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    Download milib JAR 2.3.0 with all dependencies


    Yet another Java library for Next Generation Sequencing (NGS) data processing.

    Files of the artifact milib version 2.3.0 from the group com.milaboratory.

    Test

    Download milib (2.3.0)
    Artifact milib
    Group com.milaboratory
    Version 2.3.0
    Last update 26. January 2023
    Organization not specified
    URL http://milaboratory.com/
    License Apache License, Version 2.0
    Dependencies amount 5
    Dependencies pipe, jackson-databind, commons-compress, commons-math3, trove4j,
    There are maybe transitive dependencies!
    The newest version!
    Show more of this group  Show more artifacts with this name
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    3 downloads

    Source code of milib version 2.3.0

    META-INF
    META-INF.META-INF.MANIFEST.MF
    com.milaboratory.app
    com.milaboratory.app.com.milaboratory.app.ApplicationException.kt
    com.milaboratory.app.com.milaboratory.app.InputFileType.kt
    com.milaboratory.app.com.milaboratory.app.ValidationException.kt
    com.milaboratory.app.com.milaboratory.app.logger.kt
    com.milaboratory.cli
    com.milaboratory.cli.com.milaboratory.cli.Action
    com.milaboratory.cli.com.milaboratory.cli.ActionHelpProvider
    com.milaboratory.cli.com.milaboratory.cli.ActionHelper
    com.milaboratory.cli.com.milaboratory.cli.ActionParameters
    com.milaboratory.cli.com.milaboratory.cli.ActionParametersParser
    com.milaboratory.cli.com.milaboratory.cli.ActionParametersWithOutput
    com.milaboratory.cli.com.milaboratory.cli.AllowNoArguments
    com.milaboratory.cli.com.milaboratory.cli.AppVersionInfo
    com.milaboratory.cli.com.milaboratory.cli.DeprecatedParameter
    com.milaboratory.cli.com.milaboratory.cli.HiddenAction
    com.milaboratory.cli.com.milaboratory.cli.JCommanderBasedMain
    com.milaboratory.cli.com.milaboratory.cli.ProcessException
    com.milaboratory.core
    com.milaboratory.core.com.milaboratory.core.PairedEndReadsLayout
    com.milaboratory.core.com.milaboratory.core.Range
    com.milaboratory.core.com.milaboratory.core.Target
    com.milaboratory.core.alignment
    com.milaboratory.core.alignment.com.milaboratory.core.alignment.AbstractAlignmentScoring
    com.milaboratory.core.alignment.com.milaboratory.core.alignment.AffineGapAlignmentScoring
    com.milaboratory.core.alignment.com.milaboratory.core.alignment.Aligner
    com.milaboratory.core.alignment.com.milaboratory.core.alignment.AlignerCustom
    com.milaboratory.core.alignment.com.milaboratory.core.alignment.Alignment
    com.milaboratory.core.alignment.com.milaboratory.core.alignment.AlignmentCache
    com.milaboratory.core.alignment.com.milaboratory.core.alignment.AlignmentElement
    com.milaboratory.core.alignment.com.milaboratory.core.alignment.AlignmentElementType
    com.milaboratory.core.alignment.com.milaboratory.core.alignment.AlignmentHelper
    com.milaboratory.core.alignment.com.milaboratory.core.alignment.AlignmentIterator
    com.milaboratory.core.alignment.com.milaboratory.core.alignment.AlignmentIteratorForward
    com.milaboratory.core.alignment.com.milaboratory.core.alignment.AlignmentIteratorReverse
    com.milaboratory.core.alignment.com.milaboratory.core.alignment.AlignmentScoring
    com.milaboratory.core.alignment.com.milaboratory.core.alignment.AlignmentTrimmer
    com.milaboratory.core.alignment.com.milaboratory.core.alignment.AlignmentUtils
    com.milaboratory.core.alignment.com.milaboratory.core.alignment.BLASTMatrix
    com.milaboratory.core.alignment.com.milaboratory.core.alignment.BandedAffineAligner
    com.milaboratory.core.alignment.com.milaboratory.core.alignment.BandedAligner
    com.milaboratory.core.alignment.com.milaboratory.core.alignment.BandedAlignerParameters
    com.milaboratory.core.alignment.com.milaboratory.core.alignment.BandedLinearAligner
    com.milaboratory.core.alignment.com.milaboratory.core.alignment.BandedMatrix
    com.milaboratory.core.alignment.com.milaboratory.core.alignment.BandedSemiLocalResult
    com.milaboratory.core.alignment.com.milaboratory.core.alignment.CachedIntArray
