// --------------------------------------------------------------------------------
//
// 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 encodeValue(final BCF2Encoder encoder, final Object value, final org.broadinstitute.variant.bcf2.BCF2Type type, final int minValues) throws java.io.IOException
//JAVA TO C# CONVERTER WARNING: 'final' parameters are not allowed in .NET:
public override void encodeValue(BCF2Encoder encoder, object value, BCF2Type type, int minValues)
{
int count = 0;
if (value != null)
{
encoder.encodeRawInt((int?)value, type);
count++;
}
for (; count < minValues; count++)
{
encoder.encodeRawMissingValue(type);
}
}
//JAVA TO C# CONVERTER WARNING: Method 'throws' clauses are not available in .NET:
//ORIGINAL LINE: public void encodeValue(final BCF2Encoder encoder, final Object value, final org.broadinstitute.variant.bcf2.BCF2Type type, final int minValues) throws java.io.IOException
//JAVA TO C# CONVERTER WARNING: 'final' parameters are not allowed in .NET:
public override void encodeValue(BCF2Encoder encoder, object value, BCF2Type type, int minValues)
{
int count = 0;
foreach (Integer i in toList(typeof(Integer), value))
{
if (i != null) // necessary because .,. => [null, null] in VC
{
encoder.encodeRawInt(i, type);
count++;
}
}
for (; count < minValues; count++)
{
encoder.encodeRawMissingValue(type);
}
}