public void VariantGenerator_RefAllelesAddedToMergeAlleles()
{
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("CAGCTGAACT"));
var sequenceProvider = mockSequenceProvider.Object;
var position1 = AnnotationUtilities.GetSimplePosition("chr1 2 . A T . PASS . GT 0|1 0|0 0|1 0|0", sequenceProvider.RefNameToChromosome);
var position2 = AnnotationUtilities.GetSimplePosition("chr1 4 . C A . PASS . GT 1|1 1|1 1|1 1|1", sequenceProvider.RefNameToChromosome);
var position3 = AnnotationUtilities.GetSimplePosition("chr1 6 . G C . PASS . GT 1|1 1|1 1|1 1|1", sequenceProvider.RefNameToChromosome);
var position4 = AnnotationUtilities.GetSimplePosition("chr1 8 . A G . PASS . GT 0|1 0|1 0|0 0|0", sequenceProvider.RefNameToChromosome);
var functionBlockRanges = new List <int> {
4, 6, 8, 10
};
var recomposer = new VariantGenerator(sequenceProvider);
var recomposedPositions = recomposer.Recompose(new List <ISimplePosition> {
position1, position2, position3, position4
}, functionBlockRanges).ToList();
Assert.Single(recomposedPositions);
Assert.Equal("chr1 2 . AGCTGAA AGATCAA,AGATCAG,TGATCAA,TGATCAG . PASS RECOMPOSED GT 1|4 1|2 1|3 1|1", string.Join("\t", recomposedPositions[0].VcfFields));
}
public void VariantGenerator_HomozygousSitesAndPhasedSites_Recomposed()
{
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 position1 = AnnotationUtilities.GetSimplePosition("chr1 2 . A T . PASS . GT 1/1 1/1 1/1", sequenceProvider.RefNameToChromosome);
var position2 = AnnotationUtilities.GetSimplePosition("chr1 3 . G A,G 45 PASS . GT:PS 1|1:2 1|2:2 1|2:2", sequenceProvider.RefNameToChromosome);
var position3 = AnnotationUtilities.GetSimplePosition("chr1 4 . C A 45 PASS . GT 1/1 1/1 1/1", sequenceProvider.RefNameToChromosome);
var position4 = AnnotationUtilities.GetSimplePosition("chr1 5 . T A,G 45 PASS . GT:PS 1|1:4 1|2:2 1|2:4", sequenceProvider.RefNameToChromosome);
var position5 = AnnotationUtilities.GetSimplePosition("chr1 6 . G C 30 PASS . GT 1/1 1/1 1/1", sequenceProvider.RefNameToChromosome);
var functionBlockRanges = new List <int> {
4, 5, 6, 7, 8
};
var recomposer = new VariantGenerator(sequenceProvider);
var recomposedPositions = recomposer.Recompose(new List <ISimplePosition> {
position1, position2, position3, position4, position5
}, functionBlockRanges).ToList();
Assert.Equal(3, recomposedPositions.Count);
Assert.Equal("chr1 2 . AGC TAA,TGA 45 PASS RECOMPOSED GT:PS . . 1|2:2", string.Join("\t", recomposedPositions[0].VcfFields));
Assert.Equal("chr1 2 . AGCTG TAAAC,TGAGC 30 PASS RECOMPOSED GT:PS 1|1 1|2:2 .", string.Join("\t", recomposedPositions[1].VcfFields));
Assert.Equal("chr1 4 . CTG AAC,AGC 30 PASS RECOMPOSED GT:PS . . 1|2:4", string.Join("\t", recomposedPositions[2].VcfFields));
}
public void VariantGenerator_MinGQUsed_DotAndNullIgnored()
{
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 position1 = AnnotationUtilities.GetSimplePosition("chr1 2 . A T,G . PASS . GT:PS:GQ 0|1:123:. 2/2:.:14.2 0|2:456:.", sequenceProvider.RefNameToChromosome);
var position2 = AnnotationUtilities.GetSimplePosition("chr1 4 . C A,G . PASS . GT:PS:GQ 1|1:301:. 1|2:.:18 1|2:456:15.6", sequenceProvider.RefNameToChromosome);
