/bio/Tests/Bio.TestAutomation/IO/BAM/BAMBvtTestCases.cs

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/****************************************************************************

 * BAMBvtTestCases.cs

 * 

 *   This file contains the BAM - Parsers and Formatters Bvt test cases.

 * 

***************************************************************************/



using System;

using System.Linq;

using System.Collections.Generic;

using System.IO;

using System.Text;



using Bio.TestAutomation.Util;

using Bio.Util.Logging;



using Microsoft.VisualStudio.TestTools.UnitTesting;

using Bio.IO.SAM;

using Bio.IO.BAM;

using Bio.IO.FastA;

using Bio.IO;

using System.Globalization;

using Bio;



namespace Bio.TestAutomation.IO.BAM

{

    /// <summary>

    /// BAM Bvt parser and formatter Test case implementation.

    /// </summary>

    [TestClass]

    public class BAMBvtTestCases

    {

        #region Enums



        /// <summary>

        /// BAM Parser ctor parameters used for different test cases.

        /// </summary>

        enum BAMParserParameters

        {

            StreamReader,

            FileName,

            ParseRangeFileName,

            ParseRangeWithIndex,

            ParserWithEncoding,

            IndexFile,

            IndexStreamWriter,

            StreamWriter,

            ParseRangeUsingRefSeq,

            ParseRangeUsingRefSeqAndFlag,

            ParseRangeUsingRefSeqUsingIndex,

            ParseRangeUsingIndexesAndFlag,

            Default

        }



        /// <summary>

        /// PairedReadType method parameters

        /// </summary>

        enum GetPairedReadTypeParameters

        {

            PaireReadTypeUsingLibraryName,

            PaireReadTypeUsingCloneLibraryInfo,

            PaireReadTypeUsingMeanAndDeviation,

            PaireReadTypeUsingReadsAndLibraryInfo,

            PaireReadTypeUsingReadsAndLibrary,

            GetInsertLength,

            Default

        }



        /// <summary>

        /// Get Paired parameters

        /// </summary>

        enum GetPairedReadParameters

        {

            GetPairedReadWithParameters,

            GetPairedReadWithLibraryName,

            GetPairedReadWithCloneLibraryInfo,

            Default

        }



        #endregion Enums



        #region Global Variables



        Utility utilityObj = new Utility(@"TestUtils\SAMBAMTestData\SAMBAMTestsConfig.xml");



        #endregion Global Variables



        #region Constructor



        /// <summary>

        /// Static constructor to open log and make other settings needed for test

        /// </summary>

        static BAMBvtTestCases()

        {

            Trace.Set(Trace.SeqWarnings);

            if (!ApplicationLog.Ready)

            {

                ApplicationLog.Open("bio.automation.log");

            }

        }



        #endregion Constructor



        #region BAM Parser Test Cases



        /// <summary>

        /// Validate BAM Parse(Stream) by passing valid BAM file

        /// Input : Small size BAM file.

        /// Output : Validation of aligned sequence.

        /// </summary>

        [TestMethod]

        [Priority(0)]

        [TestCategory("Priority0")]

        public void ValidateBAMParserWithStreamReader()

        {

            ValidateBAMParser(Constants.SmallSizeBAMFileNode,

                BAMParserParameters.StreamReader, false);

        }



        /// <summary>

        /// Validate BAM Parse(filename) by passing valid BAM file

        /// Input : Small size BAM file.

        /// Output : Validation of aligned sequence.

        /// </summary>

        [TestMethod]

        [Priority(0)]

        [TestCategory("Priority0")]

        public void ValidateBAMParserWithFilePath()

        {

            ValidateBAMParser(Constants.SmallSizeBAMFileNode,

                BAMParserParameters.FileName, false);

        }



        /// <summary>

        /// Validate BAM ParseRange(filename,RefIndex) by passing valid BAM file

        /// Input : Small size BAM file.

        /// Output : Validation of aligned sequence.

        /// </summary>

        [TestMethod]

        [Priority(0)]

        [TestCategory("Priority0")]

        public void ValidateBAMParserRangeWithFilePath()

        {

            ValidateBAMParser(Constants.SmallSizeBAMFileNode,

                BAMParserParameters.ParseRangeFileName, false);

        }



        /// <summary>

        /// Validate BAM ParseRange(filename,refSeqName) 

        /// by passing valid BAM file

        /// Input : Small size BAM file.

        /// Output : Validation of aligned sequence.

        /// </summary>

        [TestMethod]

        [Priority(0)]

        [TestCategory("Priority0")]

        public void ValidateBAMParseRangeUsingRefSeqName()

        {

            ValidateBAMParser(Constants.BAMFileWithSequenceRangeRefSeqsNode,

                BAMParserParameters.ParseRangeUsingRefSeq, false);

        }



        /// <summary>

        /// Validate BAM ParseRange(filename,refSeqName,flag) 

        /// by passing valid BAM file

        /// Input : Small size BAM file.

        /// Output : Validation of aligned sequence.

        /// </summary>

        [TestMethod]

        [Priority(0)]

        [TestCategory("Priority0")]

        public void ValidateBAMParseRangeUsingRefSeqNameAndFlag()

        {

            ValidateBAMParser(Constants.BAMFileWithSequenceRangeRefSeqsNode,

                BAMParserParameters.ParseRangeUsingRefSeqAndFlag, false);

        }



        /// <summary>

        /// Validate BAM ParseRange(filename,refSeqName,Start,end) 

        /// by passing valid BAM file

        /// Input : Small size BAM file.

        /// Output : Validation of aligned sequence.

