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    Download fgbio_2.13 JAR 2.4.0 with all dependencies


    fgbio

    Files of the artifact fgbio_2.13 version 2.4.0 from the group com.fulcrumgenomics.

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    Download fgbio_2.13 (2.4.0)
    Artifact fgbio_2.13
    Group com.fulcrumgenomics
    Version 2.4.0
    Last update 01. November 2024
    Organization Fulcrum Genomics LLC
    URL http://github.com/fulcrumgenomics/fgbio
    License MIT License
    Dependencies amount 10
    Dependencies scala-compiler, scala-library, scala-reflect, scala-xml_2.13, commons_2.13, sopt_2.13, htsjdk, commons-math3, enumeratum_2.13, gkl,
    There are maybe transitive dependencies!
    The newest version!
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    Source code of fgbio_2.13 version 2.4.0

    META-INF
    META-INF.META-INF.MANIFEST.MF
    com.fulcrumgenomics
    com.fulcrumgenomics.com.fulcrumgenomics.FgBioDef.scala
    com.fulcrumgenomics.com.fulcrumgenomics.Writer.scala
    com.fulcrumgenomics.alignment
    com.fulcrumgenomics.alignment.com.fulcrumgenomics.alignment.Aligner.scala
    com.fulcrumgenomics.alignment.com.fulcrumgenomics.alignment.Alignment.scala
    com.fulcrumgenomics.alignment.com.fulcrumgenomics.alignment.Matrix.scala
    com.fulcrumgenomics.alignment.com.fulcrumgenomics.alignment.package.scala
    com.fulcrumgenomics.bam
    com.fulcrumgenomics.bam.com.fulcrumgenomics.bam.AutoGenerateReadGroupsByName.scala
    com.fulcrumgenomics.bam.com.fulcrumgenomics.bam.Bams.scala
    com.fulcrumgenomics.bam.com.fulcrumgenomics.bam.BaseCounts.scala
    com.fulcrumgenomics.bam.com.fulcrumgenomics.bam.CallOverlappingConsensusBases.scala
    com.fulcrumgenomics.bam.com.fulcrumgenomics.bam.ClipBam.scala
    com.fulcrumgenomics.bam.com.fulcrumgenomics.bam.DownsampleAndNormalizeBam.scala
    com.fulcrumgenomics.bam.com.fulcrumgenomics.bam.ErrorRateByReadPosition.R
    com.fulcrumgenomics.bam.com.fulcrumgenomics.bam.ErrorRateByReadPosition.scala
    com.fulcrumgenomics.bam.com.fulcrumgenomics.bam.EstimatePoolingFractions.scala
    com.fulcrumgenomics.bam.com.fulcrumgenomics.bam.FilterBam.scala
    com.fulcrumgenomics.bam.com.fulcrumgenomics.bam.FindSwitchbackReads.R
    com.fulcrumgenomics.bam.com.fulcrumgenomics.bam.FindSwitchbackReads.scala
    com.fulcrumgenomics.bam.com.fulcrumgenomics.bam.FindTechnicalReads.scala
    com.fulcrumgenomics.bam.com.fulcrumgenomics.bam.OverlappingBasesConsensusCaller.scala
    com.fulcrumgenomics.bam.com.fulcrumgenomics.bam.RandomizeBam.scala
    com.fulcrumgenomics.bam.com.fulcrumgenomics.bam.ReadAndRefPosIterator.scala
    com.fulcrumgenomics.bam.com.fulcrumgenomics.bam.RemoveSamTags.scala
    com.fulcrumgenomics.bam.com.fulcrumgenomics.bam.SamRecordClipper.scala
    com.fulcrumgenomics.bam.com.fulcrumgenomics.bam.SetMateInformation.scala
    com.fulcrumgenomics.bam.com.fulcrumgenomics.bam.SortBam.scala
    com.fulcrumgenomics.bam.com.fulcrumgenomics.bam.SplitBam.scala
    com.fulcrumgenomics.bam.com.fulcrumgenomics.bam.TrimPrimers.scala
    com.fulcrumgenomics.bam.com.fulcrumgenomics.bam.UpdateReadGroups.scala
    com.fulcrumgenomics.bam.com.fulcrumgenomics.bam.ZipperBams.scala
    com.fulcrumgenomics.bam.api
    com.fulcrumgenomics.bam.api.com.fulcrumgenomics.bam.api.HeaderHelper.scala
