// Copyright (c) 2014-2015, 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.
//
//  * Redistributions in binary form must reproduce the above
//    copyright notice, this list of conditions and the following
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//    with the distribution.
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// GRANTED BY THIS LICENSE. THIS SOFTWARE IS PROVIDED BY PACIFIC
// BIOSCIENCES AND ITS CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED
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// SUCH DAMAGE.

// Author: Derek Barnett

#ifdef PBBAM_TESTING
#define private public
#endif

#include "TestData.h"
#include <gtest/gtest.h>
#include <pbbam/EntireFileQuery.h>
#include <string>
using namespace PacBio;
using namespace PacBio::BAM;
using namespace std;

const string inputBamFn = tests::Data_Dir + "/ex2.bam";

TEST(EntireFileQueryTest, CountRecords)
{
    EXPECT_NO_THROW(
    {
        // open input BAM file
        BamFile bamFile(inputBamFn);

        // count records
        int count = 0;
        EntireFileQuery entireFile(bamFile);
        for (const BamRecord& record : entireFile) {
            (void)record;
            ++count;
        }

        EXPECT_EQ(3307, count);
    });
}

TEST(EntireFileQueryTest, NonConstBamRecord)
{
    EXPECT_NO_THROW(
    {
        // open input BAM file
        BamFile bamFile(inputBamFn);

        // count records
        int count = 0;
        EntireFileQuery entireFile(bamFile);
        for (BamRecord& record : entireFile) {
            (void)record;
            ++count;
        }

        EXPECT_EQ(3307, count);
    });
}

TEST(BamRecordTest, HandlesDeletionOK)
{
    // this file raised no error in Debug mode, but segfaulted when
    // trying to access the aligned qualities in Release mode

    EXPECT_NO_THROW(
    {
        // open input BAM file
        const string problemBamFn = tests::Data_Dir + "/segfault.bam";
        BamFile bamFile(problemBamFn);

        // count records
        int count = 0;
        EntireFileQuery entireFile(bamFile);
        for (const BamRecord& record : entireFile) {

            const auto rawQualities     = record.Qualities(Orientation::GENOMIC, false);
            const auto alignedQualities = record.Qualities(Orientation::GENOMIC, true);

            const string rawExpected =
                "IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII";

            // 1=1D98=
            const string alignedExpected =
                "I!IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII";

            EXPECT_EQ(rawExpected,     rawQualities.Fastq());
            EXPECT_EQ(alignedExpected, alignedQualities.Fastq());

            ++count;
        }

        EXPECT_EQ(1, count);
    });
}


TEST(BamRecordTest, ReferenceName)
{
    // check reference name of first record
//    {
        const string exampleBam  = tests::Data_Dir + "/ex2.bam";
        BamFile bamFile(exampleBam);
        EntireFileQuery records(bamFile);

        auto it = records.begin();
        auto record = *it;

//        EXPECT_EQ("seq1", records.begin()->ReferenceName());
//    }

//    // unmapped records have no reference name, should throw
//    {
//        const string exampleBam  = tests::Data_Dir + "/unmap1.bam";
//        BamFile bamFile(exampleBam);
//        staging::EntireFileQuery records(bamFile);

//        EXPECT_THROW(records.begin()->ReferenceName(), std::exception);
//    }
}

// add add'l special cases as needed