    com.milaboratory.core.alignment.com.milaboratory.core.alignment.IO
    com.milaboratory.core.alignment.com.milaboratory.core.alignment.LinearGapAlignmentScoring
    com.milaboratory.core.alignment.com.milaboratory.core.alignment.ScoringMatrixIO
    com.milaboratory.core.alignment.com.milaboratory.core.alignment.ScoringUtils
    com.milaboratory.core.alignment.com.milaboratory.core.alignment.SubstitutionMatrix
    com.milaboratory.core.alignment.com.milaboratory.core.alignment.UniversalSemiGlobalAlignmentResult
    com.milaboratory.core.alignment.batch
    com.milaboratory.core.alignment.batch.com.milaboratory.core.alignment.batch.AbstractBatchAligner
    com.milaboratory.core.alignment.batch.com.milaboratory.core.alignment.batch.AlignmentHit
    com.milaboratory.core.alignment.batch.com.milaboratory.core.alignment.batch.AlignmentHitImpl
    com.milaboratory.core.alignment.batch.com.milaboratory.core.alignment.batch.AlignmentResult
    com.milaboratory.core.alignment.batch.com.milaboratory.core.alignment.batch.AlignmentResultImpl
    com.milaboratory.core.alignment.batch.com.milaboratory.core.alignment.batch.BatchAligner
    com.milaboratory.core.alignment.batch.com.milaboratory.core.alignment.batch.BatchAlignerWithBase
    com.milaboratory.core.alignment.batch.com.milaboratory.core.alignment.batch.BatchAlignerWithBaseParameters
    com.milaboratory.core.alignment.batch.com.milaboratory.core.alignment.batch.BatchAlignerWithBaseWithFilter
    com.milaboratory.core.alignment.batch.com.milaboratory.core.alignment.batch.BatchAlignmentUtil
    com.milaboratory.core.alignment.batch.com.milaboratory.core.alignment.batch.HasSequence
    com.milaboratory.core.alignment.batch.com.milaboratory.core.alignment.batch.LeftmostBatchAlignerAdapter
    com.milaboratory.core.alignment.batch.com.milaboratory.core.alignment.batch.PipedAlignmentResult
    com.milaboratory.core.alignment.batch.com.milaboratory.core.alignment.batch.PipedAlignmentResultImpl
    com.milaboratory.core.alignment.batch.com.milaboratory.core.alignment.batch.PipedBatchAligner
    com.milaboratory.core.alignment.batch.com.milaboratory.core.alignment.batch.PipedBatchAlignerWithBase
    com.milaboratory.core.alignment.batch.com.milaboratory.core.alignment.batch.SequenceExtractor
    com.milaboratory.core.alignment.batch.com.milaboratory.core.alignment.batch.SimpleBatchAligner
    com.milaboratory.core.alignment.batch.com.milaboratory.core.alignment.batch.SimpleBatchAlignerParameters
    com.milaboratory.core.alignment.batch.com.milaboratory.core.alignment.batch.WithBase
    com.milaboratory.core.alignment.benchmark
    com.milaboratory.core.alignment.benchmark.com.milaboratory.core.alignment.benchmark.Benchmark
    com.milaboratory.core.alignment.benchmark.com.milaboratory.core.alignment.benchmark.BenchmarkInput
    com.milaboratory.core.alignment.benchmark.com.milaboratory.core.alignment.benchmark.BenchmarkResults
    com.milaboratory.core.alignment.benchmark.com.milaboratory.core.alignment.benchmark.Challenge
    com.milaboratory.core.alignment.benchmark.com.milaboratory.core.alignment.benchmark.ChallengeParameters
    com.milaboratory.core.alignment.benchmark.com.milaboratory.core.alignment.benchmark.ChallengeProvider
    com.milaboratory.core.alignment.benchmark.com.milaboratory.core.alignment.benchmark.KAlignerQuery
    com.milaboratory.core.alignment.blast
    com.milaboratory.core.alignment.blast.com.milaboratory.core.alignment.blast.AABlastAligner
    com.milaboratory.core.alignment.blast.com.milaboratory.core.alignment.blast.AABlastAlignerExt
    com.milaboratory.core.alignment.blast.com.milaboratory.core.alignment.blast.AABlastHit
    com.milaboratory.core.alignment.blast.com.milaboratory.core.alignment.blast.AABlastHitExt
    com.milaboratory.core.alignment.blast.com.milaboratory.core.alignment.blast.Blast
    com.milaboratory.core.alignment.blast.com.milaboratory.core.alignment.blast.BlastAligner
    com.milaboratory.core.alignment.blast.com.milaboratory.core.alignment.blast.BlastAlignerAbstract
    com.milaboratory.core.alignment.blast.com.milaboratory.core.alignment.blast.BlastAlignerExt
    com.milaboratory.core.alignment.blast.com.milaboratory.core.alignment.blast.BlastAlignerExtAbstract
