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    Download biodata-tools JAR 3.2.2 with all dependencies


    Files of the artifact biodata-tools version 3.2.2 from the group org.opencb.biodata.

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    Artifact biodata-tools
    Group org.opencb.biodata
    Version 3.2.2
    Last update 08. October 2024
    Tags: file formats entities typically equivalents bioinformatics biological their used different
    Organization not specified
    URL http://maven.apache.org
    License not specified
    Dependencies amount 7
    Dependencies biodata-formats, biodata-models, commons-lib, datastore-core, jackson-databind, guava, junit,
    There are maybe transitive dependencies!
    There is a newer version: 3.3.0
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    Source code of biodata-tools version 3.2.2

    META-INF
    META-INF.META-INF.MANIFEST.MF
    META-INF.maven.org.opencb.biodata.biodata-tools
    META-INF.maven.org.opencb.biodata.biodata-tools.META-INF.maven.org.opencb.biodata.biodata-tools.pom.properties
    META-INF.maven.org.opencb.biodata.biodata-tools.META-INF.maven.org.opencb.biodata.biodata-tools.pom.xml
    org.opencb.biodata.tools.alignment
    org.opencb.biodata.tools.alignment.org.opencb.biodata.tools.alignment.AlignmentOptions
    org.opencb.biodata.tools.alignment.org.opencb.biodata.tools.alignment.BamManager
    org.opencb.biodata.tools.alignment.org.opencb.biodata.tools.alignment.BamUtils
    org.opencb.biodata.tools.alignment.converters
    org.opencb.biodata.tools.alignment.converters.org.opencb.biodata.tools.alignment.converters.AlignmentBiConverter
    org.opencb.biodata.tools.alignment.converters.org.opencb.biodata.tools.alignment.converters.SAMRecordToAvroReadAlignmentBiConverter
    org.opencb.biodata.tools.alignment.converters.org.opencb.biodata.tools.alignment.converters.SAMRecordToProtoReadAlignmentBiConverter
    org.opencb.biodata.tools.alignment.coverage
    org.opencb.biodata.tools.alignment.coverage.org.opencb.biodata.tools.alignment.coverage.AvroRegionCoverageCalculator
    org.opencb.biodata.tools.alignment.coverage.org.opencb.biodata.tools.alignment.coverage.RegionCoverageCalculator
    org.opencb.biodata.tools.alignment.coverage.org.opencb.biodata.tools.alignment.coverage.SamRecordRegionCoverageCalculator
    org.opencb.biodata.tools.alignment.exceptions
    org.opencb.biodata.tools.alignment.exceptions.org.opencb.biodata.tools.alignment.exceptions.AlignmentCoverageException
    org.opencb.biodata.tools.alignment.filters
    org.opencb.biodata.tools.alignment.filters.org.opencb.biodata.tools.alignment.filters.AlignmentFilters
    org.opencb.biodata.tools.alignment.filters.org.opencb.biodata.tools.alignment.filters.ReadAlignmentFilters
    org.opencb.biodata.tools.alignment.filters.org.opencb.biodata.tools.alignment.filters.SamRecordFilters
    org.opencb.biodata.tools.alignment.iterators
    org.opencb.biodata.tools.alignment.iterators.org.opencb.biodata.tools.alignment.iterators.AvroFileIterator
    org.opencb.biodata.tools.alignment.iterators.org.opencb.biodata.tools.alignment.iterators.BamIterator
    org.opencb.biodata.tools.alignment.iterators.org.opencb.biodata.tools.alignment.iterators.SAMRecordToAvroReadAlignmentBamIterator
    org.opencb.biodata.tools.alignment.iterators.org.opencb.biodata.tools.alignment.iterators.SAMRecordToProtoReadAlignmentBamIterator
    org.opencb.biodata.tools.alignment.iterators.org.opencb.biodata.tools.alignment.iterators.SamRecordBamIterator
    org.opencb.biodata.tools.alignment.stats
    org.opencb.biodata.tools.alignment.stats.org.opencb.biodata.tools.alignment.stats.AlignmentGlobalStats
    org.opencb.biodata.tools.alignment.stats.org.opencb.biodata.tools.alignment.stats.AlignmentGlobalStatsCalculator
    org.opencb.biodata.tools.alignment.stats.org.opencb.biodata.tools.alignment.stats.AvroAlignmentGlobalStatsCalculator
    org.opencb.biodata.tools.alignment.stats.org.opencb.biodata.tools.alignment.stats.ProtoAlignmentGlobalStatsCalculator
