public void GetProteinPosition_Forward_Insertion()
{
int proteinStart = MappedPositionUtilities.GetProteinPosition(225);
int proteinEnd = MappedPositionUtilities.GetProteinPosition(224);
Assert.Equal(75, proteinStart);
Assert.Equal(75, proteinEnd);
}
public void GetProteinPosition_Reverse_Deletion()
{
int proteinStart = MappedPositionUtilities.GetProteinPosition(-1);
int proteinEnd = MappedPositionUtilities.GetProteinPosition(-1);
Assert.Equal(-1, proteinStart);
Assert.Equal(-1, proteinEnd);
}
private static IMappedPosition GetMappedPosition(ITranscriptRegion[] regions, ITranscriptRegion startRegion,
int startIndex, ITranscriptRegion endRegion, int endIndex, IInterval variant, bool onReverseStrand,
ICodingRegion codingRegion, byte startExonPhase, bool isInsertion)
{
(int cdnaStart, int cdnaEnd) = MappedPositionUtilities.GetCdnaPositions(startRegion, endRegion, variant, onReverseStrand, isInsertion);
if (onReverseStrand)
{
Swap.Int(ref cdnaStart, ref cdnaEnd);
}
(int cdsStart, int cdsEnd) = MappedPositionUtilities.GetCdsPositions(codingRegion, cdnaStart, cdnaEnd,
startExonPhase, isInsertion);
int proteinStart = MappedPositionUtilities.GetProteinPosition(cdsStart);
int proteinEnd = MappedPositionUtilities.GetProteinPosition(cdsEnd);
(int exonStart, int exonEnd, int intronStart, int intronEnd) = regions.GetExonsAndIntrons(startIndex, endIndex);
return(new MappedPosition(cdnaStart, cdnaEnd, cdsStart, cdsEnd, proteinStart, proteinEnd, exonStart,
exonEnd, intronStart, intronEnd, startIndex, endIndex));
}