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edu.berkeley.cs.amplab.adam : adam-core

Maven & Gradle

Mar 28, 2014
2 usages
912 stars

ADAM: Core

Table Of Contents

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Download edu.berkeley.cs.amplab.adam : adam-core JAR file - Latest Versions:

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0.7.x

View Java Class Source Code in JAR file

  1. Download JD-GUI to open JAR file and explore Java source code file (.class .java)
  2. Click menu "File → Open File..." or just drag-and-drop the JAR file in the JD-GUI window adam-core-0.7.2.jar file.
    Once you open a JAR file, all the java classes in the JAR file will be displayed.

edu.berkeley.cs.amplab.adam.predicates

├─ edu.berkeley.cs.amplab.adam.predicates.GenotypeVarFilterPASSPredicate.class - [JAR]

├─ edu.berkeley.cs.amplab.adam.predicates.LocusPredicate.class - [JAR]

edu.berkeley.cs.amplab.adam.metrics

├─ edu.berkeley.cs.amplab.adam.metrics.BaseQualityScores.class - [JAR]

├─ edu.berkeley.cs.amplab.adam.metrics.BooleanComparisons.class - [JAR]

├─ edu.berkeley.cs.amplab.adam.metrics.BucketComparisons.class - [JAR]

├─ edu.berkeley.cs.amplab.adam.metrics.Collection.class - [JAR]

├─ edu.berkeley.cs.amplab.adam.metrics.CombinedComparisons.class - [JAR]

├─ edu.berkeley.cs.amplab.adam.metrics.DefaultComparisons.class - [JAR]

├─ edu.berkeley.cs.amplab.adam.metrics.DupeMismatch.class - [JAR]

├─ edu.berkeley.cs.amplab.adam.metrics.LongComparisons.class - [JAR]

├─ edu.berkeley.cs.amplab.adam.metrics.MapQualityScores.class - [JAR]

├─ edu.berkeley.cs.amplab.adam.metrics.MappedPosition.class - [JAR]

├─ edu.berkeley.cs.amplab.adam.metrics.OverMatched.class - [JAR]

├─ edu.berkeley.cs.amplab.adam.metrics.PointComparisons.class - [JAR]

edu.berkeley.cs.amplab.adam.converters

├─ edu.berkeley.cs.amplab.adam.converters.FastaConverter.class - [JAR]

├─ edu.berkeley.cs.amplab.adam.converters.GenotypesToVariantsConverter.class - [JAR]

├─ edu.berkeley.cs.amplab.adam.converters.SAMRecordConverter.class - [JAR]

├─ edu.berkeley.cs.amplab.adam.converters.VariantAnnotationConverter.class - [JAR]

├─ edu.berkeley.cs.amplab.adam.converters.VariantContextConverter.class - [JAR]

edu.berkeley.cs.amplab.adam.algorithms.realignmenttarget

├─ edu.berkeley.cs.amplab.adam.algorithms.realignmenttarget.GenericRange.class - [JAR]

├─ edu.berkeley.cs.amplab.adam.algorithms.realignmenttarget.IndelRange.class - [JAR]

├─ edu.berkeley.cs.amplab.adam.algorithms.realignmenttarget.IndelRangeSerializer.class - [JAR]

├─ edu.berkeley.cs.amplab.adam.algorithms.realignmenttarget.IndelRealignmentTarget.class - [JAR]

├─ edu.berkeley.cs.amplab.adam.algorithms.realignmenttarget.RangeAccumulator.class - [JAR]

├─ edu.berkeley.cs.amplab.adam.algorithms.realignmenttarget.RealignmentTargetFinder.class - [JAR]

├─ edu.berkeley.cs.amplab.adam.algorithms.realignmenttarget.SNPRange.class - [JAR]

├─ edu.berkeley.cs.amplab.adam.algorithms.realignmenttarget.SNPRangeSerializer.class - [JAR]

├─ edu.berkeley.cs.amplab.adam.algorithms.realignmenttarget.TargetOrdering.class - [JAR]

├─ edu.berkeley.cs.amplab.adam.algorithms.realignmenttarget.TreeSetSerializer.class - [JAR]

├─ edu.berkeley.cs.amplab.adam.algorithms.realignmenttarget.ZippedTargetOrdering.class - [JAR]

edu.berkeley.cs.amplab.adam.algorithms.smithwaterman

├─ edu.berkeley.cs.amplab.adam.algorithms.smithwaterman.SmithWaterman.class - [JAR]

├─ edu.berkeley.cs.amplab.adam.algorithms.smithwaterman.SmithWatermanConstantGapScoring.class - [JAR]

├─ edu.berkeley.cs.amplab.adam.algorithms.smithwaterman.SmithWatermanGapScoringFromFn.class - [JAR]

edu.berkeley.cs.amplab.adam.rdd

├─ edu.berkeley.cs.amplab.adam.rdd.AdamContext.class - [JAR]

