/// <summary>
/// Writes the SAM object to file in SAM/BAM format.
/// </summary>
private void PerformFormat()
{
if (_isSAM)
{
BAMFormatter format = new BAMFormatter();
try
{
format.Format(_sequenceAlignmentMap, _outputFile);
}
catch
{
throw new InvalidOperationException(Resources.WriteBAM);
}
}
else
{
SAMFormatter format = new SAMFormatter();
try
{
format.Format(_sequenceAlignmentMap, _outputFile);
}
catch
{
throw new InvalidOperationException(Resources.WriteSAM);
}
}
}
public void TestFormatter()
{
string filePath = @"TestUtils\SAM\SeqAlignment1.sam".TestDir();
string outputfilePath = "samtest.sam";
ISequenceAlignmentParser parser = new SAMParser();
IList <ISequenceAlignment> alignments = parser.Parse(filePath).ToList();
Assert.IsTrue(alignments != null);
Assert.AreEqual(alignments.Count, 1);
Assert.AreEqual(alignments[0].AlignedSequences.Count, 2);
try
{
SAMFormatter formatter = new SAMFormatter();
formatter.Format(alignments[0], outputfilePath);
alignments = parser.Parse(outputfilePath).ToList();
Assert.IsTrue(alignments != null);
Assert.AreEqual(alignments.Count, 1);
Assert.AreEqual(alignments[0].AlignedSequences.Count, 2);
}
finally
{
File.Delete(outputfilePath);
}
}
public void ValidateSAMFormatterWithTextWriterAndAlignments()
{
// Gets the expected sequence from the Xml
string filePath = utilityObj.xmlUtil.GetTextValue(
Constants.SmallSAMFileNode, Constants.FilePathNode);
ISequenceAlignmentParser parser = new SAMParser();
try
{
IList <ISequenceAlignment> alignments = parser.Parse(filePath);
SAMFormatter formatter = new SAMFormatter();
try
{
using (TextWriter writer =
new StreamWriter(Constants.SAMTempFileName))
{
formatter.Format(alignments, writer);
}
Assert.Fail();
}
catch (NotSupportedException)
{
ApplicationLog.WriteLine(string.Format((IFormatProvider)null,
"SAM Parser BVT : Validated the exception successfully"));
Console.WriteLine(string.Format((IFormatProvider)null,
"SAM Parser BVT : Validated the exception successfully"));
}
}
finally
{
(parser as SAMParser).Dispose();
}
}
/// <summary>
/// Writes the SAM object to file in SAM/BAM format.
/// </summary>
private void PerformFormat()
{
if (_isSAM)
{
BAMFormatter format = new BAMFormatter();
try
{
format.Format(_sequenceAlignmentMap, OutputFilename);
}
catch (Exception ex)
{
throw new InvalidOperationException(Resources.WriteBAM + Environment.NewLine + ex.Message);
}
}
else
{
SAMFormatter format = new SAMFormatter();
try
{
format.Format(_sequenceAlignmentMap, OutputFilename);
}
catch (Exception ex)
{
throw new InvalidOperationException(Resources.WriteSAM + Environment.NewLine + ex.Message);
}
}
}
/// <summary>
/// Validate formatter all format method overloads with filePath\textwriter
/// </summary>
/// <param name="nodeName">xml node name</param>
/// <param name="formatTypes">enum type to execute different overload</param>
void ValidateSAMFormatter(string nodeName,
ParseOrFormatTypes formatTypes)
{
// Gets the expected sequence from the Xml
string filePath = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.FilePathNode);
string expectedSequenceFile = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.ExpectedSequence);
ISequenceAlignmentParser parser = new SAMParser();
try
{
IList <ISequenceAlignment> alignments = parser.Parse(filePath);
SAMFormatter formatter = new SAMFormatter();
switch (formatTypes)
{
case ParseOrFormatTypes.ParseOrFormatText:
using (TextWriter writer =
new StreamWriter(Constants.SAMTempFileName))
{
formatter.Format(alignments[0], writer);
}
break;
case ParseOrFormatTypes.ParseOrFormatFileName:
formatter.Format(alignments[0], Constants.SAMTempFileName);
break;
}
alignments = parser.Parse(Constants.SAMTempFileName);
// Get expected sequences
using (FastAParser parserObj = new FastAParser(expectedSequenceFile))
{
IEnumerable <ISequence> expectedSequences = parserObj.Parse();
IList <ISequence> expectedSequencesList = expectedSequences.ToList();
// Validate parsed output with expected output
int count = 0;
for (int index = 0; index < alignments.Count; index++)
{
for (int ialigned = 0; ialigned <
alignments[index].AlignedSequences.Count; ialigned++)
{
for (int iseq = 0; iseq <
alignments[index].AlignedSequences[ialigned].Sequences.Count; iseq++)
{
Assert.AreEqual(new string(expectedSequencesList[count].Select(a => (char)a).ToArray()),
new string(alignments[index].AlignedSequences[ialigned].Sequences[iseq].Select(a => (char)a).ToArray()));
count++;
}
}
}
}
}
finally
{
(parser as SAMParser).Dispose();
}
}
/// <summary>
/// General method to validate SAM Formatter method.
