public void ParseVcfLine_NonInformativeAlleles_Alone_NotFiltered()
{
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 refMinorProvider = new Mock <IRefMinorProvider>();
var seqProvider = ParserTestUtils.GetSequenceProvider(13133, "T", 'A', ChromosomeUtilities.RefNameToChromosome);
var variantFactory = new VariantFactory(seqProvider);
var position1 = AnnotationUtilities.ParseVcfLine(vcfLine1, refMinorProvider.Object, variantFactory, seqProvider.RefNameToChromosome);
var position2 = AnnotationUtilities.ParseVcfLine(vcfLine2, refMinorProvider.Object, variantFactory, seqProvider.RefNameToChromosome);
var position3 = AnnotationUtilities.ParseVcfLine(vcfLine3, refMinorProvider.Object, variantFactory, seqProvider.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 not filtered
Assert.Equal("<*>", annotatedVariants1[0].Variant.AltAllele);
Assert.Equal("*", annotatedVariants2[0].Variant.AltAllele);
Assert.Equal("<M>", annotatedVariants3[0].Variant.AltAllele);
}
public void ParseVcfLine_NonInformativeAlleles_WithNormalAllele_NotFiltered()
{
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 refMinorProvider = new Mock <IRefMinorProvider>();
var seqProvider = ParserTestUtils.GetSequenceProvider(13133, "T", 'A', ChromosomeUtilities.RefNameToChromosome);
var refNameToChromosome = seqProvider.RefNameToChromosome;
var variantFactory = new VariantFactory(seqProvider);
var position1 = AnnotationUtilities.ParseVcfLine(vcfLine1, refMinorProvider.Object, variantFactory, refNameToChromosome);
var position2 = AnnotationUtilities.ParseVcfLine(vcfLine2, refMinorProvider.Object, variantFactory, refNameToChromosome);
var position3 = AnnotationUtilities.ParseVcfLine(vcfLine3, refMinorProvider.Object, variantFactory, refNameToChromosome);
var position4 = AnnotationUtilities.ParseVcfLine(vcfLine4, refMinorProvider.Object, 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[] { "<M>", "A" }, annotatedVariants3.Select(x => x.Variant.AltAllele).ToArray());
Assert.Equal(new[] { "A", "<NON_REF>" }, annotatedVariants4.Select(x => x.Variant.AltAllele).ToArray());
}
public void GetNextPosition()
{
const string vcfLine = "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";
var lines = new[]
{
"##fileformat=VCFv4.1", "##FILTER=<ID=PASS,Description=\"All filters passed\">", "##fileDate=20160920",
"#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NHL-16", vcfLine
};
AddLines(lines);
var refMinorProvider = new Mock <IRefMinorProvider>();
var seqProvider = ParserTestUtils.GetSequenceProvider(13133, "T", 'A', ChromosomeUtilities.RefNameToChromosome);
IPosition observedResult;
using (var reader = FileUtilities.GetStreamReader(_ms))
using (var vcfReader = VcfReader.Create(reader, reader, seqProvider, refMinorProvider.Object, new NullRecomposer(), new NullVcfFilter(), _vidCreator, null))
{
observedResult = vcfReader.GetNextPosition();
}
var expectedResult = new Position(ChromosomeUtilities.Chr1, 13133, 13133, "T", new[] { "C" }, 36, new[] { "PASS" }, null,
null, null, vcfLine.Split('\t'), new[] { false }, false);
Assert.NotNull(observedResult);
Assert.Equal(expectedResult.End, observedResult.End);
Assert.Equal(expectedResult.AltAlleles, observedResult.AltAlleles);
Assert.Equal(expectedResult.Filters, observedResult.Filters);
Assert.Equal(expectedResult.Quality, observedResult.Quality);
