internal static List <T> FlattenWithSameId <T>(List <T> genes) where T : IFlatGene <T>
{
if (genes == null || genes.Count == 1)
{
return(genes);
}
var flatGenes = new List <T>();
var seedGene = genes[0].Clone();
foreach (var gene in genes)
{
if (IntervalUtilities.Overlaps(seedGene.Start, seedGene.End, gene.Start, gene.End))
{
seedGene.End = Math.Max(seedGene.End, gene.End);
continue;
}
flatGenes.Add(seedGene);
seedGene = gene.Clone();
}
flatGenes.Add(seedGene);
return(flatGenes);
}
internal static bool IsBeforeCoding(int variantRefBegin, int variantRefEnd, int transcriptStart, int codingRegionStart)
{
// special case to handle insertions before the CDS start
if (variantRefBegin == variantRefEnd + 1 && variantRefBegin == codingRegionStart)
{
return(true);
}
bool result = IntervalUtilities.Overlaps(variantRefBegin, variantRefEnd, transcriptStart, codingRegionStart - 1);
return(result);
}
internal static bool IsAfterCoding(int variantRefBegin, int variantRefEnd, int transcriptEnd, int codingRegionEnd)
{
// special case to handle insertions after the CDS end
if (variantRefBegin == variantRefEnd + 1 && variantRefEnd == codingRegionEnd)
{
return(true);
}
var result = IntervalUtilities.Overlaps(variantRefBegin, variantRefEnd, codingRegionEnd + 1, transcriptEnd);
return(result);
}
public FeatureVariantEffects(IInterval feature, VariantType vt, IInterval variant, bool isSv)
{
_isSv = isSv;
_completelyOverlaps = IntervalUtilities.Contains(variant.Start, variant.End, feature.Start, feature.End);
_overlaps = feature.Overlaps(variant);
_completelyWithin = variant.Start >= feature.Start && variant.End <= feature.End;
_lossOrDeletion = vt == VariantType.copy_number_loss || vt == VariantType.deletion || vt == VariantType.copy_number_loss;
_gainOrDuplication = vt == VariantType.copy_number_gain || vt == VariantType.duplication || vt == VariantType.tandem_duplication || vt == VariantType.copy_number_gain;
_isInsertionDeletion = vt == VariantType.indel;
_isInsertion = vt == VariantType.insertion;
}
private static void ReplaceHgncIds(IEnumerable <MutableGene> genes, IReadOnlyDictionary <string, HgncGene> geneIdToHgncGene)
{
foreach (var gene in genes)
{
gene.HgncId = -1;
if (!geneIdToHgncGene.TryGetValue(gene.GeneId, out var hgncGene))
{
continue;
}
if (!IntervalUtilities.Overlaps(hgncGene.Start, hgncGene.End, gene.Start, gene.End))
{
continue;
}
gene.HgncId = hgncGene.HgncId;
}
}
private static void AddCoordinatesFromMultipleGenes(HgncGene hgncGene, EnsemblGene ensemblGene, IEnumerable <RefSeqGene> refSeqGenes)
{
if (ensemblGene == null)
{
return;
}
AddCoordinatesFromGene(hgncGene, ensemblGene);
foreach (var refSeqGene in refSeqGenes)
{
if (!IntervalUtilities.Overlaps(hgncGene.Start, hgncGene.End, refSeqGene.Start, refSeqGene.End))
{
continue;
}
AddCoordinatesFromGene(hgncGene, refSeqGene);
}
}
public void Contains_Theory(int start1, int end1, int start2, int end2, bool expectedResult)
{
var observedResult = IntervalUtilities.Contains(start1, end1, start2, end2);
Assert.Equal(expectedResult, observedResult);
}
