public void vid_compute_correctly(string refAllele, string altAllele, string expId)
{
var chrom = new Mock <IChromosome>();
chrom.Setup(x => x.EnsemblName).Returns("1");
var variant = SmallVariantCreator.Create(chrom.Object, 100, refAllele, altAllele, false, false);
Assert.Equal(expId, variant.VariantId);
}
public void Create_Insertion_ReturnVariant()
{
var variant = SmallVariantCreator.Create(ChromosomeUtilities.Chr1, 101, 100, "", "CG", false, false, null, null, false);
Assert.False(variant.IsRefMinor);
Assert.Equal(AnnotationBehavior.SmallVariants, variant.Behavior);
Assert.Equal("1", variant.Chromosome.EnsemblName);
Assert.Equal(101, variant.Start);
Assert.Equal(100, variant.End);
Assert.Equal("", variant.RefAllele);
Assert.Equal("CG", variant.AltAllele);
Assert.Equal(VariantType.insertion, variant.Type);
Assert.False(variant.IsDecomposed);
Assert.False(variant.IsRecomposed);
Assert.Null(variant.LinkedVids);
}
private static IAnnotatedPosition GetPosition(IChromosome chrom, int start, string refAllele, string[] altAlleles)
{
var position = new Mock <IAnnotatedPosition>();
var annotatedVariants = new List <IAnnotatedVariant>();
foreach (string altAllele in altAlleles)
{
VariantType type = SmallVariantCreator.GetVariantType(refAllele, altAllele);
int end = start + altAllele.Length - 1;
annotatedVariants.Add(new AnnotatedVariant(new Variant(chrom, start, end, refAllele, altAllele, type, null, false, false, false,
null, null, AnnotationBehavior.SmallVariantBehavior)));
}
position.SetupGet(x => x.AnnotatedVariants).Returns(annotatedVariants.ToArray);
return(position.Object);
}
private static void UpdateVariantType(ClinvarVariant variant)
{
var refAllele = variant.RefAllele;
var altAllele = variant.AltAllele;
if (refAllele == null || altAllele == null)
{
return;
}
var variantType = SmallVariantCreator.GetVariantType(refAllele, altAllele);
switch (variantType)
{
case VariantType.deletion:
variant.VariantType = "Deletion";
break;
case VariantType.insertion:
variant.VariantType = "Insertion";
break;
case VariantType.indel:
variant.VariantType = "Indel";
break;
case VariantType.duplication:
variant.VariantType = "Duplication";
break;
case VariantType.SNV:
variant.VariantType = "SNV";
break;
case VariantType.MNV:
variant.VariantType = "MNV";
break;
}
}
public void Small_variant_created_correctly()
{
var chrom = new Mock <IChromosome>();
chrom.Setup(x => x.EnsemblName).Returns("1");
var variant = SmallVariantCreator.Create(chrom.Object, 100, "A", "ACG", false, false, null);
Assert.False(variant.IsRefMinor);
Assert.True(variant.Behavior.NeedFlankingTranscript);
Assert.True(variant.Behavior.NeedSaPosition);
Assert.False(variant.Behavior.NeedSaInterval);
Assert.False(variant.Behavior.ReducedTranscriptAnnotation);
Assert.False(variant.Behavior.StructuralVariantConsequence);
Assert.Equal("1", variant.Chromosome.EnsemblName);
Assert.Equal(101, variant.Start);
Assert.Equal(100, variant.End);
Assert.Equal("", variant.RefAllele);
Assert.Equal("CG", variant.AltAllele);
Assert.Equal(VariantType.insertion, variant.Type);
Assert.False(variant.IsDecomposed);
Assert.False(variant.IsRecomposed);
Assert.Null(variant.LinkedVids);
}
internal static (int Start, int End, string Ref, string Alt, List <int> VarPosIndexesInAlleleBlock, List <string> decomposedVids) GetPositionsAndRefAltAlleles(AlleleBlock alleleBlock, AlleleSet alleleSet, string totalRefSequence, int regionStart, List <ISimplePosition> simplePositions)