        /// </summary>

        [TestMethod]

        [Priority(0)]

        [TestCategory("Priority0")]

        public void ValidateBAMParseRangeUsingStartAndEndIndex()

        {

            ValidateBAMParser(Constants.SeqRangeBAMFileNode,

                BAMParserParameters.ParseRangeUsingRefSeqUsingIndex, false);

        }



        /// <summary>

        /// Validate BAM ParseRange(filename,refSeqName,Start,end,bool) 

        /// by passing valid BAM file

        /// Input : Small size BAM file.

        /// Output : Validation of aligned sequence.

        /// </summary>

        [TestMethod]

        [Priority(0)]

        [TestCategory("Priority0")]

        public void ValidateBAMParseRangeUsingStartAndEndIndexWithFlag()

        {

            ValidateBAMParser(Constants.SeqRangeBAMFileNode,

                BAMParserParameters.ParseRangeUsingIndexesAndFlag, false);

        }



        /// <summary>

        /// Validate BAM GetPairedRead(Mean,Deviation)

        /// by passing valid BAM file

        /// Input : Small size BAM file.

        /// Output : Validation of aligned sequence.

        /// </summary>

        [TestMethod]

        [Priority(0)]

        [TestCategory("Priority0")]

        public void ValidatePairedReadUsingMeanAndDeviation()

        {

            ValidatePairedReads(Constants.PairedReadForSmallFileNodeName,

                GetPairedReadParameters.GetPairedReadWithParameters);

        }



        /// <summary>

        /// Validate BAM GetPairedRead()

        /// by passing valid BAM file

        /// Input : Small size BAM file.

        /// Output : Validation of aligned sequence.

        /// </summary>

        [TestMethod]

        [Priority(0)]

        [TestCategory("Priority0")]

        public void ValidatePairedReads()

        {

            ValidatePairedReads(Constants.PairedReadForSmallFileNodeName,

                GetPairedReadParameters.Default);

        }



        /// <summary>

        /// Validate BAM GetPairedRead(libraryName)

        /// by passing valid BAM file

        /// Input : Small size BAM file.

        /// Output : Validation of aligned sequence.

        /// </summary>

        [TestMethod]

        [Priority(0)]

        [TestCategory("Priority0")]

        public void ValidatePairedReadUsingLibraryName()

        {

            ValidatePairedReads(Constants.PairedReadForSmallFileNodeName,

                GetPairedReadParameters.GetPairedReadWithLibraryName);

        }



        /// <summary>

        /// Validate BAM GetPairedRead(CloneLibraryInfo)

        /// by passing valid BAM file

        /// Input : Small size BAM file.

        /// Output : Validation of aligned sequence.

        /// </summary>

        [TestMethod]

        [Priority(0)]

        [TestCategory("Priority0")]

        public void ValidatePairedReadUsingCloneLibraryInfo()

        {

            ValidatePairedReads(Constants.PairedReadForSmallFileNodeName,

                GetPairedReadParameters.GetPairedReadWithCloneLibraryInfo);

        }



        /// <summary>

        /// Validate BAM GetPairedReadType(PairedRead,CloneLibraryInfo)

        /// by passing valid BAM file

        /// Input : Small size BAM file.

        /// Output : Validation of aligned sequence.

        /// </summary>

        [TestMethod]

        [Priority(0)]

        [TestCategory("Priority0")]

        public void ValidatePairedReadTypeUsingCloneLibraryInfo()

        {

            ValidatePairedReadTypes(Constants.PairedReadTypesNode,

                GetPairedReadTypeParameters.PaireReadTypeUsingCloneLibraryInfo);

        }





        /// <summary>

        /// Validate BAM GetPairedReadType(PairedRead,Library)

        /// by passing valid BAM file

        /// Input : Small size BAM file.

        /// Output : Validation of aligned sequence.

        /// </summary>

        [TestMethod]

        [Priority(0)]

        [TestCategory("Priority0")]

        public void ValidatePairedReadTypeUsingLibrary()

        {

            ValidatePairedReadTypes(Constants.PairedReadTypesNode,

                GetPairedReadTypeParameters.PaireReadTypeUsingLibraryName);

        }



        /// <summary>

        /// Validate BAM GetPairedReadType(PairedRead,Mean,Devn)

        /// by passing valid BAM file

        /// Input : Small size BAM file.

        /// Output : Validation of aligned sequence.

        /// </summary>

        [TestMethod]

        [Priority(0)]

        [TestCategory("Priority0")]

        public void ValidatePairedReadTypeUsingMeanAndDeviation()

        {

            ValidatePairedReadTypes(Constants.PairedReadTypesForMeanAndDeviationNode,

                GetPairedReadTypeParameters.PaireReadTypeUsingMeanAndDeviation);

        }



        /// <summary>

        /// Validate BAM GetPairedReadType(Read1,Read2,Library)

        /// by passing valid BAM file

        /// Input : Small size BAM file.

        /// Output : Validation of aligned sequence.

        /// </summary>

        [TestMethod]

        [Priority(0)]

        [TestCategory("Priority0")]

        public void ValidatePairedReadTypeUsingReadsAndLibrary()

        {

            ValidatePairedReadTypes(Constants.PairedReadTypesForLibraryInfoNode,

                GetPairedReadTypeParameters.PaireReadTypeUsingReadsAndLibrary);

        }



        /// <summary>

        /// Validate BAM GetPairedReadType(Read1,Read2,CloneLibraryInfo)

        /// by passing valid BAM file

        /// Input : Small size BAM file.

        /// Output : Validation of aligned sequence.

        /// </summary>

        [TestMethod]

        [Priority(0)]

        [TestCategory("Priority0")]

        public void ValidatePairedReadTypeUsingReadsAndCloneLibraryInfo()

        {

            ValidatePairedReadTypes(Constants.PairedReadTypesForLibraryInfoNode,

                GetPairedReadTypeParameters.PaireReadTypeUsingReadsAndLibraryInfo);

        }



        /// <summary>

        /// Validate BAM GetInsertLength(Read1,Read2)

        /// by passing valid BAM file

        /// Input : Small size BAM file.