    com.fulcrumgenomics.bam.api.com.fulcrumgenomics.bam.api.SamIterator.scala
    com.fulcrumgenomics.bam.api.com.fulcrumgenomics.bam.api.SamOrder.scala
    com.fulcrumgenomics.bam.api.com.fulcrumgenomics.bam.api.SamRecord.scala
    com.fulcrumgenomics.bam.api.com.fulcrumgenomics.bam.api.SamRecordCodec.scala
    com.fulcrumgenomics.bam.api.com.fulcrumgenomics.bam.api.SamSource.scala
    com.fulcrumgenomics.bam.api.com.fulcrumgenomics.bam.api.SamWriter.scala
    com.fulcrumgenomics.bam.pileup
    com.fulcrumgenomics.bam.pileup.com.fulcrumgenomics.bam.pileup.Pileup.scala
    com.fulcrumgenomics.bam.pileup.com.fulcrumgenomics.bam.pileup.PileupBuilder.scala
    com.fulcrumgenomics.bam.pileup.com.fulcrumgenomics.bam.pileup.RandomAccessPileupBuilder.scala
    com.fulcrumgenomics.bam.pileup.com.fulcrumgenomics.bam.pileup.StreamingPileupBuilder.scala
    com.fulcrumgenomics.basecalling
    com.fulcrumgenomics.basecalling.com.fulcrumgenomics.basecalling.ExtractBasecallingParamsForPicard.scala
    com.fulcrumgenomics.basecalling.com.fulcrumgenomics.basecalling.ExtractIlluminaRunInfo.scala
    com.fulcrumgenomics.cmdline
    com.fulcrumgenomics.cmdline.com.fulcrumgenomics.cmdline.ClpGroups.scala
    com.fulcrumgenomics.cmdline.com.fulcrumgenomics.cmdline.FgBioMain.scala
    com.fulcrumgenomics.cmdline.com.fulcrumgenomics.cmdline.FgBioTool.scala
    com.fulcrumgenomics.coord
    com.fulcrumgenomics.coord.com.fulcrumgenomics.coord.LocatableOrdering.scala
    com.fulcrumgenomics.fasta
    com.fulcrumgenomics.fasta.com.fulcrumgenomics.fasta.CollectAlternateContigNames.scala
    com.fulcrumgenomics.fasta.com.fulcrumgenomics.fasta.HardMaskFasta.scala
    com.fulcrumgenomics.fasta.com.fulcrumgenomics.fasta.ReferenceSequenceIterator.scala
    com.fulcrumgenomics.fasta.com.fulcrumgenomics.fasta.SequenceDictionary.scala
    com.fulcrumgenomics.fasta.com.fulcrumgenomics.fasta.SortSequenceDictionary.scala
    com.fulcrumgenomics.fasta.com.fulcrumgenomics.fasta.UpdateFastaContigNames.scala
    com.fulcrumgenomics.fastq
    com.fulcrumgenomics.fastq.com.fulcrumgenomics.fastq.DemuxFastqs.scala
    com.fulcrumgenomics.fastq.com.fulcrumgenomics.fastq.FastqRecord.scala
    com.fulcrumgenomics.fastq.com.fulcrumgenomics.fastq.FastqSource.scala
    com.fulcrumgenomics.fastq.com.fulcrumgenomics.fastq.FastqToBam.scala
    com.fulcrumgenomics.fastq.com.fulcrumgenomics.fastq.FastqWriter.scala
    com.fulcrumgenomics.fastq.com.fulcrumgenomics.fastq.QualityEncoding.scala
    com.fulcrumgenomics.fastq.com.fulcrumgenomics.fastq.SortFastq.scala
    com.fulcrumgenomics.fastq.com.fulcrumgenomics.fastq.TrimFastq.scala
    com.fulcrumgenomics.illumina
    com.fulcrumgenomics.illumina.com.fulcrumgenomics.illumina.RunInfo.scala
    com.fulcrumgenomics.illumina.com.fulcrumgenomics.illumina.Sample.scala
    com.fulcrumgenomics.illumina.com.fulcrumgenomics.illumina.SampleSheet.scala
    com.fulcrumgenomics.internal
    com.fulcrumgenomics.internal.com.fulcrumgenomics.internal.BuildToolDocs.scala
    com.fulcrumgenomics.internal.com.fulcrumgenomics.internal.FgMetricsDoclet.scala
    com.fulcrumgenomics.internal.com.fulcrumgenomics.internal.InternalTools.scala
    com.fulcrumgenomics.math
    com.fulcrumgenomics.math.com.fulcrumgenomics.math.BinomialDistribution.scala
    com.fulcrumgenomics.math.com.fulcrumgenomics.math.FishersExactTest.scala
    com.fulcrumgenomics.personal.nhomer
