org.bdgenomics.cannoli

# cli

#### package cli

Visibility

1. Public
2. All

### Type Members

1. #### final class About extends AnyRef

2. #### class BcftoolsNorm extends BDGSparkCommand[BcftoolsNormArgs] with Logging

   Bcftools norm command line wrapper.

3. #### class BcftoolsNormArgs extends BcftoolsNormFnArgs with ADAMSaveAnyArgs with ParquetArgs

   Bcftools norm command line arguments.

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

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

5. #### class BcftoolsNormFnArgs extends Args4jBase

   Bcftools norm function arguments.

6. #### class BedtoolsIntersect extends BDGSparkCommand[BedtoolsIntersectArgs] with Logging

   Bedtools intersect command line wrapper.

7. #### class BedtoolsIntersectArgs extends BedtoolsIntersectFnArgs with ADAMSaveAnyArgs with ParquetArgs

   Bedtools intersect command line arguments.

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

   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

   Bedtools intersect function arguments.

10. #### class Bowtie extends BDGSparkCommand[BowtieArgs] with Logging

    Bowtie command line wrapper.

11. #### class Bowtie2 extends BDGSparkCommand[Bowtie2Args] with Logging

    Bowtie 2 command line wrapper.

12. #### class Bowtie2Args extends Bowtie2FnArgs with ADAMSaveAnyArgs with ParquetArgs

    Bowtie 2 command line arguments.

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

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

14. #### class Bowtie2FnArgs extends Args4jBase

    Bowtie 2 function arguments.

15. #### class BowtieArgs extends BowtieFnArgs with ADAMSaveAnyArgs with ParquetArgs

    Bowtie command line arguments.

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

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

17. #### class BowtieFnArgs extends Args4jBase

    Bowtie function arguments.

18. #### class Bwa extends BDGSparkCommand[BwaArgs] with Logging

    Bwa command line wrapper.

19. #### class BwaArgs extends BwaFnArgs with ADAMSaveAnyArgs with ParquetArgs

    Bwa command line arguments.

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

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

21. #### class BwaFnArgs extends Args4jBase

    Bwa function arguments.

22. #### class Cannoli extends Logging

    Cannoli main.

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

    Cannoli function.

    Cannoli function.

    X

      Cannoli function argument type parameter.

    Y

      Cannoli function result type parameter.

24. #### class CannoliModule extends AbstractModule with ScalaModule

    Cannoli module, binds the default list of command groups.

25. #### class Freebayes extends BDGSparkCommand[FreebayesArgs] with Logging

    Freebayes command line wrapper.

26. #### class FreebayesArgs extends FreebayesFnArgs with ADAMSaveAnyArgs with ParquetArgs

    Freebayes command line arguments.

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

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

28. #### class FreebayesFnArgs extends Args4jBase

    Freebayes function arguments.

29. #### class InterleaveFastq extends BDGSparkCommand[InterleaveFastqArgs] with Logging

    Interleaves two FASTQ files.

30. #### class InterleaveFastqArgs extends Args4jBase

31. #### class SampleReads extends BDGSparkCommand[SampleReadsArgs] with Logging

    Sample reads from interleaved FASTQ format.

32. #### class SampleReadsArgs extends Args4jBase with ADAMSaveAnyArgs with ParquetArgs

33. #### class SamtoolsMpileup extends BDGSparkCommand[SamtoolsMpileupArgs] with Logging

    Samtools mpileup command line wrapper.

34. #### class SamtoolsMpileupArgs extends SamtoolsMpileupFnArgs with ADAMSaveAnyArgs with ParquetArgs

    Samtools mpileup command line arguments.

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

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

36. #### class SamtoolsMpileupFnArgs extends Args4jBase

    Samtools mpileup function arguments.

37. #### class SnpEff extends BDGSparkCommand[SnpEffArgs] with Logging

    SnpEff command line wrapper.

38. #### class SnpEffArgs extends SnpEffFnArgs with ADAMSaveAnyArgs with ParquetArgs

    SnpEff command line arguments.

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

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

40. #### class SnpEffFnArgs extends Args4jBase

    SnpEff function arguments.

41. #### class VtNormalize extends BDGSparkCommand[VtNormalizeArgs] with Logging

    Vt normalize command line wrapper.

42. #### class VtNormalizeArgs extends VtNormalizeFnArgs with ADAMSaveAnyArgs with ParquetArgs

    Vt normalize command line arguments.

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

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

44. #### class VtNormalizeFnArgs extends Args4jBase

    Vt normalize function arguments.

### Value Members

1. #### object BcftoolsNorm extends BDGCommandCompanion

2. #### object BedtoolsIntersect extends BDGCommandCompanion

3. #### object Bowtie extends BDGCommandCompanion

4. #### object Bowtie2 extends BDGCommandCompanion

5. #### object Bwa extends BDGCommandCompanion

6. #### object Cannoli

7. #### object Freebayes extends BDGCommandCompanion

8. #### object InterleaveFastq extends BDGCommandCompanion

9. #### object SampleReads extends BDGCommandCompanion

10. #### object SamtoolsMpileup extends BDGCommandCompanion

11. #### object SnpEff extends BDGCommandCompanion

12. #### object VtNormalize extends BDGCommandCompanion

### Ungrouped