    org.opencb.biodata.tools.alignment.stats.org.opencb.biodata.tools.alignment.stats.SamRecordAlignmentGlobalStatsCalculator
    org.opencb.biodata.tools.alignment.stats.org.opencb.biodata.tools.alignment.stats.SequenceInfo
    org.opencb.biodata.tools.alignment.stats.org.opencb.biodata.tools.alignment.stats.SequenceKmers
    org.opencb.biodata.tools.alignment.stats.org.opencb.biodata.tools.alignment.stats.SequenceKmersCalculator
    org.opencb.biodata.tools.alignment.stats.org.opencb.biodata.tools.alignment.stats.SequenceStats
    org.opencb.biodata.tools.alignment.stats.org.opencb.biodata.tools.alignment.stats.SequenceStatsCalculator
    org.opencb.biodata.tools.clinical
    org.opencb.biodata.tools.clinical.org.opencb.biodata.tools.clinical.ClinicalVariantCreator
    org.opencb.biodata.tools.clinical.org.opencb.biodata.tools.clinical.DefaultClinicalVariantCreator
    org.opencb.biodata.tools.clinical.org.opencb.biodata.tools.clinical.DiseasePanelParsers
    org.opencb.biodata.tools.clinical.org.opencb.biodata.tools.clinical.TeamClinicalVariantCreator
    org.opencb.biodata.tools.clinical.org.opencb.biodata.tools.clinical.TieringClinicalVariantCreator
    org.opencb.biodata.tools.commons
    org.opencb.biodata.tools.commons.org.opencb.biodata.tools.commons.BiConverter
    org.opencb.biodata.tools.commons.org.opencb.biodata.tools.commons.ChunkFrequencyManager
    org.opencb.biodata.tools.commons.org.opencb.biodata.tools.commons.CommonsFilters
    org.opencb.biodata.tools.commons.org.opencb.biodata.tools.commons.Converter
    org.opencb.biodata.tools.feature
    org.opencb.biodata.tools.feature.org.opencb.biodata.tools.feature.BedManager
    org.opencb.biodata.tools.feature.org.opencb.biodata.tools.feature.BigWigManager
    org.opencb.biodata.tools.feature.org.opencb.biodata.tools.feature.FeatureManager
    org.opencb.biodata.tools.feature.org.opencb.biodata.tools.feature.WigUtils
    org.opencb.biodata.tools.pedigree
    org.opencb.biodata.tools.pedigree.org.opencb.biodata.tools.pedigree.MendelianError
    org.opencb.biodata.tools.pedigree.org.opencb.biodata.tools.pedigree.ModeOfInheritance
    org.opencb.biodata.tools.sequence
    org.opencb.biodata.tools.sequence.org.opencb.biodata.tools.sequence.FastaIndex
    org.opencb.biodata.tools.sequence.org.opencb.biodata.tools.sequence.FastaIndexManager
    org.opencb.biodata.tools.sequence.org.opencb.biodata.tools.sequence.FastqRecordToReadBiConverter
    org.opencb.biodata.tools.sequence.org.opencb.biodata.tools.sequence.SamtoolsFastaIndex
    org.opencb.biodata.tools.sequence.org.opencb.biodata.tools.sequence.SequenceAdaptor
    org.opencb.biodata.tools.variant
    org.opencb.biodata.tools.variant.org.opencb.biodata.tools.variant.LeftAligner
    org.opencb.biodata.tools.variant.org.opencb.biodata.tools.variant.VariantDeduplicationTask
    org.opencb.biodata.tools.variant.org.opencb.biodata.tools.variant.VariantJsonReader
    org.opencb.biodata.tools.variant.org.opencb.biodata.tools.variant.VariantNormalizer
    org.opencb.biodata.tools.variant.org.opencb.biodata.tools.variant.VariantOptions
    org.opencb.biodata.tools.variant.org.opencb.biodata.tools.variant.VariantReferenceBlockCreatorTask
    org.opencb.biodata.tools.variant.org.opencb.biodata.tools.variant.VariantSorterTask
    org.opencb.biodata.tools.variant.org.opencb.biodata.tools.variant.VariantVcfHtsjdkReader
    org.opencb.biodata.tools.variant.org.opencb.biodata.tools.variant.VcfFileReader
    org.opencb.biodata.tools.variant.org.opencb.biodata.tools.variant.VcfManager
    org.opencb.biodata.tools.variant.org.opencb.biodata.tools.variant.VcfUtils
    org.opencb.biodata.tools.variant.algorithm
    org.opencb.biodata.tools.variant.algorithm.org.opencb.biodata.tools.variant.algorithm.IdentityByDescentClustering
    org.opencb.biodata.tools.variant.algorithm.org.opencb.biodata.tools.variant.algorithm.IdentityByStateClustering
    org.opencb.biodata.tools.variant.converters
    org.opencb.biodata.tools.variant.converters.org.opencb.biodata.tools.variant.converters.VCFExporter