Assert.Equal(expectedResult.VcfFields, observedResult.VcfFields);
}
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.GetGlobalMajorAllele(chromosome, 10628385)).Returns("T");
var seqProvider = ParserTestUtils.GetSequenceProvider(10628385, "C", 'A',
new Dictionary <string, IChromosome> {
["1"] = chromosome
});
var refNameToChromosome = seqProvider.RefNameToChromosome;
var variantFactory = new VariantFactory(seqProvider);
var position = AnnotationUtilities.ParseVcfLine(vcfLine, refMinorProvider.Object, 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());
}
public void GetAllPositions()
{
var seqProvider = ParserTestUtils.GetSequenceProvider(10329, "AC", 'A', _chromDict);
var positions = PreLoadUtilities.GetPositions(GetVcfStream(), null, seqProvider);
Assert.Equal(2, positions.Count);
Assert.Equal(4, positions[Chrom1].Count);
Assert.Equal(4, positions[Chrom2].Count);
}
public void GetPositions_inRange()
{
var chromosome = new Chromosome("chr1", "1", 0);
var annotationRange = new GenomicRange(new GenomicPosition(chromosome, 10019), new GenomicPosition(chromosome, 10290));
var seqProvider = ParserTestUtils.GetSequenceProvider(10329, "AC", 'A', _chromDict);
var positions = PreLoadUtilities.GetPositions(GetVcfStream(), annotationRange, seqProvider);
Assert.Single(positions);
Assert.Equal(3, positions[Chrom1].Count);
}
public void GetPositions_inRange()
{
var annotationRange = new GenomicRange(new GenomicPosition(ChromosomeUtilities.Chr1, 10019), new GenomicPosition(ChromosomeUtilities.Chr1, 10290));
var seqProvider = ParserTestUtils.GetSequenceProvider(10329, "AC", 'A', ChromosomeUtilities.RefNameToChromosome);
(var positions, _) = PreLoadUtilities.GetPositions(GetVcfStream(), annotationRange, seqProvider, null);
Assert.Single(positions);
Assert.Equal(3, positions[ChromosomeUtilities.Chr1].Count);
}
public void ValidateVcfHeader_ExceptionThrown_NoChromHeaderLine()
{
var headers = new[] { "##fileformat=VCFv4.1", "##FILTER=<ID=PASS,Description=\"All filters passed\">", "##fileDate=20160920" };
AddLines(headers);
var seqProvider = ParserTestUtils.GetSequenceProvider(1000, "A", 'T', _refNameToChromosome);
var reader = FileUtilities.GetStreamReader(_ms);
Assert.Throws <UserErrorException>(() => VcfReader.Create(reader, reader, seqProvider, null, null, new NullVcfFilter()));
}
public void CheckContigId_IncorrectAutoAndSexChromLength_ThrowException(string contigLine)
{
var headers = new[] { "##fileformat=VCFv4.1", contigLine, "#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT"};
AddLines(headers);
var seqProvider = ParserTestUtils.GetSequenceProvider(1000, "A", 'T', _refNameToChromosome);
using (var reader = FileUtilities.GetStreamReader(_ms))
Assert.Throws <UserErrorException>(() => VcfReader.Create(reader, reader, seqProvider, null, null, new NullVcfFilter()));
}
public void ValidateVcfHeader_ExceptionThrown_NoFileFormat()
{
var headers = new[] { "##Some comments", "#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NHL-16 NHL-17"};
AddLines(headers);
var seqProvider = ParserTestUtils.GetSequenceProvider(1000, "A", 'T', _refNameToChromosome);
var reader = FileUtilities.GetStreamReader(_ms);
Assert.Throws <UserErrorException>(() => VcfReader.Create(reader, reader, seqProvider, null, null, new NullVcfFilter()));
}
public void GetAllPositions()
{
//we only need the sequence provider for variant rotation.
