# cannoli - Cannoli_2.11: Core 0.8.0 API - org.bdgenomics.cannoli
cannoli - Cannoli 2.11 Core 0.8.0 API - org.bdgenomics.cannoli
Keywords: cannoli Cannoli 2.11 Core 0.8.0 API org.bdgenomics.cannoli

org.bdgenomics

# cannoli

#### package cannoli

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 Bwa extends CannoliFn[FragmentDataset, AlignmentDataset]

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

16. #### class BwaArgs extends Args4jBase

    Bwa function arguments.

17. #### 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.

18. #### class Freebayes extends CannoliFn[AlignmentDataset, VariantContextDataset]

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

19. #### class FreebayesArgs extends Args4jBase

    Freebayes function arguments.

20. #### class Gem extends CannoliFn[FragmentDataset, AlignmentDataset]

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

21. #### class GemArgs extends Args4jBase

    GEM-Mapper function arguments.

22. #### class MagicBlast extends CannoliFn[FragmentDataset, AlignmentDataset]

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

23. #### class MagicBlastArgs extends Args4jBase

    Magic-BLAST function arguments.

24. #### class Minimap2 extends CannoliFn[FragmentDataset, AlignmentDataset]

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

25. #### class Minimap2Args extends Args4jBase

    Minimap2 function arguments.

26. #### class SamtoolsMpileup extends CannoliFn[AlignmentDataset, VariantContextDataset]

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

27. #### class SamtoolsMpileupArgs extends Args4jBase

    Samtools mpileup function arguments.

28. #### class SingleEndBowtie2 extends CannoliFn[AlignmentDataset, AlignmentDataset]

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

29. #### class SingleEndBowtie2Args extends Args4jBase

    Single-end read Bowtie 2 function arguments.

30. #### class SingleEndStar extends CannoliFn[AlignmentDataset, AlignmentDataset]

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

31. #### class SingleEndStarArgs extends Args4jBase

    Single-end read STAR-Mapper function arguments.

32. #### class SnpEff extends CannoliFn[VariantContextDataset, VariantContextDataset]

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

33. #### class SnpEffArgs extends Args4jBase

    SnpEff function arguments.

34. #### class Star extends CannoliFn[FragmentDataset, AlignmentDataset]

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

35. #### class StarArgs extends Args4jBase

    STAR-Mapper function arguments.

36. #### class Vep extends CannoliFn[VariantContextDataset, VariantContextDataset]

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

37. #### class VepArgs extends Args4jBase

    Vep function arguments.

38. #### class VtNormalize extends CannoliFn[VariantContextDataset, VariantContextDataset]

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

39. #### class VtNormalizeArgs extends Args4jBase

    Vt normalize function arguments.

### Value Members

1. #### object Cannoli

   Implicits on Cannoli function source data sets.

2. #### package builder

### Ungrouped