while ( NGS_AlignmentIteratorNext ( m_align, ctx ) )
    {

        uint64_t newPos = NGS_AlignmentGetAlignmentPosition ( m_align, m_ctx );
        uint64_t newLen = NGS_AlignmentGetAlignmentLength ( m_align, m_ctx );
        bool     newIsPrimary = NGS_AlignmentIsPrimary ( m_align, m_ctx );
        int      newMapq = NGS_AlignmentGetMappingQuality( m_align, m_ctx );

        PrintAlignment ();

/*        REQUIRE_LE (prevPos, newPos);
        if ( prevPos == newPos )
        {
            REQUIRE_GE ( prevLen, newLen );
            if ( prevLen == newLen )
            {
                REQUIRE ( prevIsPrimary || ! newIsPrimary);
                if ( prevIsPrimary == newIsPrimary )
                {
                    REQUIRE_GE ( prevMapq, newMapq );
                }
            }
        }*/
        prevPos = newPos;
        prevLen = newLen;
        prevIsPrimary = newIsPrimary;
        prevMapq = newMapq;
    }

    EXIT;
}
#endif
//////////////////////////////////////////// Main
extern "C"
{

#include <kapp/args.h>

ver_t CC KAppVersion ( void )
{
    return 0x1000000;
}
rc_t CC UsageSummary (const char * progname)
{
    return 0;
}

rc_t CC Usage ( const Args * args )
{
    return 0;
}

const char UsageDefaultName[] = "test-ngs_csra1_refwin";

rc_t CC KMain ( int argc, char *argv [] )
{
    rc_t m_coll=NgsCsra1RefWinTestSuite(argc, argv);
    return m_coll;
}

}