        /// Output : Validation of aligned sequence.

        /// </summary>

        [TestMethod]

        [Priority(0)]

        [TestCategory("Priority0")]

        public void ValidateInsertLengthForPairedReads()

        {

            ValidatePairedReadTypes(Constants.PairedReadTypesForLibraryInfoNode,

                GetPairedReadTypeParameters.GetInsertLength);

        }



        /// <summary>

        /// Validates the GetInsertLength method with a bool value passed for validate

        /// Input : Small size BAM file.

        /// Output : Validation of aligned sequence.

        /// </summary>

        /// </summary>

        [System.Diagnostics.CodeAnalysis.SuppressMessage("Microsoft.Usage", "CA2202:Do not dispose objects multiple times"), System.Diagnostics.CodeAnalysis.SuppressMessage("Microsoft.Usage", "CA1806:DoNotIgnoreMethodResults", MessageId = "System.String.Split(System.Char[])"), TestMethod]

        [Priority(0)]

        [TestCategory("Priority0")]

        public void ValidateGetInsertLengthWithValidate()

        {

            // Get input and output values from xml node.

            string bamFilePath = utilityObj.xmlUtil.GetTextValue(Constants.PairedReadTypesForLibraryInfoNode,

                Constants.FilePathNode);

            string mean = utilityObj.xmlUtil.GetTextValue(

                Constants.PairedReadTypesForLibraryInfoNode, Constants.MeanNode);

            string deviation = utilityObj.xmlUtil.GetTextValue(

                Constants.PairedReadTypesForLibraryInfoNode, Constants.DeviationValueNode);

            string[] insertLength = utilityObj.xmlUtil.GetTextValue(

               Constants.PairedReadTypesForLibraryInfoNode, Constants.InsertLengthNode).Split(',');

            IList<PairedRead> pairedReads = null;

            using (BAMParser bamParser = new BAMParser())

            {

                SequenceAlignmentMap seqAlignmentMapObj = bamParser.Parse(bamFilePath);

                int i = 0;

                try

                {

                    pairedReads = seqAlignmentMapObj.GetPairedReads(float.Parse(mean, (IFormatProvider)null),

                        float.Parse(deviation, (IFormatProvider)null));

                    foreach (PairedRead read in pairedReads)

                    {

                        //pass true for validate parameter

                        int length = PairedRead.GetInsertLength(read.Read1, read.Read2, true);

                        Assert.AreEqual(length.ToString((IFormatProvider)null), insertLength[i]);

                        i++;

                    }

                    ApplicationLog.WriteLine(string.Format((IFormatProvider)null,

                                "BAM Parser BVT : Validated GetInsertLength Successfully"));

                }

                finally

                {

                    bamParser.Dispose();

                }

            }

        }





        #endregion BAM Parser Test Cases



        #region BAM Formatter Test Cases



        /// <summary>

        /// Validate format(seqAlignment,bamFile,indexFile) by 

        /// parsing formatting valid BAM file.

        /// Input : Small size BAM file and index file.

        /// Output : Validation of aligned sequence.

        /// </summary>

        [TestMethod]

        [Priority(0)]

        [TestCategory("Priority0")]

        public void ValidateBAMFormatterWithIndexFile()

        {

            ValidateBAMFormatter(Constants.SmallSizeBAMFileNode,

                BAMParserParameters.IndexFile);

        }



        /// <summary>

        /// Validate format(seqAlignment, Stream) by 

        /// parsing formatting valid BAM file.

        /// Input : Small size BAM file.

        /// Output : Validation of aligned sequence.

        /// </summary>

        [TestMethod]

        [Priority(0)]

        [TestCategory("Priority0")]

        public void ValidateBAMFormatterWithStreamWriter()

        {

            ValidateBAMFormatter(Constants.SmallSizeBAMFileNode,

                BAMParserParameters.StreamWriter);

        }



        /// <summary>

        /// Validate format(seqAlignment, filename) by

        /// parsing formatting valid BAM file.

        /// Input : Small size BAM file.

        /// Output : Validation of aligned sequence.

        /// </summary>

        [TestMethod]

        [Priority(0)]

        [TestCategory("Priority0")]

        public void ValidateBAMFormatterWithFilename()

        {

            ValidateBAMFormatter(Constants.SmallSizeBAMFileNode,

                BAMParserParameters.FileName);

        }



        /// <summary>

        /// Validate create bam index file

        /// </summary>

        [TestMethod]

        [Priority(0)]

        [TestCategory("Priority0")]

        public void ValidateCreateBAMIndexFile()

        {

               string bamFilePath = utilityObj.xmlUtil.GetTextValue(Constants.MediumSizeBAMFileNode,

                        Constants.FilePathNode);

                BAMFormatter.CreateBAMIndexFile(bamFilePath);

        }



        #endregion BAM Formatter Test Cases.



        #region BAM Sort Test Cases



        /// <summary>

        /// Validates BAM Sort on ReadNames

        /// </summary>

        [TestMethod]

        [Priority(0)]

        [TestCategory("Priority0")]

        public void ValidateSortByReadNames()

        {

            using (BAMParser parser = new BAMParser())

            {

                string bamFilePath = utilityObj.xmlUtil.GetTextValue(Constants.MediumSizeBAMFileNode,

                    Constants.FilePathNode);

                SequenceAlignmentMap seqAlignment = parser.Parse(bamFilePath);

                this.ValidateSort(seqAlignment, BAMSortByFields.ReadNames);

            }

        }



        /// <summary>

        /// Validates BAM Sort by ChromosomeCoordinates

        /// </summary>

        [TestMethod]

        [Priority(0)]

        [TestCategory("Priority0")]

        public void ValidateSortByChromosomeCoordinates()

