public void Create_Dragen_3_3_DUP()
{
// chr1 1715898 DRAGEN:GAIN:1715899-1750149 N <DUP> . PASS SVTYPE=CNV;END=1750149;REFLEN=34251 GT:SM:CN:BC:QS:FT:DN ./.:1.07189:2:6:33:PASS:. ./1:1.53631:3:6:49:PASS:. ./.:1.012:2:6:38:PASS:Inherited
var infoData = new InfoData(null, null, 1750149, null, null, null, null, null, null,
"CNV", null, null, null);
var observedResults = CnvCreator.Create(ChromosomeUtilities.Chr1, 1715898, infoData.End.Value, "N", "<DUP>", null);
Assert.Equal(ChromosomeUtilities.Chr1, observedResults.Chromosome);
Assert.Equal(1715899, observedResults.Start);
Assert.Equal(1750149, observedResults.End);
Assert.Equal("N", observedResults.RefAllele);
Assert.Equal("<DUP>", observedResults.AltAllele);
Assert.Equal(VariantType.copy_number_gain, observedResults.Type);
}
public void Create_Canvas_AlleleSpecificCopyNumber()
{
//chr1 854895 Canvas:COMPLEXCNV:chr1:854896-861879 N <CN0>,<CN3> . PASS SVTYPE=CNV;END=861879;CNVLEN=6984;CIPOS=-291,291;CIEND=-291,291 GT:RC:BC:CN:MCC:MCCQ:QS:FT:DQ 0/1:59.45:12:1:1:.:25.34:PASS:. 0/1:59.45:12:1:1:.:25.34:PASS:. 1/2:165.40:12:3:3:16.80:16.71:PASS:.
var infoData = new InfoData(new[] { -291, -291 }, new[] { -291, -291 }, 861879, null, null, null, null, null, null,
"CNV", null, null);
var observedResults = CnvCreator.Create(ChromosomeUtilities.Chr1, 854895, infoData.End.Value, "N", "<CN0>", null);
Assert.Equal(ChromosomeUtilities.Chr1, observedResults.Chromosome);
Assert.Equal(854896, observedResults.Start);
Assert.Equal(861879, observedResults.End);
Assert.Equal("N", observedResults.RefAllele);
Assert.Equal("<CN0>", observedResults.AltAllele);
Assert.Equal(VariantType.copy_number_variation, observedResults.Type);
}
public void Create_Dragen_3_3_DEL()
{
// chr1 907965 DRAGEN:LOSS:907966-909406 N <DEL> . SampleFT SVTYPE=CNV;END=909406;REFLEN=1441 GT:SM:CN:BC:QS:FT:DN 0/1:0.516574:1:1:24:cnvLength:. 0/1:0.409726:1:1:26:cnvLength:. 0/1:0.496663:1:1:23:cnvLength:Inherited
var infoData = new InfoData(null, null, 909406, null, null, null, null, null, null,
"CNV", null, null, null);
var observedResults = CnvCreator.Create(ChromosomeUtilities.Chr1, 907965, infoData.End.Value, "N", "<DEL>", null);
Assert.Equal(ChromosomeUtilities.Chr1, observedResults.Chromosome);
Assert.Equal(907966, observedResults.Start);
Assert.Equal(909406, observedResults.End);
Assert.Equal("N", observedResults.RefAllele);
Assert.Equal("<DEL>", observedResults.AltAllele);
Assert.Equal(VariantType.copy_number_loss, observedResults.Type);
}
public void Create_Canvas_TotalCopyNumber()
{
// 1 723707 Canvas:GAIN:1:723708:2581225 N <CNV> 41 PASS SVTYPE=CNV;END=2581225 RC:BC:CN:MCC . 129:3123:3:2
var infoData = new InfoData(null, null, 2581225, null, null, null, null, null, null,
"CNV", null, null);
var observedResults = CnvCreator.Create(ChromosomeUtilities.Chr1, 723707, infoData.End.Value, "N", "<CNV>", null);
Assert.Equal(ChromosomeUtilities.Chr1, observedResults.Chromosome);
Assert.Equal(723708, observedResults.Start);
Assert.Equal(2581225, observedResults.End);
Assert.Equal("N", observedResults.RefAllele);
Assert.Equal("<CNV>", observedResults.AltAllele);
Assert.Equal(VariantType.copy_number_variation, observedResults.Type);
}