org.bdgenomics.cannoli

# cli

#### package cli

Visibility

1. Public
2. All

### Type Members

1. #### final class About extends AnyRef

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

   Bcftools mpileup command line wrapper.

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

   Bcftools mpileup command line arguments.

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

   Bcftools norm command line wrapper.

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

   Bcftools norm command line arguments.

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

   Bedtools intersect command line wrapper.

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

   Bedtools intersect command line arguments.

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

   Bowtie command line wrapper.

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

   Bowtie 2 command line wrapper.

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

    Bowtie 2 command line arguments.

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

    Bowtie command line arguments.

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

    Bwa command line wrapper.

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

    Bwa command line arguments.

14. #### class Cannoli extends Logging

    Cannoli main.

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

    Cannoli module, binds the default list of command groups.

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

    Freebayes command line wrapper.

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

    Freebayes command line arguments.

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

    GEM-Mapper command line wrapper.

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

    GEM-Mapper command line arguments.

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

    Interleaves two FASTQ files.

21. #### class InterleaveFastqArgs extends Args4jBase

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

    Minimap2 command line wrapper.

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

    Minimap2 command line arguments.

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

    Sample reads from interleaved FASTQ format.

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

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

    Samtools mpileup command line wrapper.

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

    Samtools mpileup command line arguments.

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

    SnpEff command line wrapper.

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

    SnpEff command line arguments.

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

    Vep command line wrapper.

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

    Vep command line arguments.

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

    Vt normalize command line wrapper.

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

    Vt normalize command line arguments.

### Value Members

1. #### object BcftoolsMpileup extends BDGCommandCompanion

2. #### object BcftoolsNorm extends BDGCommandCompanion

3. #### object BedtoolsIntersect extends BDGCommandCompanion

4. #### object Bowtie extends BDGCommandCompanion

5. #### object Bowtie2 extends BDGCommandCompanion

6. #### object Bwa extends BDGCommandCompanion

7. #### object Cannoli

8. #### object Freebayes extends BDGCommandCompanion

9. #### object Gem extends BDGCommandCompanion

10. #### object InterleaveFastq extends BDGCommandCompanion

11. #### object Minimap2 extends BDGCommandCompanion

12. #### object SampleReads extends BDGCommandCompanion

13. #### object SamtoolsMpileup extends BDGCommandCompanion

14. #### object SnpEff extends BDGCommandCompanion

15. #### object Vep extends BDGCommandCompanion

16. #### object VtNormalize extends BDGCommandCompanion

### Ungrouped