public void ValidateSAMParseAlignedSeqWithSeqPointer()
{
// Get values from XML node.
string expectedSequence = Utility._xmlUtil.GetTextValue(
Constants.SAMFileWithAllFieldsNode, Constants.ExpectedSeqWithPointersNode);
string samFilePath = Utility._xmlUtil.GetTextValue(
Constants.SAMFileWithAllFieldsNode, Constants.FilePathNode);
string lineNumberForPointer = Utility._xmlUtil.GetTextValue(
Constants.SAMFileWithAllFieldsNode, Constants.LineNumberToPointNode);
// Parse a SAM file
SAMParser parserObj = new SAMParser();
parserObj.EnforceDataVirtualization = true;
SequenceAlignmentMap seqList = parserObj.Parse(samFilePath);
Assert.IsNotNull(seqList);
// Get a pointer object
SequencePointer pointerObj = GetSequencePointer(Int32.Parse(lineNumberForPointer));
pointerObj.IndexOffsets[0] = 156;
pointerObj.IndexOffsets[1] = 304;
// Parse a SAM file using Sequence Pointer.
SAMAlignedSequence alignedSeq = (SAMAlignedSequence)parserObj.ParseAlignedSequence(pointerObj);
// Validate parsed SAM aligned sequence.
Assert.AreEqual(expectedSequence,
alignedSeq.QuerySequence.ToString());
Console.WriteLine(string.Format(null,
"SAM Parser BVT : Sequence alignment aligned seq {0} validate successfully",
alignedSeq.Sequences[0].ToString()));
ApplicationLog.WriteLine(string.Format(null,
"SAM Parser BVT : Sequence alignment aligned seq validate successfully"));
}