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 with ParquetLoadSaveArgs

3. #### class ADAM2Vcf extends BDGSparkCommand[ADAM2VcfArgs] with DictionaryCommand with Logging

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

5. #### class ADAMMain extends Logging

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

7. #### final class About extends AnyRef

8. #### class Adam2Fastq extends BDGSparkCommand[Adam2FastqArgs]

9. #### class Adam2FastqArgs extends Args4jBase with ParquetLoadSaveArgs

10. #### class AlleleCount extends BDGSparkCommand[AlleleCountArgs] with Logging

11. #### class AlleleCountArgs extends Args4jBase with ParquetArgs

12. #### class CalculateDepth extends BDGSparkCommand[CalculateDepthArgs]

13. #### class CalculateDepthArgs extends Args4jBase with ParquetArgs

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

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

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

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

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

19. #### trait DictionaryCommand extends AnyRef

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

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

22. #### class Features2ADAM extends BDGSparkCommand[Features2ADAMArgs]

23. #### class Features2ADAMArgs extends Args4jBase with ParquetSaveArgs

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

25. #### class FlagStatArgs extends Args4jBase with ParquetArgs

26. #### class Flatten extends BDGSparkCommand[FlattenArgs] with Logging

27. #### class FlattenArgs extends Args4jBase with ParquetSaveArgs

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

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

30. #### class ListDict extends BDGSparkCommand[ListDictArgs]

31. #### class ListDictArgs extends Args4jBase with ParquetArgs

32. #### class PluginExecutor extends BDGSparkCommand[PluginExecutorArgs]

33. #### class PluginExecutorArgs extends Args4jBase with ParquetArgs

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

35. #### class PrintADAMArgs extends Args4jBase

36. #### class PrintGenes extends BDGSparkCommand[PrintGenesArgs] with Serializable

37. #### class PrintGenesArgs extends Args4jBase with ParquetArgs with Serializable

38. #### class PrintTags extends BDGSparkCommand[PrintTagsArgs]

39. #### class PrintTagsArgs extends Args4jBase with ParquetArgs

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

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

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

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

44. #### class Vcf2ADAM extends BDGSparkCommand[Vcf2ADAMArgs] with DictionaryCommand with Logging

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

46. #### class VcfAnnotation2ADAM extends BDGSparkCommand[VcfAnnotation2ADAMArgs] with Logging

47. #### class VcfAnnotation2ADAMArgs extends Args4jBase with ParquetSaveArgs

48. #### 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.

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

50. #### class Wig2BedArgs extends Args4jBase

51. #### class WigFix2Bed extends BDGCommand

### Value Members

1. #### object ADAM2Fasta extends BDGCommandCompanion

2. #### object ADAM2Vcf extends BDGCommandCompanion

3. #### object ADAMMain

4. #### object Adam2Fastq extends BDGCommandCompanion

5. #### object AlleleCount extends BDGCommandCompanion

6. #### object AlleleCountHelper extends Serializable

7. #### object CalculateDepth extends BDGCommandCompanion

   CalculateDepth (accessible as the command 'depth' through the CLI) takes two arguments, an Read file and a VCF (or equivalent) file, and calculates the number of reads (the 'depth') from the Read file which overlap each of the variants given by the VCF.

   CalculateDepth (accessible as the command 'depth' through the CLI) takes two arguments, an Read file and a VCF (or equivalent) file, and calculates the number of reads (the 'depth') from the Read file which overlap each of the variants given by the VCF. It then reports, on standard out, the location and name of each variant along with the calculated depth.

8. #### object CountContigKmers extends BDGCommandCompanion

9. #### object CountReadKmers extends BDGCommandCompanion

10. #### object Fasta2ADAM extends BDGCommandCompanion

11. #### object Features2ADAM extends BDGCommandCompanion

12. #### object FlagStat extends BDGCommandCompanion

13. #### object Flatten extends BDGCommandCompanion

14. #### object Fragments2Reads extends BDGCommandCompanion

15. #### object ListDict extends BDGCommandCompanion

16. #### object PluginExecutor extends BDGCommandCompanion

    This set of classes executes a plugin along with the associated input location.

    This set of classes executes a plugin along with the associated input location.

    Example usage: adam plugin org.bdgenomics.adam.plugins.Take10Plugin reads12.sam

    `org.bdgenomics.adam.plugins.Take10Plugin` is a simple example plugin. The org.bdgenomics.adam.plugins.ADAMPlugin interface defines the class that will run using this command.

17. #### object PrintADAM extends BDGCommandCompanion

18. #### object PrintGenes extends BDGCommandCompanion with Serializable

19. #### object PrintTags extends BDGCommandCompanion

    Reads in the tagStrings field of every record, and prints out the set of unique tags found in those fields along with the number of records that have each particular tag.

20. #### object Reads2Fragments extends BDGCommandCompanion

21. #### object Transform extends BDGCommandCompanion

22. #### object Vcf2ADAM extends BDGCommandCompanion

23. #### object VcfAnnotation2ADAM extends BDGCommandCompanion

24. #### object View extends BDGCommandCompanion

25. #### object WigFix2Bed extends BDGCommandCompanion

    WigFix2Bed (accessible as the command "wigfix2bed" through the CLI) takes fixed wiggle file and converts it to a BED formatted file.

    WigFix2Bed (accessible as the command "wigfix2bed" through the CLI) takes fixed wiggle file and converts it to a BED formatted file. The wiggle file is a text based format that implements run-length encoding, without any guarantees where the sync markers are. This makes it difficult to use as a "splittable" format, and necessitates processing the file locally.

### Ungrouped