    com.milaboratory.core.alignment.blast.com.milaboratory.core.alignment.blast.BlastAlignerParameters
    com.milaboratory.core.alignment.blast.com.milaboratory.core.alignment.blast.BlastDB
    com.milaboratory.core.alignment.blast.com.milaboratory.core.alignment.blast.BlastDBBuilder
    com.milaboratory.core.alignment.blast.com.milaboratory.core.alignment.blast.BlastHit
    com.milaboratory.core.alignment.blast.com.milaboratory.core.alignment.blast.BlastHitExt
    com.milaboratory.core.alignment.blast.com.milaboratory.core.alignment.blast.BlastStrand
    com.milaboratory.core.alignment.blast.com.milaboratory.core.alignment.blast.BlastTask
    com.milaboratory.core.alignment.blast.com.milaboratory.core.alignment.blast.NBlastAligner
    com.milaboratory.core.alignment.blast.com.milaboratory.core.alignment.blast.NBlastAlignerExt
    com.milaboratory.core.alignment.blast.com.milaboratory.core.alignment.blast.NBlastHit
    com.milaboratory.core.alignment.blast.com.milaboratory.core.alignment.blast.NBlastHitExt
    com.milaboratory.core.alignment.kaligner1
    com.milaboratory.core.alignment.kaligner1.com.milaboratory.core.alignment.kaligner1.AbstractKAlignerParameters
    com.milaboratory.core.alignment.kaligner1.com.milaboratory.core.alignment.kaligner1.KAligner
    com.milaboratory.core.alignment.kaligner1.com.milaboratory.core.alignment.kaligner1.KAlignerParameters
    com.milaboratory.core.alignment.kaligner1.com.milaboratory.core.alignment.kaligner1.KAlignmentHit
    com.milaboratory.core.alignment.kaligner1.com.milaboratory.core.alignment.kaligner1.KAlignmentResult
    com.milaboratory.core.alignment.kaligner1.com.milaboratory.core.alignment.kaligner1.KAlignmentResultP
    com.milaboratory.core.alignment.kaligner1.com.milaboratory.core.alignment.kaligner1.KMapper
    com.milaboratory.core.alignment.kaligner1.com.milaboratory.core.alignment.kaligner1.KMappingHit
    com.milaboratory.core.alignment.kaligner1.com.milaboratory.core.alignment.kaligner1.KMappingResult
    com.milaboratory.core.alignment.kaligner2
    com.milaboratory.core.alignment.kaligner2.com.milaboratory.core.alignment.kaligner2.KAligner2
    com.milaboratory.core.alignment.kaligner2.com.milaboratory.core.alignment.kaligner2.KAligner2Statistics
    com.milaboratory.core.alignment.kaligner2.com.milaboratory.core.alignment.kaligner2.KAlignerParameters2
    com.milaboratory.core.alignment.kaligner2.com.milaboratory.core.alignment.kaligner2.KAlignmentHit2
    com.milaboratory.core.alignment.kaligner2.com.milaboratory.core.alignment.kaligner2.KAlignmentResult2
    com.milaboratory.core.alignment.kaligner2.com.milaboratory.core.alignment.kaligner2.KMapper2
    com.milaboratory.core.alignment.kaligner2.com.milaboratory.core.alignment.kaligner2.KMappingHit2
    com.milaboratory.core.alignment.kaligner2.com.milaboratory.core.alignment.kaligner2.KMappingResult2
    com.milaboratory.core.alignment.kaligner2.com.milaboratory.core.alignment.kaligner2.OffsetPacksAccumulator
    com.milaboratory.core.clustering
    com.milaboratory.core.clustering.com.milaboratory.core.clustering.Cluster
    com.milaboratory.core.clustering.com.milaboratory.core.clustering.Clustering
    com.milaboratory.core.clustering.com.milaboratory.core.clustering.ClusteringStrategy
    com.milaboratory.core.clustering.com.milaboratory.core.clustering.SequenceExtractor
    com.milaboratory.core.io
    com.milaboratory.core.io.com.milaboratory.core.io.CompressionType
    com.milaboratory.core.io.binary
    com.milaboratory.core.io.binary.com.milaboratory.core.io.binary.AlignmentSerializer
    com.milaboratory.core.io.binary.com.milaboratory.core.io.binary.RangeSerializer
    com.milaboratory.core.io.binary.com.milaboratory.core.io.binary.package-info
    com.milaboratory.core.io.sequence
    com.milaboratory.core.io.sequence.com.milaboratory.core.io.sequence.AbstractMultiReader
    com.milaboratory.core.io.sequence.com.milaboratory.core.io.sequence.AbstractSequenceReader
    com.milaboratory.core.io.sequence.com.milaboratory.core.io.sequence.ConcatenatingSingleReader
    com.milaboratory.core.io.sequence.com.milaboratory.core.io.sequence.IO
    com.milaboratory.core.io.sequence.com.milaboratory.core.io.sequence.IllegalFileFormatException