        {

            using (BAMParser parser = new BAMParser())

            {

                string bamFilePath = utilityObj.xmlUtil.GetTextValue(Constants.MediumSizeBAMFileNode,

                    Constants.FilePathNode);

                Assert.IsNotNull(bamFilePath);



                SequenceAlignmentMap seqAlignment = parser.Parse(bamFilePath);

                this.ValidateSort(seqAlignment, BAMSortByFields.ChromosomeCoordinates);

            }

        }



        /// <summary>

        /// Validates BAM Sort by ChromosomeNameAndCoordinates

        /// </summary>

        [TestMethod]

        [Priority(0)]

        [TestCategory("Priority0")]

        public void ValidateSortByChromosomeNameAndCoordinates()

        {

            using (BAMParser parser = new BAMParser())

            {

                string bamFilePath = utilityObj.xmlUtil.GetTextValue(Constants.MediumSizeBAMFileNode,

                    Constants.FilePathNode);

                Assert.IsNotNull(bamFilePath);



                SequenceAlignmentMap seqAlignment = parser.Parse(bamFilePath);

                this.ValidateSort(seqAlignment, BAMSortByFields.ChromosomeNameAndCoordinates);

            }

        }



        #endregion BAM Sort Test Cases



        #region SAM BAM InterConversion Test Cases



        /// <summary>

        /// Validate BAM to SAM file conversion.

        /// Input : BAM file.

        /// Output : SAM file.

        /// </summary>

        [TestMethod]

        [Priority(0)]

        [TestCategory("Priority0")]

        public void ValidateBAMToSAMConversion()

        {

            // Get values from xml config file.

            string expectedSamFilePath = utilityObj.xmlUtil.GetTextValue(Constants.BAMToSAMConversionNode,

               Constants.FilePathNode1);

            string bamFilePath = utilityObj.xmlUtil.GetTextValue(Constants.BAMToSAMConversionNode,

                Constants.FilePathNode);



            using (BAMParser bamParserObj = new BAMParser())

            {

                using (SAMParser samParserObj = new SAMParser())

                {

                    SAMFormatter samFormatterObj = new SAMFormatter();

                    SequenceAlignmentMap samSeqAlignment = null;

                    SequenceAlignmentMap bamSeqAlignment = null;



                    // Parse expected SAM file.

                    SequenceAlignmentMap expextedSamAlignmentObj = samParserObj.Parse(

                        expectedSamFilePath);



                    // Parse a BAM file.

                    bamSeqAlignment = bamParserObj.Parse(bamFilePath);



                    // Format BAM sequenceAlignment object to SAM file.

                    samFormatterObj.Format(bamSeqAlignment, Constants.SAMTempFileName);



                    // Parse a formatted SAM file.

                    samSeqAlignment = samParserObj.Parse(Constants.SAMTempFileName);



                    // Validate converted SAM file with expected SAM file.

                    Assert.IsTrue(CompareSequencedAlignmentHeader(samSeqAlignment, expextedSamAlignmentObj));



                    // Validate SAM file aligned sequences.

                    Assert.IsTrue(CompareAlignedSequences(samSeqAlignment, expextedSamAlignmentObj));

                }

            }



            // Log message to VSTest GUI.

            ApplicationLog.WriteLine(string.Format((IFormatProvider)null,

                "BAM Parser BVT : Validated the BAM->SAM conversion successfully"));

            Console.WriteLine(string.Format((IFormatProvider)null,

                "BAM Parser BVT : Validated the BAM->SAM conversion successfully"));



            // Delete temporary file.

            File.Delete(Constants.SAMTempFileName);

            ApplicationLog.WriteLine("Deleted the temp file created.");

        }



        /// <summary>

        /// Validate SAM to BAM file conversion.

        /// Input : SAM file.

        /// Output : BAM file.

        /// </summary>

        [TestMethod]

        [Priority(0)]

        [TestCategory("Priority0")]

        public void ValidateSAMToBAMConversion()

        {

            // Get values from xml config file.

            string expectedBamFilePath = utilityObj.xmlUtil.GetTextValue(

                Constants.BAMToSAMConversionNode, Constants.FilePathNode);

            string samFilePath = utilityObj.xmlUtil.GetTextValue(

                Constants.BAMToSAMConversionNode, Constants.FilePathNode1);



            using (BAMParser bamParserObj = new BAMParser())

            {

                using (SAMParser samParserObj = new SAMParser())

                {

                    BAMFormatter bamFormatterObj = new BAMFormatter();

                    SequenceAlignmentMap samSeqAlignment = null;

                    SequenceAlignmentMap bamSeqAlignment = null;



                    // Parse expected BAM file.

                    SequenceAlignmentMap expextedBamAlignmentObj = bamParserObj.Parse(

                        expectedBamFilePath);



                    // Parse a SAM file.

                    samSeqAlignment = samParserObj.Parse(samFilePath);



                    // Format SAM sequenceAlignment object to BAM file.

                    bamFormatterObj.Format(samSeqAlignment, Constants.BAMTempFileName);



                    // Parse a formatted BAM file.

                    bamSeqAlignment = bamParserObj.Parse(Constants.BAMTempFileName);



                    // Validate converted BAM file with expected BAM file.

                    Assert.IsTrue(CompareSequencedAlignmentHeader(bamSeqAlignment, expextedBamAlignmentObj));



                    // Validate BAM file aligned sequences.

                    Assert.IsTrue(CompareAlignedSequences(bamSeqAlignment, expextedBamAlignmentObj));

                }

            }



            // Log message to VSTest GUI.

            ApplicationLog.WriteLine(string.Format((IFormatProvider)null,

                "BAM Parser BVT : Validated the SAM->BAM conversion successfully"));

            Console.WriteLine(string.Format((IFormatProvider)null,

                "BAM Parser BVT : Validated the SAM->BAM conversion successfully"));



            // Delete temporary file.