var position3 = AnnotationUtilities.GetSimplePosition("chr1 6 . G C . PASS . GT . 1|0 0/1", sequenceProvider.RefNameToChromosome);
var functionBlockRanges = new List <int> {
4, 6, 8
};
var recomposer = new VariantGenerator(sequenceProvider);
var recomposedPositions = recomposer.Recompose(new List <ISimplePosition> {
position1, position2, position3
}, functionBlockRanges).ToList();
Assert.Equal(2, recomposedPositions.Count);
Assert.Equal("chr1 2 . AGC AGA,GGG,TGA . PASS RECOMPOSED GT:GQ:PS 1|3:.:123 . 1|2:15.6:456", string.Join("\t", recomposedPositions[0].VcfFields));
Assert.Equal("chr1 2 . AGCTG GGATC,GGGTG . PASS RECOMPOSED GT:GQ . 1|2:14.2 .", string.Join("\t", recomposedPositions[1].VcfFields));
}
public void VariantGenerator_AllTrailingMissingValuesDroped()
{
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 position1 = AnnotationUtilities.GetSimplePosition("chr1 2 . A T,G . PASS . GT:GQ:PS 0|1:.:123 2/2 1|1:17:456", sequenceProvider.RefNameToChromosome);
var position2 = AnnotationUtilities.GetSimplePosition("chr1 4 . C A,G . PASS . GT:GQ:PS ./. 1|2 1|2:15.6:456", sequenceProvider.RefNameToChromosome);
var position3 = AnnotationUtilities.GetSimplePosition("chr1 6 . G C . PASS . GT:GQ:PS ./. 1|0 1|1:13:456", sequenceProvider.RefNameToChromosome);
var functionBlockRanges = new List <int> {
4, 6, 8
};
var recomposer = new VariantGenerator(sequenceProvider);
var recomposedPositions = recomposer.Recompose(new List <ISimplePosition> {
position1, position2, position3
}, functionBlockRanges).ToList();
Assert.Single(recomposedPositions);
Assert.Equal("chr1 2 . AGCTG GGATC,GGGTG,TGATC,TGGTC . PASS RECOMPOSED GT:GQ:PS . 1|2 3|4:13:456", string.Join("\t", recomposedPositions[0].VcfFields));
}
public void VariantGenerator_FilterTag_DotTreatedAsPass()
{
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 position1 = AnnotationUtilities.GetSimplePosition("chr1 2 . A T,G . PASS . GT:PS 0|1:123 2/2:. 0|2:456", sequenceProvider.RefNameToChromosome);
var position2 = AnnotationUtilities.GetSimplePosition("chr1 4 . C A,G . . . GT:PS 1|1:301 1|2:. 1|2:456", sequenceProvider.RefNameToChromosome);
var position3 = AnnotationUtilities.GetSimplePosition("chr1 6 . G C . FailedForSomeReason . GT:PS . 1|0:. 0/1:456", sequenceProvider.RefNameToChromosome);
var functionBlockRanges = new List <int> {
4, 6, 8
};
var recomposer = new VariantGenerator(sequenceProvider);
var recomposedPositions = recomposer.Recompose(new List <ISimplePosition> {
position1, position2, position3
}, functionBlockRanges).ToList();
Assert.Equal(2, recomposedPositions.Count);
Assert.Equal("chr1 2 . AGC AGA,GGG,TGA . PASS RECOMPOSED GT:PS 1|3:123 . 1|2:456", string.Join("\t", recomposedPositions[0].VcfFields));
Assert.Equal("chr1 2 . AGCTG GGATC,GGGTG . FilteredVariantsRecomposed RECOMPOSED GT . 1|2 .", string.Join("\t", recomposedPositions[1].VcfFields));
}
public void VariantGenerator_FilterTag_PassedMnvOverridesFailedOne()
{
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 position1 = AnnotationUtilities.GetSimplePosition("chr1 2 . A T . PASS . GT 0|1 0|1", sequenceProvider.RefNameToChromosome);
var position2 = AnnotationUtilities.GetSimplePosition("chr1 4 . C A . FailedForSomeReason . GT 0|0 0|1", sequenceProvider.RefNameToChromosome);
