//JAVA TO C# CONVERTER TODO TASK: Most Java annotations will not have direct .NET equivalent attributes:
//ORIGINAL LINE: @Requires("vc != null") public void start(final BCF2Encoder encoder, final org.broadinstitute.variant.variantcontext.VariantContext vc) throws java.io.IOException
//JAVA TO C# CONVERTER WARNING: Method 'throws' clauses are not available in .NET:
//JAVA TO C# CONVERTER WARNING: 'final' parameters are not allowed in .NET:
public virtual void start(BCF2Encoder encoder, VariantContext vc)
{
fieldEncoder.writeFieldKey(encoder);
}
//JAVA TO C# CONVERTER WARNING: Method 'throws' clauses are not available in .NET:
//ORIGINAL LINE: public void start(final BCF2Encoder encoder, final org.broadinstitute.variant.variantcontext.VariantContext vc) throws java.io.IOException
//JAVA TO C# CONVERTER WARNING: 'final' parameters are not allowed in .NET:
public override void start(BCF2Encoder encoder, VariantContext vc)
{
if (vc.NAlleles > BCF2Utils.MAX_ALLELES_IN_GENOTYPES)
{
throw new IllegalStateException("Current BCF2 encoder cannot handle sites " + "with > " + BCF2Utils.MAX_ALLELES_IN_GENOTYPES + " alleles, but you have " + vc.NAlleles + " at " + vc.Chr + ":" + vc.Start);
}
encodingType = BCF2Type.INT8;
buildAlleleMap(vc);
nValuesPerGenotype = vc.getMaxPloidy(2);
base.start(encoder, vc);
}
//JAVA TO C# CONVERTER WARNING: Method 'throws' clauses are not available in .NET:
//ORIGINAL LINE: public void addGenotype(final BCF2Encoder encoder, final org.broadinstitute.variant.variantcontext.VariantContext vc, final org.broadinstitute.variant.variantcontext.Genotype g) throws java.io.IOException
//JAVA TO C# CONVERTER WARNING: 'final' parameters are not allowed in .NET:
public override void addGenotype(BCF2Encoder encoder, VariantContext vc, Genotype g)
{
//JAVA TO C# CONVERTER WARNING: The original Java variable was marked 'final':
//ORIGINAL LINE: final int samplePloidy = g.getPloidy();
int samplePloidy = g.Ploidy;
for (int i = 0; i < nValuesPerGenotype; i++)
{
if (i < samplePloidy)
{
// we encode the actual allele
//JAVA TO C# CONVERTER WARNING: The original Java variable was marked 'final':
//ORIGINAL LINE: final org.broadinstitute.variant.variantcontext.Allele a = g.getAllele(i);
Allele a = g.getAllele(i);
//JAVA TO C# CONVERTER WARNING: The original Java variable was marked 'final':
//ORIGINAL LINE: final int offset = getAlleleOffset(a);
int offset = getAlleleOffset(a);
//JAVA TO C# CONVERTER WARNING: The original Java variable was marked 'final':
//ORIGINAL LINE: final int encoded = ((offset+1) << 1) | (g.isPhased() ? 0x01 : 0x00);
int encoded = ((offset + 1) << 1) | (g.Phased ? 0x01 : 0x00);
encoder.encodeRawBytes(encoded, encodingType);
}
else
{
// we need to pad with missing as we have ploidy < max for this sample
encoder.encodeRawBytes(encodingType.MissingBytes, encodingType);
}
}
}
//JAVA TO C# CONVERTER WARNING: Method 'throws' clauses are not available in .NET:
//ORIGINAL LINE: public void addGenotype(final BCF2Encoder encoder, final org.broadinstitute.variant.variantcontext.VariantContext vc, final org.broadinstitute.variant.variantcontext.Genotype g) throws java.io.IOException
//JAVA TO C# CONVERTER WARNING: 'final' parameters are not allowed in .NET:
public override void addGenotype(BCF2Encoder encoder, VariantContext vc, Genotype g)
{
FieldEncoder.encodeValue(encoder, ige.getValues(g), encodingType, nValuesPerGenotype);
}
//JAVA TO C# CONVERTER WARNING: Method 'throws' clauses are not available in .NET:
//ORIGINAL LINE: public void addGenotype(final BCF2Encoder encoder, final org.broadinstitute.variant.variantcontext.VariantContext vc, final org.broadinstitute.variant.variantcontext.Genotype g) throws java.io.IOException
//JAVA TO C# CONVERTER WARNING: 'final' parameters are not allowed in .NET:
public override void addGenotype(BCF2Encoder encoder, VariantContext vc, Genotype g)
{
//JAVA TO C# CONVERTER WARNING: The original Java variable was marked 'final':
//ORIGINAL LINE: final String fieldValue = g.getFilters();
string fieldValue = g.Filters;
FieldEncoder.encodeValue(encoder, fieldValue, encodingType, nValuesPerGenotype);
}
//JAVA TO C# CONVERTER WARNING: Method 'throws' clauses are not available in .NET:
//ORIGINAL LINE: public void start(final BCF2Encoder encoder, final org.broadinstitute.variant.variantcontext.VariantContext vc) throws java.io.IOException
//JAVA TO C# CONVERTER WARNING: 'final' parameters are not allowed in .NET:
public override void start(BCF2Encoder encoder, VariantContext vc)
{
// the only value that is dynamic are integers
//JAVA TO C# CONVERTER WARNING: The original Java variable was marked 'final':
//ORIGINAL LINE: final java.util.List<Integer> values = new java.util.ArrayList<Integer>(vc.getNSamples());
IList<int?> values = new List<int?>(vc.NSamples);
foreach (Genotype g in vc.Genotypes)
{
foreach (Object i in BCF2Utils.toList(g.getExtendedAttribute(Field, null)))
{
if (i != null) // we know they are all integers
{
values.Add((int?)i);
}
}
}
encodingType = BCF2Utils.determineIntegerType(values);
base.start(encoder, vc);
}
//JAVA TO C# CONVERTER WARNING: Method 'throws' clauses are not available in .NET:
//ORIGINAL LINE: public void start(final BCF2Encoder encoder, final org.broadinstitute.variant.variantcontext.VariantContext vc) throws java.io.IOException
//JAVA TO C# CONVERTER WARNING: 'final' parameters are not allowed in .NET:
public override void start(BCF2Encoder encoder, VariantContext vc)
{
// TODO
// TODO this piece of code consumes like 10% of the runtime alone because fo the vc.getGenotypes() iteration
// TODO
encodingType = BCF2Type.INT8;
foreach (Genotype g in vc.Genotypes)
{
//JAVA TO C# CONVERTER WARNING: The original Java variable was marked 'final':
//ORIGINAL LINE: final int[] pls = ige.getValues(g);
int[] pls = ige.getValues(g);
//JAVA TO C# CONVERTER WARNING: The original Java variable was marked 'final':
//ORIGINAL LINE: final org.broadinstitute.variant.bcf2.BCF2Type plsType = getFieldEncoder().getType(pls);
BCF2Type plsType = FieldEncoder.getType(pls);
encodingType = BCF2Utils.maxIntegerType(encodingType, plsType);
if (encodingType == BCF2Type.INT32)
{
break; // stop early
}
}
base.start(encoder, vc);
}
//JAVA TO C# CONVERTER TODO TASK: Most Java annotations will not have direct .NET equivalent attributes:
//ORIGINAL LINE: @Requires({"encodingType != null", "nValuesPerGenotype >= 0"}) public void addGenotype(final BCF2Encoder encoder, final org.broadinstitute.variant.variantcontext.VariantContext vc, final org.broadinstitute.variant.variantcontext.Genotype g) throws java.io.IOException
//JAVA TO C# CONVERTER WARNING: Method 'throws' clauses are not available in .NET:
//JAVA TO C# CONVERTER WARNING: 'final' parameters are not allowed in .NET:
public virtual void addGenotype(BCF2Encoder encoder, VariantContext vc, Genotype g)
{
//JAVA TO C# CONVERTER WARNING: The original Java variable was marked 'final':
