public VariantFactory(IDictionary <string, IChromosome> refNameToChromosome, IRefMinorProvider refMinorProvider,
bool enableVerboseTranscript)
{
_refNameToChromosome = refNameToChromosome;
_refMinorProvider = refMinorProvider;
_enableVerboseTranscript = enableVerboseTranscript;
}
private static bool IsRefMinor(IRefMinorProvider refMinorProvider, IChromosome chrom, int position)
{
if (refMinorProvider == null)
{
return(false);
}
return(!string.IsNullOrEmpty(refMinorProvider.GetGlobalMajorAllele(chrom, position)));
}
public static VcfReader Create(StreamReader headerReader, StreamReader vcfLineReader, ISequenceProvider sequenceProvider,
IRefMinorProvider refMinorProvider, IRecomposer recomposer, IVcfFilter vcfFilter, IVariantIdCreator vidCreator, IMitoHeteroplasmyProvider mitoHeteroplasmyProvider, bool enableDq = false)
{
var vcfReader = new VcfReader(headerReader, vcfLineReader, sequenceProvider, refMinorProvider, vcfFilter, vidCreator, mitoHeteroplasmyProvider, enableDq);
vcfReader.ParseHeader();
vcfReader.SetRecomposer(recomposer);
return(vcfReader);
}
public static VcfReader Create(StreamReader headerReader, StreamReader vcfLineReader, ISequenceProvider sequenceProvider,
IRefMinorProvider refMinorProvider, IRecomposer recomposer, IVcfFilter vcfFilter, IVariantIdCreator vidCreator)
{
var vcfReader = new VcfReader(headerReader, vcfLineReader, sequenceProvider, refMinorProvider, vcfFilter, vidCreator);
vcfReader.ParseHeader();
vcfReader.SetRecomposer(recomposer);
return(vcfReader);
}
public VcfReader(Stream stream, IDictionary <string, IChromosome> refNameToChromosome,
IRefMinorProvider refMinorProvider, bool enableVerboseTranscript, IRecomposer recomposer)
{
_reader = new StreamReader(stream);
_variantFactory = new VariantFactory(refNameToChromosome, refMinorProvider, enableVerboseTranscript);
_refNameToChromosome = refNameToChromosome;
bool hasSampleColumn = ParseHeader();
_recomposer = hasSampleColumn ? recomposer : new NullRecomposer();
}
private VcfReader(StreamReader headerReader, StreamReader vcfLineReader, ISequenceProvider sequenceProvider,
IRefMinorProvider refMinorProvider, IVcfFilter vcfFilter)
{
_headerReader = headerReader;
_reader = vcfLineReader;
_variantFactory = new VariantFactory(sequenceProvider);
_refMinorProvider = refMinorProvider;
_vcfFilter = vcfFilter;
_refNameToChromosome = sequenceProvider.RefNameToChromosome;
}
public static IVcfReader GetVcfReader(string vcfPath, IDictionary <string, IChromosome> chromosomeDictionary,
IRefMinorProvider refMinorProvider, bool verboseTranscript, IRecomposer recomposer)
{
var useStdInput = vcfPath == "-";
var peekStream =
new PeekStream(useStdInput
? Console.OpenStandardInput()
: GZipUtilities.GetAppropriateReadStream(vcfPath));
return(new VcfReader(peekStream, chromosomeDictionary, refMinorProvider, verboseTranscript, recomposer));
}
private VcfReader(StreamReader headerReader, StreamReader vcfLineReader, ISequenceProvider sequenceProvider,
IRefMinorProvider refMinorProvider, IVcfFilter vcfFilter, IVariantIdCreator vidCreator, IMitoHeteroplasmyProvider mitoHeteroplasmyProvider)
{
_headerReader = headerReader;
_reader = vcfLineReader;
_variantFactory = new VariantFactory(sequenceProvider.Sequence, vidCreator);
_sequenceProvider = sequenceProvider;
_refMinorProvider = refMinorProvider;
_vcfFilter = vcfFilter;
_refNameToChromosome = sequenceProvider.RefNameToChromosome;
_mitoHeteroplasmyProvider = mitoHeteroplasmyProvider;
}
public static IPosition ToPosition(ISimplePosition simplePosition, IRefMinorProvider refMinorProvider, ISequenceProvider sequenceProvider, IMitoHeteroplasmyProvider mitoHeteroplasmyProvider, VariantFactory variantFactory, bool enableDq = false)
{
if (simplePosition == null)
{
return(null);
}
sequenceProvider.LoadChromosome(simplePosition.Chromosome);
string[] vcfFields = simplePosition.VcfFields;
string[] altAlleles = vcfFields[VcfCommon.AltIndex].OptimizedSplit(',');
