//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; // TODO -- can be restructured to avoid toList operation if (isAtomic) { // fast path for fields with 1 fixed float value if (value != null) { encoder.encodeRawFloat((double?)value); count++; } } else { // handle generic case //JAVA TO C# CONVERTER WARNING: The original Java variable was marked 'final': //ORIGINAL LINE: final java.util.List<Double> doubles = toList(Double.class, value); IList <double?> doubles = toList(typeof(double?), value); foreach (Double d in doubles) { if (d != null) // necessary because .,. => [null, null] in VC { encoder.encodeRawFloat(d); count++; } } } for (; count < minValues; count++) { encoder.encodeRawMissingValue(type); } }
// -------------------------------------------------------------------------------- // // 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); } }