            File.Delete(Constants.BAMTempFileName);

            ApplicationLog.WriteLine("Deleted the temp file created.");

        }



        #endregion SAM BAM InterConversion Test Cases



        #region Helper Methods

        /// <summary>

        /// calls the Sort() method in BAMSort and checks if a BAMSortedIndex is returned.

        /// </summary>

        /// <param name="seqAlignment">SequenceAlignmentMap to be sorted</param>

        /// <param name="sortType">The sort type to be used when sorting using BAMSort</param>

        void ValidateSort(SequenceAlignmentMap seqAlignment, BAMSortByFields sortType)

        {

            BAMSort sorter = new BAMSort(seqAlignment, sortType);

            IList<BAMSortedIndex> sortedIndex = sorter.Sort();

            Assert.IsNotNull(sortedIndex);

            Assert.IsTrue(IsSortedIndex(sortedIndex,sortType));

        }



        /// <summary>

        /// Checks if the BAMSorted Index is sorted

        /// </summary>

        /// <param name="sortedIndex">The BAMSortedIndex that needs to be checked for proper sorting</param>

        /// <param name="sortType">The sort type to be used when sorting using BAMSort</param>

        /// <returns>true if properly sorted</returns>

        bool IsSortedIndex(IList<BAMSortedIndex> sortedIndex, BAMSortByFields sortType)

        {

            bool isSorted = true;

            string matchFile1 = utilityObj.xmlUtil.GetTextValue(Constants.MediumSizeBAMFileNode,

                    Constants.MediumSizeBAMSortOutputMatchReadNames);

            string matchFile2 = utilityObj.xmlUtil.GetTextValue(Constants.MediumSizeBAMFileNode,

                    Constants.MediumSizeBAMSortOutputMatchChromosomeCoordinates);

            string matchFile3 = utilityObj.xmlUtil.GetTextValue(Constants.MediumSizeBAMFileNode,

                    Constants.MediumSizeBAMSortOutputMatchChromosomeNameAndCoordinates);

            string temp = string.Empty;



            switch (sortType)

            {

                case BAMSortByFields.ReadNames:

                        temp = File.ReadAllText(matchFile1);

                        Assert.AreEqual(temp, getSortedOutput(sortedIndex));

                        break;

                case BAMSortByFields.ChromosomeCoordinates:

                        temp = File.ReadAllText(matchFile2);

                        Assert.AreEqual(temp, getSortedOutput(sortedIndex));

                        break;

                case BAMSortByFields.ChromosomeNameAndCoordinates:

                        temp = File.ReadAllText(matchFile3);

                        Assert.AreEqual(temp, getSortedOutput(sortedIndex));

                        break;

                default:

                        break;

            }

            return isSorted;

        }



        /// <summary>

        /// Gets the sorted outpur from the BAMSortedIndex 

        /// </summary>

        /// <param name="sortedIndex">The BAMSortedIndex for which sortedindex values are required.</param>

        /// <returns>Sorted index values as a string</returns>

        [System.Diagnostics.CodeAnalysis.SuppressMessage("Microsoft.Performance", "CA1822:MarkMembersAsStatic")]

        private string getSortedOutput(IList<BAMSortedIndex> sortedIndex)

        {

            using (BAMParser parser = new BAMParser())

            {

                BAMSortedIndex index = sortedIndex.ElementAt(0);

                IEnumerator<int> sortedIndexList = index.GetEnumerator();

                StringBuilder temp = new StringBuilder();

                temp.Append(sortedIndexList.Current.ToString((IFormatProvider)null));

                while (sortedIndexList.MoveNext())

                {

                    temp.Append("|" + sortedIndexList.Current.ToString((IFormatProvider)null));

                }

                Assert.IsNotNull(temp);

                Assert.AreNotEqual(0, temp.Length);

                sortedIndexList.Dispose();

                return temp.ToString();

            }

        }



        /// <summary>

        /// Parse BAM and validate parsed aligned sequences and its properties.

        /// </summary>

        /// <param name="nodeName">Different xml nodes used for different test cases</param>

        /// <param name="BAMParserPam">BAM Parse method parameters</param>

        /// <param name="IsEncoding">True for BAMParser ctor with encoding.

        /// False otherwise </param>

        void ValidateBAMParser(string nodeName,

            BAMParserParameters BAMParserPam,

            bool IsReferenceIndex)

        {

            // Get input and output values from xml node.

            string bamFilePath = utilityObj.xmlUtil.GetTextValue(nodeName,

                Constants.FilePathNode);

            string expectedAlignedSeqFilePath = utilityObj.xmlUtil.GetTextValue(

                nodeName, Constants.ExpectedSequence);

            string refIndexValue = utilityObj.xmlUtil.GetTextValue(

                nodeName, Constants.RefIndexNode);

            string startIndexValue = utilityObj.xmlUtil.GetTextValue(

                nodeName, Constants.StartIndexNode);

            string endIndexValue = utilityObj.xmlUtil.GetTextValue(

                nodeName, Constants.EndIndexNode);

            string alignedSeqCount = utilityObj.xmlUtil.GetTextValue(

                nodeName, Constants.AlignedSeqCountNode);

            string refSeqName = utilityObj.xmlUtil.GetTextValue(

               nodeName, Constants.ChromosomeNameNode);

            SequenceAlignmentMap seqAlignment = null;

            BAMParser bamParser = null;

            try

            {

                bamParser = new BAMParser();



                // Parse a BAM file with different parameters.

                switch (BAMParserPam)

                {

                    case BAMParserParameters.StreamReader:

                        using (Stream stream = new FileStream(bamFilePath, FileMode.Open,

                            FileAccess.Read))

                        {

                            seqAlignment = bamParser.Parse(stream);

