org.bdgenomics.adam

# cli

#### package cli

Visibility

1. Public
2. All

### Type Members

1. #### class ADAM2Vcf extends ADAMSparkCommand[ADAM2VcfArgs] with DictionaryCommand with Logging

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

3. #### trait ADAMCommand extends Runnable

4. #### trait ADAMCommandCompanion extends AnyRef

5. #### trait ADAMSparkCommand [A <: Args4jBase] extends ADAMCommand with Logging

6. #### class Adam2Fastq extends ADAMSparkCommand[Adam2FastqArgs]

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

8. #### class AlleleCount extends ADAMSparkCommand[AlleleCountArgs] with Logging

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

10. #### class Args4jBase extends AnyRef

11. #### class Bam2ADAM extends ADAMCommand

12. #### class Bam2ADAMArgs extends Args4jBase with ParquetArgs

13. #### class BuildInformation extends ADAMCommand

14. #### class CalculateDepth extends ADAMSparkCommand[CalculateDepthArgs]

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

16. #### class CompareADAM extends ADAMSparkCommand[CompareADAMArgs] with Serializable

17. #### class CompareADAMArgs extends Args4jBase with ParquetArgs with Serializable

18. #### class CountKmers extends ADAMSparkCommand[CountKmersArgs] with Logging

19. #### class CountKmersArgs extends Args4jBase with ParquetArgs

20. #### trait DictionaryCommand extends AnyRef

21. #### class Fasta2ADAM extends ADAMSparkCommand[Fasta2ADAMArgs] with Logging

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

23. #### class Features2ADAM extends ADAMSparkCommand[Features2ADAMArgs]

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

25. #### class FindReads extends ADAMSparkCommand[FindReadsArgs] with Serializable

26. #### class FindReadsArgs extends Args4jBase with ParquetArgs with Serializable

27. #### class FlagStat extends ADAMSparkCommand[FlagStatArgs]

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

29. #### case class FreqJson (base: Long, freq: Long) extends Product with Serializable

30. #### class GenotypeConcordance extends ADAMSparkCommand[GenotypeConcordanceArgs] with Logging

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

32. #### class ListDict extends ADAMSparkCommand[ListDictArgs]

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

34. #### trait LoadFileArgs extends AnyRef

35. #### class MpileupArgs extends Args4jBase

36. #### class MpileupCommand extends ADAMSparkCommand[MpileupArgs] with Logging

37. #### trait ParquetArgs extends Args4jBase with ADAMParquetArgs

38. #### trait ParquetLoadSaveArgs extends Args4jBase with ParquetSaveArgs with LoadFileArgs with SaveFileArgs

39. #### trait ParquetSaveArgs extends Args4jBase with ParquetArgs with ADAMSaveArgs

40. #### class PluginExecutor extends ADAMSparkCommand[PluginExecutorArgs]

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

42. #### class PrintADAM extends ADAMSparkCommand[PrintADAMArgs]

43. #### class PrintADAMArgs extends Args4jBase

44. #### class PrintGenes extends ADAMSparkCommand[PrintGenesArgs] with Serializable

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

46. #### class PrintTags extends ADAMSparkCommand[PrintTagsArgs]

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

48. #### class Reads2Ref extends ADAMSparkCommand[Reads2RefArgs]

49. #### class Reads2RefArgs extends Args4jBase with ParquetSaveArgs

50. #### trait SaveFileArgs extends AnyRef

51. #### class SummarizeGenotypes extends ADAMSparkCommand[SummarizeGenotypesArgs] with Logging

52. #### class SummarizeGenotypesArgs extends Args4jBase with ParquetArgs

53. #### case class TrackJson (readName: String, start: Long, end: Long, track: Long) extends Product with Serializable

54. #### class Transform extends ADAMSparkCommand[TransformArgs] with Logging

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

56. #### case class VariationJson (contigName: String, alleles: String, start: Long, end: Long, track: Long) extends Product with Serializable

57. #### class Vcf2ADAM extends ADAMSparkCommand[Vcf2ADAMArgs] with DictionaryCommand with Logging

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

59. #### class VcfAnnotation2ADAM extends ADAMSparkCommand[VcfAnnotation2ADAMArgs] with Logging

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

61. #### class View extends ADAMSparkCommand[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.

62. #### class ViewArgs extends Args4jBase with ParquetArgs with ADAMSaveArgs

63. #### class VizReads extends ADAMSparkCommand[VizReadsArgs]

64. #### class VizReadsArgs extends Args4jBase with ParquetArgs

65. #### class VizServlet extends ScalatraServlet with JacksonJsonSupport

66. #### class Wig2BedArgs extends Args4jBase

67. #### class WigFix2Bed extends ADAMCommand

### Value Members

1. #### object ADAM2Vcf extends ADAMCommandCompanion

2. #### object ADAMMain extends Logging

3. #### object Adam2Fastq extends ADAMCommandCompanion

4. #### object AlleleCount extends ADAMCommandCompanion

5. #### object AlleleCountHelper extends Serializable

6. #### object Args4j

7. #### object Bam2ADAM extends ADAMCommandCompanion

8. #### object BuildInformation extends ADAMCommandCompanion

9. #### object CalculateDepth extends ADAMCommandCompanion

   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.

10. #### object CompareADAM extends ADAMCommandCompanion with Serializable

    CompareADAM is a tool for pairwise comparison of ADAM files (or merged sets of ADAM files, see the note on the -recurse{1,2} optional parameters, below).

11. #### object CountKmers extends ADAMCommandCompanion

12. #### object Fasta2ADAM extends ADAMCommandCompanion

13. #### object Features2ADAM extends ADAMCommandCompanion

14. #### object FindReads extends ADAMCommandCompanion with Serializable

    FindReads is an auxiliary command to CompareADAM -- whereas CompareADAM takes two ADAM files (which presumably contain the same reads, processed differently), joins them based on read-name, and computes aggregates of one or more metrics (BucketComparisons) across those joined reads -- FindReads performs the same join-and-metric-computation, but takes a second argument as well: a boolean condition on the value(s) of the metric(s) computed.

15. #### object FlagStat extends ADAMCommandCompanion

16. #### object GenotypeConcordance extends ADAMCommandCompanion

17. #### object ListDict extends ADAMCommandCompanion

18. #### object MpileupCommand extends ADAMCommandCompanion

19. #### object PluginExecutor extends ADAMCommandCompanion

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

20. #### object PrintADAM extends ADAMCommandCompanion

21. #### object PrintGenes extends ADAMCommandCompanion with Serializable

22. #### object PrintTags extends ADAMCommandCompanion

    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.

23. #### object Reads2Ref extends ADAMCommandCompanion

24. #### object SummarizeGenotypes extends ADAMCommandCompanion

25. #### object Transform extends ADAMCommandCompanion

26. #### object Vcf2ADAM extends ADAMCommandCompanion

27. #### object VcfAnnotation2ADAM extends ADAMCommandCompanion

28. #### object View extends ADAMCommandCompanion

29. #### object VizReads extends ADAMCommandCompanion

30. #### object WigFix2Bed extends ADAMCommandCompanion

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

### Ungrouped