/** * 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)) ); }
new NamingConcatFeatureMapper<BaseInformationRecords.BaseInformationOrBuilder>(firstBaseMappers), new DensityMapper("numVariationsInRead", 10, sbiProperties, record -> TraversalHelper.forAllSampleCounts(record, BaseInformationRecords.CountInfoOrBuilder::getNumVariationsInReadsList)), new DensityMapper("readMappingQuality.forward", 10, sbiProperties, baseInformationOrBuilder -> TraversalHelper.forNSampleCounts(sampleIndices, baseInformationOrBuilder, BaseInformationRecords.CountInfo::getReadMappingQualityForwardStrandList)), new DensityMapper("readMappingQuality.reverse", 10, sbiProperties, baseInformationOrBuilder -> TraversalHelper.forNSampleCounts(sampleIndices, baseInformationOrBuilder, BaseInformationRecords.CountInfo::getReadMappingQualityReverseStrandList)), new DensityMapper("baseQuality.forward", 10, sbiProperties, baseInformationOrBuilder -> TraversalHelper.forNSampleCounts(sampleIndices, baseInformationOrBuilder, BaseInformationRecords.CountInfo::getQualityScoresForwardStrandList)), new DensityMapper("baseQuality.reverse", 10, sbiProperties, baseInformationOrBuilder -> TraversalHelper.forNSampleCounts(sampleIndices, baseInformationOrBuilder, BaseInformationRecords.CountInfo::getQualityScoresReverseStrandList)), new DensityMapper("insertSizes", 10, sbiProperties, (BaseInformationRecords.BaseInformationOrBuilder baseInformationOrBuilder) -> { return TraversalHelper.forNSampleCounts(sampleIndices, baseInformationOrBuilder, BaseInformationRecords.CountInfo::getInsertSizesList); },
new NamingConcatFeatureMapper<BaseInformationRecords.BaseInformationOrBuilder>(readIndexMappers)), new GenomicContextMapper(sbiProperties), 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)) ));
new FractionDifferences4(), new MagnitudeFeatures2(), new DensityMapper("numVariationsInRead", 20, 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 DensityMapper("insertSizes", 10, sbiProperties, (BaseInformationRecords.BaseInformationOrBuilder baseInformationOrBuilder) -> { return TraversalHelper.forAllSampleCounts(baseInformationOrBuilder, BaseInformationRecords.CountInfo::getInsertSizesList); },
new NamingConcatFeatureMapper<BaseInformationRecords.BaseInformationOrBuilder>(readIndexMappers)), new GenomicContextMapper(sbiProperties), 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))
new NamingConcatFeatureMapper<BaseInformationRecords.BaseInformationOrBuilder>(firstBaseMappers), new DensityMapper("numVariationsInRead", 10, sbiProperties, record -> TraversalHelper.forAllSampleCounts(record, BaseInformationRecords.CountInfoOrBuilder::getNumVariationsInReadsList)), new DensityMapper("readMappingQuality.forward", 10, sbiProperties, baseInformationOrBuilder -> TraversalHelper.forNSampleCounts(sampleIndices, baseInformationOrBuilder, BaseInformationRecords.CountInfo::getReadMappingQualityForwardStrandList)), new DensityMapper("readMappingQuality.reverse", 10, sbiProperties, baseInformationOrBuilder -> TraversalHelper.forNSampleCounts(sampleIndices, baseInformationOrBuilder, BaseInformationRecords.CountInfo::getReadMappingQualityReverseStrandList)), new DensityMapper("baseQuality.forward", 10, sbiProperties, baseInformationOrBuilder -> TraversalHelper.forNSampleCounts(sampleIndices, baseInformationOrBuilder, BaseInformationRecords.CountInfo::getQualityScoresForwardStrandList)), new DensityMapper("baseQuality.reverse", 10, sbiProperties, baseInformationOrBuilder -> TraversalHelper.forNSampleCounts(sampleIndices, baseInformationOrBuilder, BaseInformationRecords.CountInfo::getQualityScoresReverseStrandList)), new DensityMapper("insertSizes", 10, sbiProperties, (BaseInformationRecords.BaseInformationOrBuilder baseInformationOrBuilder) -> { return TraversalHelper.forNSampleCounts(sampleIndices, baseInformationOrBuilder, BaseInformationRecords.CountInfo::getInsertSizesList); },
new FractionDifferences4(), new MagnitudeFeatures2(), new DensityMapper("numVariationsInRead", 20, 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 DensityMapper("insertSizes", 10, sbiProperties, (BaseInformationRecords.BaseInformationOrBuilder baseInformationOrBuilder) -> { return TraversalHelper.forAllSampleCounts(baseInformationOrBuilder, BaseInformationRecords.CountInfo::getInsertSizesList); },
new FractionDifferences4(), new MagnitudeFeatures2(), new DensityMapper("numVariationsInRead", 20, 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 DensityMapper("insertSizes", 10, sbiProperties, (BaseInformationRecords.BaseInformationOrBuilder baseInformationOrBuilder) -> { return TraversalHelper.forAllSampleCounts(baseInformationOrBuilder, BaseInformationRecords.CountInfo::getInsertSizesList); },
new FractionDifferences4Trio(1), new MagnitudeFeatures2Trio(), new DensityMapper("numVariationsInRead", 20, 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 DensityMapper("insertSizes", 10, sbiProperties, (BaseInformationRecords.BaseInformationOrBuilder baseInformationOrBuilder) -> { return TraversalHelper.forAllSampleCounts(baseInformationOrBuilder, BaseInformationRecords.CountInfo::getInsertSizesList); },
