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

org.bdgenomics.cannoli

# cli

#### package cli

Visibility

1. Public
2. All

### Type Members

1. #### final class About extends AnyRef

2. #### class BcftoolsCall extends BDGSparkCommand[BcftoolsCallArgs] with Logging

   Bcftools call command line wrapper.

3. #### class BcftoolsCallArgs extends cannoli.BcftoolsCallArgs with ADAMSaveAnyArgs with ParquetArgs

   Bcftools call command line arguments.

4. #### class BcftoolsMpileup extends BDGSparkCommand[BcftoolsMpileupArgs] with Logging

   Bcftools mpileup command line wrapper.

5. #### class BcftoolsMpileupArgs extends cannoli.BcftoolsMpileupArgs with ADAMSaveAnyArgs with ParquetArgs

   Bcftools mpileup command line arguments.

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

   Bcftools norm command line wrapper.

7. #### class BcftoolsNormArgs extends cannoli.BcftoolsNormArgs with ADAMSaveAnyArgs with ParquetArgs

   Bcftools norm command line arguments.

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

   Bedtools intersect command line wrapper.

9. #### class BedtoolsIntersectArgs extends cannoli.BedtoolsIntersectArgs with ADAMSaveAnyArgs with ParquetArgs

   Bedtools intersect command line arguments.

10. #### class Blastn extends BDGSparkCommand[BlastnArgs] with Logging

    Blastn command line wrapper.

11. #### class BlastnArgs extends cannoli.BlastnArgs with ADAMSaveAnyArgs with ParquetArgs

    Blastn command line arguments.

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

    Bowtie command line wrapper.

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

    Bowtie 2 command line wrapper.

14. #### class Bowtie2Args extends cannoli.Bowtie2Args with ADAMSaveAnyArgs with ParquetArgs

    Bowtie 2 command line arguments.

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

    Bowtie command line arguments.

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

    Bwa command line wrapper.

17. #### class BwaArgs extends cannoli.BwaArgs with ADAMSaveAnyArgs with ParquetArgs

    Bwa command line arguments.

18. #### class Cannoli extends Logging

    Cannoli main.

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

    Cannoli module, binds the default list of command groups.

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

    Freebayes command line wrapper.

21. #### class FreebayesArgs extends cannoli.FreebayesArgs with ADAMSaveAnyArgs with ParquetArgs

    Freebayes command line arguments.

22. #### class Gem extends BDGSparkCommand[GemArgs] with Logging

    GEM-Mapper command line wrapper.

23. #### class GemArgs extends cannoli.GemArgs with ADAMSaveAnyArgs with ParquetArgs

    GEM-Mapper command line arguments.

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

    Interleaves two FASTQ files.

25. #### class InterleaveFastqArgs extends Args4jBase

26. #### class MagicBlast extends BDGSparkCommand[MagicBlastArgs] with Logging

    MagicBlast command line wrapper.

27. #### class MagicBlastArgs extends cannoli.MagicBlastArgs with ADAMSaveAnyArgs with ParquetArgs

    Magic-BLAST command line arguments.

28. #### class Minimap2 extends BDGSparkCommand[Minimap2Args] with Logging

    Minimap2 command line wrapper.

29. #### class Minimap2Args extends cannoli.Minimap2Args with ADAMSaveAnyArgs with ParquetArgs

    Minimap2 command line arguments.

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

    Sample reads from interleaved FASTQ format.

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

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

    Samtools mpileup command line wrapper.

33. #### class SamtoolsMpileupArgs extends cannoli.SamtoolsMpileupArgs with ADAMSaveAnyArgs with ParquetArgs

    Samtools mpileup command line arguments.

34. #### class SingleEndBowtie2 extends BDGSparkCommand[SingleEndBowtie2Args] with Logging

    Single-end read Bowtie 2 command line wrapper.

35. #### class SingleEndBowtie2Args extends cannoli.SingleEndBowtie2Args with ADAMSaveAnyArgs with ParquetArgs

    Single-end read Bowtie 2 command line arguments.

36. #### class SingleEndStar extends BDGSparkCommand[SingleEndStarArgs] with Logging

    Single-end read STAR-Mapper command line wrapper.

37. #### class SingleEndStarArgs extends cannoli.SingleEndStarArgs with ADAMSaveAnyArgs with ParquetArgs

    Single-end read STAR-Mapper command line arguments.

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

    SnpEff command line wrapper.

39. #### class SnpEffArgs extends cannoli.SnpEffArgs with ADAMSaveAnyArgs with ParquetArgs

    SnpEff command line arguments.

40. #### class Star extends BDGSparkCommand[StarArgs] with Logging

    STAR-Mapper command line wrapper.

41. #### class StarArgs extends cannoli.StarArgs with ADAMSaveAnyArgs with ParquetArgs

    STAR-Mapper command line arguments.

42. #### class Vep extends BDGSparkCommand[VepArgs] with Logging

    Vep command line wrapper.

43. #### class VepArgs extends cannoli.VepArgs with ADAMSaveAnyArgs with ParquetArgs

    Vep command line arguments.

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

    Vt normalize command line wrapper.

45. #### class VtNormalizeArgs extends cannoli.VtNormalizeArgs with ADAMSaveAnyArgs with ParquetArgs

    Vt normalize command line arguments.

### Value Members

1. #### object BcftoolsCall extends BDGCommandCompanion

2. #### object BcftoolsMpileup extends BDGCommandCompanion

3. #### object BcftoolsNorm extends BDGCommandCompanion

4. #### object BedtoolsIntersect extends BDGCommandCompanion

5. #### object Blastn extends BDGCommandCompanion

6. #### object Bowtie extends BDGCommandCompanion

7. #### object Bowtie2 extends BDGCommandCompanion

8. #### object Bwa extends BDGCommandCompanion

9. #### object Cannoli

10. #### object Freebayes extends BDGCommandCompanion

11. #### object Gem extends BDGCommandCompanion

12. #### object InterleaveFastq extends BDGCommandCompanion

13. #### object MagicBlast extends BDGCommandCompanion

14. #### object Minimap2 extends BDGCommandCompanion

15. #### object SampleReads extends BDGCommandCompanion

16. #### object SamtoolsMpileup extends BDGCommandCompanion

17. #### object SingleEndBowtie2 extends BDGCommandCompanion

18. #### object SingleEndStar extends BDGCommandCompanion

19. #### object SnpEff extends BDGCommandCompanion

20. #### object Star extends BDGCommandCompanion

21. #### object Vep extends BDGCommandCompanion

22. #### object VtNormalize extends BDGCommandCompanion

### Ungrouped