/// </summary>
/// <param name="nodeName">xml node name</param>
/// <param name="parseTypes">enum type to execute different overload</param>
void ValidateSAMFormatterSeqAlign(
string nodeName,
ParseOrFormatTypes parseTypes)
{
// Gets the expected sequence from the Xml
string filePath = _utilityObj._xmlUtil.GetTextValue(
nodeName, Constants.FilePathNode);
string expectedSequenceFile = _utilityObj._xmlUtil.GetTextValue(
nodeName, Constants.ExpectedSequence);
using (SAMParser parser = new SAMParser())
{
SequenceAlignmentMap alignments = parser.Parse(filePath);
SAMFormatter formatter = new SAMFormatter();
switch (parseTypes)
{
case ParseOrFormatTypes.ParseOrFormatText:
using (TextWriter writer =
new StreamWriter(Constants.SAMTempFileName))
{
formatter.Format(alignments, writer);
}
break;
case ParseOrFormatTypes.ParseOrFormatFileName:
formatter.Format(alignments, Constants.SAMTempFileName);
break;
case ParseOrFormatTypes.ParseOrFormatFileNameWithFlag:
formatter.Format(alignments, Constants.SAMTempFileName);
break;
}
alignments = parser.Parse(Constants.SAMTempFileName);
// Get expected sequences
using (FastaParser parserObj = new FastaParser())
{
IList <ISequence> expectedSequences =
parserObj.Parse(expectedSequenceFile);
// Validate parsed output with expected output
for (int index = 0;
index < alignments.QuerySequences.Count;
index++)
{
for (int count = 0;
count < alignments.QuerySequences[index].Sequences.Count;
count++)
{
Assert.AreEqual(expectedSequences[index].ToString(),
alignments.QuerySequences[index].Sequences[count].ToString());
}
}
}
}
}
public void ValidateSAMFormatterProperties()
{
SAMFormatter parser = new SAMFormatter();
Assert.AreEqual(Constants.SAMFormatterDescription, parser.Description.Replace("\r\n", "\n"));
Assert.AreEqual(Constants.SAMFileType, parser.SupportedFileTypes);
Assert.AreEqual(Constants.SAMName, parser.Name);
ApplicationLog.WriteLine("Successfully validated all the properties of SAM Parser class.");
}
/// <summary>
/// Writes BAM header to the specified stream in BAM format.
