public void ValidateBAMParseAlignedSeqWithSeqPointer()
{
// Get values from XML node.
string expectedSequence = _utilityObj._xmlUtil.GetTextValue(
Constants.BAMToSAMConversionNode, Constants.ExpectedSeqWithPointersNode);
string samFilePath = _utilityObj._xmlUtil.GetTextValue(
Constants.BAMToSAMConversionNode, Constants.FilePathNode);
string startingLineForPointer = _utilityObj._xmlUtil.GetTextValue(
Constants.BAMToSAMConversionNode, Constants.LineNumberToPointNode);
string startIndex = _utilityObj._xmlUtil.GetTextValue(
Constants.BAMToSAMConversionNode, Constants.StartIndexNode);
string endIndex = _utilityObj._xmlUtil.GetTextValue(
Constants.BAMToSAMConversionNode, Constants.EndIndexNode);
// Parse a BAM file
using (BAMParser parserObj = new BAMParser())
{
parserObj.EnforceDataVirtualization = true;
SequenceAlignmentMap seqList = parserObj.Parse(samFilePath);
Assert.IsNotNull(seqList);
// Get a pointer object
SequencePointer pointerObj =
GetBAMSequencePointer(Int32.Parse(startingLineForPointer, (IFormatProvider)null),
Int32.Parse(startIndex, (IFormatProvider)null), Int32.Parse(endIndex, (IFormatProvider)null));
// Parse a BAM 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((IFormatProvider)null,
"BAM Parser BVT : Sequence alignment aligned seq {0} validate successfully",
alignedSeq.Sequences[0].ToString()));
ApplicationLog.WriteLine(string.Format((IFormatProvider)null,
"BAM Parser BVT : Sequence alignment aligned seq validate successfully"));
}
}
