public void ParseVcfLine_line_with_only_non_informative_alleles_position_unchanged_but_variants_ignored()
{
const string vcfLine1 = "chr1 13133 . T <*> 36.00 PASS SNVSB=0.0;SNVHPOL=4 GT:GQ:GQX:DP:DPF:AD 0/1:62:20:7:1:3,4";
const string vcfLine2 = "chr1 13133 . T * 36.00 PASS SNVSB=0.0;SNVHPOL=4 GT:GQ:GQX:DP:DPF:AD 0/1:62:20:7:1:3,4";
const string vcfLine3 = "chr1 13133 . T <M> 36.00 PASS SNVSB=0.0;SNVHPOL=4 GT:GQ:GQX:DP:DPF:AD 0/1:62:20:7:1:3,4";
var chromosome = new Chromosome("chr1", "1", 0);
var refMinorProvider = new Mock <IRefMinorProvider>();
refMinorProvider.Setup(x => x.IsReferenceMinor(chromosome, 13133)).Returns(false);
var refNameToChromosome = new Dictionary <string, IChromosome> {
["chr1"] = chromosome
};
var variantFactory = new VariantFactory(refNameToChromosome, refMinorProvider.Object, false);
var position1 = VcfReaderUtils.ParseVcfLine(vcfLine1, variantFactory, refNameToChromosome);
var position2 = VcfReaderUtils.ParseVcfLine(vcfLine2, variantFactory, refNameToChromosome);
var position3 = VcfReaderUtils.ParseVcfLine(vcfLine3, variantFactory, refNameToChromosome);
var annotatedVariants1 = Annotator.GetAnnotatedVariants(position1.Variants);
var annotatedVariants2 = Annotator.GetAnnotatedVariants(position2.Variants);
var annotatedVariants3 = Annotator.GetAnnotatedVariants(position3.Variants);
// SimplePositions unchanged
Assert.Equal("<*>", position1.AltAlleles[0]);
Assert.Equal("*", position2.AltAlleles[0]);
Assert.Equal("<M>", position3.AltAlleles[0]);
// Variants are null
Assert.Null(annotatedVariants1);
Assert.Null(annotatedVariants2);
Assert.Null(annotatedVariants3);
}
public void ParseVcfLine_line_with_only_NonRef_is_refMinor()
{
const string vcfLine = "1 10628385 . C <NON_REF> . LowGQX;HighDPFRatio END=10628385;BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:24:9:18";
var chromosome = new Chromosome("chr1", "1", 0);
var refMinorProvider = new Mock <IRefMinorProvider>();
refMinorProvider.Setup(x => x.IsReferenceMinor(chromosome, 10628385)).Returns(true);
refMinorProvider.Setup(x => x.GetGlobalMajorAlleleForRefMinor(chromosome, 10628385)).Returns("T");
var refNameToChromosome = new Dictionary <string, IChromosome> {
["1"] = chromosome
};
var variantFactory = new VariantFactory(refNameToChromosome, refMinorProvider.Object, false);
var position = VcfReaderUtils.ParseVcfLine(vcfLine, variantFactory, refNameToChromosome);
var annotatedVariants = Annotator.GetAnnotatedVariants(position.Variants);
Assert.Equal("C", position.RefAllele);
Assert.Equal(new[] { "<NON_REF>" }, position.AltAlleles);
Assert.Equal("T", position.Variants[0].RefAllele);
Assert.Equal("C", position.Variants[0].AltAllele);
// Variants
Assert.Equal(new[] { "C" }, annotatedVariants.Select(x => x.Variant.AltAllele).ToArray());
}
internal static IAnnotatedPosition GetAnnotatedPosition(string cacheFilePrefix, List <string> saPaths,
string vcfLine, bool enableVerboseTranscripts)
{
var refMinorProvider = ProviderUtilities.GetRefMinorProvider(saPaths);
var annotatorAndRef = GetAnnotatorAndReferenceDict(cacheFilePrefix, saPaths);
var annotator = annotatorAndRef.Annotator;
var refNames = annotatorAndRef.RefNames;
var variantFactory = new VariantFactory(refNames, refMinorProvider, enableVerboseTranscripts);
var position = VcfReaderUtils.ParseVcfLine(vcfLine, variantFactory, refNames);
var annotatedPosition = annotator.Annotate(position);
return(annotatedPosition);
}
public void Test_crash_caused_by_variant_trimming()
{
const string vcfLine1 = "chr1 8021910 rs373653682 GGTGCTGGACGGTGTCCCT G . . .";
var chromosome = new Chromosome("chr1", "1", 0);
var refMinorProvider = new Mock <IRefMinorProvider>();
refMinorProvider.Setup(x => x.IsReferenceMinor(chromosome, 8021910)).Returns(false);