    com.fulcrumgenomics.personal.nhomer.com.fulcrumgenomics.personal.nhomer.GenerateRegionsFromFasta.scala
    com.fulcrumgenomics.personal.nhomer.com.fulcrumgenomics.personal.nhomer.SplitTag.scala
    com.fulcrumgenomics.personal.tfenne
    com.fulcrumgenomics.personal.tfenne.com.fulcrumgenomics.personal.tfenne.StripFastqReadNumbers.scala
    com.fulcrumgenomics.personal.tfenne.com.fulcrumgenomics.personal.tfenne.SummarizeGff.scala
    com.fulcrumgenomics.rnaseq
    com.fulcrumgenomics.rnaseq.com.fulcrumgenomics.rnaseq.CollectErccMetrics.R
    com.fulcrumgenomics.rnaseq.com.fulcrumgenomics.rnaseq.CollectErccMetrics.scala
    com.fulcrumgenomics.rnaseq.com.fulcrumgenomics.rnaseq.ErccStandardMixtures.txt
    com.fulcrumgenomics.rnaseq.com.fulcrumgenomics.rnaseq.EstimateRnaSeqInsertSize.scala
    com.fulcrumgenomics.testing
    com.fulcrumgenomics.testing.com.fulcrumgenomics.testing.ReferenceSetBuilder.scala
    com.fulcrumgenomics.testing.com.fulcrumgenomics.testing.SamBuilder.scala
    com.fulcrumgenomics.testing.com.fulcrumgenomics.testing.VariantContextSetBuilder.scala
    com.fulcrumgenomics.testing.com.fulcrumgenomics.testing.VcfBuilder.scala
    com.fulcrumgenomics.umi
    com.fulcrumgenomics.umi.com.fulcrumgenomics.umi.AnnotateBamWithUmis.scala
    com.fulcrumgenomics.umi.com.fulcrumgenomics.umi.CallDuplexConsensusReads.scala
    com.fulcrumgenomics.umi.com.fulcrumgenomics.umi.CallMolecularConsensusReads.scala
    com.fulcrumgenomics.umi.com.fulcrumgenomics.umi.CollectDuplexSeqMetrics.R
    com.fulcrumgenomics.umi.com.fulcrumgenomics.umi.CollectDuplexSeqMetrics.scala
    com.fulcrumgenomics.umi.com.fulcrumgenomics.umi.ConsensusCaller.scala
    com.fulcrumgenomics.umi.com.fulcrumgenomics.umi.ConsensusCallingIterator.scala
    com.fulcrumgenomics.umi.com.fulcrumgenomics.umi.ConsensusTags.scala
    com.fulcrumgenomics.umi.com.fulcrumgenomics.umi.CopyUmiFromReadName.scala
    com.fulcrumgenomics.umi.com.fulcrumgenomics.umi.CorrectUmis.scala
    com.fulcrumgenomics.umi.com.fulcrumgenomics.umi.DuplexConsensusCaller.scala
    com.fulcrumgenomics.umi.com.fulcrumgenomics.umi.ExtractUmisFromBam.scala
    com.fulcrumgenomics.umi.com.fulcrumgenomics.umi.FilterConsensusReads.scala
    com.fulcrumgenomics.umi.com.fulcrumgenomics.umi.GroupReadsByUmi.scala
    com.fulcrumgenomics.umi.com.fulcrumgenomics.umi.ReviewConsensusVariants.scala
    com.fulcrumgenomics.umi.com.fulcrumgenomics.umi.SimpleConsensusCaller.scala
    com.fulcrumgenomics.umi.com.fulcrumgenomics.umi.UmiConsensusCaller.scala
    com.fulcrumgenomics.umi.com.fulcrumgenomics.umi.Umis.scala
    com.fulcrumgenomics.umi.com.fulcrumgenomics.umi.VanillaUmiConsensusCaller.scala
    com.fulcrumgenomics.util
    com.fulcrumgenomics.util.com.fulcrumgenomics.util.Amplicon.scala
    com.fulcrumgenomics.util.com.fulcrumgenomics.util.AmpliconDetector.scala
    com.fulcrumgenomics.util.com.fulcrumgenomics.util.AssignPrimers.scala
    com.fulcrumgenomics.util.com.fulcrumgenomics.util.DnaFoldPrediction
    com.fulcrumgenomics.util.com.fulcrumgenomics.util.DnaFoldPredictor
    com.fulcrumgenomics.util.com.fulcrumgenomics.util.GeneAnnotations.scala
    com.fulcrumgenomics.util.com.fulcrumgenomics.util.GenomicSpan.scala
    com.fulcrumgenomics.util.com.fulcrumgenomics.util.IlluminaAdapters.scala
    com.fulcrumgenomics.util.com.fulcrumgenomics.util.IntervalListSource.scala