                        }

                        break;

                    case BAMParserParameters.FileName:

                        seqAlignment = bamParser.Parse(bamFilePath);

                        break;

                    case BAMParserParameters.ParseRangeFileName:

                        seqAlignment = bamParser.ParseRange(bamFilePath,

                            Convert.ToInt32(refIndexValue, (IFormatProvider)null));

                        break;

                    case BAMParserParameters.ParseRangeWithIndex:

                        seqAlignment = bamParser.ParseRange(bamFilePath,

                            Convert.ToInt32(refIndexValue, (IFormatProvider)null),

                            Convert.ToInt32(startIndexValue, (IFormatProvider)null),

                            Convert.ToInt32(endIndexValue, (IFormatProvider)null));

                        break;

                    case BAMParserParameters.ParseRangeUsingRefSeq:

                        seqAlignment = bamParser.ParseRange(bamFilePath, refSeqName);

                        break;

                    case BAMParserParameters.ParseRangeUsingRefSeqAndFlag:

                        seqAlignment = bamParser.ParseRange(bamFilePath, refSeqName);

                        break;

                    case BAMParserParameters.ParseRangeUsingRefSeqUsingIndex:

                        seqAlignment = bamParser.ParseRange(bamFilePath, refSeqName,

                            Convert.ToInt32(startIndexValue, (IFormatProvider)null),

                            Convert.ToInt32(endIndexValue, (IFormatProvider)null));

                        break;

                    case BAMParserParameters.ParseRangeUsingIndexesAndFlag:

                        seqAlignment = bamParser.ParseRange(bamFilePath, refSeqName,

                            Convert.ToInt32(startIndexValue, (IFormatProvider)null),

                            Convert.ToInt32(endIndexValue, (IFormatProvider)null));

                        break;

                }



                // Validate BAM Header record fileds.

                if (!IsReferenceIndex)

                {

                    ValidateBAMHeaderRecords(nodeName, seqAlignment);

                }



                IList<SAMAlignedSequence> alignedSeqs = seqAlignment.QuerySequences;

                Assert.AreEqual(alignedSeqCount, alignedSeqs.Count.ToString((IFormatProvider)null));

                // Get expected sequences

                using (FastAParser parserObj = new FastAParser(expectedAlignedSeqFilePath))

                {

                    IEnumerable<ISequence> expectedSequences = parserObj.Parse();

                    IList<ISequence> expectedSequencesList = expectedSequences.ToList();

                    // Validate aligned sequences from BAM file.

                    for (int index = 0; index < alignedSeqs.Count; index++)

                    {

                        Assert.AreEqual(

                            new string(expectedSequencesList[index].Select(a => (char)a).ToArray()),

                            new string(alignedSeqs[index].QuerySequence.Select(a => (char)a).ToArray()));

                        // Log to VSTest GUI.

                        ApplicationLog.WriteLine(string.Format((IFormatProvider)null,

                            "BAM Parser BVT : Validated Aligned sequence :{0} successfully",

                            alignedSeqs[index].QuerySequence.ToString()));

                        Console.WriteLine(string.Format((IFormatProvider)null,

                            "BAM Parser BVT : Validated the aligned sequence :{0} successfully",

                            alignedSeqs[index].QuerySequence.ToString()));

                    }

                }

            }

            finally

            {

                bamParser.Dispose();

            }

        }



        /// <summary>

        /// Validate BAM file Header fields.

        /// </summary>

        /// <param name="nodeName">XML nodename used for different test cases</param>

        /// <param name="seqAlignment">seqAlignment object</param>

        void ValidateBAMHeaderRecords(string nodeName,

            SequenceAlignmentMap seqAlignment)

        {

            string expectedHeaderTagValues = utilityObj.xmlUtil.GetTextValue(

               nodeName, Constants.RecordTagValuesNode);

            string expectedHeaderTagKeys = utilityObj.xmlUtil.GetTextValue(

                nodeName, Constants.RecordTagKeysNode);

            string expectedHeaderTypes = utilityObj.xmlUtil.GetTextValue(

                nodeName, Constants.HeaderTyepsNodes);

            string[] expectedHeaderTagsValues = expectedHeaderTagValues.Split(',');

            string[] expectedHeaderKeys = expectedHeaderTagKeys.Split(',');

            string[] expectedHeaders = expectedHeaderTypes.Split(',');

            SAMAlignmentHeader header = seqAlignment.Header;

            IList<SAMRecordField> recordFields = header.RecordFields;

            int tagKeysCount = 0;

            int tagValuesCount = 0;



            for (int index = 0; index < recordFields.Count; index++)

            {

                Assert.AreEqual(expectedHeaders[index].Replace("/", ""),

                    recordFields[index].Typecode.ToString((IFormatProvider)null).Replace("/", ""));

                for (int tags = 0; tags < recordFields[index].Tags.Count; tags++)

                {

                    Assert.AreEqual(expectedHeaderKeys[tagKeysCount].Replace("/", ""),

                        recordFields[index].Tags[tags].Tag.ToString((IFormatProvider)null).Replace("/", ""));

                    Assert.AreEqual(expectedHeaderTagsValues[tagValuesCount].Replace("/", ""),

                        recordFields[index].Tags[tags].Value.ToString((IFormatProvider)null).Replace("/", "").Replace("\r", "").Replace("\n", ""));

                    tagKeysCount++;

                    tagValuesCount++;

                }

            }

        }



        /// <summary>

        /// Validate formatted BAM file.