    org.opencb.biodata.tools.variant.converters.org.opencb.biodata.tools.variant.converters.VariantContextConverter
    org.opencb.biodata.tools.variant.converters.avro
    org.opencb.biodata.tools.variant.converters.avro.org.opencb.biodata.tools.variant.converters.avro.VCFHeaderToAvroVcfHeaderConverter
    org.opencb.biodata.tools.variant.converters.avro.org.opencb.biodata.tools.variant.converters.avro.VCFHeaderToVariantFileHeaderConverter
    org.opencb.biodata.tools.variant.converters.avro.org.opencb.biodata.tools.variant.converters.avro.VCFHeaderToVariantFileMetadataConverter
    org.opencb.biodata.tools.variant.converters.avro.org.opencb.biodata.tools.variant.converters.avro.VariantAvroToVariantContextConverter
    org.opencb.biodata.tools.variant.converters.avro.org.opencb.biodata.tools.variant.converters.avro.VariantContextToVariantConverter
    org.opencb.biodata.tools.variant.converters.avro.org.opencb.biodata.tools.variant.converters.avro.VariantFileHeaderToVCFHeaderConverter
    org.opencb.biodata.tools.variant.converters.avro.org.opencb.biodata.tools.variant.converters.avro.VariantSourceToVCFHeaderConverter
    org.opencb.biodata.tools.variant.converters.avro.org.opencb.biodata.tools.variant.converters.avro.VariantStatsToPopulationFrequencyConverter
    org.opencb.biodata.tools.variant.converters.avro.org.opencb.biodata.tools.variant.converters.avro.VariantStatsToTsvConverter
    org.opencb.biodata.tools.variant.converters.avro.org.opencb.biodata.tools.variant.converters.avro.VariantStudyMetadataToVCFHeaderConverter
    org.opencb.biodata.tools.variant.converters.ga4gh
    org.opencb.biodata.tools.variant.converters.ga4gh.org.opencb.biodata.tools.variant.converters.ga4gh.Ga4ghCallSetConverter
    org.opencb.biodata.tools.variant.converters.ga4gh.org.opencb.biodata.tools.variant.converters.ga4gh.Ga4ghVariantConverter
    org.opencb.biodata.tools.variant.converters.ga4gh.org.opencb.biodata.tools.variant.converters.ga4gh.Ga4ghVariantSetConverter
    org.opencb.biodata.tools.variant.converters.ga4gh.factories
    org.opencb.biodata.tools.variant.converters.ga4gh.factories.org.opencb.biodata.tools.variant.converters.ga4gh.factories.AvroGa4GhVariantFactory
    org.opencb.biodata.tools.variant.converters.ga4gh.factories.org.opencb.biodata.tools.variant.converters.ga4gh.factories.Ga4ghVariantFactory
    org.opencb.biodata.tools.variant.converters.ga4gh.factories.org.opencb.biodata.tools.variant.converters.ga4gh.factories.ProtoGa4GhVariantFactory
    org.opencb.biodata.tools.variant.converters.proto
    org.opencb.biodata.tools.variant.converters.proto.org.opencb.biodata.tools.variant.converters.proto.VariantAvroToVariantProtoConverter
    org.opencb.biodata.tools.variant.converters.proto.org.opencb.biodata.tools.variant.converters.proto.VariantContextToVariantProtoConverter
    org.opencb.biodata.tools.variant.converters.proto.org.opencb.biodata.tools.variant.converters.proto.VariantProtoToVariantContextConverter
    org.opencb.biodata.tools.variant.converters.proto.org.opencb.biodata.tools.variant.converters.proto.VariantToProtoVcfRecord
    org.opencb.biodata.tools.variant.converters.proto.org.opencb.biodata.tools.variant.converters.proto.VariantToVcfSliceConverter
    org.opencb.biodata.tools.variant.converters.proto.org.opencb.biodata.tools.variant.converters.proto.VcfRecordProtoToVariantConverter
    org.opencb.biodata.tools.variant.converters.proto.org.opencb.biodata.tools.variant.converters.proto.VcfSliceToVariantListConverter
    org.opencb.biodata.tools.variant.exceptions
    org.opencb.biodata.tools.variant.exceptions.org.opencb.biodata.tools.variant.exceptions.VariantNormalizerException
    org.opencb.biodata.tools.variant.filters
    org.opencb.biodata.tools.variant.filters.org.opencb.biodata.tools.variant.filters.VariantAvroFilters
    org.opencb.biodata.tools.variant.filters.org.opencb.biodata.tools.variant.filters.VariantContextFilters
    org.opencb.biodata.tools.variant.filters.org.opencb.biodata.tools.variant.filters.VariantFilters
