public FeatureMapperV12() { super(new SimpleFeatureCalculator(true), new IndelFeatures(), new ReadIndexFeatures(), new FractionDifferences2() ); } }
public float produceFeatureInternal(BaseInformationRecords.BaseInformationOrBuilder record, int featureIndex) { assert featureIndex >= 0 && featureIndex < MAX_GENOTYPES : "Only MAX_GENOTYPES features"; // germline counts written first: final IndelGenotypeCount genotypeCount = (IndelGenotypeCount) getAllCounts(record, false, true).get(featureIndex); return genotypeCount.getIsIndel() ? 1F : 0F; }
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 float produceFeature(BaseInformationRecords.BaseInformationOrBuilder record, int featureIndex) { return produceFeatureInternal(record, featureIndex); }
public FeatureMapperV18() { super(new SimpleFeatureCalculator(true), new IndelFeatures(), new ReadIndexFeaturesFix(), new FractionDifferences4(), new MagnitudeFeatures2() ); } }
public FeatureMapperV16() { super(new SimpleFeatureCalculator(true), new IndelFeatures(), new ReadIndexFeatures(), new FractionDifferences4(), new MagnitudeFeatures2() ); } }
public FeatureMapperV14() { super(new SimpleFeatureCalculator(true), new IndelFeatures(), new ReadIndexFeatures(), new FractionDifferences3(), new MagnitudeFeatures3() ); } }
public FeatureMapperV13() { super(new SimpleFeatureCalculator(true), new IndelFeatures(), new ReadIndexFeatures(), new FractionDifferences3(), new MagnitudeFeatures2() ); } }
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() ); } }
/** * 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 IndelFeatures(), new GenomicContextMapper(sbiProperties),
new IndelFeatures(), new GenomicContextMapper(sbiProperties),
new IndelFeatures(), new GenomicContextMapper(sbiProperties),
new IndelFeatures(), new GenomicContextMapper(sbiProperties),
new IndelFeatures(), new GenomicContextMapper(sbiProperties),