├─ edu.berkeley.cs.amplab.adam.rdd.AdamNucleotideContigFragmentRDDFunctions.class - [JAR]

├─ edu.berkeley.cs.amplab.adam.rdd.AdamPileupRDDFunctions.class - [JAR]

├─ edu.berkeley.cs.amplab.adam.rdd.AdamRDDFunctions.class - [JAR]

├─ edu.berkeley.cs.amplab.adam.rdd.AdamRecordRDDFunctions.class - [JAR]

├─ edu.berkeley.cs.amplab.adam.rdd.AdamRodRDDFunctions.class - [JAR]

├─ edu.berkeley.cs.amplab.adam.rdd.AdamSequenceDictionaryRDDAggregator.class - [JAR]

├─ edu.berkeley.cs.amplab.adam.rdd.AdamSpecificRecordSequenceDictionaryRDDAggregator.class - [JAR]

├─ edu.berkeley.cs.amplab.adam.rdd.DuplicateMetrics.class - [JAR]

├─ edu.berkeley.cs.amplab.adam.rdd.FlagStat.class - [JAR]

├─ edu.berkeley.cs.amplab.adam.rdd.FlagStatMetrics.class - [JAR]

├─ edu.berkeley.cs.amplab.adam.rdd.GenomicRegionPartitioner.class - [JAR]

├─ edu.berkeley.cs.amplab.adam.rdd.GenotypesSummary.class - [JAR]

├─ edu.berkeley.cs.amplab.adam.rdd.GenotypesSummaryCounts.class - [JAR]

├─ edu.berkeley.cs.amplab.adam.rdd.GenotypesSummaryFormatting.class - [JAR]

├─ edu.berkeley.cs.amplab.adam.rdd.MarkDuplicates.class - [JAR]

├─ edu.berkeley.cs.amplab.adam.rdd.MultiContigNonoverlappingRegions.class - [JAR]

├─ edu.berkeley.cs.amplab.adam.rdd.NonoverlappingRegions.class - [JAR]

├─ edu.berkeley.cs.amplab.adam.rdd.PileupAggregator.class - [JAR]

├─ edu.berkeley.cs.amplab.adam.rdd.Reads2PileupProcessor.class - [JAR]

├─ edu.berkeley.cs.amplab.adam.rdd.RealignIndels.class - [JAR]

├─ edu.berkeley.cs.amplab.adam.rdd.RegionJoin.class - [JAR]

edu.berkeley.cs.amplab.adam.projections

├─ edu.berkeley.cs.amplab.adam.projections.ADAMDatabaseVariantAnnotationField.class - [JAR]

├─ edu.berkeley.cs.amplab.adam.projections.ADAMNucleotideContigFragmentField.class - [JAR]

├─ edu.berkeley.cs.amplab.adam.projections.ADAMRecordField.class - [JAR]

├─ edu.berkeley.cs.amplab.adam.projections.ADAMVariantField.class - [JAR]

├─ edu.berkeley.cs.amplab.adam.projections.FieldEnumeration.class - [JAR]

├─ edu.berkeley.cs.amplab.adam.projections.FieldValue.class - [JAR]

├─ edu.berkeley.cs.amplab.adam.projections.Filter.class - [JAR]

├─ edu.berkeley.cs.amplab.adam.projections.Projection.class - [JAR]

├─ edu.berkeley.cs.amplab.adam.projections.VariantCallingAnnotationsField.class - [JAR]

edu.berkeley.cs.amplab.adam.projections.variation

├─ edu.berkeley.cs.amplab.adam.projections.variation.ADAMGenotypeField.class - [JAR]

edu.berkeley.cs.amplab.adam.io

├─ edu.berkeley.cs.amplab.adam.io.InterleavedFastqInputFormat.class - [JAR]

edu.berkeley.cs.amplab.adam.core.util

├─ edu.berkeley.cs.amplab.adam.core.util.BuildInformation.class - [JAR]

edu.berkeley.cs.amplab.adam.rdd.recalibration

├─ edu.berkeley.cs.amplab.adam.rdd.recalibration.AbstractCovariate.class - [JAR]

├─ edu.berkeley.cs.amplab.adam.rdd.recalibration.Aggregate.class - [JAR]

├─ edu.berkeley.cs.amplab.adam.rdd.recalibration.BaseQualityRecalibration.class - [JAR]

├─ edu.berkeley.cs.amplab.adam.rdd.recalibration.Covariate.class - [JAR]

├─ edu.berkeley.cs.amplab.adam.rdd.recalibration.CovariateKey.class - [JAR]

├─ edu.berkeley.cs.amplab.adam.rdd.recalibration.CovariateSpace.class - [JAR]