bool isReference = altAlleles.Length == 1 && VcfCommon.ReferenceAltAllele.Contains(altAlleles[0]);
string globalMajorAllele = isReference
? refMinorProvider?.GetGlobalMajorAllele(simplePosition.Chromosome, simplePosition.Start)
: null;
bool isRefMinor = isReference && globalMajorAllele != null;
if (isReference && !isRefMinor)
{
return(GetReferencePosition(simplePosition));
}
var infoData = VcfInfoParser.Parse(vcfFields[VcfCommon.InfoIndex]);
int end = ExtractEnd(infoData, simplePosition.Start, simplePosition.RefAllele.Length);
double?quality = vcfFields[VcfCommon.QualIndex].GetNullableValue <double>(double.TryParse);
string[] filters = vcfFields[VcfCommon.FilterIndex].OptimizedSplit(';');
ISample[] samples = vcfFields.ToSamples(variantFactory.FormatIndices, simplePosition, mitoHeteroplasmyProvider, enableDq);
IVariant[] variants = variantFactory.CreateVariants(simplePosition.Chromosome, simplePosition.Start, end,
simplePosition.RefAllele, altAlleles, infoData, simplePosition.IsDecomposed,
simplePosition.IsRecomposed, simplePosition.LinkedVids, globalMajorAllele);
return(new Position(simplePosition.Chromosome, simplePosition.Start, end, simplePosition.RefAllele,
altAlleles, quality, filters, variants, samples, infoData, vcfFields, simplePosition.IsDecomposed,
simplePosition.IsRecomposed));
}
public static (IPosition, string[]) GetPositionAndSampleNames(this SingleConfig config, ISequenceProvider sequenceProvider,
IRefMinorProvider refMinorProvider) => (ToPosition(config.variant.GetVcfFields(), sequenceProvider, refMinorProvider), config.variant.sampleNames);
internal static IPosition ParseVcfLine(string vcfLine, IRefMinorProvider refMinorProvider, VariantFactory variantFactory, IDictionary <string, IChromosome> refNameToChromosome)
{
var simplePosition = GetSimplePosition(vcfLine, refNameToChromosome);
return(Position.ToPosition(simplePosition, refMinorProvider, variantFactory));
}
public static (ImmutableDictionary <IChromosome, List <int> > PositionsByChromosome, int Count) GetPositions(Stream vcfStream, GenomicRange genomicRange,
ISequenceProvider sequenceProvider, IRefMinorProvider refMinorProvider)
{
var positionsByChromosome = new Dictionary <IChromosome, List <int> >();
var rangeChecker = new GenomicRangeChecker(genomicRange);
var refNameToChrom = sequenceProvider.RefNameToChromosome;
using (var reader = new StreamReader(vcfStream))
{
string line;
string currentReferenceName = "";
IChromosome chromosome = null;
while ((line = reader.ReadLine()) != null)
{
if (line.StartsWith('#'))
{
continue;
}
string[] cols = line.OptimizedSplit('\t');
string referenceName = cols[VcfCommon.ChromIndex];
if (referenceName != currentReferenceName)
{
if (!refNameToChrom.TryGetValue(referenceName, out chromosome))
{
continue;
}
currentReferenceName = referenceName;
}
(int position, bool foundError) = cols[VcfCommon.PosIndex].OptimizedParseInt32();
if (foundError)
{
throw new InvalidDataException($"Unable to convert the VCF position to an integer: {cols[VcfCommon.PosIndex]}");
}
if (rangeChecker.OutOfRange(chromosome, position))
{
break;
}
string refAllele = cols[VcfCommon.RefIndex];
string altAllele = cols[VcfCommon.AltIndex];
if (altAllele == "." && !IsRefMinor(refMinorProvider, chromosome, position))
{
continue;
}
sequenceProvider.LoadChromosome(chromosome);
TryAddPosition(positionsByChromosome, chromosome, position, refAllele, altAllele, sequenceProvider.Sequence);
}
}
int count = SortPositionsAndGetCount(positionsByChromosome);
return(positionsByChromosome.ToImmutableDictionary(), count);
}
internal static IPosition ParseVcfLine(string vcfLine, IRefMinorProvider refMinorProvider, ISequenceProvider sequenceProvider, VariantFactory variantFactory)
{
var simplePosition = GetSimplePosition(vcfLine, sequenceProvider.RefNameToChromosome);
return(Position.ToPosition(simplePosition, refMinorProvider, sequenceProvider, variantFactory));
}
