org.bdgenomics

# cannoli

#### package cannoli

Visibility

1. Public
2. All

### Type Members

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

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

2. #### class BcftoolsMpileupArgs extends Args4jBase

   Bcftools mpileup function arguments.

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

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

4. #### class BcftoolsNormArgs extends Args4jBase

   Bcftools norm function arguments.

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

   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

   Bedtools intersect function arguments.

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

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

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

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

9. #### class Bowtie2Args extends Args4jBase

   Bowtie 2 function arguments.

10. #### class BowtieArgs extends Args4jBase

    Bowtie function arguments.

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

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

12. #### class BwaArgs extends Args4jBase

    Bwa function arguments.

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

    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

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

15. #### class FreebayesArgs extends Args4jBase

    Freebayes function arguments.

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

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

17. #### class GemArgs extends Args4jBase

    GEM-Mapper function arguments.

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

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

19. #### class Minimap2Args extends Args4jBase

    Minimap2 function arguments.

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

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

21. #### class SamtoolsMpileupArgs extends Args4jBase

    Samtools mpileup function arguments.

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

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

23. #### class SnpEffArgs extends Args4jBase

    SnpEff function arguments.

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

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

25. #### class VepArgs extends Args4jBase

    Vep function arguments.

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

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

27. #### class VtNormalizeArgs extends Args4jBase

    Vt normalize function arguments.

### Value Members

1. #### object Cannoli

   Implicits on Cannoli function source data sets.

2. #### package builder

### Ungrouped