/// </summary>
/// <param name="header">SAMAlignmentHeader object</param>
/// <param name="writer">Stream to write.</param>
public void WriteHeader(SAMAlignmentHeader header, Stream writer)
{
if (header == null)
{
throw new ArgumentNullException("header");
}
if (writer == null)
{
throw new ArgumentNullException("writer");
}
string samHeader;
if (_refSequences == null)
{
_refSequences = SortSequenceRanges(header.GetReferenceSequenceRanges());
}
using (StringWriter strwriter = new StringWriter(CultureInfo.InvariantCulture))
{
SAMFormatter.WriteHeader(header, strwriter);
samHeader = strwriter.ToString();
}
int samHeaderLen = samHeader.Length;
byte[] bytes = System.Text.ASCIIEncoding.ASCII.GetBytes(samHeader);
byte[] bamMagicNumber = new byte[4] {
66, 65, 77, 1
};
// write BAM magic number
writer.Write(bamMagicNumber, 0, 4);
// Length of the header text
writer.Write(Helper.GetLittleEndianByteArray(samHeaderLen), 0, 4);
//Plain header text in SAM
writer.Write(bytes, 0, bytes.Length);
// number of reference sequences
writer.Write(Helper.GetLittleEndianByteArray(_refSequences.Count), 0, 4);
for (int i = 0; i < _refSequences.Count; i++)
{
int len = _refSequences[i].ID.Length;
byte[] array = System.Text.ASCIIEncoding.ASCII.GetBytes(_refSequences[i].ID);
writer.Write(Helper.GetLittleEndianByteArray(len + 1), 0, 4);
writer.Write(array, 0, len);
writer.WriteByte((byte)'\0');
writer.Write(Helper.GetLittleEndianByteArray((int)_refSequences[i].End), 0, 4);
}
}
/// <summary>
/// Validate formatter all format method overloads with filePath\textwriter
/// </summary>
/// <param name="nodeName">xml node name</param>
/// <param name="formatTypes">enum type to execute different overload</param>
void ValidateSAMFormatter(string nodeName,
ParseOrFormatTypes formatTypes)
{
// Gets the expected sequence from the Xml
string filePath = Utility._xmlUtil.GetTextValue(
nodeName, Constants.FilePathNode);
string expectedSequenceFile = Utility._xmlUtil.GetTextValue(
nodeName, Constants.ExpectedSequence);
ISequenceAlignmentParser parser = new SAMParser();
IList <ISequenceAlignment> alignments = parser.Parse(filePath);
SAMFormatter formatter = new SAMFormatter();
switch (formatTypes)
{
case ParseOrFormatTypes.ParseOrFormatText:
using (TextWriter writer =
new StreamWriter(Constants.SAMTempFileName))
{
formatter.Format(alignments[0], writer);
}
break;
case ParseOrFormatTypes.ParseOrFormatFileName:
formatter.Format(alignments[0], Constants.SAMTempFileName);
break;
case ParseOrFormatTypes.ParseOrFormatFileNameWithFlag:
formatter.Format(alignments, Constants.SAMTempFileName);
break;
}
alignments = parser.Parse(Constants.SAMTempFileName);
// Get expected sequences
FastaParser parserObj = new FastaParser();
IList <ISequence> expectedSequences = parserObj.Parse(expectedSequenceFile);
// Validate parsed output with expected output
int count = 0;
for (int index = 0; index < alignments.Count; index++)
{
for (int ialigned = 0; ialigned <
alignments[index].AlignedSequences.Count; ialigned++)
{
for (int iseq = 0; iseq <
alignments[index].AlignedSequences[ialigned].Sequences.Count; iseq++)
{
Assert.AreEqual(expectedSequences[count].ToString(),
alignments[index].AlignedSequences[ialigned].Sequences[iseq].ToString());
count++;
}
}
}
}
/// <summary>
/// Writes aligned sequence to output stream.
/// </summary>
/// <param name="header">Alignment header.</param>
/// <param name="alignedSequence">Aligned sequence to write.</param>
private void WriteAlignedSequence(SAMAlignmentHeader header, SAMAlignedSequence alignedSequence)
{
if (UnCompressedBAM || BAMOutput)
{
// Incase of compressed bamoutput uncompressed file will be compressed before sending it to output stream.
bamformatter.WriteAlignedSequence(header, alignedSequence, bamUncompressedOutStream);
}
else
{
SAMFormatter.WriteSAMAlignedSequence(alignedSequence, writer);
}
}
/// <summary>
/// Writes BAM header to the specified stream in BAM format.
/// </summary>
/// <param name="header">SAMAlignmentHeader object</param>
/// <param name="writer">Stream to write.</param>
public void WriteHeader(SAMAlignmentHeader header, Stream writer)
{
if (header == null)
{
throw new ArgumentNullException("header");
}
if (writer == null)
{
throw new ArgumentNullException("writer");
}
string samHeader;
if (this.refSequences == null)
{
this.refSequences = header.GetReferenceSequenceRanges();
}
using (StringWriter strwriter = new StringWriter(CultureInfo.InvariantCulture))
{
SAMFormatter.WriteHeader(strwriter, header);
samHeader = strwriter.ToString();
}
int samHeaderLen = samHeader.Length;
byte[] bytes = Encoding.UTF8.GetBytes(samHeader);
byte[] bamMagicNumber = { 66, 65, 77, 1 };
// write BAM magic number
writer.Write(bamMagicNumber, 0, 4);
// Length of the header text
writer.Write(Helper.GetLittleEndianByteArray(samHeaderLen), 0, 4);
//Plain header text in SAM
writer.Write(bytes, 0, bytes.Length);
// number of reference sequences
writer.Write(Helper.GetLittleEndianByteArray(this.refSequences.Count), 0, 4);
foreach (SequenceRange range in this.refSequences)
{
int len = range.ID.Length;
byte[] array = Encoding.UTF8.GetBytes(range.ID);
writer.Write(Helper.GetLittleEndianByteArray(len + 1), 0, 4);
writer.Write(array, 0, len);
writer.WriteByte((byte)'\0');
writer.Write(Helper.GetLittleEndianByteArray((int)range.End), 0, 4);
}
}
/// <summary>
/// General method to validate SAM Formatter method.
