public void TestConvertFromSolexaToSanger()
{
byte[] bs;
byte[] bs1 = new byte[1];
bs1[0] = (byte)59;
bs = QualitativeSequence.ConvertFromSolexaToSanger(bs1);
Assert.IsNotNull((object)bs);
Assert.AreEqual <int>(1, bs.Length);
Assert.AreEqual <byte>((byte)33, bs[0]);
}
public void TestConvertFromSolexaToSanger()
{
byte[] sangerScores;
byte[] solexaScores = new byte[1];
solexaScores[0] = (byte)59;
sangerScores = QualitativeSequence.ConvertFromSolexaToSanger(solexaScores);
Assert.IsNotNull((object)sangerScores);
Assert.AreEqual <int>(1, sangerScores.Length);
Assert.AreEqual <byte>((byte)33, sangerScores[0]);
}
public void ConvertSolexaToSangerAndIllumina()
{
// Gets the actual sequence and the Qual score from the Xml
string solexaSequence = utilityObj.xmlUtil.GetTextValue(
Constants.SolexaToSangerAndIlluminaNode, Constants.SolexaSequence);
string expectedSangerSequence = utilityObj.xmlUtil.GetTextValue(
Constants.SolexaToSangerAndIlluminaNode, Constants.SangerSequence);
string expectedIlluminaSequence = utilityObj.xmlUtil.GetTextValue(
Constants.SolexaToSangerAndIlluminaNode, Constants.IlluminaSequence);
string solexaQualScore = utilityObj.xmlUtil.GetTextValue(
Constants.SolexaToSangerAndIlluminaNode, Constants.SolexaQualScore);
string expectedSangerQualScore = utilityObj.xmlUtil.GetTextValue(
Constants.SolexaToSangerAndIlluminaNode, Constants.SangerQualScore);
string expectedIlluminaQualScore = utilityObj.xmlUtil.GetTextValue(
Constants.SolexaToSangerAndIlluminaNode, Constants.IlluminaQualScore);
byte[] byteValue = ASCIIEncoding.ASCII.GetBytes(solexaQualScore);
//string sangerQualScore = null;
//string illuminaQualScore = null;
//byte[] qualScores = new byte[solexaSequence.Count()];
//for (int i = 0; i < solexaSequence.Count(); i++)
//{
// qualScores[i] = (byte)'{';
//}
Byte[] solexaSequenceinBytes = encodingObj.GetBytes(solexaSequence);
// Create a Solexa qualitative sequence.
//QualitativeSequence solexaQualSequence = new QualitativeSequence(Alphabets.DNA,
// FastQFormatType.Solexa, solexaSequence, byteValue);
//QualitativeSequence solexaQualSequence = new QualitativeSequence(Alphabets.DNA,********************
// FastQFormatType.Solexa, solexaSequenceinBytes, byteValue);
//// Convert Solexa to Sanger.
//QualitativeSequence sangerQualSequence = solexaQualSequence.ConvertTo(
// FastQFormatType.Sanger);
//sangerQualScore = ASCIIEncoding.ASCII.GetString(sangerQualSequence.Scores);
byte[] sangerQualScore = QualitativeSequence.ConvertFromSolexaToSanger(byteValue);
// Validate converted sanger score.
string qualSequence = new string(encodingObj.GetChars(sangerQualScore));
Assert.AreEqual(expectedSangerQualScore, qualSequence);
//Assert.AreEqual(sangerQualSequence.ToString(), expectedSangerSequence);
ApplicationLog.WriteLine(string.Format((IFormatProvider)null,
"Qualitative Sequence BVT:Qualitative Sanger score type {0} is as expected.",
sangerQualScore));
//Console.WriteLine(string.Format((IFormatProvider)null,
// "Qualitative Sequence BVT:Qualitative Sanger score type {0} is as expected.",
// sangerQualSequence.ToString()));
// Convert Solexa to Illumina.
//QualitativeSequence illuminaQualSequence =
// solexaQualSequence.ConvertTo(FastQFormatType.Illumina);
//illuminaQualScore = ASCIIEncoding.ASCII.GetString(illuminaQualSequence.Scores);
byte[] illuminaQualScore = QualitativeSequence.ConvertFromSolexaToIllumina(byteValue);
string qualSequenceIllumina = new string(encodingObj.GetChars(illuminaQualScore));
Assert.AreEqual(expectedIlluminaQualScore, qualSequenceIllumina);
// Validate converted illumina score.
//Assert.AreEqual(illuminaQualScore, expectedIlluminaQualScore);
//Assert.AreEqual(illuminaQualSequence.ToString(), expectedIlluminaSequence);
ApplicationLog.WriteLine(string.Format((IFormatProvider)null,
"Qualitative Sequence BVT:Qualitative Illumina score type {0} is as expected.",
illuminaQualScore));
//Console.WriteLine(string.Format((IFormatProvider)null,
// "Qualitative Sequence BVT:Qualitative Illumina score type {0} is as expected.",
// illuminaQualSequence.ToString()));
}
