Package

org.bdgenomics.adam

cli

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package cli

Visibility
  1. Public
  2. All

Type Members

  1. class ADAM2Fasta extends BDGSparkCommand[ADAM2FastaArgs] with Logging

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  2. class ADAM2FastaArgs extends Args4jBase with ParquetLoadSaveArgs

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  3. class ADAM2Fastq extends BDGSparkCommand[ADAM2FastqArgs]

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  4. class ADAM2FastqArgs extends Args4jBase with ParquetLoadSaveArgs

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  5. class ADAM2Vcf extends BDGSparkCommand[ADAM2VcfArgs] with DictionaryCommand with Logging

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  6. class ADAM2VcfArgs extends Args4jBase with ParquetArgs

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  7. class ADAMMain extends Logging

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  8. class ADAMModule extends AbstractModule with ScalaModule

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  9. final class About extends AnyRef

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  10. class AlleleCount extends BDGSparkCommand[AlleleCountArgs] with Logging

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  11. class AlleleCountArgs extends Args4jBase with ParquetArgs

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  12. class CalculateDepth extends BDGSparkCommand[CalculateDepthArgs]

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  13. class CalculateDepthArgs extends Args4jBase with ParquetArgs

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

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  15. class CountContigKmers extends BDGSparkCommand[CountContigKmersArgs] with Logging

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  16. class CountContigKmersArgs extends Args4jBase with ParquetArgs

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  17. class CountReadKmers extends BDGSparkCommand[CountReadKmersArgs] with Logging

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  18. class CountReadKmersArgs extends Args4jBase with ParquetArgs

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  19. trait DictionaryCommand extends AnyRef

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  20. class Fasta2ADAM extends BDGSparkCommand[Fasta2ADAMArgs] with Logging

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  21. class Fasta2ADAMArgs extends Args4jBase with ParquetSaveArgs

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  22. class FlagStat extends BDGSparkCommand[FlagStatArgs]

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  23. class FlagStatArgs extends Args4jBase with ParquetArgs

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  24. class Flatten extends BDGSparkCommand[FlattenArgs] with Logging

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  25. class FlattenArgs extends Args4jBase with ParquetSaveArgs

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  26. class Fragments2Reads extends BDGSparkCommand[Fragments2ReadsArgs] with Logging

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  27. class Fragments2ReadsArgs extends Args4jBase with ADAMSaveAnyArgs with ParquetArgs

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  28. class ListDict extends BDGSparkCommand[ListDictArgs]

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  29. class ListDictArgs extends Args4jBase with ParquetArgs

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  30. class MergeShards extends BDGSparkCommand[MergeShardsArgs]

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    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

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  32. class PrintADAM extends BDGSparkCommand[PrintADAMArgs]

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  33. class PrintADAMArgs extends Args4jBase

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  34. class Reads2Coverage extends BDGSparkCommand[Reads2CoverageArgs]

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  35. class Reads2CoverageArgs extends Args4jBase with ParquetArgs

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  36. class Reads2Fragments extends BDGSparkCommand[Reads2FragmentsArgs] with Logging

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  37. class Reads2FragmentsArgs extends Args4jBase with ADAMSaveAnyArgs with ParquetArgs

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  38. class Transform extends BDGSparkCommand[TransformArgs] with Logging

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  39. class TransformArgs extends Args4jBase with ADAMSaveAnyArgs with ParquetArgs

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  40. class TransformFeatures extends BDGSparkCommand[TransformFeaturesArgs]

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  41. class TransformFeaturesArgs extends Args4jBase with ParquetSaveArgs

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

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  43. class Vcf2ADAMArgs extends Args4jBase with ParquetSaveArgs

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  44. class VcfAnnotation2ADAM extends BDGSparkCommand[VcfAnnotation2ADAMArgs] with Logging

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  45. class VcfAnnotation2ADAMArgs extends Args4jBase with ParquetSaveArgs

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  46. class View extends BDGSparkCommand[ViewArgs]

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    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

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  48. class Wig2BedArgs extends Args4jBase

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  49. class WigFix2Bed extends BDGCommand

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Value Members

  1. object ADAM2Fasta extends BDGCommandCompanion

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  2. object ADAM2Fastq extends BDGCommandCompanion

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  3. object ADAM2Vcf extends BDGCommandCompanion

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  4. object ADAMMain

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  5. object AlleleCount extends BDGCommandCompanion

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  6. object AlleleCountHelper extends Serializable

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  7. object CalculateDepth extends BDGCommandCompanion

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    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

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  9. object CountReadKmers extends BDGCommandCompanion

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  10. object Fasta2ADAM extends BDGCommandCompanion

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  11. object FlagStat extends BDGCommandCompanion

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  12. object Flatten extends BDGCommandCompanion

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  13. object Fragments2Reads extends BDGCommandCompanion

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  14. object ListDict extends BDGCommandCompanion

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  15. object MergeShards extends BDGCommandCompanion

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  16. object PrintADAM extends BDGCommandCompanion

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  17. object Reads2Coverage extends BDGCommandCompanion

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    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

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  19. object Transform extends BDGCommandCompanion

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  20. object TransformFeatures extends BDGCommandCompanion

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  21. object Vcf2ADAM extends BDGCommandCompanion

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  22. object VcfAnnotation2ADAM extends BDGCommandCompanion

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  23. object View extends BDGCommandCompanion

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  24. object WigFix2Bed extends BDGCommandCompanion

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    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.

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