├─ edu.berkeley.cs.amplab.adam.rdd.recalibration.DinucCovariate.class - [JAR]

├─ edu.berkeley.cs.amplab.adam.rdd.recalibration.Observation.class - [JAR]

├─ edu.berkeley.cs.amplab.adam.rdd.recalibration.ObservationAccumulator.class - [JAR]

├─ edu.berkeley.cs.amplab.adam.rdd.recalibration.ObservationTable.class - [JAR]

├─ edu.berkeley.cs.amplab.adam.rdd.recalibration.RecalibrationTable.class - [JAR]

├─ edu.berkeley.cs.amplab.adam.rdd.recalibration.Recalibrator.class - [JAR]

edu.berkeley.cs.amplab.adam.serialization

├─ edu.berkeley.cs.amplab.adam.serialization.AdamKryoProperties.class - [JAR]

├─ edu.berkeley.cs.amplab.adam.serialization.AdamKryoRegistrator.class - [JAR]

├─ edu.berkeley.cs.amplab.adam.serialization.AvroSerializer.class - [JAR]

├─ edu.berkeley.cs.amplab.adam.serialization.InputStreamWithDecoder.class - [JAR]

edu.berkeley.cs.amplab.adam.plugins

├─ edu.berkeley.cs.amplab.adam.plugins.AccessControl.class - [JAR]

├─ edu.berkeley.cs.amplab.adam.plugins.AdamPlugin.class - [JAR]

├─ edu.berkeley.cs.amplab.adam.plugins.EmptyAccessControl.class - [JAR]

edu.berkeley.cs.amplab.adam.metrics.filters

├─ edu.berkeley.cs.amplab.adam.metrics.filters.CombinedFilter.class - [JAR]

├─ edu.berkeley.cs.amplab.adam.metrics.filters.ComparisonsFilter.class - [JAR]

├─ edu.berkeley.cs.amplab.adam.metrics.filters.GeneratorFilter.class - [JAR]

edu.berkeley.cs.amplab.adam.metrics.aggregators

├─ edu.berkeley.cs.amplab.adam.metrics.aggregators.Aggregated.class - [JAR]

├─ edu.berkeley.cs.amplab.adam.metrics.aggregators.AggregatedCollection.class - [JAR]

├─ edu.berkeley.cs.amplab.adam.metrics.aggregators.Aggregator.class - [JAR]

├─ edu.berkeley.cs.amplab.adam.metrics.aggregators.CombinedAggregator.class - [JAR]

├─ edu.berkeley.cs.amplab.adam.metrics.aggregators.HistogramAggregator.class - [JAR]

├─ edu.berkeley.cs.amplab.adam.metrics.aggregators.UniqueAggregator.class - [JAR]

├─ edu.berkeley.cs.amplab.adam.metrics.aggregators.UniqueWritable.class - [JAR]

├─ edu.berkeley.cs.amplab.adam.metrics.aggregators.Writable.class - [JAR]

edu.berkeley.cs.amplab.adam.rich

├─ edu.berkeley.cs.amplab.adam.rich.DecadentRead.class - [JAR]

├─ edu.berkeley.cs.amplab.adam.rich.IlluminaOptics.class - [JAR]

├─ edu.berkeley.cs.amplab.adam.rich.ReferenceLocation.class - [JAR]

├─ edu.berkeley.cs.amplab.adam.rich.ReferenceMappingContext.class - [JAR]

├─ edu.berkeley.cs.amplab.adam.rich.RichADAMGenotype.class - [JAR]

├─ edu.berkeley.cs.amplab.adam.rich.RichADAMRecord.class - [JAR]

├─ edu.berkeley.cs.amplab.adam.rich.RichADAMVariant.class - [JAR]

├─ edu.berkeley.cs.amplab.adam.rich.RichCigar.class - [JAR]

├─ edu.berkeley.cs.amplab.adam.rich.RichRDDReferenceRecords.class - [JAR]

edu.berkeley.cs.amplab.adam.rdd.variation

├─ edu.berkeley.cs.amplab.adam.rdd.variation.ADAMGenotypeRDDFunctions.class - [JAR]

├─ edu.berkeley.cs.amplab.adam.rdd.variation.ADAMVCFOutputFormat.class - [JAR]

├─ edu.berkeley.cs.amplab.adam.rdd.variation.ADAMVariantContextRDDFunctions.class - [JAR]

├─ edu.berkeley.cs.amplab.adam.rdd.variation.ADAMVariationContext.class - [JAR]

├─ edu.berkeley.cs.amplab.adam.rdd.variation.ConcordanceTable.class - [JAR]

edu.berkeley.cs.amplab.adam.models

├─ edu.berkeley.cs.amplab.adam.models.ADAMRod.class - [JAR]

├─ edu.berkeley.cs.amplab.adam.models.ADAMVariantContext.class - [JAR]

