public float produceFeature(BaseInformationRecords.BaseInformationOrBuilder record, int featureIndex) { float producedFeat = produceFeatureInternal(record, featureIndex); return normalize(producedFeat, FRACTION_NORM); }
public void mapFeatures(BaseInformationRecords.BaseInformationOrBuilder record, INDArray inputs, int indexOfRecord) { indices[0] = 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 float produceFeatureInternal(BaseInformationRecords.BaseInformationOrBuilder record, int featureIndex) { assert featureIndex >= 0 && featureIndex < MAX_GENOTYPES : "Only MAX_GENOTYPES features"; ObjectArrayList<? extends GenotypeCount> germlineCounts = getAllCounts(record, false, true); ObjectArrayList<? extends GenotypeCount> somaticCounts = getAllCounts(record, true, true); // note that we normalize the counts to frequency before substracting: int germlineCount = germlineCounts.get(featureIndex).totalCount(); int somaticCount = somaticCounts.get(featureIndex).totalCount(); float germFrequency = ((float) germlineCount / (float) totalCountsGermline); float somaticFrequency = ((float) somaticCount / (float) totalCountsSomatic); // then multiply again by somatic counts to reintroduce size effect: return (float) (Math.max(0f,(somaticFrequency - germFrequency)) * somaticCount); }
public FeatureMapperV12() { super(new SimpleFeatureCalculator(true), new IndelFeatures(), new ReadIndexFeatures(), new FractionDifferences2() ); } }
public void prepareToNormalize(BaseInformationRecords.BaseInformationOrBuilder record, int indexOfRecord) { totalCountsGermline = 0; totalCountsSomatic = 0; ObjectArrayList<? extends GenotypeCount> germlineCounts = getAllCounts(record, false, true); ObjectArrayList<? extends GenotypeCount> somaticCounts = getAllCounts(record, true, true); for (int i = 0; i < germlineCounts.size(); i++) { totalCountsGermline += (germlineCounts.get(i).totalCount()); totalCountsSomatic += (somaticCounts.get(i).totalCount()); } assert(totalCountsGermline>0):"0 total"; assert(totalCountsSomatic>0):"0 total"; }
public FeatureMapperV9() { 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() ); } }
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() ); } }