@Override public float produceFeature(BaseInformationRecords.BaseInformationOrBuilder record, int featureIndex) { // compare genotype indices after sorting: final ObjectArrayList<? extends GenotypeCount> sortedCountsSample0 = getAllCounts(record, getGenotypeCountFactory(), false, true); final ObjectArrayList<? extends GenotypeCount> sortedCountsSample1 = getAllCounts(record, getGenotypeCountFactory(), false, false); int genotypeIndexSample0 = sortedCountsSample0.get(featureIndex).genotypeIndex; int genotypeIndexSample1 = sortedCountsSample1.get(featureIndex).genotypeIndex; return genotypeIndexSample0 == genotypeIndexSample1 ? 1f : .0f; }
@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 FeatureMapperV9() { super(new SimpleFeatureCalculator(true), new SimpleFeatureCalculator(false), new SortedGenotypeAgreementMapper(), //new MagnitudeFeatures(), // new QualityFeatures(), new ReadIndexFeatures(), new FractionDifferences2() ); } }
public FeatureMapperV4() { super(new SimpleFeatureCalculator(true), new SortedGenotypeAgreementMapper(), new MagnitudeFeatures(), new QualityFeatures(), new ReadIndexFeatures() ); } }
public FeatureMapperV9_2() { super(new SimpleFeatureCalculator(true), new SimpleFeatureCalculator(false), new SortedGenotypeAgreementMapper(), //new MagnitudeFeatures(), // new QualityFeatures(), new ReadIndexFeatures(), new FractionDifferences4() ); } }
public FeatureMapperV10() { super(new SimpleFeatureCalculator(true), new SimpleFeatureCalculator(false), new SortedGenotypeAgreementMapper(), //new MagnitudeFeatures(), new QualityFeatures(), new ReadIndexFeatures(), new FractionDifferences2() ); } }
public FeatureMapperV7() { super(new SimpleFeatureCalculator(true), new SortedGenotypeAgreementMapper(), new MagnitudeFeatures(), new QualityFeatures(), new ReadIndexFeatures(), new FractionDifferences2() ); } }