var position3 = AnnotationUtilities.GetSimplePosition("chr1 6 . G C . PASS . GT 0|1 0|1", sequenceProvider.RefNameToChromosome);
var functionBlockRanges = new List <int> {
6, 8, 10
};
var recomposer = new VariantGenerator(sequenceProvider);
var recomposedPositions = recomposer.Recompose(new List <ISimplePosition> {
position1, position2, position3
}, functionBlockRanges).ToList();
Assert.Single(recomposedPositions);
Assert.Equal("chr1 2 . AGCTG TGATC,TGCTC . PASS RECOMPOSED GT 0|2 0|1", string.Join("\t", recomposedPositions[0].VcfFields));
}
public void VariantGenerator_HomoReferenceGenotype_Output()
{
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 position1 = AnnotationUtilities.GetSimplePosition("chr1 1 . C A . PASS . GT:PS 0|1:1584593 0/0:.", sequenceProvider.RefNameToChromosome);
var position2 = AnnotationUtilities.GetSimplePosition("chr1 2 . A C . PASS . GT:PS 0|1:1584593 0/0:.", sequenceProvider.RefNameToChromosome);
var functionBlockRanges = new List <int> {
3, 4
};
var recomposer = new VariantGenerator(sequenceProvider);
var recomposedPositions = recomposer.Recompose(new List <ISimplePosition> {
position1, position2
}, functionBlockRanges).ToList();
Assert.Single(recomposedPositions);
Assert.Equal("chr1 1 . CA AC . PASS RECOMPOSED GT:PS 0|1:1584593 0|0", string.Join("\t", recomposedPositions[0].VcfFields));
}
public void VariantGenerator_OverlappingDeletionAtTheEnd_Ignored()
{
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("CAGCTGAATCGCGA"));
var sequenceProvider = mockSequenceProvider.Object;
var position1 = AnnotationUtilities.GetSimplePosition("chr1 2 . A T . PASS . GT 0|1 0/0", sequenceProvider.RefNameToChromosome);
var position2 = AnnotationUtilities.GetSimplePosition("chr1 4 . C A . PASS . GT 1|1 0/0", sequenceProvider.RefNameToChromosome);
var position3 = AnnotationUtilities.GetSimplePosition("chr1 4 . CTGAATCGCGA C . PASS . GT 0/0 0|1", sequenceProvider.RefNameToChromosome);
var functionBlockRanges = new List <int> {
4, 6, 6
};
var recomposer = new VariantGenerator(sequenceProvider);
var recomposedPositions = recomposer.Recompose(new List <ISimplePosition> {
position1, position2, position3
}, functionBlockRanges).ToList();
Assert.Single(recomposedPositions);
Assert.Equal("chr1 2 . AGC AGA,TGA . PASS RECOMPOSED GT 1|2 0|0", string.Join("\t", recomposedPositions[0].VcfFields));
}
public void VariantGenerator_ForceGenotype_ConsistentAllele_Recompose()
{
var mockSequenceProvider = new Mock <ISequenceProvider>();
mockSequenceProvider.SetupGet(x => x.RefNameToChromosome)
.Returns(ChromosomeUtilities.RefNameToChromosome);
mockSequenceProvider.SetupGet(x => x.Sequence).Returns(new SimpleSequence("CAGCTGAATCGCGA"));
var sequenceProvider = mockSequenceProvider.Object;
var position1 = AnnotationUtilities.GetSimplePosition("chr1 2 . A T . PASS . GT 1|1 0/0", sequenceProvider.RefNameToChromosome);
var position2 = AnnotationUtilities.GetSimplePosition("chr1 4 . C G . PASS . GT 0|1 0|1", sequenceProvider.RefNameToChromosome);
var position3 = AnnotationUtilities.GetSimplePosition("chr1 4 . C G,A . PASS . GT 0|1 0/0", sequenceProvider.RefNameToChromosome);
var functionBlockRanges = new List <int> {
4, 6, 6
};
