private VcfReader(StreamReader headerReader, StreamReader vcfLineReader, ISequenceProvider sequenceProvider,
IRefMinorProvider refMinorProvider, IVcfFilter vcfFilter, IVariantIdCreator vidCreator)
{
_headerReader = headerReader;
_reader = vcfLineReader;
_variantFactory = new VariantFactory(sequenceProvider.Sequence, vidCreator);
_sequenceProvider = sequenceProvider;
_refMinorProvider = refMinorProvider;
_vcfFilter = vcfFilter;
_refNameToChromosome = sequenceProvider.RefNameToChromosome;
}
private VcfReader(StreamReader headerReader, StreamReader vcfLineReader, ISequenceProvider sequenceProvider,
IRefMinorProvider refMinorProvider, IVcfFilter vcfFilter, IVariantIdCreator vidCreator, IMitoHeteroplasmyProvider mitoHeteroplasmyProvider, bool enableDq = false)
{
_headerReader = headerReader;
_reader = vcfLineReader;
_variantFactory = new VariantFactory(sequenceProvider.Sequence, vidCreator);
_sequenceProvider = sequenceProvider;
_refMinorProvider = refMinorProvider;
_vcfFilter = vcfFilter;
_refNameToChromosome = sequenceProvider.RefNameToChromosome;
_mitoHeteroplasmyProvider = mitoHeteroplasmyProvider;
EnableDq = enableDq;
}
public static IVariant[] Create(IVariantIdCreator vidCreator, ISequence sequence, IChromosome chromosome, int start, int end,
string refAllele, string altAllele, string globalMajorAllele)
{
bool isRefMinor = end == start && globalMajorAllele != null;
if (!isRefMinor)
{
return(null);
}
string vid = vidCreator.Create(sequence, VariantCategory.SmallVariant, null, chromosome, start, end, refAllele, altAllele, null);
return(new[]
{
SmallVariantCreator.Create(chromosome, start, end, globalMajorAllele, refAllele, false, false, null, vid, true)
});
}
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 VariantFactory(ISequence sequence, IVariantIdCreator vidCreator)
{
_sequence = sequence;
_vidCreator = vidCreator;
}
public VariantGenerator(ISequenceProvider sequenceProvider, IVariantIdCreator vidCreator)
{
_sequenceProvider = sequenceProvider;
_vidCreator = vidCreator;
}
decomposedVids) GetPositionsAndRefAltAlleles(AlleleBlock alleleBlock, AlleleSet alleleSet,
string totalRefSequence, int regionStart, List <ISimplePosition> simplePositions, ISequence sequence, IVariantIdCreator vidCreator)
{
int numPositions = alleleBlock.AlleleIndexes.Length;
int firstPositionIndex = alleleBlock.PositionIndex;
int lastPositionIndex = alleleBlock.PositionIndex + numPositions - 1;
int blockStart = alleleSet.Starts[firstPositionIndex];
int blockEnd = alleleSet.Starts[lastPositionIndex];
string lastRefAllele = alleleSet.VariantArrays[lastPositionIndex][0];
int blockRefLength = blockEnd - blockStart + lastRefAllele.Length;
string refSequence = totalRefSequence.Substring(blockStart - regionStart, blockRefLength);
var refSequenceStart = 0;
var altSequenceSegments = new LinkedList <string>();
var variantPosIndexesInAlleleBlock = new List <int>();
var vidListsNeedUpdate = new List <List <string> >();
var decomposedVids = new List <string>();
if (FindConflictAllele(alleleBlock, alleleSet))
{
return(default);
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);
}