protected internal override void noteCurrentRecord(VariantContext vc)
{
base.noteCurrentRecord(vc); // first, check for errors
// then, update mostUpstreamWritableLoc:
int mostUpstreamWritableIndex = vc.Start - maxCachingStartDistance;
this.mostUpstreamWritableLoc = Math.Max(BEFORE_MOST_UPSTREAM_LOC, mostUpstreamWritableIndex);
}
//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: private byte[] buildSamplesData(final VariantContext vc) throws IOException
//JAVA TO C# CONVERTER WARNING: 'final' parameters are not allowed in .NET:
private sbyte[] buildSamplesData(VariantContext vc)
{
//JAVA TO C# CONVERTER WARNING: The original Java variable was marked 'final':
//ORIGINAL LINE: final org.broadinstitute.variant.bcf2.BCF2Codec.LazyData lazyData = getLazyData(vc);
BCF2Codec.LazyData lazyData = getLazyData(vc); // has critical side effects
if (lazyData != null)
{
// we never decoded any data from this BCF file, so just pass it back
return lazyData.bytes;
}
// we have to do work to convert the VC into a BCF2 byte stream
//JAVA TO C# CONVERTER WARNING: The original Java variable was marked 'final':
//ORIGINAL LINE: final List<String> genotypeFields = VCFWriter.calcVCFGenotypeKeys(vc, header);
IList<string> genotypeFields = VCFWriter.calcVCFGenotypeKeys(vc, header);
foreach (String field in genotypeFields)
{
//JAVA TO C# CONVERTER WARNING: The original Java variable was marked 'final':
//ORIGINAL LINE: final BCF2FieldWriter.GenotypesWriter writer = fieldManager.getGenotypeFieldWriter(field);
BCF2FieldWriter.GenotypesWriter writer = fieldManager.getGenotypeFieldWriter(field);
if (writer == null)
{
errorUnexpectedFieldToWrite(vc, field, "FORMAT");
}
Debug.Assert(writer != null);
writer.start(encoder, vc);
foreach (String name in sampleNames)
{
Genotype g = vc.getGenotype(name);
if (g == null)
{
g = GenotypeBuilder.createMissing(name, writer.nValuesPerGenotype);
}
writer.addGenotype(encoder, vc, g);
}
writer.done(encoder, vc);
}
return encoder.RecordBytes;
}
//JAVA TO C# CONVERTER WARNING: Method 'throws' clauses are not available in .NET:
//ORIGINAL LINE: private void buildFilter(VariantContext vc) throws IOException
private void buildFilter(VariantContext vc)
{
if (vc.Filtered)
{
encodeStringsByRef(vc.Filters);
}
else if (vc.filtersWereApplied())
{
encodeStringsByRef(Collections.singleton(VCFConstants.PASSES_FILTERS_v4));
}
else
{
encoder.encodeTypedMissing(BCF2Type.INT8);
}
}
//JAVA TO C# CONVERTER WARNING: Method 'throws' clauses are not available in .NET:
//ORIGINAL LINE: private void buildID(VariantContext vc) throws IOException
private void buildID(VariantContext vc)
{
encoder.encodeTypedString(vc.ID);
}
//JAVA TO C# CONVERTER WARNING: 'final' parameters are not allowed in .NET:
//ORIGINAL LINE: private org.broadinstitute.variant.bcf2.BCF2Codec.LazyData getLazyData(final VariantContext vc)
private BCF2Codec.LazyData getLazyData(VariantContext vc)
{
if (vc.Genotypes.LazyWithData)
{
//JAVA TO C# CONVERTER WARNING: The original Java variable was marked 'final':
//ORIGINAL LINE: final LazyGenotypesContext lgc = (LazyGenotypesContext)vc.getGenotypes();
LazyGenotypesContext lgc = (LazyGenotypesContext)vc.Genotypes;
if (lgc.UnparsedGenotypeData is BCF2Codec.LazyData && canSafelyWriteRawGenotypesBytes((BCF2Codec.LazyData) lgc.UnparsedGenotypeData))
{
return (BCF2Codec.LazyData)lgc.UnparsedGenotypeData;
}
else
{
lgc.decode(); // WARNING -- required to avoid keeping around bad lazy data for too long
}
}
return null;
}
public override void add(VariantContext vc)
{
if (doNotWriteGenotypes)
{
vc = (new VariantContextBuilder(vc)).noGenotypes().make();
}
vc = vc.fullyDecode(header, false);
base.add(vc); // allow on the fly indexing
try
{
//JAVA TO C# CONVERTER WARNING: The original Java variable was marked 'final':
//ORIGINAL LINE: final byte[] infoBlock = buildSitesData(vc);
sbyte[] infoBlock = buildSitesData(vc);
//JAVA TO C# CONVERTER WARNING: The original Java variable was marked 'final':
//ORIGINAL LINE: final byte[] genotypesBlock = buildSamplesData(vc);
sbyte[] genotypesBlock = buildSamplesData(vc);
// write the two blocks to disk
writeBlock(infoBlock, genotypesBlock);
}
catch (IOException e)
{
throw new Exception("Error writing record to BCF2 file: " + vc.ToString(), e);
}
}
/// <summary>
/// add a record to the file
/// </summary>
/// <param name="vc"> the Variant Context object </param>
public virtual void add(VariantContext vc)
{
// if we are doing on the fly indexing, add the record ***before*** we write any bytes
if (indexer != null)
{
indexer.addFeature(vc, positionalOutputStream.Position);
}
}
//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 TODO TASK: Most Java annotations will not have direct .NET equivalent attributes:
//ORIGINAL LINE: @Ensures({"result >= 0"}) private final int computeMaxSizeOfGenotypeFieldFromValues(final org.broadinstitute.variant.variantcontext.VariantContext vc)
//JAVA TO C# CONVERTER WARNING: 'final' parameters are not allowed in .NET:
private int computeMaxSizeOfGenotypeFieldFromValues(VariantContext vc)
{
int size = -1;
foreach (Genotype g in vc.Genotypes)
{
size = Math.Max(size, numElements(vc, g));
}
return size;
}
//JAVA TO C# CONVERTER TODO TASK: Most Java annotations will not have direct .NET equivalent attributes:
//ORIGINAL LINE: @Ensures({"result >= 0"}) protected int numElements(final org.broadinstitute.variant.variantcontext.VariantContext vc, final org.broadinstitute.variant.variantcontext.Genotype g)
//JAVA TO C# CONVERTER WARNING: 'final' parameters are not allowed in .NET:
protected internal virtual int numElements(VariantContext vc, Genotype g)
{
return FieldEncoder.numElements(vc, g.getExtendedAttribute(Field));
}
//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: 'final' parameters are not allowed in .NET:
//ORIGINAL LINE: private final void buildAlleleMap(final org.broadinstitute.variant.variantcontext.VariantContext vc)
private void buildAlleleMap(VariantContext vc)
{
// these are fast path options to determine the offsets for
//JAVA TO C# CONVERTER WARNING: The original Java variable was marked 'final':
//ORIGINAL LINE: final int nAlleles = vc.getNAlleles();
int nAlleles = vc.NAlleles;
@ref = vc.Reference;
alt1 = nAlleles > 1 ? vc.getAlternateAllele(0) : null;
if (nAlleles > 2)
{
// for multi-allelics we need to clear the map, and add additional looks
alleleMapForTriPlus.Clear();
//JAVA TO C# CONVERTER WARNING: The original Java variable was marked 'final':
//ORIGINAL LINE: final java.util.List<org.broadinstitute.variant.variantcontext.Allele> alleles = vc.getAlleles();
IList<Allele> alleles = vc.Alleles;
for (int i = 2; i < alleles.Count; i++)
{
alleleMapForTriPlus[alleles[i]] = i;
}
}
}
//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)
{
// 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 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: 'final' parameters are not allowed in .NET:
//ORIGINAL LINE: protected int numElements(final org.broadinstitute.variant.variantcontext.VariantContext vc, final org.broadinstitute.variant.variantcontext.Genotype g)
protected internal override int numElements(VariantContext vc, Genotype g)
{
return ige.getSize(g);
}
// --------------------------------------------------------------------------------
//
// implicit block
//
// The first four records of BCF are inline untype encoded data of:
//
// 4 byte integer chrom offset
// 4 byte integer start
// 4 byte integer ref length
// 4 byte float qual
//
// --------------------------------------------------------------------------------
//JAVA TO C# CONVERTER WARNING: Method 'throws' clauses are not available in .NET:
//ORIGINAL LINE: private byte[] buildSitesData(VariantContext vc) throws IOException
private sbyte[] buildSitesData(VariantContext vc)
{
//JAVA TO C# CONVERTER WARNING: The original Java variable was marked 'final':
//ORIGINAL LINE: final int contigIndex = contigDictionary.get(vc.getChr());
int contigIndex = contigDictionary[vc.Chr];
if (contigIndex == -1)
{
throw new IllegalStateException(string.Format("Contig {0} not found in sequence dictionary from reference", vc.Chr));
}
// note use of encodeRawValue to not insert the typing byte
encoder.encodeRawValue(contigIndex, BCF2Type.INT32);
// pos. GATK is 1 based, BCF2 is 0 based
encoder.encodeRawValue(vc.Start - 1, BCF2Type.INT32);
// ref length. GATK is closed, but BCF2 is open so the ref length is GATK end - GATK start + 1
// for example, a SNP is in GATK at 1:10-10, which has ref length 10 - 10 + 1 = 1
encoder.encodeRawValue(vc.End - vc.Start + 1, BCF2Type.INT32);
// qual
if (vc.hasLog10PError())
{
encoder.encodeRawFloat((float) vc.PhredScaledQual);
}
else
{
encoder.encodeRawMissingValue(BCF2Type.FLOAT);
}
// info fields
//JAVA TO C# CONVERTER WARNING: The original Java variable was marked 'final':
//ORIGINAL LINE: final int nAlleles = vc.getNAlleles();
int nAlleles = vc.NAlleles;
//JAVA TO C# CONVERTER WARNING: The original Java variable was marked 'final':
//ORIGINAL LINE: final int nInfo = vc.getAttributes().size();
int nInfo = vc.Attributes.Count;
//JAVA TO C# CONVERTER WARNING: The original Java variable was marked 'final':
//ORIGINAL LINE: final int nGenotypeFormatFields = getNGenotypeFormatFields(vc);
int nGenotypeFormatFields = getNGenotypeFormatFields(vc);
//JAVA TO C# CONVERTER WARNING: The original Java variable was marked 'final':
//ORIGINAL LINE: final int nSamples = header.getNGenotypeSamples();
int nSamples = header.NGenotypeSamples;
encoder.encodeRawInt((nAlleles << 16) | (nInfo & 0x0000FFFF), BCF2Type.INT32);
encoder.encodeRawInt((nGenotypeFormatFields << 24) | (nSamples & 0x00FFFFF), BCF2Type.INT32);
buildID(vc);
buildAlleles(vc);
buildFilter(vc);
buildInfo(vc);
return encoder.RecordBytes;
}
//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);
}
/// <summary>
/// Try to get the nGenotypeFields as efficiently as possible.