├─ edu.berkeley.cs.amplab.adam.models.Attribute.class - [JAR]

├─ edu.berkeley.cs.amplab.adam.models.Consensus.class - [JAR]

├─ edu.berkeley.cs.amplab.adam.models.ReadBucket.class - [JAR]

├─ edu.berkeley.cs.amplab.adam.models.ReadBucketSerializer.class - [JAR]

├─ edu.berkeley.cs.amplab.adam.models.RecordGroupDictionary.class - [JAR]

├─ edu.berkeley.cs.amplab.adam.models.ReferenceMapping.class - [JAR]

├─ edu.berkeley.cs.amplab.adam.models.ReferencePosition.class - [JAR]

├─ edu.berkeley.cs.amplab.adam.models.ReferencePositionPair.class - [JAR]

├─ edu.berkeley.cs.amplab.adam.models.ReferencePositionPairSerializer.class - [JAR]

├─ edu.berkeley.cs.amplab.adam.models.ReferencePositionSerializer.class - [JAR]

├─ edu.berkeley.cs.amplab.adam.models.ReferencePositionWithOrientation.class - [JAR]

├─ edu.berkeley.cs.amplab.adam.models.ReferencePositionWithOrientationSerializer.class - [JAR]

├─ edu.berkeley.cs.amplab.adam.models.ReferenceRegion.class - [JAR]

├─ edu.berkeley.cs.amplab.adam.models.ReferenceRegionSerializer.class - [JAR]

├─ edu.berkeley.cs.amplab.adam.models.SequenceDictionary.class - [JAR]

├─ edu.berkeley.cs.amplab.adam.models.SequenceRecord.class - [JAR]

├─ edu.berkeley.cs.amplab.adam.models.SingleReadBucket.class - [JAR]

├─ edu.berkeley.cs.amplab.adam.models.SingleReadBucketSerializer.class - [JAR]

├─ edu.berkeley.cs.amplab.adam.models.SnpTable.class - [JAR]

├─ edu.berkeley.cs.amplab.adam.models.TagType.class - [JAR]

edu.berkeley.cs.amplab.adam.util

├─ edu.berkeley.cs.amplab.adam.util.AdamVCFOutputFormat.class - [JAR]

├─ edu.berkeley.cs.amplab.adam.util.AttributeUtils.class - [JAR]

├─ edu.berkeley.cs.amplab.adam.util.Base.class - [JAR]

├─ edu.berkeley.cs.amplab.adam.util.DeletionEvent.class - [JAR]

├─ edu.berkeley.cs.amplab.adam.util.Histogram.class - [JAR]

├─ edu.berkeley.cs.amplab.adam.util.ImplicitJavaConversions.class - [JAR]

├─ edu.berkeley.cs.amplab.adam.util.InsertionEvent.class - [JAR]

├─ edu.berkeley.cs.amplab.adam.util.IntervalListReader.class - [JAR]

├─ edu.berkeley.cs.amplab.adam.util.MapTools.class - [JAR]

├─ edu.berkeley.cs.amplab.adam.util.MatchEvent.class - [JAR]

├─ edu.berkeley.cs.amplab.adam.util.MdTag.class - [JAR]

├─ edu.berkeley.cs.amplab.adam.util.MdTagEvent.class - [JAR]

├─ edu.berkeley.cs.amplab.adam.util.MismatchEvent.class - [JAR]

├─ edu.berkeley.cs.amplab.adam.util.NormalizationUtils.class - [JAR]

├─ edu.berkeley.cs.amplab.adam.util.ParquetFileTraversable.class - [JAR]

├─ edu.berkeley.cs.amplab.adam.util.ParquetLogger.class - [JAR]

├─ edu.berkeley.cs.amplab.adam.util.PhredUtils.class - [JAR]

├─ edu.berkeley.cs.amplab.adam.util.Pileup.class - [JAR]

├─ edu.berkeley.cs.amplab.adam.util.PileupEvent.class - [JAR]

├─ edu.berkeley.cs.amplab.adam.util.PileupTraversable.class - [JAR]

├─ edu.berkeley.cs.amplab.adam.util.QualityScore.class - [JAR]

├─ edu.berkeley.cs.amplab.adam.util.RegExp.class - [JAR]

├─ edu.berkeley.cs.amplab.adam.util.Util.class - [JAR]

├─ edu.berkeley.cs.amplab.adam.util.VcfHeaderBuilder.class - [JAR]

├─ edu.berkeley.cs.amplab.adam.util.VcfHeaderUtils.class - [JAR]

├─ edu.berkeley.cs.amplab.adam.util.VcfStringUtils.class - [JAR]

edu.berkeley.cs.amplab.adam.rdd.comparisons

├─ edu.berkeley.cs.amplab.adam.rdd.comparisons.ComparisonTraversalEngine.class - [JAR]

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