/// <summary>
/// Validate different paired read types
/// </summary>
/// <param name="nodeName">XML node name</param>
/// <param name="pams">GetPairedReadTypes method parameters</param>
private void ValidatePairedReadTypes(string nodeName, GetPairedReadTypeParameters pams)
{
// Get input and output values from xml node.
string bamFilePath = this.utilityObj.xmlUtil.GetTextValue(nodeName,
Constants.FilePathNode);
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[] pairedReadType = this.utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.PairedReadTypeNode).Split(',');
string[] insertLength = this.utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.InsertLengthNode).Split(',');
var bamParser = new BAMParser();
SequenceAlignmentMap seqAlignmentMapObj = bamParser.ParseOne<SequenceAlignmentMap>(bamFilePath);
CloneLibraryInformation libraryInfo;
int i = 0;
try
{
IList<PairedRead> pairedReads;
switch (pams)
{
case GetPairedReadTypeParameters.PaireReadTypeUsingLibraryName:
pairedReads = seqAlignmentMapObj.GetPairedReads(float.Parse(mean, null),
float.Parse(deviation, null));
foreach (PairedRead read in pairedReads)
{
PairedReadType type = PairedRead.GetPairedReadType(read, library);
Assert.AreEqual(type.ToString(), pairedReadType[i]);
i++;
}
break;
case GetPairedReadTypeParameters.PaireReadTypeUsingCloneLibraryInfo:
pairedReads = seqAlignmentMapObj.GetPairedReads(float.Parse(mean, null),
float.Parse(deviation, null));
libraryInfo = CloneLibrary.Instance.GetLibraryInformation(library);
foreach (PairedRead read in pairedReads)
{
PairedReadType type = PairedRead.GetPairedReadType(read, libraryInfo);
Assert.AreEqual(type.ToString(), pairedReadType[i]);
i++;
}
break;
case GetPairedReadTypeParameters.PaireReadTypeUsingMeanAndDeviation:
pairedReads = seqAlignmentMapObj.GetPairedReads(float.Parse(mean, null),
float.Parse(deviation, null));
foreach (PairedRead read in pairedReads)
{
PairedReadType type = PairedRead.GetPairedReadType(read, float.Parse(mean, null),
float.Parse(deviation, null));
Assert.AreEqual(type.ToString(), pairedReadType[i]);
i++;
}
break;
case GetPairedReadTypeParameters.PaireReadTypeUsingReadsAndLibrary:
pairedReads = seqAlignmentMapObj.GetPairedReads(float.Parse(mean, null),
float.Parse(deviation, null));
foreach (PairedRead read in pairedReads)
{
PairedReadType type = PairedRead.GetPairedReadType(read.Read1,
read.Read2, library);
Assert.AreEqual(type.ToString(), pairedReadType[i]);
i++;
}
break;
case GetPairedReadTypeParameters.PaireReadTypeUsingReadsAndLibraryInfo:
pairedReads = seqAlignmentMapObj.GetPairedReads(float.Parse(mean, null),
float.Parse(deviation, null));
libraryInfo = CloneLibrary.Instance.GetLibraryInformation(library);
foreach (PairedRead read in pairedReads)
{
PairedReadType type = PairedRead.GetPairedReadType(read.Read1,
read.Read2, libraryInfo);
Assert.AreEqual(type.ToString(), pairedReadType[i]);
i++;
}
break;
case GetPairedReadTypeParameters.GetInsertLength:
pairedReads = seqAlignmentMapObj.GetPairedReads(float.Parse(mean, null),
float.Parse(deviation, null));
libraryInfo = CloneLibrary.Instance.GetLibraryInformation(library);
foreach (PairedRead read in pairedReads)
{
int length = PairedRead.GetInsertLength(read.Read1, read.Read2);
Assert.AreEqual(length.ToString((IFormatProvider) null), insertLength[i]);
i++;
}
break;
}
ApplicationLog.WriteLine(string.Format(null,
"BAM Parser BVT : Validated Paired read Type Successfully"));
}
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);
CloneLibraryInformation libraryInfo;
int i = 0;
try
{
switch (pams)
{
case GetPairedReadTypeParameters.PaireReadTypeUsingLibraryName:
pairedReads = seqAlignmentMapObj.GetPairedReads(float.Parse(mean, (IFormatProvider)null),
float.Parse(deviation, (IFormatProvider)null));
foreach (PairedRead read in pairedReads)
{
PairedReadType type = PairedRead.GetPairedReadType(read, library);
Assert.AreEqual(type.ToString(), pairedReadType[i]);
i++;
}
break;
case GetPairedReadTypeParameters.PaireReadTypeUsingCloneLibraryInfo:
pairedReads = seqAlignmentMapObj.GetPairedReads(float.Parse(mean, (IFormatProvider)null),
float.Parse(deviation, (IFormatProvider)null));
libraryInfo = CloneLibrary.Instance.GetLibraryInformation(library);
foreach (PairedRead read in pairedReads)
{
PairedReadType type = PairedRead.GetPairedReadType(read, libraryInfo);
Assert.AreEqual(type.ToString(), pairedReadType[i]);
i++;
}
break;
case GetPairedReadTypeParameters.PaireReadTypeUsingMeanAndDeviation:
pairedReads = seqAlignmentMapObj.GetPairedReads(float.Parse(mean, (IFormatProvider)null),
float.Parse(deviation, (IFormatProvider)null));
foreach (PairedRead read in pairedReads)
{
PairedReadType type = PairedRead.GetPairedReadType(read, float.Parse(mean, (IFormatProvider)null),
float.Parse(deviation, (IFormatProvider)null));
Assert.AreEqual(type.ToString(), pairedReadType[i]);
i++;
}
break;
case GetPairedReadTypeParameters.PaireReadTypeUsingReadsAndLibrary:
pairedReads = seqAlignmentMapObj.GetPairedReads(float.Parse(mean, (IFormatProvider)null),
float.Parse(deviation, (IFormatProvider)null));
foreach (PairedRead read in pairedReads)
{
PairedReadType type = PairedRead.GetPairedReadType(read.Read1,
read.Read2, library);
Assert.AreEqual(type.ToString(), pairedReadType[i]);
i++;
}
break;
case GetPairedReadTypeParameters.PaireReadTypeUsingReadsAndLibraryInfo:
pairedReads = seqAlignmentMapObj.GetPairedReads(float.Parse(mean, (IFormatProvider)null),
float.Parse(deviation, (IFormatProvider)null));
libraryInfo = CloneLibrary.Instance.GetLibraryInformation(library);
foreach (PairedRead read in pairedReads)
{
PairedReadType type = PairedRead.GetPairedReadType(read.Read1,
read.Read2, libraryInfo);
Assert.AreEqual(type.ToString(), pairedReadType[i]);
i++;
}
break;
case GetPairedReadTypeParameters.GetInsertLength:
pairedReads = seqAlignmentMapObj.GetPairedReads(float.Parse(mean, (IFormatProvider)null),
float.Parse(deviation, (IFormatProvider)null));
libraryInfo = CloneLibrary.Instance.GetLibraryInformation(library);
foreach (PairedRead read in pairedReads)
{
int length = PairedRead.GetInsertLength(read.Read1, read.Read2);
Assert.AreEqual(length.ToString((IFormatProvider)null), insertLength[i]);
i++;
}
break;
}
ApplicationLog.WriteLine(string.Format((IFormatProvider)null,
"BAM Parser BVT : Validated Paired read Type Successfully"));
}
finally
{
bamParser.Dispose();
}
}
