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, true).get(featureIndex); return genotypeCount.getDistinctReadIndices(); } else { // tumor counts written next: featureIndex -= MAX_GENOTYPES; final ReadIndexWithCounts genotypeCount = (ReadIndexWithCounts) getAllCounts(record, true, 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 FeatureMapperV18() { super(new SimpleFeatureCalculator(true), new IndelFeatures(), new ReadIndexFeaturesFix(), new FractionDifferences4(), new MagnitudeFeatures2() ); } }
/** * Configure the feature mapper for a specific set of sbi files. This method accesses the properties of the reader. * * @param sbiProperties properties from an sbi reader. */ public void configure(Properties sbiProperties) { delegate = new NamingConcatFeatureMapper<BaseInformationRecords.BaseInformationOrBuilder>( new SimpleFeatureCalculator(true), new IndelFeatures(), new GenomicContextMapper(sbiProperties), new ReadIndexFeaturesFix(), new FractionDifferences4(), new MagnitudeFeatures2(), new DensityMapper("numVariationsInRead", 20, sbiProperties, baseInformationOrBuilder -> TraversalHelper.forSampleCounts(sampleIndex,baseInformationOrBuilder, BaseInformationRecords.CountInfo::getNumVariationsInReadsList)), new DensityMapper("readMappingQuality.forward", 10, sbiProperties, baseInformationOrBuilder -> TraversalHelper.forSampleCounts(sampleIndex,baseInformationOrBuilder, BaseInformationRecords.CountInfo::getReadMappingQualityForwardStrandList)), new DensityMapper("readMappingQuality.reverse", 10, sbiProperties, baseInformationOrBuilder -> TraversalHelper.forSampleCounts(sampleIndex,baseInformationOrBuilder, BaseInformationRecords.CountInfo::getReadMappingQualityReverseStrandList)), new DensityMapper("baseQuality.forward", 10, sbiProperties, baseInformationOrBuilder -> TraversalHelper.forSampleCounts(sampleIndex,baseInformationOrBuilder, BaseInformationRecords.CountInfo::getQualityScoresForwardStrandList)), new DensityMapper("baseQuality.reverse", 10, sbiProperties, baseInformationOrBuilder -> TraversalHelper.forSampleCounts(sampleIndex,baseInformationOrBuilder, BaseInformationRecords.CountInfo::getQualityScoresReverseStrandList)) ); }
/** * Configure the feature mapper for a specific set of sbi files. This method accesses the properties of the reader. * * @param sbiProperties properties from an sbi reader. */ public void configure(Properties sbiProperties) { delegate = new NamingConcatFeatureMapper<>(new SimpleFeatureCalculator(true), new IndelFeatures(), new GenomicContextMapper(sbiProperties), new ReadIndexFeaturesFix(), new FractionDifferences4(), new MagnitudeFeatures2(), new DensityMapper("numVariationsInRead", 10, sbiProperties, baseInformationOrBuilder -> TraversalHelper.forAllSampleCounts(baseInformationOrBuilder, BaseInformationRecords.CountInfo::getNumVariationsInReadsList)), new DensityMapper("readMappingQuality.forward", 10, sbiProperties, baseInformationOrBuilder -> TraversalHelper.forAllSampleCounts(baseInformationOrBuilder, BaseInformationRecords.CountInfo::getReadMappingQualityForwardStrandList)), new DensityMapper("readMappingQuality.reverse", 10, sbiProperties, baseInformationOrBuilder -> TraversalHelper.forAllSampleCounts(baseInformationOrBuilder, BaseInformationRecords.CountInfo::getReadMappingQualityReverseStrandList)), new DensityMapper("baseQuality.forward", 10, sbiProperties, baseInformationOrBuilder -> TraversalHelper.forAllSampleCounts(baseInformationOrBuilder, BaseInformationRecords.CountInfo::getQualityScoresForwardStrandList)), new DensityMapper("baseQuality.reverse", 10, sbiProperties, baseInformationOrBuilder -> TraversalHelper.forAllSampleCounts(baseInformationOrBuilder, BaseInformationRecords.CountInfo::getQualityScoresReverseStrandList)) ); }
new GenomicContextMapper(1, record -> recordTo(1, record, 2)), new GenomicContextMapper(1, record -> recordTo(1, record, 3)), new ReadIndexFeaturesFix(), new FractionDifferences4(), new MagnitudeFeatures2(),
new GenomicContextMapper(1, record -> recordTo(1, record, 2)), new GenomicContextMapper(1, record -> recordTo(1, record, 3)), new ReadIndexFeaturesFix(), new FractionDifferences4(), new MagnitudeFeatures2(),
new GenomicContextMapper(1, record -> recordTo(1, record, 2)), new GenomicContextMapper(1, record -> recordTo(1, record, 3)), new ReadIndexFeaturesFix(), new FractionDifferences4(), new MagnitudeFeatures2(),
new GenomicContextMapper(1, record -> recordTo(1, record, 2)), new GenomicContextMapper(1, record -> recordTo(1, record, 3)), new ReadIndexFeaturesFix(), new FractionDifferences4(), new MagnitudeFeatures2(),
new GenomicContextMapper(1, record -> recordTo(1, record, 2)), new GenomicContextMapper(1, record -> recordTo(1, record, 3)), new ReadIndexFeaturesFix(), new FractionDifferences4(), new MagnitudeFeatures2(),