        /// </summary>

        /// <param name="nodeName">Different xml nodes used for different test cases</param>

        /// <param name="BAMParserPam">BAM Format method parameters</param>

        void ValidateBAMFormatter(string nodeName,

             BAMParserParameters BAMParserPam)

        {

            // Get input and output values from xml node.

            string bamFilePath = utilityObj.xmlUtil.GetTextValue(nodeName,

                Constants.FilePathNode);

            string expectedAlignedSeqFilePath = utilityObj.xmlUtil.GetTextValue(

                nodeName, Constants.ExpectedSequence);

            string alignedSeqCount = utilityObj.xmlUtil.GetTextValue(

                nodeName, Constants.AlignedSeqCountNode);



            Stream stream = null;

            SequenceAlignmentMap seqAlignment = null;

            using (BAMParser bamParserObj = new BAMParser())

            {

                // Parse a BAM file.

                seqAlignment = bamParserObj.Parse(bamFilePath);

                // Create a BAM formatter object.

                BAMFormatter formatterObj = new BAMFormatter();

                // Write/Format aligned sequences to BAM file.

                switch (BAMParserPam)

                {

                    case BAMParserParameters.StreamWriter:

                        using (stream = new

                            FileStream(Constants.BAMTempFileName,

                            FileMode.Create, FileAccess.Write))

                        {

                            formatterObj.Format(seqAlignment, stream);

                        }

                        break;

                    case BAMParserParameters.FileName:

                        formatterObj.Format(seqAlignment, Constants.BAMTempFileName);

                        break;

                    case BAMParserParameters.IndexFile:

                        formatterObj.Format(seqAlignment, Constants.BAMTempFileName,

                            Constants.BAMTempIndexFile);

                        File.Exists(Constants.BAMTempIndexFile);

                        break;

                    default:

                        break;

                }



                // Parse formatted BAM file and validate aligned sequences.

                SequenceAlignmentMap expectedSeqAlignmentMap = bamParserObj.Parse(

                    Constants.BAMTempFileName);



                // Validate Parsed BAM file Header record fileds.

                ValidateBAMHeaderRecords(nodeName, expectedSeqAlignmentMap);

                IList<SAMAlignedSequence> alignedSeqs = expectedSeqAlignmentMap.QuerySequences;

                Assert.AreEqual(alignedSeqCount, alignedSeqs.Count.ToString((IFormatProvider)null));



                // Get expected sequences

                using (FastAParser parserObj = new FastAParser(expectedAlignedSeqFilePath))

                {

                    IEnumerable<ISequence> expectedSequences = parserObj.Parse();

                    IList<ISequence> expectedSequencesList = expectedSequences.ToList();

                    // Validate aligned sequences from BAM file.

                    for (int index = 0; index < alignedSeqs.Count; index++)

                    {

                        Assert.AreEqual(

                             new string(expectedSequencesList[index].Select(a => (char)a).ToArray()),

                             new string(alignedSeqs[index].QuerySequence.Select(a => (char)a).ToArray()));

                        // Log to VSTest GUI.

                        ApplicationLog.WriteLine(string.Format((IFormatProvider)null,

                            "BAM Formatter BVT : Validated Aligned sequence :{0} successfully",

                            alignedSeqs[index].QuerySequence.ToString()));

                        Console.WriteLine(string.Format((IFormatProvider)null,

                            "BAM Formatter BVT : Validated the aligned sequence :{0} successfully",

                            alignedSeqs[index].QuerySequence.ToString()));

                    }

                }

            }

            File.Delete(Constants.BAMTempFileName);

            File.Delete(Constants.BAMTempIndexFile);

        }



        /// <summary>

        ///  Comapare Sequence Alignment Header fields

        /// </summary>

        /// <param name="actualAlignment">Actual sequence alignment object</param>

        /// <param name="expectedAlignment">Expected sequence alignment object</param>

        /// <returns></returns>

        private static bool CompareSequencedAlignmentHeader(SequenceAlignmentMap actualAlignment,

             SequenceAlignmentMap expectedAlignment)

        {

            SAMAlignmentHeader aheader = actualAlignment.Header;

            IList<SAMRecordField> arecordFields = aheader.RecordFields;

            SAMAlignmentHeader expectedheader = expectedAlignment.Header;

            IList<SAMRecordField> expectedrecordFields = expectedheader.RecordFields;

            int tagKeysCount = 0;

            int tagValuesCount = 0;



            for (int index = 0; index < expectedrecordFields.Count; index++)

            {

                if (0 != string.Compare(expectedrecordFields[index].Typecode.ToString((IFormatProvider)null),

                    arecordFields[index].Typecode.ToString((IFormatProvider)null), StringComparison.CurrentCulture))

                {

                    return false;

                }

                for (int tags = 0; tags < expectedrecordFields[index].Tags.Count; tags++)

                {

                    if ((0 != string.Compare(expectedrecordFields[index].Tags[tags].Tag.ToString((IFormatProvider)null),

                        arecordFields[index].Tags[tags].Tag.ToString((IFormatProvider)null), StringComparison.CurrentCulture))

                        || (0 != string.Compare(expectedrecordFields[index].Tags[tags].Value.ToString((IFormatProvider)null),

                        arecordFields[index].Tags[tags].Value.ToString((IFormatProvider)null), StringComparison.CurrentCulture)))

                    {

                        Console.WriteLine(string.Format((IFormatProvider)null,

                            "BAM Parser BVT : Sequence alignment header does not match"));

                        ApplicationLog.WriteLine(string.Format((IFormatProvider)null,

                           "BAM Parser BVT : Sequence alignment header does not match"));

                        return false;

                    }

                    tagKeysCount++;

                    tagValuesCount++;

                }

            }



            return true;

        }



        /// <summary>

        /// Compare BAM file aligned sequences.

