public float produceFeatureInternal(BaseInformationRecords.BaseInformationOrBuilder record, int featureIndex) { assert featureIndex >= 0 && featureIndex < MAX_GENOTYPES * 2 : "Only MAX_GENOTYPES*2 features"; if (featureIndex < MAX_GENOTYPES) { // germline counts written first: final ReadIndexWithCounts genotypeCount = (ReadIndexWithCounts) getAllCounts(record, false).get(featureIndex); return genotypeCount.getDistinctReadIndices(); } else { // tumor counts written next: featureIndex -= MAX_GENOTYPES; final ReadIndexWithCounts genotypeCount = (ReadIndexWithCounts) getAllCounts(record, true).get(featureIndex); return genotypeCount.getDistinctReadIndices(); } }
public float produceFeature(BaseInformationRecords.BaseInformationOrBuilder record, int featureIndex) { return normalize(produceFeatureInternal(record, featureIndex), sumReadIndex); }
@Override public void mapFeatures(BaseInformationRecords.BaseInformationOrBuilder record, INDArray inputs, int indexOfRecord) { indices[0] = indexOfRecord; prepareToNormalize(record, indexOfRecord); for (int featureIndex = 0; featureIndex < numberOfFeatures(); featureIndex++) { indices[1] = featureIndex; inputs.putScalar(indices, produceFeature(record, featureIndex)); } }
public FeatureMapperV8() { super(new SimpleFeatureCalculator(true), new SortedGenotypeAgreementMapper(), //new MagnitudeFeatures(), // new QualityFeatures(), new ReadIndexFeatures(), new FractionDifferences2() ); } }
public FeatureMapperV6() { super(new FractionDifferences(), new MagnitudeFeatures(), new ReadIndexFeatures(), new QualityFeatures()); } }
public FeatureMapperV5() { super(new MagnitudeFeatures(), new SimpleFeatureCalculator(false), new QualityFeatures(), new ReadIndexFeatures()); } }
public FeatureMapperV12() { super(new SimpleFeatureCalculator(true), new IndelFeatures(), new ReadIndexFeatures(), new FractionDifferences2() ); } }
public FeatureMapperV9_2() { super(new SimpleFeatureCalculator(true), new SimpleFeatureCalculator(false), new SortedGenotypeAgreementMapper(), //new MagnitudeFeatures(), // new QualityFeatures(), new ReadIndexFeatures(), new FractionDifferences4() ); } }
public FeatureMapperV16() { super(new SimpleFeatureCalculator(true), new IndelFeatures(), new ReadIndexFeatures(), new FractionDifferences4(), new MagnitudeFeatures2() ); } }
public FeatureMapperV4() { super(new SimpleFeatureCalculator(true), new SortedGenotypeAgreementMapper(), new MagnitudeFeatures(), new QualityFeatures(), new ReadIndexFeatures() ); } }
public FeatureMapperV13() { super(new SimpleFeatureCalculator(true), new IndelFeatures(), new ReadIndexFeatures(), new FractionDifferences3(), new MagnitudeFeatures2() ); } }
public FeatureMapperV9() { super(new SimpleFeatureCalculator(true), new SimpleFeatureCalculator(false), new SortedGenotypeAgreementMapper(), //new MagnitudeFeatures(), // new QualityFeatures(), new ReadIndexFeatures(), new FractionDifferences2() ); } }
public FeatureMapperV14() { super(new SimpleFeatureCalculator(true), new IndelFeatures(), new ReadIndexFeatures(), new FractionDifferences3(), new MagnitudeFeatures3() ); } }
public FeatureMapperVT() { super(new SimpleFeatureCalculator(false), new SimpleFeatureCalculator(true), new MagnitudeFeatures(), new QualityFeatures(), new ReadIndexFeatures() ); } }
public FeatureMapperV7() { super(new SimpleFeatureCalculator(true), new SortedGenotypeAgreementMapper(), new MagnitudeFeatures(), new QualityFeatures(), new ReadIndexFeatures(), new FractionDifferences2() ); } }
public FeatureMapperV11() { super(new SimpleFeatureCalculator(false), new SimpleFeatureCalculator(true), new MagnitudeFeatures(), new QualityFeatures(), new ReadIndexFeatures(), new FractionDifferences2() ); } }
public FeatureMapperV10() { super(new SimpleFeatureCalculator(true), new SimpleFeatureCalculator(false), new SortedGenotypeAgreementMapper(), //new MagnitudeFeatures(), new QualityFeatures(), new ReadIndexFeatures(), new FractionDifferences2() ); } }
public FeatureMapperV17() { super(new SimpleFeatureCalculator(true), new IndelFeatures(), new ReadIndexFeatures(), new FractionDifferences4(), new MagnitudeFeatures2(), new GenomicPositionMapper() ); } }
public FeatureMapperV15() { super(new SimpleFeatureCalculator(true), new IndelFeatures(), new ReadIndexFeatures(), new FractionDifferences3(), new MagnitudeFeatures2(), new GenomicPositionMapper() ); } }