    com.milaboratory.core.io.sequence.com.milaboratory.core.io.sequence.MultiRead
    com.milaboratory.core.io.sequence.com.milaboratory.core.io.sequence.MultiReader
    com.milaboratory.core.io.sequence.com.milaboratory.core.io.sequence.MultiSequenceWriter
    com.milaboratory.core.io.sequence.com.milaboratory.core.io.sequence.PairedRead
    com.milaboratory.core.io.sequence.com.milaboratory.core.io.sequence.PairedReader
    com.milaboratory.core.io.sequence.com.milaboratory.core.io.sequence.PairedSequenceWriter
    com.milaboratory.core.io.sequence.com.milaboratory.core.io.sequence.SequenceRead
    com.milaboratory.core.io.sequence.com.milaboratory.core.io.sequence.SequenceReadUtil
    com.milaboratory.core.io.sequence.com.milaboratory.core.io.sequence.SequenceReadWrapper
    com.milaboratory.core.io.sequence.com.milaboratory.core.io.sequence.SequenceReader
    com.milaboratory.core.io.sequence.com.milaboratory.core.io.sequence.SequenceWriter
    com.milaboratory.core.io.sequence.com.milaboratory.core.io.sequence.SingleRead
    com.milaboratory.core.io.sequence.com.milaboratory.core.io.sequence.SingleReadImpl
    com.milaboratory.core.io.sequence.com.milaboratory.core.io.sequence.SingleReadLazy
    com.milaboratory.core.io.sequence.com.milaboratory.core.io.sequence.SingleReader
    com.milaboratory.core.io.sequence.com.milaboratory.core.io.sequence.SingleSequenceWriter
    com.milaboratory.core.io.sequence.fasta
    com.milaboratory.core.io.sequence.fasta.com.milaboratory.core.io.sequence.fasta.FastaReader
    com.milaboratory.core.io.sequence.fasta.com.milaboratory.core.io.sequence.fasta.FastaRecord
    com.milaboratory.core.io.sequence.fasta.com.milaboratory.core.io.sequence.fasta.FastaSequenceReaderWrapper
    com.milaboratory.core.io.sequence.fasta.com.milaboratory.core.io.sequence.fasta.FastaSequenceWriterWrapper
    com.milaboratory.core.io.sequence.fasta.com.milaboratory.core.io.sequence.fasta.FastaWriter
    com.milaboratory.core.io.sequence.fasta.com.milaboratory.core.io.sequence.fasta.RandomAccessFastaIndex
    com.milaboratory.core.io.sequence.fasta.com.milaboratory.core.io.sequence.fasta.RandomAccessFastaReader
    com.milaboratory.core.io.sequence.fastq
    com.milaboratory.core.io.sequence.fastq.com.milaboratory.core.io.sequence.fastq.AbstractMultiFastqWriter
    com.milaboratory.core.io.sequence.fastq.com.milaboratory.core.io.sequence.fastq.FastqRecordsReader
    com.milaboratory.core.io.sequence.fastq.com.milaboratory.core.io.sequence.fastq.MultiFastqWriter
    com.milaboratory.core.io.sequence.fastq.com.milaboratory.core.io.sequence.fastq.PairedFastqReader
    com.milaboratory.core.io.sequence.fastq.com.milaboratory.core.io.sequence.fastq.PairedFastqWriter
    com.milaboratory.core.io.sequence.fastq.com.milaboratory.core.io.sequence.fastq.QualityFormat
    com.milaboratory.core.io.sequence.fastq.com.milaboratory.core.io.sequence.fastq.RandomAccessFastqReader
    com.milaboratory.core.io.sequence.fastq.com.milaboratory.core.io.sequence.fastq.RandomAccessPairedFastqReader
    com.milaboratory.core.io.sequence.fastq.com.milaboratory.core.io.sequence.fastq.SingleFastqIndexer
    com.milaboratory.core.io.sequence.fastq.com.milaboratory.core.io.sequence.fastq.SingleFastqReader
    com.milaboratory.core.io.sequence.fastq.com.milaboratory.core.io.sequence.fastq.SingleFastqWriter
    com.milaboratory.core.io.sequence.fastq.com.milaboratory.core.io.sequence.fastq.WrongQualityFormat
    com.milaboratory.core.io.util
    com.milaboratory.core.io.util.com.milaboratory.core.io.util.AbstractRandomAccessReader
    com.milaboratory.core.io.util.com.milaboratory.core.io.util.FileIndex
    com.milaboratory.core.io.util.com.milaboratory.core.io.util.FileIndexBuilder
    com.milaboratory.core.io.util.com.milaboratory.core.io.util.IOUtil
    com.milaboratory.core.merger
    com.milaboratory.core.merger.com.milaboratory.core.merger.MergerParameters
    com.milaboratory.core.merger.com.milaboratory.core.merger.MismatchOnlyPairedReadMerger
    com.milaboratory.core.merger.com.milaboratory.core.merger.PairedReadMergingResult
    com.milaboratory.core.merger.com.milaboratory.core.merger.QualityMergingAlgorithm
