/// <summary>
/// Gets the Delta for list of query sequences.
/// </summary>
/// <param name="referenceSequence">The reference sequence.</param>
/// <param name="originalQuerySequences">The query sequence.</param>
/// <returns>Returns list of IEnumerable Delta Alignment.</returns>
private IEnumerable<IEnumerable<DeltaAlignment>> GetDelta(IEnumerable<ISequence> referenceSequence, IEnumerable<ISequence> originalQuerySequences)
{
IEnumerable<ISequence> querySequences =
Forward ? originalQuerySequences
: (Reverse
? ReverseComplementSequenceList(originalQuerySequences)
: AddReverseComplementsToSequenceList(originalQuerySequences));
foreach (ISequence refSeq in referenceSequence)
{
NUCmer nucmer = new NUCmer(refSeq)
{
FixedSeparation = FixedSeparation,
BreakLength = BreakLength,
LengthOfMUM = MinMatch,
MaximumSeparation = MaxGap,
MinimumScore = MinCluster,
SeparationFactor = (float) DiagFactor
};
foreach (ISequence qs in querySequences)
{
_queryCount++;
yield return nucmer.GetDeltaAlignments(qs, !MaxMatch, qs.IsMarkedAsReverseComplement());
}
}
}
/// <summary>
/// Aligns reads to reference genome using NUCmer.
/// </summary>
/// <param name="nodeName">Name of parent Node which contains the data in xml.</param>
/// <param name="isFilePath">Represents sequence is in a file or not.</param>
/// <returns>Delta i.e. output from NUCmer</returns>
IList<IEnumerable<DeltaAlignment>> GetDeltaAlignment(string nodeName, bool isFilePath)
{
string[] referenceSequences = null;
string[] searchSequences = null;
List<ISequence> referenceSeqList = new List<ISequence>();
List<ISequence> searchSeqList = new List<ISequence>();
IList<IEnumerable<DeltaAlignment>> results = new List<IEnumerable<DeltaAlignment>>();
if (isFilePath)
{
// Gets the reference sequence from the FastA file
string filePath = utilityObj.xmlUtil.GetTextValue(nodeName,
Constants.FilePathNode1);
Assert.IsNotNull(filePath);
ApplicationLog.WriteLine(string.Format((IFormatProvider)null,
"Comparative BVT : Successfully validated the File Path '{0}'.", filePath));
using (FastASequencePositionParser parser = new FastASequencePositionParser(filePath))
{
IEnumerable<ISequence> referenceList = parser.Parse();
foreach (ISequence seq in referenceList)
{
referenceSeqList.Add(seq);
}
// Gets the query sequence from the FastA file
string queryFilePath = utilityObj.xmlUtil.GetTextValue(nodeName,
Constants.FilePathNode2);
Assert.IsNotNull(queryFilePath);
ApplicationLog.WriteLine(string.Format((IFormatProvider)null,
"Comparative BVT : Successfully validated the File Path '{0}'.", queryFilePath));
using (FastASequencePositionParser queryParser = new FastASequencePositionParser(queryFilePath))
{
IEnumerable<ISequence> querySeqList = queryParser.Parse();
foreach (ISequence seq in querySeqList)
{
searchSeqList.Add(seq);
}
}
}
}
else
{
// Gets the reference & search sequences from the configurtion file
referenceSequences = utilityObj.xmlUtil.GetTextValues(nodeName,
Constants.ReferenceSequencesNode);
searchSequences = utilityObj.xmlUtil.GetTextValues(nodeName,
Constants.SearchSequencesNode);
IAlphabet seqAlphabet = Utility.GetAlphabet(utilityObj.xmlUtil.GetTextValue(nodeName,
Constants.AlphabetNameNode));
for (int i = 0; i < referenceSequences.Length; i++)
{
ISequence referSeq = new Sequence(seqAlphabet, encodingObj.GetBytes(referenceSequences[i]));
referenceSeqList.Add(referSeq);
}
string[] seqArray = searchSequences.ElementAt(0).Split(',');
searchSeqList.AddRange(seqArray.Select(t => new Sequence(seqAlphabet, encodingObj.GetBytes(t))).Cast<ISequence>());
}
foreach (ISequence reference in referenceSeqList)
{
NUCmer nucmerAligner = new NUCmer((Sequence)reference);
string fixedSeparation = utilityObj.xmlUtil.GetTextValue(nodeName,
Constants.FixedSeparationNode);
string minimumScore = utilityObj.xmlUtil.GetTextValue(nodeName,
Constants.MinimumScoreNode);
string separationFactor = utilityObj.xmlUtil.GetTextValue(nodeName,
Constants.SeparationFactorNode);
string LengthOfMUM = utilityObj.xmlUtil.GetTextValue(nodeName,
Constants.MUMLengthNode);
nucmerAligner.FixedSeparation = int.Parse(fixedSeparation);
nucmerAligner.MinimumScore = int.Parse(minimumScore);
nucmerAligner.SeparationFactor = int.Parse(separationFactor);
nucmerAligner.LengthOfMUM = int.Parse(LengthOfMUM);
foreach (ISequence querySeq in searchSeqList)
{
results.Add(nucmerAligner.GetDeltaAlignments(querySeq, true));
}
}
return results;
}
