org.bdgenomics.cannoli

# cli

#### package cli

Visibility

1. Public
2. All

### Type Members

1. #### final class About extends AnyRef

2. #### class Bcftools extends BDGSparkCommand[BcftoolsArgs] with Logging

   Bcftools.

3. #### class BcftoolsArgs extends Args4jBase with ADAMSaveAnyArgs with ParquetArgs

4. #### class Bedtools extends BDGSparkCommand[BedtoolsArgs] with Logging

   Bedtools.

5. #### class BedtoolsArgs extends Args4jBase with ADAMSaveAnyArgs with ParquetArgs

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

   Bowtie.

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

   Bowtie 2.

8. #### class Bowtie2Args extends Args4jBase with ADAMSaveAnyArgs with ParquetArgs

9. #### class BowtieArgs extends Args4jBase with ADAMSaveAnyArgs with ParquetArgs

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

    Bwa.

11. #### class BwaArgs extends Args4jBase with ADAMSaveAnyArgs with ParquetArgs

12. #### class Cannoli extends Logging

    Cannoli main.

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

    Cannoli module, binds the default list of command groups.

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

    Freebayes.

15. #### class FreebayesArgs extends Args4jBase with ADAMSaveAnyArgs with ParquetArgs

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

    Interleaves two FASTQ files.

17. #### class InterleaveFastqArgs extends Args4jBase

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

    Sample reads from interleaved FASTQ format.

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

20. #### class Samtools extends BDGSparkCommand[SamtoolsArgs] with Logging

    Samtools.

21. #### class SamtoolsArgs extends Args4jBase with ADAMSaveAnyArgs with ParquetArgs

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

    SnpEff.

23. #### class SnpEffArgs extends Args4jBase with ADAMSaveAnyArgs with ParquetArgs

24. #### class Vt extends BDGSparkCommand[VtArgs] with Logging

    Vt.

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

### Value Members

1. #### object Bcftools extends BDGCommandCompanion

2. #### object Bedtools 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 Samtools extends BDGCommandCompanion

11. #### object SnpEff extends BDGCommandCompanion

12. #### object Vt extends BDGCommandCompanion

### Ungrouped