Package

org.bdgenomics

cannoli

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package cannoli

Visibility
  1. Public
  2. All

Type Members

  1. class BcftoolsMpileup extends CannoliFn[AlignmentRecordDataset, VariantContextDataset] with Logging

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    Bcftools mpileup wrapper as a function AlignmentRecordDataset → VariantContextDataset, for use in cannoli-shell or notebooks.

  2. class BcftoolsMpileupArgs extends Args4jBase

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    Bcftools mpileup function arguments.

  3. class BcftoolsNorm extends CannoliFn[VariantContextDataset, VariantContextDataset] with Logging

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    Bcftools norm wrapper as a function VariantContextDataset → VariantContextDataset, for use in cannoli-shell or notebooks.

  4. class BcftoolsNormArgs extends Args4jBase

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    Bcftools norm function arguments.

  5. class BedtoolsIntersect extends CannoliFn[FeatureDataset, FeatureDataset] with Logging

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    Bedtools intersect wrapper as a function FeatureDataset → FeatureDataset, for use in cannoli-shell or notebooks.

    Bedtools intersect wrapper as a function FeatureDataset → FeatureDataset, for use in cannoli-shell or notebooks.

    val args = new BedtoolsIntersectFnArgs() args.b = "foo.bed" args.useDocker = true val features = ... val pipedFeatures = new BedtoolsIntersectFn(args, sc).apply(features)

  6. class BedtoolsIntersectArgs extends Args4jBase

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    Bedtools intersect function arguments.

  7. class Bowtie extends CannoliFn[FragmentDataset, AlignmentRecordDataset] with Logging

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    Bowtie wrapper as a function FragmentDataset → AlignmentRecordDataset, for use in cannoli-shell or notebooks.

  8. class Bowtie2 extends CannoliFn[FragmentDataset, AlignmentRecordDataset] with Logging

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    Bowtie 2 wrapper as a function FragmentDataset → AlignmentRecordDataset, for use in cannoli-shell or notebooks.

  9. class Bowtie2Args extends Args4jBase

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    Bowtie 2 function arguments.

  10. class BowtieArgs extends Args4jBase

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    Bowtie function arguments.

  11. class Bwa extends CannoliFn[FragmentDataset, AlignmentRecordDataset] with Logging

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    Bwa wrapper as a function FragmentDataset → AlignmentRecordDataset, for use in cannoli-shell or notebooks.

  12. class BwaArgs extends Args4jBase

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    Bwa function arguments.

  13. abstract class CannoliFn[X, Y] extends (X) ⇒ Y

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    Cannoli function.

    Cannoli function.

    X

    Cannoli function argument type parameter.

    Y

    Cannoli function result type parameter.

  14. class Freebayes extends CannoliFn[AlignmentRecordDataset, VariantContextDataset] with Logging

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    Freebayes wrapper as a function AlignmentRecordDataset → VariantContextDataset, for use in cannoli-shell or notebooks.

  15. class FreebayesArgs extends Args4jBase

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    Freebayes function arguments.

  16. class Gem extends CannoliFn[FragmentDataset, AlignmentRecordDataset] with Logging

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    GEM-Mapper wrapper as a function FragmentDataset → AlignmentRecordDataset, for use in cannoli-shell or notebooks.

  17. class GemArgs extends Args4jBase

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    GEM-Mapper function arguments.

  18. class Minimap2 extends CannoliFn[FragmentDataset, AlignmentRecordDataset] with Logging

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    Minimap2 wrapper as a function FragmentDataset → AlignmentRecordDataset, for use in cannoli-shell or notebooks.

  19. class Minimap2Args extends Args4jBase

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    Minimap2 function arguments.

  20. class SamtoolsMpileup extends CannoliFn[AlignmentRecordDataset, VariantContextDataset] with Logging

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    Samtools mpileup wrapper as a function AlignmentRecordDataset → VariantContextDataset, for use in cannoli-shell or notebooks.

  21. class SamtoolsMpileupArgs extends Args4jBase

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    Samtools mpileup function arguments.

  22. class SnpEff extends CannoliFn[VariantContextDataset, VariantContextDataset] with Logging

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    SnpEff wrapper as a function VariantContextDataset → VariantContextDataset, for use in cannoli-shell or notebooks.

  23. class SnpEffArgs extends Args4jBase

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    SnpEff function arguments.

  24. class Vep extends CannoliFn[VariantContextDataset, VariantContextDataset] with Logging

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    Vep wrapper as a function VariantContextDataset → VariantContextDataset, for use in cannoli-shell or notebooks.

  25. class VepArgs extends Args4jBase

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    Vep function arguments.

  26. class VtNormalize extends CannoliFn[VariantContextDataset, VariantContextDataset] with Logging

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    Vt normalize wrapper as a function VariantContextDataset → VariantContextDataset, for use in cannoli-shell or notebooks.

  27. class VtNormalizeArgs extends Args4jBase

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    Vt normalize function arguments.

Value Members

  1. object Cannoli

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    Implicits on Cannoli function source data sets.

  2. package builder

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