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 ADAM2Vcf extends BDGSparkCommand[ADAM2VcfArgs] with Logging

6. #### class ADAM2VcfArgs extends Args4jBase with ParquetArgs

7. #### class ADAMMain extends Logging

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

9. #### final class About extends AnyRef

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

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

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

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

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

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

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

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

18. #### class FlagStatArgs extends Args4jBase

19. #### class Fragments2Reads extends BDGSparkCommand[Fragments2ReadsArgs] with Logging

20. #### class Fragments2ReadsArgs extends Args4jBase with ADAMSaveAnyArgs with ParquetArgs

21. #### 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.

22. #### class MergeShardsArgs extends Args4jBase

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

24. #### class PrintADAMArgs extends Args4jBase

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

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

27. #### class Reads2Fragments extends BDGSparkCommand[Reads2FragmentsArgs] with Logging

28. #### class Reads2FragmentsArgs extends Args4jBase with ADAMSaveAnyArgs with ParquetArgs

29. #### class Transform extends BDGSparkCommand[TransformArgs] with Logging

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

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

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

33. #### class Vcf2ADAM extends BDGSparkCommand[Vcf2ADAMArgs] with Logging

34. #### class Vcf2ADAMArgs extends Args4jBase with ParquetSaveArgs

35. #### 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.

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

### Value Members

1. #### object ADAM2Fasta extends BDGCommandCompanion

2. #### object ADAM2Fastq extends BDGCommandCompanion

3. #### object ADAM2Vcf extends BDGCommandCompanion

4. #### object ADAMMain

5. #### object CountContigKmers extends BDGCommandCompanion

6. #### object CountReadKmers extends BDGCommandCompanion

7. #### object Fasta2ADAM extends BDGCommandCompanion

8. #### object FlagStat extends BDGCommandCompanion

9. #### object Fragments2Reads extends BDGCommandCompanion

10. #### object MergeShards extends BDGCommandCompanion

11. #### object PrintADAM extends BDGCommandCompanion

12. #### 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.

13. #### object Reads2Fragments extends BDGCommandCompanion

14. #### object Transform extends BDGCommandCompanion

15. #### object TransformFeatures extends BDGCommandCompanion

16. #### object Vcf2ADAM extends BDGCommandCompanion

17. #### object View extends BDGCommandCompanion

### Ungrouped