/// </summary>
/// <param name="nodeName">xml node name</param>
/// <param name="parseTypes">enum type to execute different overload</param>
void ValidateSAMFormatterSeqAlign(
string nodeName,
ParseOrFormatTypes parseTypes)
{
// Gets the expected sequence from the Xml
string filePath = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.FilePathNode).TestDir();
string expectedSequenceFile = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.ExpectedSequence).TestDir();
SAMParser parser = new SAMParser();
{
SequenceAlignmentMap alignments = parser.ParseOne <SequenceAlignmentMap>(filePath);
SAMFormatter formatter = new SAMFormatter();
switch (parseTypes)
{
case ParseOrFormatTypes.ParseOrFormatText:
using (var writer =
File.Create(Constants.SAMTempFileName))
{
formatter.Format(writer, alignments);
}
break;
case ParseOrFormatTypes.ParseOrFormatFileName:
formatter.Format(alignments, Constants.SAMTempFileName);
break;
}
alignments = parser.ParseOne <SequenceAlignmentMap>(Constants.SAMTempFileName);
// Get expected sequences
FastAParser parserObj = new FastAParser();
{
IEnumerable <ISequence> expectedSequences =
parserObj.Parse(expectedSequenceFile);
IList <ISequence> expectedSequencesList = expectedSequences.ToList();
// Validate parsed output with expected output
for (int index = 0;
index < alignments.QuerySequences.Count;
index++)
{
for (int count = 0;
count < alignments.QuerySequences[index].Sequences.Count;
count++)
{
Assert.AreEqual(new string(expectedSequencesList[index].Select(a => (char)a).ToArray()),
new string(alignments.QuerySequences[index].Sequences[count].Select(a => (char)a).ToArray()));
}
}
}
}
}
public void ValidateSAMFormatterFormatString()
{
string filePath = Utility._xmlUtil.GetTextValue(
Constants.SamFormatterFileNode,
Constants.FilePathNode);
ISequenceAlignmentParser parser = new SAMParser();
IList <ISequenceAlignment> alignment = parser.Parse(filePath);
SAMFormatter formatter = new SAMFormatter();
string writer = formatter.FormatString(alignment[0]);
Assert.AreEqual(writer, Constants.FormatterString);
}
public void ValidateSAMFormatterFormatString()
{
string filePath = utilityObj.xmlUtil.GetTextValue(
Constants.SamFormatterFileNode,
Constants.FilePathNode).TestDir();
ISequenceAlignmentParser parser = new SAMParser();
IList <ISequenceAlignment> alignment = parser.Parse(filePath).ToList();
SAMFormatter formatter = new SAMFormatter();
string writer = formatter.FormatString(alignment[0]);
Assert.AreEqual(writer, Constants.FormatterString.Replace("\r\n", Environment.NewLine));
}
public void SAMProperties()
{
ISequenceAlignmentParser parser = new SAMParser();
Assert.AreEqual(parser.Name, Properties.Resource.SAM_NAME);
Assert.AreEqual(parser.Description, Properties.Resource.SAMPARSER_DESCRIPTION);
Assert.AreEqual(parser.FileTypes, Properties.Resource.SAM_FILEEXTENSION);
ISequenceAlignmentFormatter formatter = new SAMFormatter();
Assert.AreEqual(formatter.Name, Properties.Resource.SAM_NAME);
Assert.AreEqual(formatter.Description, Properties.Resource.SAMFORMATTER_DESCRIPTION);
Assert.AreEqual(formatter.FileTypes, Properties.Resource.SAM_FILEEXTENSION);
}
public void InvalidateSAMWriteTextWriter()
{
SAMAlignmentHeader header = new SAMAlignmentHeader();
try
{
SAMFormatter.WriteHeader(null, header);
Assert.Fail();
}
catch (ArgumentNullException)
{
ApplicationLog.WriteLine(
"SAM Formatter P2 : Successfully validated the exception");
}
}
public void ValidateBAMToSAMConversionWithDVEnabled()
{
// 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.
bamParserObj.EnforceDataVirtualization = true;
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 NUnit 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>
/// General method to validate SAM Formatter method.
