public void FixExonEndpointInsertion_VariantStart_ExonStart_Forward()
{
var startRegion = new TranscriptRegion(TranscriptRegionType.Exon, 2, 99459243, 99459360, 108, 225);
var endRegion = new TranscriptRegion(TranscriptRegionType.Intron, 1, 99456512, 99459242, 107, 108);
var result = MappedPositionUtilities.FixExonEndpointInsertion(108, -1, false, startRegion, endRegion,
new Interval(99459243, 99459242));
Assert.Equal(108, result.CdnaStart);
Assert.Equal(107, result.CdnaEnd);
}
public void FixExonEndpointInsertion_VariantEnd_ExonEnd_Forward()
{
var startRegion = new TranscriptRegion(TranscriptRegionType.Intron, 16, 89521770, 89528546, 3071, 3072);
var endRegion = new TranscriptRegion(TranscriptRegionType.Exon, 16, 89521614, 89521769, 2916, 3071);
var result = MappedPositionUtilities.FixExonEndpointInsertion(-1, 3071, false, startRegion, endRegion,
new Interval(89521770, 89521769));
Assert.Equal(3072, result.CdnaStart);
Assert.Equal(3071, result.CdnaEnd);
}
public void FixExonEndpointInsertion_VariantEnd_ExonEnd_Reverse()
{
var startRegion = new TranscriptRegion(TranscriptRegionType.Intron, 7, 243736351, 243776972, 762, 763);
var endRegion = new TranscriptRegion(TranscriptRegionType.Exon, 8, 243736228, 243736350, 763, 885);
var result = MappedPositionUtilities.FixExonEndpointInsertion(-1, 763, true, startRegion, endRegion,
new Interval(243736351, 243736350));
Assert.Equal(762, result.CdnaStart);
Assert.Equal(763, result.CdnaEnd);
}
public void FixExonEndpointInsertion_VariantStart_ExonStart_Reverse()
{
// N.B. this configuration has never been spotted in the wild
var startRegion = new TranscriptRegion(TranscriptRegionType.Exon, 2, 2000, 2199, 1, 200);
var endRegion = new TranscriptRegion(TranscriptRegionType.Intron, 2, 1999, 1000, 200, 201);
var result = MappedPositionUtilities.FixExonEndpointInsertion(200, -1, true, startRegion, endRegion,
new Interval(2000, 1999));
Assert.Equal(200, result.CdnaStart);
Assert.Equal(201, result.CdnaEnd);
}