var seqProvider = ParserTestUtils.GetSequenceProvider(10329, "AC", 'A', ChromosomeUtilities.RefNameToChromosome);
(var positions, _) = PreLoadUtilities.GetPositions(GetVcfStream(), null, seqProvider, null);
Assert.Equal(2, positions.Count);
Assert.Equal(4, positions[ChromosomeUtilities.Chr1].Count);
Assert.Equal(4, positions[ChromosomeUtilities.Chr2].Count);
}
public void RemoveConflictingAlleles_does_not_remove_duplicates()
{
var seqProvider = ParserTestUtils.GetSequenceProvider(70220313, "TGCC", 'A', _chromDict);
var topMedReader = new TopMedReader(new StreamReader(GetDupItemsStream()), seqProvider);
var items = topMedReader.GetItems().ToList();
var saItems = new List <ISupplementaryDataItem>(items);
saItems = SuppDataUtilities.RemoveConflictingAlleles(saItems, false);
Assert.Single(saItems);
}
public void CheckContigId_InferredAssemblyIsUnknown_GivenIrregularChrom(string contigLine)
{
var headers = new[] { "##fileformat=VCFv4.1", contigLine, "#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT"};
AddLines(headers);
var seqProvider = ParserTestUtils.GetSequenceProvider(1000, "A", 'T', _refNameToChromosome);
using (var reader = FileUtilities.GetStreamReader(_ms))
using (var vcfReader = VcfReader.Create(reader, reader, seqProvider, null, null, new NullVcfFilter()))
{
Assert.Equal(GenomeAssembly.Unknown, vcfReader.InferredGenomeAssembly);
}
}
public void ToString_translocation_breakend(string refAllele, string altAllele, int position, string expectedVid)
{
var chromosome1 = new Chromosome("chr1", "1", 0);
var seqProvider = ParserTestUtils.GetSequenceProvider(position, refAllele, 'A', new Dictionary <string, IChromosome> {
{ "1", chromosome1 }
});
var variantFactory = new VariantFactory(seqProvider);
var breakEnds = variantFactory.GetTranslocationBreakends(chromosome1, refAllele, altAllele, position);
Assert.NotNull(breakEnds);
Assert.Single(breakEnds);
Assert.Equal(expectedVid, breakEnds[0].ToString());
}
public void ToString_deletion()
{
var chromosome1 = new Chromosome("chr1", "1", 0);
var seqProvider = ParserTestUtils.GetSequenceProvider(1594584, "T", 'A', new Dictionary <string, IChromosome> {
{ "1", chromosome1 }
});
var variantFactory = new VariantFactory(seqProvider);
var breakEnds = variantFactory.GetSvBreakEnds("1", 1594584, VariantType.deletion, 1660503);
Assert.NotNull(breakEnds);
Assert.Equal(2, breakEnds.Length);
Assert.Equal("1:1594584:+:1:1660504:+", breakEnds[0].ToString());
Assert.Equal("1:1660504:-:1:1594584:-", breakEnds[1].ToString());
}
public void ToString_duplication()
{
var chromosome1 = new Chromosome("chr1", "1", 0);
var seqProvider = ParserTestUtils.GetSequenceProvider(37820921, "T", 'A', new Dictionary <string, IChromosome> {
{ "1", chromosome1 }
});
var variantFactory = new VariantFactory(seqProvider);
var breakEnds = variantFactory.GetSvBreakEnds("1", 37820921, VariantType.duplication, 38404543);
Assert.NotNull(breakEnds);
Assert.Equal(2, breakEnds.Length);
Assert.Equal("1:38404543:+:1:37820921:+", breakEnds[0].ToString());
Assert.Equal("1:37820921:-:1:38404543:-", breakEnds[1].ToString());
}
public void Duplicated_headlines_are_removed()
{
var headers = new[] { "##fileformat=VCFv4.1", "##FILTER=<ID=PASS,Description=\"All filters passed\">", "##fileDate=20160920", "##dataSource=ClinVar,version:unknown,release date:2016-09-01", "#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NHL-16 NHL-17"};
AddLines(headers);
IEnumerable <string> observedHeaders;
var seqProvider = ParserTestUtils.GetSequenceProvider(1000, "A", 'T', _refNameToChromosome);
using (var reader = FileUtilities.GetStreamReader(_ms))
using (var vcfReader = VcfReader.Create(reader, reader, seqProvider, null, null, new NullVcfFilter()))
{
observedHeaders = vcfReader.GetHeaderLines();
}
Assert.Equal(4, observedHeaders.Count());
}
public void HeaderLines_are_parsed()
{
var headers = new[] { "##fileformat=VCFv4.1", "##FILTER=<ID=PASS,Description=\"All filters passed\">", "##fileDate=20160920", "#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NHL-16"};
AddLines(headers);
IEnumerable <string> observedHeaders;
var seqProvider = ParserTestUtils.GetSequenceProvider(1000, "A", 'T', _refNameToChromosome);
using (var reader = FileUtilities.GetStreamReader(_ms))
using (var vcfReader = VcfReader.Create(reader, reader, seqProvider, null, null, new NullVcfFilter()))
{
observedHeaders = vcfReader.GetHeaderLines();
}
Assert.Equal(headers, observedHeaders.ToArray());
}
public void Sample_names_are_reported()
{
var headers = new[] { "##fileformat=VCFv4.1", "##FILTER=<ID=PASS,Description=\"All filters passed\">", "##fileDate=20160920", "#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NHL-16 NHL-17"};
AddLines(headers);
string[] samples;
var seqProvider = ParserTestUtils.GetSequenceProvider(1000, "A", 'T', _refNameToChromosome);
using (var reader = FileUtilities.GetStreamReader(_ms))
using (var vcfReader = VcfReader.Create(reader, reader, seqProvider, null, null, new NullVcfFilter()))
{
samples = vcfReader.GetSampleNames();
}
Assert.Equal(new[] { "NHL-16", "NHL-17" }, samples);
}
public void GetAllPositions_skip_refs()
{
//we only need the sequence provider for variant rotation.
