public void GetCdnaPosition_Snv_AfterOutframeRnaEditInsertion()
{
// NM_033517.1
var variant = new Interval(51135986, 51135986);
var observed = MappedPositionUtilities.GetCdnaPositions(_regionsNm33517[20], _regionsNm33517[20], variant, false, false);
Assert.Equal(1343, observed.CdnaStart);
}
public void GetCdnaPosition_Snv_AfterInframeRnaEditInsertion()
{
// NM_000682.6
var variant = new Interval(96780984, 96780984);
var observed = MappedPositionUtilities.GetCdnaPositions(_regionsNm682[0], _regionsNm682[0], variant, true, false);
Assert.Equal(1010, observed.CdnaStart);
}
public void GetCdnaPosition_Snv_AfterOutFrameRnaEditDeletion()
{
// NM_001317107.1
var variant = new Interval(22138550, 22138550);
var observed = MappedPositionUtilities.GetCdnaPositions(_regionsNm1317107[0], _regionsNm1317107[0], variant, true, false);
Assert.Equal(681, observed.CdnaStart);
}
public void GetCdnaPositions_Reverse_Deletion()
{
var variant = new Interval(ReverseVariantStart, ReverseVariantEnd);
var observed = MappedPositionUtilities.GetCdnaPositions(_reverseTranscriptRegions[6], _reverseTranscriptRegions[7], variant, true, false);
Assert.Equal(123, observed.CdnaStart);
Assert.Equal(-1, observed.CdnaEnd);
}
public void GetCdnaPositions_Forward_Insertion()
{
var variant = new Interval(ForwardVariantStart, ForwardVariantEnd);
var observed = MappedPositionUtilities.GetCdnaPositions(_forwardTranscriptRegions[4],
_forwardTranscriptRegions[4], variant, false, true);
Assert.Equal(486, observed.CdnaStart);
Assert.Equal(485, observed.CdnaEnd);
}
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));
}