var recomposer = new VariantGenerator(sequenceProvider, _vidCreator);
var recomposedPositions = recomposer.Recompose(new List <ISimplePosition> {
position1, position2, position3
}, functionBlockRanges).ToList();
Assert.Single(recomposedPositions);
Assert.Equal("chr1 2 . AGC TGC,TGG . PASS RECOMPOSED GT 1|2 .", string.Join("\t", recomposedPositions[0].VcfFields));
}
public void VariantGenerator_MinQualUsed_DotIgnored()
{
var mockSequenceProvider = new Mock <ISequenceProvider>();
mockSequenceProvider.SetupGet(x => x.RefNameToChromosome)
.Returns(ChromosomeUtilities.RefNameToChromosome);
mockSequenceProvider.SetupGet(x => x.Sequence).Returns(new SimpleSequence("CAGCTGAA"));
var sequenceProvider = mockSequenceProvider.Object;
var position1 = AnnotationUtilities.GetSimplePosition("chr1 2 . A T,G . PASS . GT:PS 0|1:123 2/2:. 0|2:456", sequenceProvider.RefNameToChromosome);
var position2 = AnnotationUtilities.GetSimplePosition("chr1 4 . C A,G 45 PASS . GT:PS 1|1:301 1|2:. 1|2:456", sequenceProvider.RefNameToChromosome);
var position3 = AnnotationUtilities.GetSimplePosition("chr1 6 . G C 30.1 PASS . GT . 1|0 0/1", sequenceProvider.RefNameToChromosome);
var functionBlockRanges = new List <int> {
4, 6, 8
};
var recomposer = new VariantGenerator(sequenceProvider, _vidCreator);
var recomposedPositions = recomposer.Recompose(new List <ISimplePosition> {
position1, position2, position3
}, functionBlockRanges).ToList();
Assert.Equal(2, recomposedPositions.Count);
Assert.Equal("chr1 2 . AGC AGA,GGG,TGA 45 PASS RECOMPOSED GT:PS 1|3:123 . 1|2:456", string.Join("\t", recomposedPositions[0].VcfFields));
Assert.Equal("chr1 2 . AGCTG GGATC,GGGTG 30.1 PASS RECOMPOSED GT . 1|2 .", string.Join("\t", recomposedPositions[1].VcfFields));
}
public void VariantGenerator_ConflictAltAlleles_AlleleBlockStartInTheMiddle_NoRecompositionNoException()
{
var mockSequenceProvider = new Mock <ISequenceProvider>();
mockSequenceProvider.SetupGet(x => x.RefNameToChromosome)
.Returns(ChromosomeUtilities.RefNameToChromosome);
mockSequenceProvider.SetupGet(x => x.Sequence).Returns(new SimpleSequence("CAGCTGAATCGCGA"));
var sequenceProvider = mockSequenceProvider.Object;
var position1 = AnnotationUtilities.GetSimplePosition("chr1 1 . C T . PASS . GT 0/1 0|1", sequenceProvider.RefNameToChromosome);
var position2 = AnnotationUtilities.GetSimplePosition("chr1 2 . A T . PASS . GT 0/1 0|0", sequenceProvider.RefNameToChromosome);
var position3 = AnnotationUtilities.GetSimplePosition("chr1 4 . C G . PASS . GT 1|1 1|1", sequenceProvider.RefNameToChromosome);
var position4 = AnnotationUtilities.GetSimplePosition("chr1 4 . C A . PASS . GT 1|1 0|1", sequenceProvider.RefNameToChromosome);
var functionBlockRanges = new List <int> {
3, 4, 6, 6
};
var recomposer = new VariantGenerator(sequenceProvider, _vidCreator);
var recomposedPositions = recomposer.Recompose(new List <ISimplePosition> {
position1, position2, position3, position4
}, functionBlockRanges).ToList();
Assert.Empty(recomposedPositions);
}
public void VariantGenerator_AsExpected()
{
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 position1 = SimplePosition.GetSimplePosition("chr1 2 . A T,G . PASS . GT:PS 0|1:123 2/2:789 0|2:456", sequenceProvider.RefNameToChromosome);
