Cannoli_2.12: Core 1.0 API < Back
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# Packages

-  package root
  Definition Classes
    root
-  package org
  Definition Classes
    root
-  package bdgenomics
  Definition Classes
    org
-  package cannoli
  Definition Classes
    bdgenomics
- BcftoolsCall
- BcftoolsCallArgs
- BcftoolsMpileup
- BcftoolsMpileupArgs
- BcftoolsNorm
- BcftoolsNormArgs
- BedtoolsIntersect
- BedtoolsIntersectArgs
- Blastn
- BlastnArgs
- Bowtie
- Bowtie2
- Bowtie2Args
- BowtieArgs
- BwaMem
- BwaMem2
- BwaMem2Args
- BwaMemArgs
- Cannoli
- CannoliFn
- Freebayes
- FreebayesArgs
- Gem
- GemArgs
- LongMinimap2
- LongUnimap
- MagicBlast
- MagicBlastArgs
- Minimap2
- Minimap2Args
- SamtoolsMpileup
- SamtoolsMpileupArgs
- SingleEndBowtie2
- SingleEndBowtie2Args
- SingleEndBwaMem
- SingleEndBwaMem2
- SingleEndMinimap2
- SingleEndStar
- SingleEndStarArgs
- SingleEndUnimap
- Snap
- SnapArgs
- SnpEff
- SnpEffArgs
- Star
- StarArgs
- Unimap
- UnimapArgs
- Vep
- VepArgs
- VtNormalize
- VtNormalizeArgs

p

org.bdgenomics

# cannoli 

#### package cannoli

 
Ordering

1. Alphabetic

Visibility

1. Public
2. All

### Type Members

1.  class BcftoolsCall extends CannoliFn[VariantContextDataset, VariantContextDataset]

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

2.  class BcftoolsCallArgs extends Args4jBase

   Bcftools call function arguments.

3.  class BcftoolsMpileup extends CannoliFn[AlignmentDataset, VariantContextDataset]

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

4.  class BcftoolsMpileupArgs extends Args4jBase

   Bcftools mpileup function arguments.

5.  class BcftoolsNorm extends CannoliFn[VariantContextDataset, VariantContextDataset]

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

6.  class BcftoolsNormArgs extends Args4jBase

   Bcftools norm function arguments.

7.  class BedtoolsIntersect extends CannoliFn[FeatureDataset, FeatureDataset]

   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)`

8.  class BedtoolsIntersectArgs extends Args4jBase

   Bedtools intersect function arguments.

9.  class Blastn extends CannoliFn[SequenceDataset, AlignmentDataset]

   Blastn wrapper as a function SequenceDataset → AlignmentDataset, for use in cannoli-shell or notebooks.

10.  class BlastnArgs extends Args4jBase

    Blastn function arguments.

11.  class Bowtie extends CannoliFn[FragmentDataset, AlignmentDataset]

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

12.  class Bowtie2 extends CannoliFn[FragmentDataset, AlignmentDataset]

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

13.  class Bowtie2Args extends Args4jBase

    Bowtie 2 function arguments.

14.  class BowtieArgs extends Args4jBase

    Bowtie function arguments.

15.  class BwaMem extends CannoliFn[FragmentDataset, AlignmentDataset]

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

16.  class BwaMem2 extends CannoliFn[FragmentDataset, AlignmentDataset]

    Bwa-mem2 wrapper as a function FragmentDataset → AlignmentDataset, for use in cannoli-shell or notebooks.

17.  class BwaMem2Args extends ReadGroupArgs

    Bwa-mem2 function arguments.

18.  class BwaMemArgs extends ReadGroupArgs

    Bwa mem function arguments.

19.  abstract class CannoliFn [X, Y] extends (X) ⇒ Y with Logging

    Cannoli function.

    Cannoli function.

    X

      Cannoli function argument type parameter.

    Y

      Cannoli function result type parameter.

20.  class Freebayes extends CannoliFn[AlignmentDataset, VariantContextDataset]

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

21.  class FreebayesArgs extends Args4jBase

    Freebayes function arguments.