new NamingConcatFeatureMapper<BaseInformationRecords.BaseInformationOrBuilder>(readIndexMappers)), new GenomicContextMapper(sbiProperties), 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))
new NamingConcatFeatureMapper<BaseInformationRecords.BaseInformationOrBuilder>(readIndexMappers)), new GenomicContextMapper(sbiProperties), 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)) ));
new NamingConcatFeatureMapper<BaseInformationRecords.BaseInformationOrBuilder>(readIndexMappers)), new GenomicContextMapper(sbiProperties), 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)) ));
new FractionDifferences4(), new MagnitudeFeatures2(), new DensityMapper("numVariationsInRead", 20, 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 FractionDifferences4(), new MagnitudeFeatures2(), new DensityMapper("numVariationsInRead", 20, 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 NamingConcatFeatureMapper<BaseInformationRecords.BaseInformationOrBuilder>(readIndexMappers)), new GenomicContextMapper(sbiProperties), 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))
firstBaseMappers[i] = new GenomicContextMapper(1, record -> record.getSamples(this.sampleIndex).getCounts(constantGenotypeIndex).getToSequence().substring(0, 1)); numVariationsInReadMappers[i] = new DensityMapper("numVariationsInRead", 40, sbiProperties, baseInformationOrBuilder -> TraversalHelper.forOneSampleGenotype(sampleIndex, constantGenotypeIndex, baseInformationOrBuilder, BaseInformationRecords.CountInfo::getNumVariationsInReadsList)); readMappingQualityMappers[i] = new DensityMapper("readMappingQuality.forward", 10, sbiProperties, baseInformationOrBuilder -> TraversalHelper.forOneSampleGenotype(sampleIndex, constantGenotypeIndex, baseInformationOrBuilder, BaseInformationRecords.CountInfo::getReadMappingQualityForwardStrandList)); baseQualityMappers[i] = new DensityMapper("baseQuality.forward", 10, sbiProperties, baseInformationOrBuilder -> readIndexMappers[i] = (new SingleReadIndexCountMapper(sampleIndex, genotypeIndex, false)); readMappingQualityMappers[i] = new DensityMapper("readMappingQuality.reverse", 10, sbiProperties, baseInformationOrBuilder -> TraversalHelper.forOneSampleGenotype(sampleIndex, constantGenotypeIndex, baseInformationOrBuilder, BaseInformationRecords.CountInfo::getReadMappingQualityReverseStrandList)); baseQualityMappers[i] = new DensityMapper("baseQuality.reverse", 10, sbiProperties, baseInformationOrBuilder ->
firstBaseMappers[i] = new GenomicContextMapper(1, record -> record.getSamples(this.sampleIndex).getCounts(constantGenotypeIndex).getToSequence().substring(0, 1)); numVariationsInReadMappers[i] = new DensityMapper("numVariationsInRead", 20, sbiProperties, baseInformationOrBuilder -> TraversalHelper.forOneSampleGenotype(sampleIndex, constantGenotypeIndex, baseInformationOrBuilder, BaseInformationRecords.CountInfo::getNumVariationsInReadsList)); readMappingQualityMappers[i] = new DensityMapper("readMappingQuality.forward", 10, sbiProperties, baseInformationOrBuilder -> TraversalHelper.forOneSampleGenotype(sampleIndex, constantGenotypeIndex, baseInformationOrBuilder, BaseInformationRecords.CountInfo::getReadMappingQualityForwardStrandList)); baseQualityMappers[i] = new DensityMapper("baseQuality.forward", 10, sbiProperties, baseInformationOrBuilder -> readIndexMappers[i] = (new SingleReadIndexCountMapper(sampleIndex, genotypeIndex, false)); readMappingQualityMappers[i] = new DensityMapper("readMappingQuality.reverse", 10, sbiProperties, baseInformationOrBuilder -> TraversalHelper.forOneSampleGenotype(sampleIndex, constantGenotypeIndex, baseInformationOrBuilder, BaseInformationRecords.CountInfo::getReadMappingQualityReverseStrandList)); baseQualityMappers[i] = new DensityMapper("baseQuality.reverse", 10, sbiProperties, baseInformationOrBuilder ->
queryPositions[i] = new DensityMapper("queryPosition", 10, sbiProperties, baseInformationOrBuilder -> BaseInformationRecords.CountInfo::getDistancesToReadVariationsForwardStrandList, BaseInformationRecords.CountInfo::getDistancesToReadVariationsReverseStrandList)); targetAlignedLengthMappers[i] = new DensityMapper("targetAlignedLength", 10, sbiProperties, baseInformationOrBuilder -> TraversalHelper.forOneSampleGenotype(sampleIndex, constantGenotypeIndex, baseInformationOrBuilder, BaseInformationRecords.CountInfo::getTargetAlignedLengthsList)); queryAlignedLengthMappers[i] = new DensityMapper("queryAlignedLength", 10, sbiProperties, baseInformationOrBuilder ->
queryPositions[i] = new DensityMapper("queryPosition", 10, sbiProperties, baseInformationOrBuilder -> BaseInformationRecords.CountInfo::getDistancesToReadVariationsForwardStrandList, BaseInformationRecords.CountInfo::getDistancesToReadVariationsReverseStrandList)); targetAlignedLengthMappers[i] = new DensityMapper("targetAlignedLength", 10, sbiProperties, baseInformationOrBuilder -> TraversalHelper.forOneSampleGenotype(sampleIndex, constantGenotypeIndex, baseInformationOrBuilder, BaseInformationRecords.CountInfo::getTargetAlignedLengthsList)); queryAlignedLengthMappers[i] = new DensityMapper("queryAlignedLength", 10, sbiProperties, baseInformationOrBuilder ->