/// </summary>
/// <param name="nodeName">xml node name</param>
/// <param name="parseTypes">enum type to execute different overload</param>
void ValidateSAMFormatter(string nodeName)
{
// Gets the expected sequence from the Xml
string filePath = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.FilePathNode);
string expectedSequenceFile = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.ExpectedSequence);
using (SAMParser parser = new SAMParser())
{
SequenceAlignmentMap alignments = parser.Parse(filePath);
SAMFormatter formatter = new SAMFormatter();
using (TextWriter writer =
new StreamWriter(Constants.SAMTempFileName))
{
formatter.Format(alignments, writer);
}
alignments = parser.Parse(Constants.SAMTempFileName);
// Get expected sequences
using (FastAParser parserObj = new FastAParser(expectedSequenceFile))
{
IEnumerable <ISequence> expectedSequences =
parserObj.Parse();
IList <ISequence> expectedSequencesList = expectedSequences.ToList();
// Validate parsed output with expected output
for (int index = 0;
index < alignments.QuerySequences.Count;
index++)
{
for (int count = 0;
count < alignments.QuerySequences[index].Sequences.Count;
count++)
{
Assert.AreEqual(
new string(expectedSequencesList[index].Select(a => (char)a).ToArray()),
new string(alignments.QuerySequences[index].Sequences[count].Select(a => (char)a).ToArray()));
}
}
}
}
}
/// <summary>
/// Writes the header to output stream
/// </summary>
/// <param name="header"></param>
private void WriteHeader(SAMAlignmentHeader header)
{
if (!Header && !HeaderOnly)
{
return;
}
if (UnCompressedBAM || BAMOutput)
{
// Incase of compressed bamoutput uncompressed file will be compressed before sending it to output stream.
bamformatter.WriteHeader(header, bamUncompressedOutStream);
}
else
{
SAMFormatter.WriteHeader(header, writer);
}
}
/// <summary>
/// Returns sequence alignment formatter which supports the specified file.
/// </summary>
/// <param name="fileName">File name for which the formatter is required.</param>
/// <returns>If found returns the formatter as ISequenceAlignmentFormatter else returns null.</returns>
public static ISequenceAlignmentFormatter FindFormatterByFile(string fileName)
{
ISequenceAlignmentFormatter formatter = null;
if (!string.IsNullOrEmpty(fileName))
{
if (Helper.IsSAM(fileName))
{
formatter = new SAMFormatter();
}
else
{
formatter = null;
}
}
return(formatter);
}
public void ValidateSAMFormatterWithFileNameAndAlignments()
{
// Gets the expected sequence from the Xml
string filePath = utilityObj.xmlUtil.GetTextValue(
Constants.SmallSAMFileNode.Replace("\r\n", System.Environment.NewLine), Constants.FilePathNode);
ISequenceAlignmentParser parser = new SAMParser();
IEnumerable <ISequenceAlignment> alignments = parser.Parse(filePath);
SAMFormatter formatter = new SAMFormatter();
try
{
formatter.Format(alignments, Constants.SAMTempFileName);
Assert.Fail();
}
catch (NotSupportedException)
{
ApplicationLog.WriteLine("SAM Parser BVT : Validated the exception successfully");
}
}
public void TestFormatter()
{
string filePath = @"TestData\SAM\SeqAlignment1.sam";
string outputfilePath = "samtest.sam";
ISequenceAlignmentParser parser = new SAMParser();
SAMFormatter formatter = new SAMFormatter();
IList <ISequenceAlignment> alignments = parser.Parse(filePath);
Assert.IsTrue(alignments != null);
Assert.AreEqual(alignments.Count, 1);
Assert.AreEqual(alignments[0].AlignedSequences.Count, 2);
formatter.Format(alignments[0], outputfilePath);
alignments = parser.Parse(outputfilePath);
Assert.IsTrue(alignments != null);
Assert.AreEqual(alignments.Count, 1);
Assert.AreEqual(alignments[0].AlignedSequences.Count, 2);
}
public void ValidateSeqFormatterProperties()
{
// Gets the expected sequence from the Xml
string samFormatterName = _utilityObj._xmlUtil.GetTextValue(Constants.SamFileParserNode,
Constants.ParserNameNode);
string bamFormatterName = _utilityObj._xmlUtil.GetTextValue(Constants.BamFileParserNode,
Constants.ParserNameNode);
// Get SequenceAlignmentFormatter class properties.
