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 ADAM2Fastq extends BDGSparkCommand[ADAM2FastqArgs]

4. #### class ADAM2FastqArgs extends Args4jBase with ParquetLoadSaveArgs

5. #### class ADAM2Vcf extends BDGSparkCommand[ADAM2VcfArgs] with DictionaryCommand 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. #### 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 FlagStat extends BDGSparkCommand[FlagStatArgs]

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

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

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

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

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

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

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

30. #### 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.

31. #### class MergeShardsArgs extends Args4jBase

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

33. #### class PrintADAMArgs extends Args4jBase

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

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

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

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

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

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

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

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

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

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

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

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

46. #### 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.

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

48. #### class Wig2BedArgs extends Args4jBase

49. #### class WigFix2Bed extends BDGCommand

### Value Members

1. #### object ADAM2Fasta extends BDGCommandCompanion

2. #### object ADAM2Fastq extends BDGCommandCompanion

3. #### object ADAM2Vcf extends BDGCommandCompanion

4. #### object ADAMMain

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 FlagStat extends BDGCommandCompanion

12. #### object Flatten extends BDGCommandCompanion

13. #### object Fragments2Reads extends BDGCommandCompanion

14. #### object ListDict extends BDGCommandCompanion

15. #### object MergeShards extends BDGCommandCompanion

16. #### object PrintADAM extends BDGCommandCompanion

17. #### 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.

18. #### object Reads2Fragments extends BDGCommandCompanion

19. #### object Transform extends BDGCommandCompanion

20. #### object TransformFeatures extends BDGCommandCompanion

21. #### object Vcf2ADAM extends BDGCommandCompanion

22. #### object VcfAnnotation2ADAM extends BDGCommandCompanion

23. #### object View extends BDGCommandCompanion

24. #### 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