    org.opencb.biodata.tools.variant.filters.org.opencb.biodata.tools.variant.filters.VariantProtoFilters
    org.opencb.biodata.tools.variant.iterators
    org.opencb.biodata.tools.variant.iterators.org.opencb.biodata.tools.variant.iterators.VariantContextToAvroVariantVcfIterator
    org.opencb.biodata.tools.variant.iterators.org.opencb.biodata.tools.variant.iterators.VariantContextToProtoVariantVcfIterator
    org.opencb.biodata.tools.variant.iterators.org.opencb.biodata.tools.variant.iterators.VariantContextVcfIterator
    org.opencb.biodata.tools.variant.iterators.org.opencb.biodata.tools.variant.iterators.VcfIterator
    org.opencb.biodata.tools.variant.merge
    org.opencb.biodata.tools.variant.merge.org.opencb.biodata.tools.variant.merge.VariantAlternateRearranger
    org.opencb.biodata.tools.variant.merge.org.opencb.biodata.tools.variant.merge.VariantMerger
    org.opencb.biodata.tools.variant.metadata
    org.opencb.biodata.tools.variant.metadata.org.opencb.biodata.tools.variant.metadata.VariantMetadataManager
    org.opencb.biodata.tools.variant.metadata.org.opencb.biodata.tools.variant.metadata.VariantMetadataUtils
    org.opencb.biodata.tools.variant.normalizer.extensions
    org.opencb.biodata.tools.variant.normalizer.extensions.org.opencb.biodata.tools.variant.normalizer.extensions.CustomNormalizerExtension
    org.opencb.biodata.tools.variant.normalizer.extensions.org.opencb.biodata.tools.variant.normalizer.extensions.SvVariantNormalizerExtension
    org.opencb.biodata.tools.variant.normalizer.extensions.org.opencb.biodata.tools.variant.normalizer.extensions.VafVariantNormalizerExtension
    org.opencb.biodata.tools.variant.normalizer.extensions.org.opencb.biodata.tools.variant.normalizer.extensions.VariantNormalizerExtension
    org.opencb.biodata.tools.variant.normalizer.extensions.org.opencb.biodata.tools.variant.normalizer.extensions.VariantNormalizerExtensionFactory
    org.opencb.biodata.tools.variant.normalizer.extensions.org.opencb.biodata.tools.variant.normalizer.extensions.VariantNormalizerExtensionFileToSample
    org.opencb.biodata.tools.variant.scores
    org.opencb.biodata.tools.variant.scores.org.opencb.biodata.tools.variant.scores.AcmgVariantClassifier
    org.opencb.biodata.tools.variant.scores.org.opencb.biodata.tools.variant.scores.HardyWeinbergScoreCalculatorTask
    org.opencb.biodata.tools.variant.simulator
    org.opencb.biodata.tools.variant.simulator.org.opencb.biodata.tools.variant.simulator.VariantSimulator
    org.opencb.biodata.tools.variant.simulator.org.opencb.biodata.tools.variant.simulator.VariantSimulatorConfiguration
    org.opencb.biodata.tools.variant.stats
    org.opencb.biodata.tools.variant.stats.org.opencb.biodata.tools.variant.stats.AggregationUtils
    org.opencb.biodata.tools.variant.stats.org.opencb.biodata.tools.variant.stats.SampleVariantStatsCalculator
    org.opencb.biodata.tools.variant.stats.org.opencb.biodata.tools.variant.stats.VariantAggregatedEVSStatsCalculator
    org.opencb.biodata.tools.variant.stats.org.opencb.biodata.tools.variant.stats.VariantAggregatedExacStatsCalculator
    org.opencb.biodata.tools.variant.stats.org.opencb.biodata.tools.variant.stats.VariantAggregatedStatsCalculator
    org.opencb.biodata.tools.variant.stats.org.opencb.biodata.tools.variant.stats.VariantSetStatsCalculator
    org.opencb.biodata.tools.variant.stats.org.opencb.biodata.tools.variant.stats.VariantStatsCalculator
    org.opencb.biodata.tools.variant.stats.org.opencb.biodata.tools.variant.stats.VariantStatsPedigree
    org.opencb.biodata.tools.variant.stats.writer
    org.opencb.biodata.tools.variant.stats.writer.org.opencb.biodata.tools.variant.stats.writer.VariantStatsPopulationFrequencyExporter
    org.opencb.biodata.tools.variant.stats.writer.org.opencb.biodata.tools.variant.stats.writer.VariantStatsTsvExporter
    org.opencb.biodata.tools.variant.writers
    org.opencb.biodata.tools.variant.writers.org.opencb.biodata.tools.variant.writers.EnsemblVepOutputWriter




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