/// <summary>
/// Validate GetPaired method
/// </summary>
/// <param name="nodeName">XML node name</param>
/// <param name="pams">GetPairedReads method parameters</param>
private void ValidatePairedReads(string nodeName, GetPairedReadParameters pams)
{
// Get input and output values from xml node.
string bamFilePath = this.utilityObj.xmlUtil.GetTextValue(nodeName,
Constants.FilePathNode);
string expectedAlignedSeqFilePath = this.utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.ExpectedSequence);
string mean = this.utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.MeanNode);
string deviation = this.utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.DeviationValueNode);
string library = this.utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.LibraryNameNode);
string pairedReadsCount = this.utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.PairedReadsNode);
string[] insertLength = this.utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.InsertLengthNode).Split(',');
string[] pairedReadType = this.utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.PairedReadTypeNode).Split(',');
SequenceAlignmentMap seqAlignment = null;
IList<PairedRead> pairedReads = null;
var bamParser = new BAMParser();
var parserObj = new FastAParser();
try
{
seqAlignment = bamParser.ParseOne<SequenceAlignmentMap>(bamFilePath);
IEnumerable<ISequence> expectedSequences = parserObj.Parse(expectedAlignedSeqFilePath);
switch (pams)
{
case GetPairedReadParameters.GetPairedReadWithParameters:
pairedReads = seqAlignment.GetPairedReads(float.Parse(mean, null),
float.Parse(deviation, 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(null,
"BAM Parser BVT : Validated Paired read :{0} successfully",
seq.QuerySequence));
}
i++;
}
}
finally
{
bamParser.Dispose();
}
}
/// <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 NUNIT GUI.
ApplicationLog.WriteLine(string.Format((IFormatProvider)null,
"BAM Parser BVT : Validated Paired read :{0} successfully",
seq.QuerySequence.ToString()));
}
i++;
}
}
finally
{
bamParser.Dispose();
}
}