SAMFormatter actualSamFormatter = SequenceAlignmentFormatters.SAM;
IList <ISequenceAlignmentFormatter> allFormatters = SequenceAlignmentFormatters.All;
BAMFormatter actualBamFormatterName = SequenceAlignmentFormatters.BAM;
// Validate Sequence Formatter
Assert.AreEqual(samFormatterName, actualSamFormatter.Name);
Assert.IsNotNull(allFormatters);
Assert.AreEqual(bamFormatterName, actualBamFormatterName.Name);
Console.WriteLine(string.Format((IFormatProvider)null,
"SequenceAlignmentFormatter : Type of the parser is validated successfully"));
ApplicationLog.WriteLine("Type of the parser is validated successfully");
}
public void ValidateSAMFormatterWithTextWriterAndAlignments()
{
// Gets the expected sequence from the Xml
string filePath = utilityObj.xmlUtil.GetTextValue(
Constants.SmallSAMFileNode, Constants.FilePathNode);
ISequenceAlignmentParser parser = new SAMParser();
IEnumerable <ISequenceAlignment> alignments = parser.Parse(filePath);
SAMFormatter formatter = new SAMFormatter();
try
{
using (var writer = File.Create(Constants.SAMTempFileName))
{
formatter.Format(writer, alignments);
}
Assert.Fail();
}
catch (NotSupportedException)
{
ApplicationLog.WriteLine("SAM Parser BVT : Validated the exception successfully");
}
}
public void ValidateSAMFormatterWithFileNameAndAlignments()
{
// Gets the expected sequence from the Xml
string filePath = Utility._xmlUtil.GetTextValue(
Constants.SmallSAMFileNode, Constants.FilePathNode);
ISequenceAlignmentParser parser = new SAMParser();
IList <ISequenceAlignment> alignments = parser.Parse(filePath);
SAMFormatter formatter = new SAMFormatter();
try
{
formatter.Format(alignments, Constants.SAMTempFileName);
Assert.Fail();
}
catch (NotSupportedException)
{
ApplicationLog.WriteLine(string.Format(null,
"SAM Parser BVT : Validated the exception successfully"));
Console.WriteLine(string.Format(null,
"SAM Parser BVT : Validated the exception successfully"));
}
}
/// <summary>
/// General method to validate SAM Formatter method.
/// </summary>
/// <param name="nodeName">xml node name</param>
/// <param name="parseTypes">enum type to execute different overload</param>
void ValidateSAMFormatter(string nodeName)
{
// Gets the expected sequence from the Xml
string filePath = Utility._xmlUtil.GetTextValue(
nodeName, Constants.FilePathNode);
string expectedSequenceFile = Utility._xmlUtil.GetTextValue(
nodeName, Constants.ExpectedSequence);
SAMParser parser = new SAMParser();
SequenceAlignmentMap alignments = parser.Parse(filePath);
SAMFormatter formatter = new SAMFormatter();
using (TextWriter writer =
new StreamWriter(Constants.SAMTempFileName))
{
formatter.Format(alignments, writer);
}
alignments = parser.Parse(Constants.SAMTempFileName);
// Get expected sequences
FastaParser parserObj = new FastaParser();
IList <ISequence> expectedSequences =
parserObj.Parse(expectedSequenceFile);
// Validate parsed output with expected output
for (int index = 0;
index < alignments.QuerySequences.Count;
index++)
{
for (int count = 0;
count < alignments.QuerySequences[index].Sequences.Count;
count++)
{
Assert.AreEqual(expectedSequences[index].ToString(),
alignments.QuerySequences[index].Sequences[count].ToString());
}
}
}
