public void GenerateOutput_NoRecomposable_ReturnOriginalVcfFieldList()
{
var positionMock1 = new Mock <IPosition>();
var positionMock2 = new Mock <IPosition>();
var positionMock3 = new Mock <IPosition>();
positionMock1.SetupGet(x => x.VcfFields).Returns(new[]
{ "chr1", "2", ".", "A", ".", ".", "PASS", ".", "GT", "0/0" });
var position1 = positionMock1.Object;
positionMock2.SetupGet(x => x.VcfFields).Returns(new[]
{ "chr1", "4", ".", "C", ".", ".", "PASS", ".", "GT", "0/0" });
var position2 = positionMock2.Object;
positionMock3.SetupGet(x => x.VcfFields).Returns(new[]
{ "chr1", "6", ".", "G", ".", ".", "PASS", ".", "GT", "0/0" });
var position3 = positionMock3.Object;
var positions = new List <ISimplePosition> {
position1, position2, position3
};
var recomposable = new List <bool> {
false, false, false
};
var functionBlockRanges = new List <int>();
var bufferedPositions = new BufferedPositions(positions, recomposable, functionBlockRanges);
var positionProcessor = new PositionProcessor(_positionBufferMock.Object, _variantGeneratorMock.Object);
var output = positionProcessor.GenerateOutput(bufferedPositions).ToArray();
for (int i = 0; i < output.Length; i++)
{
Assert.True(positions[i].VcfFields.SequenceEqual(output[i].VcfFields));
}
}
public void GenerateOutput_NothingRecomposed_ReturnOriginalVcfFieldList()
{
var mockSequenceProvider = new Mock <ISequenceProvider>();
mockSequenceProvider.SetupGet(x => x.RefNameToChromosome)
.Returns(new Dictionary <string, IChromosome> {
{ "chr1", new Chromosome("chr1", "1", 0) }
});
mockSequenceProvider.SetupGet(x => x.Sequence).Returns(new SimpleSequence("CAGCTGAA"));
var sequenceProvider = mockSequenceProvider.Object;
var variantGenerator = new VariantGenerator(sequenceProvider);
var position1 = AnnotationUtilities.GetSimplePosition("chr1 2 . A T . PASS . GT:PS 0|1:123", sequenceProvider.RefNameToChromosome);
var position2 = AnnotationUtilities.GetSimplePosition("chr1 4 . C G . PASS . GT 0/1", sequenceProvider.RefNameToChromosome);
var position3 = AnnotationUtilities.GetSimplePosition("chr1 6 . G C . PASS . GT 0|1", sequenceProvider.RefNameToChromosome);
var positions = new List <ISimplePosition> {
position1, position2, position3
};
var recomposable = new List <bool> {
true, true, true
};
var functionBlockRanges = new List <int> {
4, 6, 8
};
var bufferedPositions = new BufferedPositions(positions, recomposable, functionBlockRanges);
var positionProcessor = new PositionProcessor(_positionBufferMock.Object, variantGenerator);
var output = positionProcessor.GenerateOutput(bufferedPositions).ToArray();
for (int i = 0; i < output.Length; i++)
{
Assert.True(positions[i].VcfFields.SequenceEqual(output[i].VcfFields));
}
}
public void GenerateOutput_Return_OriginalAndRecomposed_VcfFieldList()
{
var mockSequenceProvider = new Mock <ISequenceProvider>();
mockSequenceProvider.SetupGet(x => x.RefNameToChromosome)
.Returns(new Dictionary <string, IChromosome> {
{ "chr1", new Chromosome("chr1", "1", 0) }
});
mockSequenceProvider.SetupGet(x => x.Sequence).Returns(new SimpleSequence("CAGCTGAA"));
var sequenceProvider = mockSequenceProvider.Object;
var variantGenerator = new VariantGenerator(sequenceProvider);
var position1 = AnnotationUtilities.GetSimplePosition("chr1 2 . A T . PASS . GT:PS 0|1:.", sequenceProvider.RefNameToChromosome);
var position2 = AnnotationUtilities.GetSimplePosition("chr1 4 . C G . PASS . GT 1/1", sequenceProvider.RefNameToChromosome);
var position3 = AnnotationUtilities.GetSimplePosition("chr1 6 . G C . PASS . GT 0|1", sequenceProvider.RefNameToChromosome);
var positions = new List <ISimplePosition> {
position1, position2, position3
};
var recomposable = new List <bool> {
true, true, true
};
var functionBlockRanges = new List <int> {
4, 6, 8
};
var bufferedPositions = new BufferedPositions(positions, recomposable, functionBlockRanges);
var positionProcessor = new PositionProcessor(_positionBufferMock.Object, variantGenerator);
var output = positionProcessor.GenerateOutput(bufferedPositions).ToArray();
var expectedOutput = new string[4][];
expectedOutput[0] = position1.VcfFields;
expectedOutput[1] = new[]
{ "chr1", "2", ".", "AGCTG", "AGGTG,TGGTC", ".", "PASS", "RECOMPOSED", "GT", "1|2" };
expectedOutput[2] = position2.VcfFields;
expectedOutput[3] = position3.VcfFields;
for (int i = 0; i < output.Length; i++)
{
Assert.True(expectedOutput[i].SequenceEqual(output[i].VcfFields));
}
}
public void GetRecomposablePositions_OnlyRecomposablePositions_Returned()
{
var positions = new List <ISimplePosition>
{
GetMockedIPositionOnChr1(99, 99),
GetMockedIPositionOnChr1(101, 101, "."),
GetMockedIPositionOnChr1(105, 105, "T"),
GetMockedIPositionOnChr1(110, 110, ".")
};
var recomposable = new List <bool> {
true, false, true, false
};
var functionBlockRanges = new List <int> {
102, 110
};
var recomposablePositions = new BufferedPositions(positions, recomposable, functionBlockRanges).GetRecomposablePositions();
Assert.Equal(2, recomposablePositions.Count);
Assert.True(positions[0].Equals(recomposablePositions[0]));
Assert.True(positions[2].Equals(recomposablePositions[1]));
}
internal IEnumerable <ISimplePosition> GenerateOutput(BufferedPositions bufferedPositions)
{
if (bufferedPositions.SimplePositions.Count == 0)
{
return(new List <ISimplePosition>()); // nothing to output
}
var recomposablePositions = bufferedPositions.GetRecomposablePositions();
if (recomposablePositions.Count <= 1)
{
return(bufferedPositions.SimplePositions); // nothing to recompose
}
var functionBlockRanges = bufferedPositions.FunctionBlockRanges;
var recomposedPositions = _variantGenerator.Recompose(recomposablePositions, functionBlockRanges).ToList();
if (recomposedPositions.Count == 0)
{
return(bufferedPositions.SimplePositions); // nothing has been recomposed
}
return(bufferedPositions.SimplePositions.Concat(recomposedPositions).OrderBy(x => x.Start));
}
