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 RightAlignmentTest(string chromosome, int refPos, string refAllele, string altAllele, int alignedPos,
string alignedRefAllele, string alignedAltAllele)
{
var sequence = new VariantAligner.ReferenceSequence("GGCCTCACATTTTAAAAGGGGCCCCCTATTATATAT");
var aligner = new VariantAligner(sequence);
var rightAlignedVar = aligner.RightAlign(refPos, refAllele, altAllele);
Assert.Equal(Tuple.Create(alignedPos, alignedRefAllele, alignedAltAllele), rightAlignedVar);
}
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);
}
