new NamingConcatFeatureMapper<>( new NamingConcatFeatureMapper<BaseInformationRecords.BaseInformationOrBuilder>(countMappers)), // different new CeilingNormalizationMapper<>( new NamingConcatFeatureMapper<BaseInformationRecords.BaseInformationOrBuilder>(countMappers),30), new InverseNormalizationMapper<BaseInformationRecords.BaseInformationOrBuilder>( new NamingConcatFeatureMapper<BaseInformationRecords.BaseInformationOrBuilder>(readIndexMappers)), // different new NamingConcatFeatureMapper<BaseInformationRecords.BaseInformationOrBuilder>(targetAlignedLengthMappers), // different new NamingConcatFeatureMapper<BaseInformationRecords.BaseInformationOrBuilder>(queryAlignedLengthMappers), // different new NamingConcatFeatureMapper<BaseInformationRecords.BaseInformationOrBuilder>(queryPositions), // different new NamingConcatFeatureMapper<BaseInformationRecords.BaseInformationOrBuilder>(distancesToReadVariations), // different new NamingConcatFeatureMapper<BaseInformationRecords.BaseInformationOrBuilder>(bamFlagMappers) // different );
new NamingConcatFeatureMapper<>( new NamingConcatFeatureMapper<BaseInformationRecords.BaseInformationOrBuilder>(countMappers)), // different new InverseNormalizationMapper<BaseInformationRecords.BaseInformationOrBuilder>( new NamingConcatFeatureMapper<BaseInformationRecords.BaseInformationOrBuilder>(readIndexMappers)), // different new NamingConcatFeatureMapper<BaseInformationRecords.BaseInformationOrBuilder>(targetAlignedLengthMappers), // different new NamingConcatFeatureMapper<BaseInformationRecords.BaseInformationOrBuilder>(queryAlignedLengthMappers), // different new NamingConcatFeatureMapper<BaseInformationRecords.BaseInformationOrBuilder>(queryPositions), // different new NamingConcatFeatureMapper<BaseInformationRecords.BaseInformationOrBuilder>(distancesToReadVariations), // different new NamingConcatFeatureMapper<BaseInformationRecords.BaseInformationOrBuilder>(bamFlagMappers) // different );
new CountReorderingMapper(sampleIndex,new NamingConcatFeatureMapper<>( new NamingConcatFeatureMapper<BaseInformationRecords.BaseInformationOrBuilder>(firstBaseMappers), new InverseNormalizationMapper<BaseInformationRecords.BaseInformationOrBuilder>( new NamingConcatFeatureMapper<BaseInformationRecords.BaseInformationOrBuilder>(countMappers)), new InverseNormalizationMapper<BaseInformationRecords.BaseInformationOrBuilder>( new NamingConcatFeatureMapper<BaseInformationRecords.BaseInformationOrBuilder>(readIndexMappers)), new GenomicContextMapper(sbiProperties), new NamingConcatFeatureMapper<BaseInformationRecords.BaseInformationOrBuilder>(matchesRefMappers), new NamingConcatFeatureMapper<BaseInformationRecords.BaseInformationOrBuilder>(numVariationsInReadMappers), new NamingConcatFeatureMapper<BaseInformationRecords.BaseInformationOrBuilder>(readMappingQualityMappers), new NamingConcatFeatureMapper<BaseInformationRecords.BaseInformationOrBuilder>(baseQualityMappers) ));
new CountReorderingMapper(sampleIndex, new NamingConcatFeatureMapper<>( new NamingConcatFeatureMapper<BaseInformationRecords.BaseInformationOrBuilder>(firstBaseMappers), new MaxNormalizationMapper<BaseInformationRecords.BaseInformationOrBuilder>( new NamingConcatFeatureMapper<BaseInformationRecords.BaseInformationOrBuilder>(countMappers)), new MaxNormalizationMapper<BaseInformationRecords.BaseInformationOrBuilder>( new NamingConcatFeatureMapper<BaseInformationRecords.BaseInformationOrBuilder>(readIndexMappers)), new GenomicContextMapper(sbiProperties), new NamingConcatFeatureMapper<BaseInformationRecords.BaseInformationOrBuilder>(matchesRefMappers), new NamingConcatFeatureMapper<BaseInformationRecords.BaseInformationOrBuilder>(numVariationsInReadMappers), new NamingConcatFeatureMapper<BaseInformationRecords.BaseInformationOrBuilder>(readMappingQualityMappers), new NamingConcatFeatureMapper<BaseInformationRecords.BaseInformationOrBuilder>(baseQualityMappers) ));
new NamingConcatFeatureMapper<>( new MaxNormalizationMapper( new NamingConcatFeatureMapper<BaseInformationRecords.BaseInformationOrBuilder>(countMappers)), new InverseNormalizationMapper( new NamingConcatFeatureMapper<BaseInformationRecords.BaseInformationOrBuilder>(countMappers)), new MaxNormalizationMapper( new NamingConcatFeatureMapper<BaseInformationRecords.BaseInformationOrBuilder>(readIndexMappers)), new InverseNormalizationMapper( new NamingConcatFeatureMapper<BaseInformationRecords.BaseInformationOrBuilder>(readIndexMappers)), new GenomicContextMapper(sbiProperties), new DensityMapper("numVariationsInRead", 20, sbiProperties, baseInformationOrBuilder ->