{
int numPositions = alleleBlock.AlleleIndexes.Length;
int firstPositionIndex = alleleBlock.PositionIndex;
int lastPositionIndex = alleleBlock.PositionIndex + numPositions - 1;
int blockStart = alleleSet.Starts[firstPositionIndex];
int blockEnd = alleleSet.Starts[lastPositionIndex];
string lastRefAllele = alleleSet.VariantArrays[lastPositionIndex][0];
int blockRefLength = blockEnd - blockStart + lastRefAllele.Length;
var refSequence = totalRefSequence.Substring(blockStart - regionStart, blockRefLength);
int refSequenceStart = 0;
var altSequenceSegments = new LinkedList <string>();
var variantPosIndexesInAlleleBlock = new List <int>();
var vidListsNeedUpdate = new List <List <string> >();
var decomposedVids = new List <string>();
for (int positionIndex = firstPositionIndex; positionIndex <= lastPositionIndex; positionIndex++)
{
int indexInBlock = positionIndex - firstPositionIndex;
int alleleIndex = alleleBlock.AlleleIndexes[indexInBlock];
//only non-reference alleles considered
if (alleleIndex == 0)
{
continue;
}
variantPosIndexesInAlleleBlock.Add(positionIndex - firstPositionIndex);
string refAllele = alleleSet.VariantArrays[positionIndex][0];
string altAllele = alleleSet.VariantArrays[positionIndex][alleleIndex];
int positionOnRefSequence = alleleSet.Starts[positionIndex] - blockStart;
int refRegionBetweenTwoAltAlleles = positionOnRefSequence - refSequenceStart;
if (refRegionBetweenTwoAltAlleles < 0)
{
string previousAltAllele = alleleSet.VariantArrays[positionIndex - 1][alleleIndex];
throw new UserErrorException($"Conflicting alternative alleles identified at {alleleSet.Chromosome.UcscName}:{alleleSet.Starts[positionIndex]}: both \"{previousAltAllele}\" and \"{altAllele}\" are present.");
}
string refSequenceBefore = refSequence.Substring(refSequenceStart, refRegionBetweenTwoAltAlleles);
altSequenceSegments.AddLast(refSequenceBefore);
altSequenceSegments.AddLast(altAllele);
refSequenceStart = positionOnRefSequence + refAllele.Length;
if (simplePositions == null)
{
continue;
}
var thisPosition = simplePositions[positionIndex];
// alleleIndex is 1-based for altAlleles
int varIndex = alleleIndex - 1;
//Only SNVs get recomposed for now
if (thisPosition.Vids[varIndex] == null)
{
thisPosition.Vids[varIndex] = SmallVariantCreator.GetVid(alleleSet.Chromosome.EnsemblName,
thisPosition.Start, thisPosition.End, thisPosition.AltAlleles[varIndex], VariantType.SNV);
thisPosition.IsDecomposed[varIndex] = true;
}
decomposedVids.Add(thisPosition.Vids[varIndex]);
if (thisPosition.LinkedVids[varIndex] == null)
{
thisPosition.LinkedVids[varIndex] = new List <string>();
}
vidListsNeedUpdate.Add(thisPosition.LinkedVids[varIndex]);
}
altSequenceSegments.AddLast(refSequence.Substring(refSequenceStart));
var recomposedAllele = string.Concat(altSequenceSegments);
var blockRefEnd = blockStart + blockRefLength - 1;
var recomposedVariantId = SmallVariantCreator.GetVid(alleleSet.Chromosome.EnsemblName, blockStart, blockRefEnd, recomposedAllele, VariantType.MNV);
vidListsNeedUpdate.ForEach(x => x.Add(recomposedVariantId));
return(blockStart, blockRefEnd, refSequence, recomposedAllele, variantPosIndexesInAlleleBlock, decomposedVids);
}
