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)); }