new CountReorderingMapper(sampleIndex, new NamingConcatFeatureMapper<>( new NamingConcatFeatureMapper<BaseInformationRecords.BaseInformationOrBuilder>(matchesRefMappers), new NamingConcatFeatureMapper<BaseInformationRecords.BaseInformationOrBuilder>(firstBaseMappers), new MaxNormalizationMapper<BaseInformationRecords.BaseInformationOrBuilder>( new NamingConcatFeatureMapper<BaseInformationRecords.BaseInformationOrBuilder>(countMappers)), new MaxNormalizationMapper<BaseInformationRecords.BaseInformationOrBuilder>( new NamingConcatFeatureMapper<BaseInformationRecords.BaseInformationOrBuilder>(readIndexMappers)), new GenomicContextMapper(sbiProperties), new DensityMapper("numVariationsInRead", 20, sbiProperties, baseInformationOrBuilder ->
new CountReorderingMapper(sampleIndex, new NamingConcatFeatureMapper<>( new NamingConcatFeatureMapper<BaseInformationRecords.BaseInformationOrBuilder>(matchesRefMappers), new NamingConcatFeatureMapper<BaseInformationRecords.BaseInformationOrBuilder>(firstBaseMappers), new MaxNormalizationMapper<BaseInformationRecords.BaseInformationOrBuilder>( new NamingConcatFeatureMapper<BaseInformationRecords.BaseInformationOrBuilder>(countMappers)), new MaxNormalizationMapper<BaseInformationRecords.BaseInformationOrBuilder>( new NamingConcatFeatureMapper<BaseInformationRecords.BaseInformationOrBuilder>(readIndexMappers)), new GenomicContextMapper(sbiProperties), new DensityMapper("numVariationsInRead", 20, sbiProperties, baseInformationOrBuilder ->
new CountReorderingMapper(sampleIndex, new NamingConcatFeatureMapper<>( new NamingConcatFeatureMapper<BaseInformationRecords.BaseInformationOrBuilder>(matchesRefMappers), new MaxNormalizationMapper<BaseInformationRecords.BaseInformationOrBuilder>( new NamingConcatFeatureMapper<BaseInformationRecords.BaseInformationOrBuilder>(countMappers)), new MaxNormalizationMapper<BaseInformationRecords.BaseInformationOrBuilder>( new NamingConcatFeatureMapper<BaseInformationRecords.BaseInformationOrBuilder>(readIndexMappers)), new GenomicContextMapper(sbiProperties), new DensityMapper("numVariationsInRead", 20, sbiProperties, baseInformationOrBuilder ->
new NamingConcatFeatureMapper<>( new NamingConcatFeatureMapper<BaseInformationRecords.BaseInformationOrBuilder>(matchesRefMappers), new MaxNormalizationMapper<BaseInformationRecords.BaseInformationOrBuilder>( new NamingConcatFeatureMapper<BaseInformationRecords.BaseInformationOrBuilder>(countMappers)), new MaxNormalizationMapper<BaseInformationRecords.BaseInformationOrBuilder>( new NamingConcatFeatureMapper<BaseInformationRecords.BaseInformationOrBuilder>(readIndexMappers)), new GenomicContextMapper(sbiProperties), new DensityMapper("numVariationsInRead", 20, sbiProperties, baseInformationOrBuilder ->
new NamingConcatFeatureMapper<>( new MeanNormalizationMapper<BaseInformationRecords.BaseInformationOrBuilder>( new NamingConcatFeatureMapper<BaseInformationRecords.BaseInformationOrBuilder>(countMappers)), new MeanNormalizationMapper<BaseInformationRecords.BaseInformationOrBuilder>( new NamingConcatFeatureMapper<BaseInformationRecords.BaseInformationOrBuilder>(readIndexMappers)), new GenomicContextMapper(sbiProperties), new DensityMapper("numVariationsInRead", 20, sbiProperties, baseInformationOrBuilder ->
a.configure(sbiProperties); b.configure(sbiProperties); delegate = new CountReorderingMapper(somaticIndex, new NamingConcatFeatureMapper<BaseInformationRecords.BaseInformationOrBuilder>( a, b, new GenomicContextMapper(sbiProperties), new NamingConcatFeatureMapper<BaseInformationRecords.BaseInformationOrBuilder>(matchesRefMappers), new NamingConcatFeatureMapper<BaseInformationRecords.BaseInformationOrBuilder>(originalGobyCountIndexMappers), new NamingConcatFeatureMapper<BaseInformationRecords.BaseInformationOrBuilder>(firstBaseMappers),
a.configure(sbiProperties); b.configure(sbiProperties); delegate = new CountReorderingMapper(somaticIndex, new NamingConcatFeatureMapper<BaseInformationRecords.BaseInformationOrBuilder>( a, b,
/** * 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)) ); }
/** * 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)) ); }
delegate = new NamingConcatFeatureMapper<BaseInformationRecords.BaseInformationOrBuilder>( new SimpleFeatureCalculator(true), new IndelFeatures(),
delegate = new NamingConcatFeatureMapper<BaseInformationRecords.BaseInformationOrBuilder>( new SimpleFeatureCalculator(true), new IndelFeatures(),
delegate = new NamingConcatFeatureMapper<BaseInformationRecords.BaseInformationOrBuilder>( new SimpleFeatureCalculator(true), new IndelFeatures(),
delegate = new NamingConcatFeatureMapper<BaseInformationRecords.BaseInformationOrBuilder>( new SimpleFeatureCalculatorTrio(true), new IndelFeaturesTrio(),
delegate = new NamingConcatFeatureMapper<BaseInformationRecords.BaseInformationOrBuilder>( new SimpleFeatureCalculator(true), new IndelFeatures(),
delegate = new NamingConcatFeatureMapper<BaseInformationRecords.BaseInformationOrBuilder>( new SimpleFeatureCalculator(true), new IndelFeatures(),