Package

org.bdgenomics.cannoli

cli

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package cli

Visibility
  1. Public
  2. All

Type Members

  1. final class About extends AnyRef

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  2. class BcftoolsNorm extends BDGSparkCommand[BcftoolsNormArgs] with Logging

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    Bcftools norm command line wrapper.

  3. class BcftoolsNormArgs extends BcftoolsNormFnArgs with ADAMSaveAnyArgs with ParquetArgs

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    Bcftools norm command line arguments.

  4. class BcftoolsNormFn extends CannoliFn[VariantContextRDD, VariantContextRDD] with Logging

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

  5. class BcftoolsNormFnArgs extends Args4jBase

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    Bcftools norm function arguments.

  6. class BedtoolsIntersect extends BDGSparkCommand[BedtoolsIntersectArgs] with Logging

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    Bedtools intersect command line wrapper.

  7. class BedtoolsIntersectArgs extends BedtoolsIntersectFnArgs with ADAMSaveAnyArgs with ParquetArgs

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    Bedtools intersect command line arguments.

  8. class BedtoolsIntersectFn extends CannoliFn[FeatureRDD, FeatureRDD] with Logging

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

    Bedtools intersect wrapper as a function FeatureRDD → FeatureRDD, 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)

  9. class BedtoolsIntersectFnArgs extends Args4jBase

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    Bedtools intersect function arguments.

  10. class Bowtie extends BDGSparkCommand[BowtieArgs] with Logging

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    Bowtie command line wrapper.

  11. class Bowtie2 extends BDGSparkCommand[Bowtie2Args] with Logging

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    Bowtie 2 command line wrapper.

  12. class Bowtie2Args extends Bowtie2FnArgs with ADAMSaveAnyArgs with ParquetArgs

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    Bowtie 2 command line arguments.

  13. class Bowtie2Fn extends CannoliFn[FragmentRDD, AlignmentRecordRDD] with Logging

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

  14. class Bowtie2FnArgs extends Args4jBase

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    Bowtie 2 function arguments.

  15. class BowtieArgs extends BowtieFnArgs with ADAMSaveAnyArgs with ParquetArgs

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    Bowtie command line arguments.

  16. class BowtieFn extends CannoliFn[FragmentRDD, AlignmentRecordRDD] with Logging

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

  17. class BowtieFnArgs extends Args4jBase

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    Bowtie function arguments.

  18. class Bwa extends BDGSparkCommand[BwaArgs] with Logging

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    Bwa command line wrapper.

  19. class BwaArgs extends BwaFnArgs with ADAMSaveAnyArgs with ParquetArgs

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    Bwa command line arguments.

  20. class BwaFn extends CannoliFn[FragmentRDD, AlignmentRecordRDD] with Logging

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

  21. class BwaFnArgs extends Args4jBase

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    Bwa function arguments.

  22. class Cannoli extends Logging

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    Cannoli main.

  23. 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.

  24. class CannoliModule extends AbstractModule with ScalaModule

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    Cannoli module, binds the default list of command groups.

  25. class Freebayes extends BDGSparkCommand[FreebayesArgs] with Logging

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    Freebayes command line wrapper.

  26. class FreebayesArgs extends FreebayesFnArgs with ADAMSaveAnyArgs with ParquetArgs

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    Freebayes command line arguments.

  27. class FreebayesFn extends CannoliFn[AlignmentRecordRDD, VariantContextRDD] with Logging

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

  28. class FreebayesFnArgs extends Args4jBase

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    Freebayes function arguments.

  29. class InterleaveFastq extends BDGSparkCommand[InterleaveFastqArgs] with Logging

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    Interleaves two FASTQ files.

  30. class InterleaveFastqArgs extends Args4jBase

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  31. class SampleReads extends BDGSparkCommand[SampleReadsArgs] with Logging

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    Sample reads from interleaved FASTQ format.

  32. class SampleReadsArgs extends Args4jBase with ADAMSaveAnyArgs with ParquetArgs

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  33. class SamtoolsMpileup extends BDGSparkCommand[SamtoolsMpileupArgs] with Logging

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    Samtools mpileup command line wrapper.

  34. class SamtoolsMpileupArgs extends SamtoolsMpileupFnArgs with ADAMSaveAnyArgs with ParquetArgs

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    Samtools mpileup command line arguments.

  35. class SamtoolsMpileupFn extends CannoliFn[AlignmentRecordRDD, VariantContextRDD] with Logging

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

  36. class SamtoolsMpileupFnArgs extends Args4jBase

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    Samtools mpileup function arguments.

  37. class SnpEff extends BDGSparkCommand[SnpEffArgs] with Logging

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    SnpEff command line wrapper.

  38. class SnpEffArgs extends SnpEffFnArgs with ADAMSaveAnyArgs with ParquetArgs

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    SnpEff command line arguments.

  39. class SnpEffFn extends CannoliFn[VariantContextRDD, VariantContextRDD] with Logging

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

  40. class SnpEffFnArgs extends Args4jBase

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    SnpEff function arguments.

  41. class VtNormalize extends BDGSparkCommand[VtNormalizeArgs] with Logging

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    Vt normalize command line wrapper.

  42. class VtNormalizeArgs extends VtNormalizeFnArgs with ADAMSaveAnyArgs with ParquetArgs

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    Vt normalize command line arguments.

  43. class VtNormalizeFn extends CannoliFn[VariantContextRDD, VariantContextRDD] with Logging

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

  44. class VtNormalizeFnArgs extends Args4jBase

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    Vt normalize function arguments.

Value Members

  1. object BcftoolsNorm extends BDGCommandCompanion

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  2. object BedtoolsIntersect extends BDGCommandCompanion

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  3. object Bowtie extends BDGCommandCompanion

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  4. object Bowtie2 extends BDGCommandCompanion

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  5. object Bwa extends BDGCommandCompanion

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  6. object Cannoli

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  7. object Freebayes extends BDGCommandCompanion

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  8. object InterleaveFastq extends BDGCommandCompanion

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  9. object SampleReads extends BDGCommandCompanion

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  10. object SamtoolsMpileup extends BDGCommandCompanion

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  11. object SnpEff extends BDGCommandCompanion

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  12. object VtNormalize extends BDGCommandCompanion

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Ungrouped