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 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 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 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 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 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);
}
private static VcfReader GetVcfReader(Stream headerStream, Stream vcfStream, IAnnotationResources annotationResources,
IVcfFilter vcfFilter, IMitoHeteroplasmyProvider mitoHeteroplasmyProvider)
{
var vcfReader = FileUtilities.GetStreamReader(vcfStream);
StreamReader headerReader;
if (headerStream == null)
{
headerReader = vcfReader;
}
else
{
headerReader = FileUtilities.GetStreamReader(headerStream);
vcfStream.Position = Tabix.VirtualPosition.From(annotationResources.InputStartVirtualPosition).BlockOffset;
}
return(VcfReader.Create(headerReader, vcfReader, annotationResources.SequenceProvider,
annotationResources.RefMinorProvider, annotationResources.Recomposer, vcfFilter, annotationResources.VidCreator, mitoHeteroplasmyProvider));
}
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());
}
}