    com.milaboratory.core.motif
    com.milaboratory.core.motif.com.milaboratory.core.motif.BitScoreCalculator
    com.milaboratory.core.motif.com.milaboratory.core.motif.BitapData
    com.milaboratory.core.motif.com.milaboratory.core.motif.BitapMatcher
    com.milaboratory.core.motif.com.milaboratory.core.motif.BitapMatcherFilter
    com.milaboratory.core.motif.com.milaboratory.core.motif.BitapMatcherImpl
    com.milaboratory.core.motif.com.milaboratory.core.motif.BitapMatcherWithScore
    com.milaboratory.core.motif.com.milaboratory.core.motif.BitapPattern
    com.milaboratory.core.motif.com.milaboratory.core.motif.BitapStateIterator
    com.milaboratory.core.motif.com.milaboratory.core.motif.LongArrayBitHelper
    com.milaboratory.core.motif.com.milaboratory.core.motif.Motif
    com.milaboratory.core.motif.com.milaboratory.core.motif.MotifBuilder
    com.milaboratory.core.motif.com.milaboratory.core.motif.MotifUtils
    com.milaboratory.core.motif.com.milaboratory.core.motif.MotifWithExactMask
    com.milaboratory.core.mutations
    com.milaboratory.core.mutations.com.milaboratory.core.mutations.CoverageCounter
    com.milaboratory.core.mutations.com.milaboratory.core.mutations.IO
    com.milaboratory.core.mutations.com.milaboratory.core.mutations.Mutation
    com.milaboratory.core.mutations.com.milaboratory.core.mutations.MutationConsensusBuilder
    com.milaboratory.core.mutations.com.milaboratory.core.mutations.MutationType
    com.milaboratory.core.mutations.com.milaboratory.core.mutations.Mutations
    com.milaboratory.core.mutations.com.milaboratory.core.mutations.MutationsBuilder
    com.milaboratory.core.mutations.com.milaboratory.core.mutations.MutationsCounter
    com.milaboratory.core.mutations.com.milaboratory.core.mutations.MutationsEnumerator
    com.milaboratory.core.mutations.com.milaboratory.core.mutations.MutationsUtil
    com.milaboratory.core.mutations.com.milaboratory.core.mutations.SequenceWeighter
    com.milaboratory.core.mutations.generator
    com.milaboratory.core.mutations.generator.com.milaboratory.core.mutations.generator.GenericNucleotideMutationModel
    com.milaboratory.core.mutations.generator.com.milaboratory.core.mutations.generator.MutationModels
    com.milaboratory.core.mutations.generator.com.milaboratory.core.mutations.generator.MutationsGenerator
    com.milaboratory.core.mutations.generator.com.milaboratory.core.mutations.generator.NucleotideMutationModel
    com.milaboratory.core.mutations.generator.com.milaboratory.core.mutations.generator.SubstitutionModel
    com.milaboratory.core.mutations.generator.com.milaboratory.core.mutations.generator.SubstitutionModelBuilder
    com.milaboratory.core.mutations.generator.com.milaboratory.core.mutations.generator.SubstitutionModels
    com.milaboratory.core.mutations.generator.com.milaboratory.core.mutations.generator.UniformMutationsGenerator
    com.milaboratory.core.sequence
    com.milaboratory.core.sequence.com.milaboratory.core.sequence.AbstractArrayAlphabet
    com.milaboratory.core.sequence.com.milaboratory.core.sequence.AbstractArraySequence
    com.milaboratory.core.sequence.com.milaboratory.core.sequence.AbstractSeq
    com.milaboratory.core.sequence.com.milaboratory.core.sequence.Alphabet
    com.milaboratory.core.sequence.com.milaboratory.core.sequence.Alphabets
    com.milaboratory.core.sequence.com.milaboratory.core.sequence.AminoAcidAlphabet
    com.milaboratory.core.sequence.com.milaboratory.core.sequence.AminoAcidSequence
    com.milaboratory.core.sequence.com.milaboratory.core.sequence.ArraySeqBuilder
    com.milaboratory.core.sequence.com.milaboratory.core.sequence.ArraySequenceBuilder
    com.milaboratory.core.sequence.com.milaboratory.core.sequence.GeneticCode
    com.milaboratory.core.sequence.com.milaboratory.core.sequence.IO
    com.milaboratory.core.sequence.com.milaboratory.core.sequence.MultiNSequenceWithQuality
    com.milaboratory.core.sequence.com.milaboratory.core.sequence.MultiNSequenceWithQualityImpl
    com.milaboratory.core.sequence.com.milaboratory.core.sequence.NSQTuple
    com.milaboratory.core.sequence.com.milaboratory.core.sequence.NSeq
    com.milaboratory.core.sequence.com.milaboratory.core.sequence.NSequenceWithQuality