        /// </summary>

        /// <param name="expectedAlignment">Expected sequence alignment object</param>

        /// <param name="actualAlignment">Actual sequence alignment object</param>

        /// <returns></returns>

        private static bool CompareAlignedSequences(SequenceAlignmentMap expectedAlignment,

             SequenceAlignmentMap actualAlignment)

        {

            IList<SAMAlignedSequence> actualAlignedSeqs = actualAlignment.QuerySequences;

            IList<SAMAlignedSequence> expectedAlignedSeqs = expectedAlignment.QuerySequences;



            for (int i = 0; i < expectedAlignedSeqs.Count; i++)

            {

                if (0 != string.Compare(new string(expectedAlignedSeqs.ElementAt(i).QuerySequence.Select(a => (char)a).ToArray()),

                           new string(actualAlignedSeqs[i].QuerySequence.Select(a => (char)a).ToArray()),

                           true, CultureInfo.CurrentCulture))

                {

                    Console.WriteLine(string.Format((IFormatProvider)null,

                           "BAM Parser BVT : Sequence alignment aligned seq does not match"));

                    ApplicationLog.WriteLine(string.Format((IFormatProvider)null,

                       "BAM Parser BVT : Sequence alignment aligned seq does match"));

                    return false;

                }

            }



            return true;

        }



        /// <summary>

        /// Validate GetPaired method

        /// </summary>

        /// <param name="nodeName">XML node name</param>

        /// <param name="pams">GetPairedReads method parameters</param>

        void ValidatePairedReads(string nodeName, GetPairedReadParameters pams)

        {

            // Get input and output values from xml node.

            string bamFilePath = utilityObj.xmlUtil.GetTextValue(nodeName,

                Constants.FilePathNode);

            string expectedAlignedSeqFilePath = utilityObj.xmlUtil.GetTextValue(

                nodeName, Constants.ExpectedSequence);

            string mean = utilityObj.xmlUtil.GetTextValue(

                nodeName, Constants.MeanNode);

            string deviation = utilityObj.xmlUtil.GetTextValue(

                nodeName, Constants.DeviationValueNode);

            string library = utilityObj.xmlUtil.GetTextValue(

                nodeName, Constants.LibraryNameNode);

            string pairedReadsCount = utilityObj.xmlUtil.GetTextValue(

                nodeName, Constants.PairedReadsNode);

            string[] insertLength = utilityObj.xmlUtil.GetTextValue(

               nodeName, Constants.InsertLengthNode).Split(',');

            string[] pairedReadType = utilityObj.xmlUtil.GetTextValue(

               nodeName, Constants.PairedReadTypeNode).Split(',');



            SequenceAlignmentMap seqAlignment = null;

            IList<PairedRead> pairedReads = null;

            BAMParser bamParser = new BAMParser();

            FastAParser parserObj = new FastAParser(expectedAlignedSeqFilePath);



            try

            {

                seqAlignment = bamParser.Parse(bamFilePath);

                IEnumerable<ISequence> expectedSequences = parserObj.Parse();



                switch (pams)

                {

                    case GetPairedReadParameters.GetPairedReadWithParameters:

                        pairedReads = seqAlignment.GetPairedReads(float.Parse(mean, (IFormatProvider)null),

                            float.Parse(deviation, (IFormatProvider)null));

                        break;

                    case GetPairedReadParameters.GetPairedReadWithLibraryName:

                        pairedReads = seqAlignment.GetPairedReads(library);

                        break;

                    case GetPairedReadParameters.GetPairedReadWithCloneLibraryInfo:

                        CloneLibraryInformation libraryInfo =

                            CloneLibrary.Instance.GetLibraryInformation(library);

                        pairedReads = seqAlignment.GetPairedReads(libraryInfo);

                        break;

                    case GetPairedReadParameters.Default:

                        pairedReads = seqAlignment.GetPairedReads();

                        break;

                }



                Assert.AreEqual(pairedReadsCount, pairedReads.Count.ToString((IFormatProvider)null));



                int i = 0;

                foreach (PairedRead read in pairedReads)

                {

                    Assert.AreEqual(insertLength[i], read.InsertLength.ToString((IFormatProvider)null));

                    Assert.AreEqual(pairedReadType[i], read.PairedType.ToString());



                    foreach (SAMAlignedSequence seq in read.Reads)

                    {

                        Assert.AreEqual(new string(expectedSequences.ElementAt(i).Select(a => (char)a).ToArray()),

                            new string(seq.QuerySequence.Select(a => (char)a).ToArray()));



                        // Log to VSTest GUI.

                        ApplicationLog.WriteLine(string.Format((IFormatProvider)null,

                            "BAM Parser BVT : Validated Paired read :{0} successfully",

                            seq.QuerySequence.ToString()));

                    }

                    i++;



                }

            }



            finally

            {

                bamParser.Dispose();

            }

        }



        /// <summary>

        /// Validate different paired read types

        /// </summary>

        /// <param name="nodeName">XML node name</param>

        /// <param name="pams">GetPairedReadTypes method parameters</param>

        void ValidatePairedReadTypes(string nodeName, GetPairedReadTypeParameters pams)

        {

            // Get input and output values from xml node.

            string bamFilePath = utilityObj.xmlUtil.GetTextValue(nodeName,

                Constants.FilePathNode);

            string mean = utilityObj.xmlUtil.GetTextValue(

                nodeName, Constants.MeanNode);

            string deviation = utilityObj.xmlUtil.GetTextValue(

                nodeName, Constants.DeviationValueNode);

            string library = utilityObj.xmlUtil.GetTextValue(

                nodeName, Constants.LibraryNameNode);

            string[] pairedReadType = utilityObj.xmlUtil.GetTextValue(

               nodeName, Constants.PairedReadTypeNode).Split(',');

            string[] insertLength = utilityObj.xmlUtil.GetTextValue(

               nodeName, Constants.InsertLengthNode).Split(',');



            IList<PairedRead> pairedReads = null;

            BAMParser bamParser = new BAMParser();

            SequenceAlignmentMap seqAlignmentMapObj = bamParser.Parse(bamFilePath);

            CloneLibrary…

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