private List <MitoMapSvItem> ExtractSvItemFromDeletionsSingle(List <string> info)
{
var junctions = info[0].OptimizedSplit(':').Select(int.Parse).ToList();
var start = junctions[0] + 1;
var end = junctions[1] - 1;
if (end < start)
{
throw new ArgumentOutOfRangeException($"Deletions with end position smaller than start position: start: {start}, end: {end}");
}
var calculatedSize = end - start + 1;
var size = int.Parse(info[1].Substring(1));
if (size <= MitomapParsingParameters.LargeDeletionCutoff)
{
return(new List <MitoMapSvItem>());
}
if (calculatedSize != size)
{
Console.WriteLine($"Incorrect size of deleted region: size of {start}-{end} should be {calculatedSize}, provided size is {size}. Provided size is used.");
}
var refSequence = _sequenceProvider.Sequence.Substring(start - 1, size);
var newStart = _variantAligner.LeftAlign(start, refSequence, "").Item1;
if (start != newStart)
{
Console.WriteLine($"Deletion of {size} bps. Original start start position: {start}; new position after left-alignment {newStart}.");
}
var mitoMapSvItem = new MitoMapSvItem(_chromosome, newStart, newStart + size - 1, VariantType.deletion);
return(new List <MitoMapSvItem> {
mitoMapSvItem
});
}
public void LeftAlignmentAlleleChange(string chromosome, int refPos, string refAllele, string altAllele,
int alignedPos, string alignedRefAllele, string alignedAltAllele)
{
var sequence = new VariantAligner.ReferenceSequence("GGCTAGCTAGCTTATTATATAT");
var aligner = new VariantAligner(sequence);
var leftAlignedVariant = aligner.LeftAlign(refPos, refAllele, altAllele);
Assert.Equal(Tuple.Create(alignedPos, alignedRefAllele, alignedAltAllele), leftAlignedVariant);
}
public void LeftAlignmentTest(string chromosome, int refPos, string refAllele, string altAllele, int alignedPos,
string alignedRefAllele, string alignedAltAllele)
{
var sequence = new VariantAligner.ReferenceSequence("TGGGGTGAGAATCATTGACATAATTGTAACAGGATAATATTCAGGAAATATGGAGATAAATAATTTTCTTCTCGACATTAAAAAAATCTAATAAAAAGTTTTATGTTTTCCCCTAACTCAGGGTCATCAGCCTTCAAGCTTCAGTCTCTGTGTGTTCACAGGTGCTGTAAACACACGCATCACTACTAATATCCCACTTCAGTGCTATTGCTGCTCCCAAAACTCCAGGTATTTTTAACCTTATAAACCTCCAGAATAATGAGACCACTGGGTTCAGTAAATTGCTTTGTTTTGAAGCACTATTAGACAAAGTGGGAGACTAGAAGATAAATCTGTCAATGACATGTCCTTTAAGACTACTTAGATTTTGTTGAATTTGTGGATCATTCCTTACTTGAGCAAATGGTAAATTAACTCTCTCTTTTCTCTCTCTCTCTAGCTGGCACACTTTTTCCAGTAGCCATTCTACTTGGTATGCTTACTTATCAGCTGTCCTCCAGGGGCCTCACATTAGATGTTTCTCTGA", 106514);
var aligner = new VariantAligner(sequence);
var leftAlignedVariant = aligner.LeftAlign(refPos, refAllele, altAllele);
Assert.Equal(Tuple.Create(alignedPos, alignedRefAllele, alignedAltAllele), leftAlignedVariant);
}
public void AlleleChangeDeletion()
{
var sequence = new VariantAligner.ReferenceSequence("AAAAAAAAAATTTTTTTTTTGGGGGGCTATTAACCCAAAAAAAAAATTTTTTTTTTGGGGGG");
var aligner = new VariantAligner(sequence);
var leftAlignedVariant = aligner.LeftAlign(29, "ATTA", "A");
Assert.Equal(Tuple.Create(28, "TAT", ""), leftAlignedVariant);
var rightAlingedVariant = aligner.RightAlign(27, "CTAT", "C");
Assert.Equal(Tuple.Create(30, "TTA", ""), rightAlingedVariant);
}