    com.milaboratory.core.sequence.com.milaboratory.core.sequence.NSequenceWithQualityBuilder
    com.milaboratory.core.sequence.com.milaboratory.core.sequence.NucleotideAlphabet
    com.milaboratory.core.sequence.com.milaboratory.core.sequence.NucleotideSequence
    com.milaboratory.core.sequence.com.milaboratory.core.sequence.Seq
    com.milaboratory.core.sequence.com.milaboratory.core.sequence.SeqBuilder
    com.milaboratory.core.sequence.com.milaboratory.core.sequence.Sequence
    com.milaboratory.core.sequence.com.milaboratory.core.sequence.SequenceBuilder
    com.milaboratory.core.sequence.com.milaboratory.core.sequence.SequenceProperties
    com.milaboratory.core.sequence.com.milaboratory.core.sequence.SequenceQuality
    com.milaboratory.core.sequence.com.milaboratory.core.sequence.SequenceQualityBuilder
    com.milaboratory.core.sequence.com.milaboratory.core.sequence.SequenceWithQuality
    com.milaboratory.core.sequence.com.milaboratory.core.sequence.SequencesUtils
    com.milaboratory.core.sequence.com.milaboratory.core.sequence.ShortSequenceSet
    com.milaboratory.core.sequence.com.milaboratory.core.sequence.TranslationParameters
    com.milaboratory.core.sequence.com.milaboratory.core.sequence.UnsafeFactory
    com.milaboratory.core.sequence.com.milaboratory.core.sequence.Wildcard
    com.milaboratory.core.sequence.provider
    com.milaboratory.core.sequence.provider.com.milaboratory.core.sequence.provider.CachedSequenceProvider
    com.milaboratory.core.sequence.provider.com.milaboratory.core.sequence.provider.SequenceProvider
    com.milaboratory.core.sequence.provider.com.milaboratory.core.sequence.provider.SequenceProviderFactory
    com.milaboratory.core.sequence.provider.com.milaboratory.core.sequence.provider.SequenceProviderIndexOutOfBoundsException
    com.milaboratory.core.sequence.provider.com.milaboratory.core.sequence.provider.SequenceProviderUtils
    com.milaboratory.core.sequence.quality
    com.milaboratory.core.sequence.quality.com.milaboratory.core.sequence.quality.AverageQualityAggregator
    com.milaboratory.core.sequence.quality.com.milaboratory.core.sequence.quality.FunctionWithIndex
    com.milaboratory.core.sequence.quality.com.milaboratory.core.sequence.quality.MaximalQualityAggregator
    com.milaboratory.core.sequence.quality.com.milaboratory.core.sequence.quality.MiniMaxQualityAggregator
    com.milaboratory.core.sequence.quality.com.milaboratory.core.sequence.quality.MinimalQualityAggregator
    com.milaboratory.core.sequence.quality.com.milaboratory.core.sequence.quality.QualityAggregationType
    com.milaboratory.core.sequence.quality.com.milaboratory.core.sequence.quality.QualityAggregator
    com.milaboratory.core.sequence.quality.com.milaboratory.core.sequence.quality.QualityTrimmer
    com.milaboratory.core.sequence.quality.com.milaboratory.core.sequence.quality.QualityTrimmerParameters
    com.milaboratory.core.sequence.quality.com.milaboratory.core.sequence.quality.ReadTrimmerListener
    com.milaboratory.core.sequence.quality.com.milaboratory.core.sequence.quality.ReadTrimmerProcessor
    com.milaboratory.core.sequence.quality.com.milaboratory.core.sequence.quality.SumQualityAggregator
    com.milaboratory.core.tree
    com.milaboratory.core.tree.com.milaboratory.core.tree.BranchingEnumerator
    com.milaboratory.core.tree.com.milaboratory.core.tree.MutationGuide
    com.milaboratory.core.tree.com.milaboratory.core.tree.NeighborhoodIterator
    com.milaboratory.core.tree.com.milaboratory.core.tree.PenaltyUtils
    com.milaboratory.core.tree.com.milaboratory.core.tree.SequenceTreeMap
    com.milaboratory.core.tree.com.milaboratory.core.tree.TreeSearchParameters
    com.milaboratory.primitivio
    com.milaboratory.primitivio.com.milaboratory.primitivio.CustomSerializerImpl
    com.milaboratory.primitivio.com.milaboratory.primitivio.DefaultSerializersProvider
    com.milaboratory.primitivio.com.milaboratory.primitivio.DefaultSerializersProviderImpl
    com.milaboratory.primitivio.com.milaboratory.primitivio.HasPrimitivIOState
    com.milaboratory.primitivio.com.milaboratory.primitivio.IOExtensions.kt
    com.milaboratory.primitivio.com.milaboratory.primitivio.JSONSerializer