var position2 = SimplePosition.GetSimplePosition("chr1 4 . C A,G . PASS . GT:PS 1|1:301 1|2:789 1|2:456", sequenceProvider.RefNameToChromosome);
var position3 = SimplePosition.GetSimplePosition("chr1 6 . G C . PASS . GT:PS . 1|0:789 0/1:.", sequenceProvider.RefNameToChromosome);
var functionBlockRanges = new List <int> {
4, 6, 8
};
var recomposer = new VariantGenerator(sequenceProvider);
var recomposedPositions = recomposer.Recompose(new List <ISimplePosition> {
position1, position2, position3
}, functionBlockRanges).ToList();
Assert.Equal(2, recomposedPositions.Count);
Assert.Equal("chr1 2 . AGC AGA,GGG . PASS RECOMPOSED GT:PS . . 1|2:456", string.Join("\t", recomposedPositions[0].VcfFields));
Assert.Equal("chr1 2 . AGCTG GGATC,GGGTG . PASS RECOMPOSED GT:PS . 1|2:789 .", string.Join("\t", recomposedPositions[1].VcfFields));
}
public void VariantGenerator_SampleColumnCorrectlyProcessed_WhenTrailingMissingValuesDroped()
{
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 position1 = SimplePosition.GetSimplePosition("chr1 2 . A T,G . PASS . GT:PS:GQ 0|1:123 2/2:.:14.2 ./.", sequenceProvider.RefNameToChromosome);
var position2 = SimplePosition.GetSimplePosition("chr1 4 . C A,G . PASS . GT:PS:GQ ./. 1|2:.:18 1|2:456:15.6", sequenceProvider.RefNameToChromosome);
var position3 = SimplePosition.GetSimplePosition("chr1 6 . G C . PASS . GT ./. 1|0 ./.", sequenceProvider.RefNameToChromosome);
var functionBlockRanges = new List <int> {
4, 6, 8
};
var recomposer = new VariantGenerator(sequenceProvider);
var recomposedPositions = recomposer.Recompose(new List <ISimplePosition> {
position1, position2, position3
}, functionBlockRanges).ToList();
Assert.Single(recomposedPositions);
Assert.Equal("chr1 2 . AGCTG GGATC,GGGTG . PASS RECOMPOSED GT:GQ . 1|2:14.2 .", string.Join("\t", recomposedPositions[0].VcfFields));
}
public void VariantGenerator_NoMnvAfterTrimming_NotRecompose()
{
var mockSequenceProvider = new Mock <ISequenceProvider>();
mockSequenceProvider.SetupGet(x => x.RefNameToChromosome)
.Returns(ChromosomeUtilities.RefNameToChromosome);
mockSequenceProvider.SetupGet(x => x.Sequence).Returns(new SimpleSequence("CAGCTGAA"));
var sequenceProvider = mockSequenceProvider.Object;
var position1 = AnnotationUtilities.GetSimplePosition("chr1 1 . C A . PASS . GT:PS 1|0:1584593 1|1:. 0|1:.", sequenceProvider.RefNameToChromosome);
var position2 = AnnotationUtilities.GetSimplePosition("chr1 2 . A C . PASS . GT:PS 0|1:1584593 0/0:. 0/0:.", sequenceProvider.RefNameToChromosome);
var functionBlockRanges = new List <int> {
3, 4
};
var recomposer = new VariantGenerator(sequenceProvider, _vidCreator);
var recomposedPositions = recomposer.Recompose(new List <ISimplePosition> {
position1, position2
}, functionBlockRanges).ToList();
Assert.Empty(recomposedPositions);
}
public void VariantGenerator_FilterTag_OnlyDecomposedVariantsConsidered()
{
var mockSequenceProvider = new Mock <ISequenceProvider>();
mockSequenceProvider.SetupGet(x => x.RefNameToChromosome)
.Returns(ChromosomeUtilities.RefNameToChromosome);
mockSequenceProvider.SetupGet(x => x.Sequence).Returns(new SimpleSequence("CAGCTGAA"));
var sequenceProvider = mockSequenceProvider.Object;