var seqProvider = ParserTestUtils.GetSequenceProvider(10329, "AC", 'A', ChromosomeUtilities.RefNameToChromosome);
var refMinorProvider = ParserTestUtils.GetRefMinorProvider(
new List <(IChromosome chrom, int position, string globalMinor)>
{
(ChromosomeUtilities.Chr1, 10275, "A")
}
);
(var positions, _) = PreLoadUtilities.GetPositions(GetRefMinorVcfStream(), null, seqProvider, refMinorProvider);
Assert.Equal(2, positions.Count);
Assert.Equal(5, positions[ChromosomeUtilities.Chr1].Count);
Assert.Equal(4, positions[ChromosomeUtilities.Chr2].Count);
}
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 refMinorProvider = new Mock <IRefMinorProvider>();
var seqProvider =
ParserTestUtils.GetSequenceProvider(10005, "C", 'A', ChromosomeUtilities.RefNameToChromosome);
var variantFactory = new VariantFactory(seqProvider.Sequence, _vidCreator);
var position = AnnotationUtilities.ParseVcfLine(vcfLine, refMinorProvider.Object, seqProvider, null, variantFactory);
var annotatedVariants = Annotator.GetAnnotatedVariants(position.Variants);
Assert.Equal("C", position.RefAllele);
Assert.Equal(new[] { "<NON_REF>" }, position.AltAlleles);
Assert.Null(position.Variants);
Assert.Null(annotatedVariants);
}
public void Test_crash_caused_by_variant_trimming()
{
const string vcfLine1 = "chr1 8021910 rs373653682 GGTGCTGGACGGTGTCCCT G . . .";
var refMinorProvider = new Mock <IRefMinorProvider>();
var seqProvider = ParserTestUtils.GetSequenceProvider(8021910, "GGTGCTGGACGGTGTCCCT", 'A', ChromosomeUtilities.RefNameToChromosome);
var variantFactory = new VariantFactory(seqProvider.Sequence, _vidCreator);
var position1 = AnnotationUtilities.ParseVcfLine(vcfLine1, refMinorProvider.Object, seqProvider, null, variantFactory);
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 GetJsonString_fisherStrand()
{
const string vcfLine = "21\t9411410\t.\tC\tT\t9.51\tDRAGENSnpHardQUAL\tAC=2;AF=1.000;AN=2;DP=2;FS=0.000;MQ=100.00;QD=9.51;SOR=1.609";
var refMinorProvider = new Mock <IRefMinorProvider>();
var seqProvider = ParserTestUtils.GetSequenceProvider(9411410, "C", 'A', ChromosomeUtilities.RefNameToChromosome);
var variantFactory = new VariantFactory(seqProvider.Sequence, new VariantId());
var position = AnnotationUtilities.ParseVcfLine(vcfLine, refMinorProvider.Object, seqProvider, null, variantFactory);
IVariant[] variants = GetVariants();
IAnnotatedVariant[] annotatedVariants = Annotator.GetAnnotatedVariants(variants);
var annotatedPosition = new AnnotatedPosition(position, annotatedVariants);
string observedResult = annotatedPosition.GetJsonString();
Assert.NotNull(observedResult);
Assert.Contains("\"fisherStrandBias\":0", observedResult);
}
public void GetJsonString_BreakEndEventId()
{
const string vcfLine = "1\t38432782\tMantaBND:2312:0:1:0:0:0:0\tG\tG]6:28863899]\t971\tPASS\tSVTYPE=BND;MATEID=MantaBND:2312:0:1:0:0:0:1;EVENT=MantaBND:2312:0:1:0:0:0:0;JUNCTION_QUAL=716;BND_DEPTH=52;MATE_BND_DEPTH=56";