    com.milaboratory.primitivio.com.milaboratory.primitivio.ObjectMapperProvider
    com.milaboratory.primitivio.com.milaboratory.primitivio.PReader
    com.milaboratory.primitivio.com.milaboratory.primitivio.PWriter
    com.milaboratory.primitivio.com.milaboratory.primitivio.PipeDataInputReader
    com.milaboratory.primitivio.com.milaboratory.primitivio.PipeReader
    com.milaboratory.primitivio.com.milaboratory.primitivio.PipeWriter
    com.milaboratory.primitivio.com.milaboratory.primitivio.PrimitivI
    com.milaboratory.primitivio.com.milaboratory.primitivio.PrimitivIO
    com.milaboratory.primitivio.com.milaboratory.primitivio.PrimitivIOStateBuilder
    com.milaboratory.primitivio.com.milaboratory.primitivio.PrimitivIState
    com.milaboratory.primitivio.com.milaboratory.primitivio.PrimitivO
    com.milaboratory.primitivio.com.milaboratory.primitivio.PrimitivOState
    com.milaboratory.primitivio.com.milaboratory.primitivio.Serializer.kt
    com.milaboratory.primitivio.com.milaboratory.primitivio.SerializersManager
    com.milaboratory.primitivio.com.milaboratory.primitivio.TypeSerializationHelper
    com.milaboratory.primitivio.com.milaboratory.primitivio.Util
    com.milaboratory.primitivio.annotations
    com.milaboratory.primitivio.annotations.com.milaboratory.primitivio.annotations.CustomSerializer
    com.milaboratory.primitivio.annotations.com.milaboratory.primitivio.annotations.Serializable
    com.milaboratory.primitivio.blocks
    com.milaboratory.primitivio.blocks.com.milaboratory.primitivio.blocks.PrimitivIBlocks
    com.milaboratory.primitivio.blocks.com.milaboratory.primitivio.blocks.PrimitivIBlocksStats
    com.milaboratory.primitivio.blocks.com.milaboratory.primitivio.blocks.PrimitivIHeaderAction
    com.milaboratory.primitivio.blocks.com.milaboratory.primitivio.blocks.PrimitivIHeaderActions
    com.milaboratory.primitivio.blocks.com.milaboratory.primitivio.blocks.PrimitivIHybrid
    com.milaboratory.primitivio.blocks.com.milaboratory.primitivio.blocks.PrimitivIOBlockHeader
    com.milaboratory.primitivio.blocks.com.milaboratory.primitivio.blocks.PrimitivIOBlocksAbstract
    com.milaboratory.primitivio.blocks.com.milaboratory.primitivio.blocks.PrimitivIOBlocksStatsAbstract
    com.milaboratory.primitivio.blocks.com.milaboratory.primitivio.blocks.PrimitivIOBlocksUtil
    com.milaboratory.primitivio.blocks.com.milaboratory.primitivio.blocks.PrimitivOBlocks
    com.milaboratory.primitivio.blocks.com.milaboratory.primitivio.blocks.PrimitivOBlocksStats
    com.milaboratory.primitivio.blocks.com.milaboratory.primitivio.blocks.PrimitivOHybrid
    com.milaboratory.util
    com.milaboratory.util.com.milaboratory.util.AbstractLongProcessReporter
    com.milaboratory.util.com.milaboratory.util.ArrayIterator
    com.milaboratory.util.com.milaboratory.util.ArraysUtils
    com.milaboratory.util.com.milaboratory.util.AtomicEnumHistogram
    com.milaboratory.util.com.milaboratory.util.AtomicHistogram
    com.milaboratory.util.com.milaboratory.util.Bit2Array
    com.milaboratory.util.com.milaboratory.util.BitArray
    com.milaboratory.util.com.milaboratory.util.BottomN
    com.milaboratory.util.com.milaboratory.util.BottomNByte
    com.milaboratory.util.com.milaboratory.util.ByteString
    com.milaboratory.util.com.milaboratory.util.Cache
    com.milaboratory.util.com.milaboratory.util.CachedPipe.kt
    com.milaboratory.util.com.milaboratory.util.CanReportProgress
    com.milaboratory.util.com.milaboratory.util.CanReportProgressAndStage
    com.milaboratory.util.com.milaboratory.util.CollectionUtils
    com.milaboratory.util.com.milaboratory.util.CompactIntArrayList
    com.milaboratory.util.com.milaboratory.util.ComparatorsUtil.kt
    com.milaboratory.util.com.milaboratory.util.CountLimitingOutputPort.kt
    com.milaboratory.util.com.milaboratory.util.CountingInputStream
    com.milaboratory.util.com.milaboratory.util.Factory
    com.milaboratory.util.com.milaboratory.util.FormatUtils
    com.milaboratory.util.com.milaboratory.util.GlobalObjectMappers
    com.milaboratory.util.com.milaboratory.util.GroupByPipe.kt
    com.milaboratory.util.com.milaboratory.util.HashFunctions
    com.milaboratory.util.com.milaboratory.util.IntArrayList
