org.bdgenomics.adam

# cli

#### package cli

Visibility

1. Public
2. All

### Type Members

1. #### class ADAM2Fasta extends BDGSparkCommand[ADAM2FastaArgs] with Logging

2. #### class ADAM2FastaArgs extends Args4jBase

3. #### class ADAM2Fastq extends BDGSparkCommand[ADAM2FastqArgs]

4. #### class ADAM2FastqArgs extends Args4jBase

5. #### class ADAMMain extends Logging

6. #### class ADAMModule extends AbstractModule with ScalaModule

7. #### final class About extends AnyRef

8. #### case class CommandGroup(name: String, commands: List[BDGCommandCompanion]) extends Product with Serializable

9. #### class CountContigKmers extends BDGSparkCommand[CountContigKmersArgs] with Logging

10. #### class CountContigKmersArgs extends Args4jBase with ParquetArgs

11. #### class CountReadKmers extends BDGSparkCommand[CountReadKmersArgs] with Logging

12. #### class CountReadKmersArgs extends Args4jBase with ParquetArgs

13. #### class Fasta2ADAM extends BDGSparkCommand[Fasta2ADAMArgs] with Logging

14. #### class Fasta2ADAMArgs extends Args4jBase with ParquetSaveArgs

15. #### class FlagStat extends BDGSparkCommand[FlagStatArgs]

16. #### class FlagStatArgs extends Args4jBase

17. #### class MergeShards extends BDGSparkCommand[MergeShardsArgs]

    A command to merge sharded files.

    A command to merge sharded files.

    This needs to be a Spark command in order to pull in the Hadoop Config via Spark. Also, this allows us to benefit from Spark's YARN/Mesos submission bits, etc.

18. #### class MergeShardsArgs extends Args4jBase

19. #### class PrintADAM extends BDGSparkCommand[PrintADAMArgs]

20. #### class PrintADAMArgs extends Args4jBase

21. #### class Reads2Coverage extends BDGSparkCommand[Reads2CoverageArgs]

22. #### class Reads2CoverageArgs extends Args4jBase with ParquetArgs

23. #### class TransformAlignments extends BDGSparkCommand[TransformAlignmentsArgs] with Logging

24. #### class TransformAlignmentsArgs extends Args4jBase with ADAMSaveAnyArgs with ParquetArgs

25. #### class TransformFeatures extends BDGSparkCommand[TransformFeaturesArgs]

26. #### class TransformFeaturesArgs extends Args4jBase with ParquetSaveArgs

27. #### class TransformFragments extends BDGSparkCommand[TransformFragmentsArgs] with Logging

28. #### class TransformFragmentsArgs extends Args4jBase with ADAMSaveAnyArgs with ParquetArgs

29. #### class TransformGenotypes extends BDGSparkCommand[TransformGenotypesArgs]

    Convert a file with genotypes into corresponding ADAM format and vice versa.

30. #### class TransformGenotypesArgs extends Args4jBase with ADAMSaveAnyArgs with ParquetArgs

31. #### class TransformVariants extends BDGSparkCommand[TransformVariantsArgs]

    Convert a file with variants into corresponding ADAM format and vice versa.

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

33. #### class View extends BDGSparkCommand[ViewArgs]

    The `adam view` command implements some of the functionality of `samtools view`, specifically the -f, -F, -c, and -o options, in an optionally distributed fashion.

    The `adam view` command implements some of the functionality of `samtools view`, specifically the -f, -F, -c, and -o options, in an optionally distributed fashion.

    It is agnostic to its input and output being SAM, BAM, or ADAM files; when printing to stdout it prints SAM.

34. #### class ViewArgs extends Args4jBase with ParquetArgs with ADAMSaveAnyArgs

### Value Members

1. #### object ADAM2Fasta extends BDGCommandCompanion

2. #### object ADAM2Fastq extends BDGCommandCompanion

3. #### object ADAMMain

4. #### object CountContigKmers extends BDGCommandCompanion

5. #### object CountReadKmers extends BDGCommandCompanion

6. #### object Fasta2ADAM extends BDGCommandCompanion

7. #### object FlagStat extends BDGCommandCompanion

8. #### object MergeShards extends BDGCommandCompanion

9. #### object PrintADAM extends BDGCommandCompanion

10. #### object Reads2Coverage extends BDGCommandCompanion

    Reads2Coverage (accessible as the command 'reads2coverage' through the CLI) takes two arguments, an INPUT and OUTPUT, and calculates the number of reads from INPUT at every location in the file.

    Reads2Coverage (accessible as the command 'reads2coverage' through the CLI) takes two arguments, an INPUT and OUTPUT, and calculates the number of reads from INPUT at every location in the file. Optional arguments are only_negative_strands, only_positive_strands and collapse. only_negative_strands and only_positive_strands save coverage computed from only negative and positive strands, respectively. Collapse specifies whether saved coverage should merge neighboring coverage with the same counts to one record.

11. #### object TransformAlignments extends BDGCommandCompanion

12. #### object TransformFeatures extends BDGCommandCompanion

13. #### object TransformFragments extends BDGCommandCompanion

14. #### object TransformGenotypes extends BDGCommandCompanion

15. #### object TransformVariants extends BDGCommandCompanion

16. #### object View extends BDGCommandCompanion

### Ungrouped