public void StageMnv(int readLength, string changedSequence, int variantPosition, int variantDepth, int referenceDepth)
{
var variantReads = GetMnvReads(changedSequence, variantPosition, readLength);
var referenceReads = GetReferenceReads(readLength);
AlignmentExtractor.StageAlignment(variantReads.Item1, variantReads.Item2, variantDepth);
AlignmentExtractor.StageAlignment(referenceReads.Item1, referenceReads.Item2, referenceDepth);
}
public void StageInsertion(int readLength, string insertion, int variantPosition, int variantDepth, int referenceDepth)
{
var variantReads = GetInsertionReads(insertion, variantPosition, readLength);
var referenceReads = GetReferenceReads(readLength);
AlignmentExtractor.StageAlignment(variantReads.Item1, variantReads.Item2, variantDepth);
AlignmentExtractor.StageAlignment(referenceReads.Item1, referenceReads.Item2, referenceDepth);
}
public void StageDeletion(int readLength, int numberDeletedBases, int variantPosition, int variantDepth, int referenceDepth)
{
var variantReads = GetDeletionReads(numberDeletedBases, variantPosition, readLength);
var referenceReads = GetReferenceReads(readLength);
AlignmentExtractor.StageAlignment(variantReads.Item1, variantReads.Item2, variantDepth, "del");
AlignmentExtractor.StageAlignment(referenceReads.Item1, referenceReads.Item2, referenceDepth, "ref");
}
public void StageStitchedVariant(BamAlignment variantRead, int variantDepth,
BamAlignment referenceRead, int referenceDepth)
{
AlignmentExtractor.StageAlignment(variantRead, variantDepth);
AlignmentExtractor.StageAlignment(referenceRead, referenceDepth);
}