    com.milaboratory.util.com.milaboratory.util.IntCombinations
    com.milaboratory.util.com.milaboratory.util.JsonOverrider
    com.milaboratory.util.com.milaboratory.util.LambdaExecutionException
    com.milaboratory.util.com.milaboratory.util.LambdaLatch
    com.milaboratory.util.com.milaboratory.util.LambdaSemaphore
    com.milaboratory.util.com.milaboratory.util.LightFileDescriptor
    com.milaboratory.util.com.milaboratory.util.LongProcess
    com.milaboratory.util.com.milaboratory.util.LongProcessReporter
    com.milaboratory.util.com.milaboratory.util.NSequenceWithQualityPrintHelper
    com.milaboratory.util.com.milaboratory.util.ObjectSerializer
    com.milaboratory.util.com.milaboratory.util.OutputPortWithExpectedSize.kt
    com.milaboratory.util.com.milaboratory.util.OutputPortWithProgress.kt
    com.milaboratory.util.com.milaboratory.util.ParseUtil
    com.milaboratory.util.com.milaboratory.util.ParserException
    com.milaboratory.util.com.milaboratory.util.ProgressAndStage
    com.milaboratory.util.com.milaboratory.util.ProgressUtil.kt
    com.milaboratory.util.com.milaboratory.util.RandomUtil
    com.milaboratory.util.com.milaboratory.util.Randomizer
    com.milaboratory.util.com.milaboratory.util.RangeMap
    com.milaboratory.util.com.milaboratory.util.Report
    com.milaboratory.util.com.milaboratory.util.ReportBuilder
    com.milaboratory.util.com.milaboratory.util.ReportHelper
    com.milaboratory.util.com.milaboratory.util.ReportUtil
    com.milaboratory.util.com.milaboratory.util.SingleIterator
    com.milaboratory.util.com.milaboratory.util.SmartProgressReporter
    com.milaboratory.util.com.milaboratory.util.SortedPipe.kt
    com.milaboratory.util.com.milaboratory.util.StreamUtil
    com.milaboratory.util.com.milaboratory.util.StringUtil
    com.milaboratory.util.com.milaboratory.util.TempFileDest
    com.milaboratory.util.com.milaboratory.util.TempFileManager
    com.milaboratory.util.com.milaboratory.util.TopN
    com.milaboratory.util.com.milaboratory.util.Util.kt
    com.milaboratory.util.com.milaboratory.util.VersionInfo
    com.milaboratory.util.io
    com.milaboratory.util.io.com.milaboratory.util.io.AsynchronousFileChannelAdapter
    com.milaboratory.util.io.com.milaboratory.util.io.ByteArrayDataOutput
    com.milaboratory.util.io.com.milaboratory.util.io.ByteBufferDataInputAdapter
    com.milaboratory.util.io.com.milaboratory.util.io.HasMutablePosition
    com.milaboratory.util.io.com.milaboratory.util.io.HasPosition
    com.milaboratory.util.io.com.milaboratory.util.io.IOUtil
    com.milaboratory.util.sorting
    com.milaboratory.util.sorting.com.milaboratory.util.sorting.AbstractHashSortingProperty
    com.milaboratory.util.sorting.com.milaboratory.util.sorting.AbstractSortingProperty
    com.milaboratory.util.sorting.com.milaboratory.util.sorting.GroupingOutputPort
    com.milaboratory.util.sorting.com.milaboratory.util.sorting.HashSorter
    com.milaboratory.util.sorting.com.milaboratory.util.sorting.HashUtils
    com.milaboratory.util.sorting.com.milaboratory.util.sorting.MappedSortingProperty
    com.milaboratory.util.sorting.com.milaboratory.util.sorting.MergeStrategy
    com.milaboratory.util.sorting.com.milaboratory.util.sorting.MergingOutputPort
    com.milaboratory.util.sorting.com.milaboratory.util.sorting.Property
    com.milaboratory.util.sorting.com.milaboratory.util.sorting.Sorter
    com.milaboratory.util.sorting.com.milaboratory.util.sorting.SortingProperty
    com.milaboratory.util.sorting.com.milaboratory.util.sorting.SortingPropertyRelation
    com.milaboratory.util.sorting.com.milaboratory.util.sorting.SortingUtil
    com.milaboratory.util.sorting.com.milaboratory.util.sorting.UnorderedMerger
    com.milaboratory.util.sorting.com.milaboratory.util.sorting.WithIndex
    matrices
    matrices.matrices.BLOSUM45
    matrices.matrices.BLOSUM50
    matrices.matrices.BLOSUM62
    matrices.matrices.BLOSUM80
    matrices.matrices.BLOSUM90
    matrices.matrices.PAM250
    matrices.matrices.PAM30
    matrices.matrices.PAM70
    parameters_resource
    parameters_resource.parameters_resource.kaligner_parameters.json




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