//ORIGINAL LINE: final Object fieldValue = g.getExtendedAttribute(getField(), null);
object fieldValue = g.getExtendedAttribute(Field, null);
FieldEncoder.encodeValue(encoder, fieldValue, encodingType, nValuesPerGenotype);
}
//JAVA TO C# CONVERTER TODO TASK: Most Java annotations will not have direct .NET equivalent attributes:
//ORIGINAL LINE: @Override @Requires({"encodingType != null", "nValuesPerGenotype >= 0 || ! getFieldEncoder().hasConstantNumElements()"}) @Ensures("nValuesPerGenotype >= 0") public void start(final BCF2Encoder encoder, final org.broadinstitute.variant.variantcontext.VariantContext vc) throws java.io.IOException
//JAVA TO C# CONVERTER WARNING: Method 'throws' clauses are not available in .NET:
//JAVA TO C# CONVERTER WARNING: 'final' parameters are not allowed in .NET:
public override void start(BCF2Encoder encoder, VariantContext vc)
{
// writes the key information
base.start(encoder, vc);
// only update if we need to
if (!FieldEncoder.hasConstantNumElements())
{
if (FieldEncoder.hasContextDeterminedNumElements())
// we are cheap -- just depends on genotype of allele counts
{
nValuesPerGenotype = FieldEncoder.numElements(vc);
}
else
// we have to go fishing through the values themselves (expensive)
{
nValuesPerGenotype = computeMaxSizeOfGenotypeFieldFromValues(vc);
}
}
encoder.encodeType(nValuesPerGenotype, encodingType);
}
//JAVA TO C# CONVERTER WARNING: Method 'throws' clauses are not available in .NET:
//ORIGINAL LINE: public void site(final BCF2Encoder encoder, final org.broadinstitute.variant.variantcontext.VariantContext vc) throws java.io.IOException
//JAVA TO C# CONVERTER WARNING: 'final' parameters are not allowed in .NET:
public override void site(BCF2Encoder encoder, VariantContext vc)
{
//JAVA TO C# CONVERTER WARNING: The original Java variable was marked 'final':
//ORIGINAL LINE: final Object rawValue = vc.getAttribute(getField(), null);
object rawValue = vc.getAttribute(Field, null);
//JAVA TO C# CONVERTER WARNING: The original Java variable was marked 'final':
//ORIGINAL LINE: final org.broadinstitute.variant.bcf2.BCF2Type type = getFieldEncoder().getType(rawValue);
BCF2Type type = FieldEncoder.getType(rawValue);
if (rawValue == null)
{
// the value is missing, just write in null
encoder.encodeType(0, type);
}
else
{
//JAVA TO C# CONVERTER WARNING: The original Java variable was marked 'final':
//ORIGINAL LINE: final int valueCount = getFieldEncoder().numElements(vc, rawValue);
int valueCount = FieldEncoder.numElements(vc, rawValue);
encoder.encodeType(valueCount, type);
FieldEncoder.encodeValue(encoder, rawValue, type, valueCount);
}
}
//JAVA TO C# CONVERTER WARNING: Method 'throws' clauses are not available in .NET: //ORIGINAL LINE: public abstract void site(final BCF2Encoder encoder, final org.broadinstitute.variant.variantcontext.VariantContext vc) throws java.io.IOException; //JAVA TO C# CONVERTER WARNING: 'final' parameters are not allowed in .NET: public abstract void site(BCF2Encoder encoder, VariantContext vc);
//JAVA TO C# CONVERTER WARNING: Method 'throws' clauses are not available in .NET:
//ORIGINAL LINE: public void done(final BCF2Encoder encoder, final org.broadinstitute.variant.variantcontext.VariantContext vc) throws java.io.IOException
//JAVA TO C# CONVERTER WARNING: 'final' parameters are not allowed in .NET:
public virtual void done(BCF2Encoder encoder, VariantContext vc) // TODO -- overload done so that we null out values and test for correctness
{
}