var refMinorProvider = new Mock <IRefMinorProvider>();
var seqProvider = ParserTestUtils.GetSequenceProvider(38432782, "G", 'C', ChromosomeUtilities.RefNameToChromosome);
var variantFactory = new VariantFactory(seqProvider.Sequence, new VariantId());
var position = AnnotationUtilities.ParseVcfLine(vcfLine, refMinorProvider.Object, seqProvider, null, variantFactory);
IVariant[] variants = GetVariants();
IAnnotatedVariant[] annotatedVariants = Annotator.GetAnnotatedVariants(variants);
var annotatedPosition = new AnnotatedPosition(position, annotatedVariants);
string observedResult = annotatedPosition.GetJsonString();
Assert.NotNull(observedResult);
Assert.Contains("\"breakendEventId\":\"MantaBND:2312:0:1:0:0:0:0\"", observedResult);
}
public void GetJsonString_StrelkaSomatic()
{
const string vcfLine = "chr1 13813 . T G . LowQscore SOMATIC;QSS=33;TQSS=1;NT=ref;QSS_NT=16;TQSS_NT=1;SGT=TT->GT;DP=266;MQ=23.89;MQ0=59;ALTPOS=69;ALTMAP=37;ReadPosRankSum=1.22;SNVSB=5.92;PNOISE=0.00;PNOISE2=0.00;VQSR=1.93";
var refMinorProvider = new Mock <IRefMinorProvider>();
var seqProvider = ParserTestUtils.GetSequenceProvider(13813, "T", 'C', ChromosomeUtilities.RefNameToChromosome);
var variantFactory = new VariantFactory(seqProvider.Sequence, new VariantId());
var position = AnnotationUtilities.ParseVcfLine(vcfLine, refMinorProvider.Object, seqProvider, variantFactory);
IVariant[] variants = GetVariants();
IAnnotatedVariant[] annotatedVariants = Annotator.GetAnnotatedVariants(variants);
var annotatedPosition = new AnnotatedPosition(position, annotatedVariants);
string observedResult = annotatedPosition.GetJsonString();
Assert.NotNull(observedResult);
Assert.Contains("\"jointSomaticNormalQuality\":16", observedResult);
Assert.Contains("\"recalibratedQuality\":1.93", observedResult);
}
public void CheckSampleConsistency_noSample()
{
const string vcfLine1 = "chr1 13133 . T C 36.00 PASS SNVSB=0.0;SNVHPOL=4";
const string vcfLine2 = "chr1 13133 . T A 36.00 PASS SNVSB=0.0;SNVHPOL=4 GT:GQ:GQX:DP:DPF:AD 0/1:62:20:7:1:3,4";
var lines = new[]
{
"##fileformat=VCFv4.1", "##FILTER=<ID=PASS,Description=\"All filters passed\">", "##fileDate=20160920",
"#CHROM POS ID REF ALT QUAL FILTER INFO", vcfLine1, vcfLine2
};
AddLines(lines);
var refMinorProvider = new Mock <IRefMinorProvider>();
var seqProvider = ParserTestUtils.GetSequenceProvider(13133, "T", 'A', ChromosomeUtilities.RefNameToChromosome);
using (var reader = FileUtilities.GetStreamReader(_ms))
using (var vcfReader = VcfReader.Create(reader, reader, seqProvider, refMinorProvider.Object, new NullRecomposer(), new NullVcfFilter(), _vidCreator, null))
{
//first line is valid. So, no exception
Assert.NotNull(vcfReader.GetNextPosition());
// second line has invalid number of sample fields, so it will throw exception
Assert.Throws <UserErrorException>(() => vcfReader.GetNextPosition());
}
}