public MitoMapSvReader(FileInfo mitoMapFileInfo, ISequenceProvider sequenceProvider) { _mitoMapFileInfo = mitoMapFileInfo; _dataType = GetDataType(); _sequenceProvider = sequenceProvider; _chromosome = sequenceProvider?.RefNameToChromosome["chrM"]; _variantAligner = new VariantAligner(sequenceProvider?.Sequence); }
public MitoMapSvReader(FileInfo mitoMapFileInfo, ReferenceSequenceProvider sequenceProvider) { _mitoMapFileInfo = mitoMapFileInfo; _dataType = GetDataType(); _sequenceProvider = sequenceProvider; _mitoGenomeModel = new CircularGenomeModel(sequenceProvider.Sequence); _variantAligner = new VariantAligner(sequenceProvider.Sequence); }
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 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); }