///
/// If this is a lazy BCF2 object just grab the field count from there,
/// otherwise do the whole counting by types test in the actual data
/// </summary>
/// <param name="vc">
/// @return </param>
//JAVA TO C# CONVERTER WARNING: 'final' parameters are not allowed in .NET:
//ORIGINAL LINE: private final int getNGenotypeFormatFields(final VariantContext vc)
private int getNGenotypeFormatFields(VariantContext vc)
{
//JAVA TO C# CONVERTER WARNING: The original Java variable was marked 'final':
//ORIGINAL LINE: final org.broadinstitute.variant.bcf2.BCF2Codec.LazyData lazyData = getLazyData(vc);
BCF2Codec.LazyData lazyData = getLazyData(vc);
return lazyData != null ? lazyData.nGenotypeFields : VCFWriter.calcVCFGenotypeKeys(vc, header).Count;
}
//JAVA TO C# CONVERTER WARNING: 'final' parameters are not allowed in .NET:
//ORIGINAL LINE: protected int numElements(final org.broadinstitute.variant.variantcontext.VariantContext vc, final org.broadinstitute.variant.variantcontext.Genotype g)
protected internal override int numElements(VariantContext vc, Genotype g)
{
return FieldEncoder.numElements(vc, g.Filters);
}
//JAVA TO C# CONVERTER WARNING: Method 'throws' clauses are not available in .NET:
//ORIGINAL LINE: private void buildAlleles(VariantContext vc) throws IOException
private void buildAlleles(VariantContext vc)
{
foreach (Allele allele in vc.Alleles)
{
//JAVA TO C# CONVERTER WARNING: The original Java variable was marked 'final':
//ORIGINAL LINE: final byte[] s = allele.getDisplayBases();
sbyte[] s = allele.DisplayBases;
if (s == null)
{
throw new IllegalStateException("BUG: BCF2Writer encountered null padded allele" + allele);
}
encoder.encodeTypedString(s);
}
}
//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: private void buildInfo(VariantContext vc) throws IOException
private void buildInfo(VariantContext vc)
{
foreach (KeyValuePair<string, object> infoFieldEntry in vc.Attributes)
{
//JAVA TO C# CONVERTER WARNING: The original Java variable was marked 'final':
//ORIGINAL LINE: final String field = infoFieldEntry.getKey();
string field = infoFieldEntry.Key;
//JAVA TO C# CONVERTER WARNING: The original Java variable was marked 'final':
//ORIGINAL LINE: final BCF2FieldWriter.SiteWriter writer = fieldManager.getSiteFieldWriter(field);
BCF2FieldWriter.SiteWriter writer = fieldManager.getSiteFieldWriter(field);
if (writer == null)
{
errorUnexpectedFieldToWrite(vc, field, "INFO");
}
writer.start(encoder, vc);
writer.site(encoder, vc);
writer.done(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);
}
}
}
/// <summary>
/// Throws a meaningful error message when a field (INFO or FORMAT) is found when writing out a file
/// but there's no header line for it.
/// </summary>
/// <param name="vc"> </param>
/// <param name="field"> </param>
/// <param name="fieldType"> </param>
//JAVA TO C# CONVERTER WARNING: 'final' parameters are not allowed in .NET:
//ORIGINAL LINE: private final void errorUnexpectedFieldToWrite(final VariantContext vc, final String field, final String fieldType)
private void errorUnexpectedFieldToWrite(VariantContext vc, string field, string fieldType)
{
throw new IllegalStateException("Found field " + field + " in the " + fieldType + " fields of VariantContext at " + vc.Chr + ":" + vc.Start + " from " + vc.Source + " but this hasn't been defined in the VCFHeader");
}
//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
{
}