    com.fulcrumgenomics.util.com.fulcrumgenomics.util.IntervalListWriter.scala
    com.fulcrumgenomics.util.com.fulcrumgenomics.util.Io.scala
    com.fulcrumgenomics.util.com.fulcrumgenomics.util.MathUtil.scala
    com.fulcrumgenomics.util.com.fulcrumgenomics.util.Metric.scala
    com.fulcrumgenomics.util.com.fulcrumgenomics.util.NcbiRefSeqGffSource.scala
    com.fulcrumgenomics.util.com.fulcrumgenomics.util.NumericTypes.scala
    com.fulcrumgenomics.util.com.fulcrumgenomics.util.PickIlluminaIndices.scala
    com.fulcrumgenomics.util.com.fulcrumgenomics.util.PickIlluminaIndicesCommand
    com.fulcrumgenomics.util.com.fulcrumgenomics.util.PickLongIndices.scala
    com.fulcrumgenomics.util.com.fulcrumgenomics.util.ProgressLogger.scala
    com.fulcrumgenomics.util.com.fulcrumgenomics.util.ReadStructure.scala
    com.fulcrumgenomics.util.com.fulcrumgenomics.util.RefFlatSource.scala
    com.fulcrumgenomics.util.com.fulcrumgenomics.util.Rscript.scala
    com.fulcrumgenomics.util.com.fulcrumgenomics.util.SampleBarcodeMetric.scala
    com.fulcrumgenomics.util.com.fulcrumgenomics.util.Sequences.scala
    com.fulcrumgenomics.util.com.fulcrumgenomics.util.Sorter.scala
    com.fulcrumgenomics.util.com.fulcrumgenomics.util.UpdateDelimitedFileContigNames.scala
    com.fulcrumgenomics.util.com.fulcrumgenomics.util.UpdateGffContigNames.scala
    com.fulcrumgenomics.util.com.fulcrumgenomics.util.UpdateIntervalListContigNames.scala
    com.fulcrumgenomics.vcf
    com.fulcrumgenomics.vcf.com.fulcrumgenomics.vcf.AssessPhasing.scala
    com.fulcrumgenomics.vcf.com.fulcrumgenomics.vcf.ByIntervalListVariantContextIterator.scala
    com.fulcrumgenomics.vcf.com.fulcrumgenomics.vcf.FixVcfPhaseSet.scala
    com.fulcrumgenomics.vcf.com.fulcrumgenomics.vcf.HapCutToVcf.scala
    com.fulcrumgenomics.vcf.com.fulcrumgenomics.vcf.JointVariantContextIterator.scala
    com.fulcrumgenomics.vcf.com.fulcrumgenomics.vcf.MakeMixtureVcf.scala
    com.fulcrumgenomics.vcf.com.fulcrumgenomics.vcf.MakeTwoSampleMixtureVcf.scala
    com.fulcrumgenomics.vcf.com.fulcrumgenomics.vcf.UpdateVcfContigNames.scala
    com.fulcrumgenomics.vcf.com.fulcrumgenomics.vcf.VariantMask.scala
    com.fulcrumgenomics.vcf.api
    com.fulcrumgenomics.vcf.api.com.fulcrumgenomics.vcf.api.Allele.scala
    com.fulcrumgenomics.vcf.api.com.fulcrumgenomics.vcf.api.AlleleSet.scala
    com.fulcrumgenomics.vcf.api.com.fulcrumgenomics.vcf.api.ArrayAttr.scala
    com.fulcrumgenomics.vcf.api.com.fulcrumgenomics.vcf.api.Genotype.scala
    com.fulcrumgenomics.vcf.api.com.fulcrumgenomics.vcf.api.GenotypeMap.scala
    com.fulcrumgenomics.vcf.api.com.fulcrumgenomics.vcf.api.Variant.scala
    com.fulcrumgenomics.vcf.api.com.fulcrumgenomics.vcf.api.VcfConversions.scala
    com.fulcrumgenomics.vcf.api.com.fulcrumgenomics.vcf.api.VcfHeader.scala
    com.fulcrumgenomics.vcf.api.com.fulcrumgenomics.vcf.api.VcfSource.scala
    com.fulcrumgenomics.vcf.api.com.fulcrumgenomics.vcf.api.VcfWriter.scala
    com.fulcrumgenomics.vcf.filtration
    com.fulcrumgenomics.vcf.filtration.com.fulcrumgenomics.vcf.filtration.FilterSomaticVcf.scala
    com.fulcrumgenomics.vcf.filtration.com.fulcrumgenomics.vcf.filtration.ReadEndSomaticVariantFilter.scala
    com.fulcrumgenomics.vcf.filtration.com.fulcrumgenomics.vcf.filtration.SomaticVariantFilter.scala
    .log4j2.xml




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