var refNameToChromosome = new Dictionary <string, IChromosome> {
["chr1"] = chromosome
};
var variantFactory = new VariantFactory(refNameToChromosome, refMinorProvider.Object, false);
var position1 = VcfReaderUtils.ParseVcfLine(vcfLine1, variantFactory, refNameToChromosome);
var annotatedVariants1 = Annotator.GetAnnotatedVariants(position1.Variants);
// SimplePositions
Assert.Equal(new[] { "G" }, position1.AltAlleles);
// Variants
Assert.Equal(new[] { "" }, annotatedVariants1.Select(x => x.Variant.AltAllele).ToArray());
}
public void ParseVcfLine_non_informative_alleles_or_NonRef_filtered_only_in_variants()
{
const string vcfLine1 = "chr1 13133 . T <*>,G 36.00 PASS SNVSB=0.0;SNVHPOL=4 GT:GQ:GQX:DP:DPF:AD 0/1:62:20:7:1:3,4";
const string vcfLine2 = "chr1 13133 . T *,C 36.00 PASS SNVSB=0.0;SNVHPOL=4 GT:GQ:GQX:DP:DPF:AD 0/1:62:20:7:1:3,4";
const string vcfLine3 = "chr1 13133 . T <M>,A 36.00 PASS SNVSB=0.0;SNVHPOL=4 GT:GQ:GQX:DP:DPF:AD 0/1:62:20:7:1:3,4";
const string vcfLine4 = "chr1 13133 . T A,<NON_REF> 36.00 PASS SNVSB=0.0;SNVHPOL=4 GT:GQ:GQX:DP:DPF:AD 0/1:62:20:7:1:3,4";
var chromosome = new Chromosome("chr1", "1", 0);
var refMinorProvider = new Mock <IRefMinorProvider>();
refMinorProvider.Setup(x => x.IsReferenceMinor(chromosome, 13133)).Returns(false);
var refNameToChromosome = new Dictionary <string, IChromosome> {
["chr1"] = chromosome
};
var variantFactory = new VariantFactory(refNameToChromosome, refMinorProvider.Object, false);
var position1 = VcfReaderUtils.ParseVcfLine(vcfLine1, variantFactory, refNameToChromosome);
var position2 = VcfReaderUtils.ParseVcfLine(vcfLine2, variantFactory, refNameToChromosome);
var position3 = VcfReaderUtils.ParseVcfLine(vcfLine3, variantFactory, refNameToChromosome);
var position4 = VcfReaderUtils.ParseVcfLine(vcfLine4, variantFactory, refNameToChromosome);
var annotatedVariants1 = Annotator.GetAnnotatedVariants(position1.Variants);
var annotatedVariants2 = Annotator.GetAnnotatedVariants(position2.Variants);
var annotatedVariants3 = Annotator.GetAnnotatedVariants(position3.Variants);
var annotatedVariants4 = Annotator.GetAnnotatedVariants(position4.Variants);
// SimplePositions
Assert.Equal(new[] { "<*>", "G" }, position1.AltAlleles);
Assert.Equal(new[] { "*", "C" }, position2.AltAlleles);
Assert.Equal(new[] { "<M>", "A" }, position3.AltAlleles);
Assert.Equal(new[] { "A", "<NON_REF>" }, position4.AltAlleles);
// Variants
Assert.Equal(new[] { "G" }, annotatedVariants1.Select(x => x.Variant.AltAllele).ToArray());
Assert.Equal(new[] { "C" }, annotatedVariants2.Select(x => x.Variant.AltAllele).ToArray());
Assert.Equal(new[] { "A" }, annotatedVariants3.Select(x => x.Variant.AltAllele).ToArray());
Assert.Equal(new[] { "A" }, annotatedVariants4.Select(x => x.Variant.AltAllele).ToArray());
}
public void ParseVcfLine_line_with_only_NonRef_is_not_refMinor()
{
const string vcfLine = "1 10005 . C <NON_REF> . LowGQX END=10034;BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:3:1:0";
var chromosome = new Chromosome("chr1", "1", 0);
var refMinorProvider = new Mock <IRefMinorProvider>();
refMinorProvider.Setup(x => x.IsReferenceMinor(chromosome, 10005)).Returns(false);
var refNameToChromosome = new Dictionary <string, IChromosome> {
["1"] = chromosome
};
var variantFactory = new VariantFactory(refNameToChromosome, refMinorProvider.Object, false);
var position = VcfReaderUtils.ParseVcfLine(vcfLine, variantFactory, refNameToChromosome);
var annotatedVariants = Annotator.GetAnnotatedVariants(position.Variants);
Assert.Equal("C", position.RefAllele);
Assert.Equal(new[] { "<NON_REF>" }, position.AltAlleles);
Assert.Equal("C", position.Variants[0].RefAllele);
Assert.Equal("<NON_REF>", position.Variants[0].AltAllele);
// Variants
Assert.Null(annotatedVariants);
}