22.  class Gem extends CannoliFn[FragmentDataset, AlignmentDataset]

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

23.  class GemArgs extends Args4jBase

    GEM-Mapper function arguments.

24.  class LongMinimap2 extends CannoliFn[SequenceDataset, AlignmentDataset]

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

25.  class LongUnimap extends CannoliFn[SequenceDataset, AlignmentDataset]

    Unimap wrapper as a function SequenceDataset → AlignmentDataset, for use in cannoli-shell or notebooks.

26.  class MagicBlast extends CannoliFn[FragmentDataset, AlignmentDataset]

    Magic-BLAST wrapper as a function FragmentDataset → AlignmentDataset, for use in cannoli-shell or notebooks.

27.  class MagicBlastArgs extends Args4jBase

    Magic-BLAST function arguments.

28.  class Minimap2 extends CannoliFn[FragmentDataset, AlignmentDataset]

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

29.  class Minimap2Args extends ReadGroupArgs

    Minimap2 function arguments.

30.  class SamtoolsMpileup extends CannoliFn[AlignmentDataset, VariantContextDataset]

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

31.  class SamtoolsMpileupArgs extends Args4jBase

    Samtools mpileup function arguments.

32.  class SingleEndBowtie2 extends CannoliFn[AlignmentDataset, AlignmentDataset]

    Single-end read Bowtie 2 wrapper as a function AlignmentDataset → AlignmentDataset, for use in cannoli-shell or notebooks.

33.  class SingleEndBowtie2Args extends Args4jBase

    Single-end read Bowtie 2 function arguments.

34.  class SingleEndBwaMem extends CannoliFn[AlignmentDataset, AlignmentDataset]

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

35.  class SingleEndBwaMem2 extends CannoliFn[AlignmentDataset, AlignmentDataset]

    Bwa-mem2 wrapper as a function AlignmentDataset → AlignmentDataset, for use in cannoli-shell or notebooks.

36.  class SingleEndMinimap2 extends CannoliFn[AlignmentDataset, AlignmentDataset]

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

37.  class SingleEndStar extends CannoliFn[AlignmentDataset, AlignmentDataset]

    Single-end read STAR-Mapper wrapper as a function AlignmentDataset → AlignmentDataset, for use in cannoli-shell or notebooks.

38.  class SingleEndStarArgs extends Args4jBase

    Single-end read STAR-Mapper function arguments.

39.  class SingleEndUnimap extends CannoliFn[AlignmentDataset, AlignmentDataset]

    Unimap wrapper as a function AlignmentDataset → AlignmentDataset, for use in cannoli-shell or notebooks.

40.  class Snap extends CannoliFn[FragmentDataset, AlignmentDataset]

    Scalable Nucleotide Alignment Program (SNAP) wrapper as a function FragmentDataset → AlignmentDataset, for use in cannoli-shell or notebooks.

41.  class SnapArgs extends ReadGroupArgs

    Scalable Nucleotide Alignment Program (SNAP) function arguments.

42.  class SnpEff extends CannoliFn[VariantContextDataset, VariantContextDataset]

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

43.  class SnpEffArgs extends Args4jBase

    SnpEff function arguments.

44.  class Star extends CannoliFn[FragmentDataset, AlignmentDataset]

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

45.  class StarArgs extends Args4jBase

    STAR-Mapper function arguments.

46.  class Unimap extends CannoliFn[FragmentDataset, AlignmentDataset]

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

47.  class UnimapArgs extends ReadGroupArgs

    Unimap function arguments.

48.  class Vep extends CannoliFn[VariantContextDataset, VariantContextDataset]

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

49.  class VepArgs extends Args4jBase

    Vep function arguments.

50.  class VtNormalize extends CannoliFn[VariantContextDataset, VariantContextDataset]

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

51.  class VtNormalizeArgs extends Args4jBase

    Vt normalize function arguments.

### Value Members

1.  object Cannoli

   Implicits on Cannoli function source data sets.

### Ungrouped