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 void SetRecomposer(IRecomposer recomposer) => _recomposer = _sampleNames == null ? new NullRecomposer() : recomposer;
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));
}