var position1 = AnnotationUtilities.GetSimplePosition("chr1 2 . A T . PASS . GT 0|1 0/1 0|0", sequenceProvider.RefNameToChromosome);
var position2 = AnnotationUtilities.GetSimplePosition("chr1 4 . C A . FailedForSomeReason . GT 0|0 0/1 0|0", sequenceProvider.RefNameToChromosome);
var position3 = AnnotationUtilities.GetSimplePosition("chr1 6 . G C . PASS . GT 1|1 0/1 0|0", sequenceProvider.RefNameToChromosome);
var functionBlockRanges = new List <int> {
6, 8, 10
};
var recomposer = new VariantGenerator(sequenceProvider, _vidCreator);
var recomposedPositions = recomposer.Recompose(new List <ISimplePosition> {
position1, position2, position3
}, functionBlockRanges).ToList();
Assert.Single(recomposedPositions);
Assert.Equal("chr1 2 . AGCTG AGCTC,TGCTC . PASS RECOMPOSED GT 1|2 . 0|0", string.Join("\t", recomposedPositions[0].VcfFields));
}
public void VariantGenerator_AsExpected()
{
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 position1 = AnnotationUtilities.GetSimplePosition("chr1 2 . A T,G . PASS . GT:PS 0|1:123 2/2:789 0|2:456", sequenceProvider.RefNameToChromosome);
var position2 = AnnotationUtilities.GetSimplePosition("chr1 4 . C A,G . PASS . GT:PS 1|1:301 1|2:789 1|2:456", sequenceProvider.RefNameToChromosome);
var position3 = AnnotationUtilities.GetSimplePosition("chr1 6 . G C . PASS . GT:PS . 1|0:789 0/1:.", sequenceProvider.RefNameToChromosome);
var functionBlockRanges = new List <int> {
4, 6, 8
};
var recomposer = new VariantGenerator(sequenceProvider);
var recomposedPositions = recomposer.Recompose(new List <ISimplePosition> {
position1, position2, position3
}, functionBlockRanges).ToList();
Assert.Equal(2, recomposedPositions.Count);
Assert.Equal("chr1 2 . AGC AGA,GGG,TGA . PASS RECOMPOSED GT:PS 1|3:123 . 1|2:456", string.Join("\t", recomposedPositions[0].VcfFields));
Assert.Equal("chr1 2 . AGCTG GGATC,GGGTG . PASS RECOMPOSED GT:PS . 1|2:789 .", string.Join("\t", recomposedPositions[1].VcfFields));
//Check LinkedVids
//SNVs
Assert.Equal(2, position1.LinkedVids.Length);
Assert.Equal(new List <string> {
"1:2:4:TGA"
}, position1.LinkedVids[0]);
position1.LinkedVids[1].Sort();
Assert.Equal(new List <string> {
"1:2:4:GGG", "1:2:6:GGATC", "1:2:6:GGGTG"
}, position1.LinkedVids[1]);
Assert.Equal(2, position2.LinkedVids.Length);
position2.LinkedVids[0].Sort();
Assert.Equal(new List <string> {
"1:2:4:AGA", "1:2:4:TGA", "1:2:6:GGATC"
}, position2.LinkedVids[0]);
position2.LinkedVids[1].Sort();
Assert.Equal(new List <string> {
"1:2:4:GGG", "1:2:6:GGGTG"
}, position2.LinkedVids[1]);
Assert.Single(position3.LinkedVids);
Assert.Equal(new List <string> {
"1:2:6:GGATC"
}, position3.LinkedVids[0]);
//MNVs
Assert.Equal(3, recomposedPositions[0].LinkedVids.Length);
Assert.Equal(new List <string> {
"1:4:A"
}, recomposedPositions[0].LinkedVids[0]);
Assert.Equal(new List <string> {
"1:2:G", "1:4:G"
}, recomposedPositions[0].LinkedVids[1]);
Assert.Equal(new List <string> {
"1:2:T", "1:4:A"
}, recomposedPositions[0].LinkedVids[2]);
Assert.Equal(2, recomposedPositions[1].LinkedVids.Length);
Assert.Equal(new List <string> {
"1:2:G", "1:4:A", "1:6:C"
}, recomposedPositions[1].LinkedVids[0]);
Assert.Equal(new List <string> {
"1:2:G", "1:4:G"
}, recomposedPositions[1].LinkedVids[1]);
}