package cli

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Type Members

  1. final class About extends AnyRef

    About.

  2. class BcftoolsCall extends BDGSparkCommand[BcftoolsCallArgs] with Logging

    Bcftools call command line wrapper.

  3. class BcftoolsCallArgs extends cannoli.BcftoolsCallArgs with ADAMSaveAnyArgs with ParquetArgs

    Bcftools call command line arguments.

  4. class BcftoolsMpileup extends BDGSparkCommand[BcftoolsMpileupArgs] with Logging

    Bcftools mpileup command line wrapper.

  5. class BcftoolsMpileupArgs extends cannoli.BcftoolsMpileupArgs with ADAMSaveAnyArgs with ParquetArgs

    Bcftools mpileup command line arguments.

  6. class BcftoolsNorm extends BDGSparkCommand[BcftoolsNormArgs] with Logging

    Bcftools norm command line wrapper.

  7. class BcftoolsNormArgs extends cannoli.BcftoolsNormArgs with ADAMSaveAnyArgs with ParquetArgs

    Bcftools norm command line arguments.

  8. class BedtoolsIntersect extends BDGSparkCommand[BedtoolsIntersectArgs] with Logging

    Bedtools intersect command line wrapper.

  9. class BedtoolsIntersectArgs extends cannoli.BedtoolsIntersectArgs with ADAMSaveAnyArgs with ParquetArgs

    Bedtools intersect command line arguments.

  10. class Blastn extends BDGSparkCommand[BlastnArgs] with Logging

    Blastn command line wrapper.

  11. class BlastnArgs extends cannoli.BlastnArgs with ADAMSaveAnyArgs with ParquetArgs

    Blastn command line arguments.

  12. class Bowtie extends BDGSparkCommand[BowtieArgs] with Logging

    Bowtie command line wrapper.

  13. class Bowtie2 extends BDGSparkCommand[Bowtie2Args] with Logging

    Bowtie 2 command line wrapper.

  14. class Bowtie2Args extends cannoli.Bowtie2Args with ADAMSaveAnyArgs with CramArgs with ParquetArgs

    Bowtie 2 command line arguments.

  15. class BowtieArgs extends cannoli.BowtieArgs with ADAMSaveAnyArgs with CramArgs with ParquetArgs

    Bowtie command line arguments.

  16. class BwaMem extends BDGSparkCommand[BwaMemArgs] with Logging

    Bwa mem command line wrapper.

  17. class BwaMem2 extends BDGSparkCommand[BwaMem2Args] with Logging

    Bwa-mem2 command line wrapper.

  18. class BwaMem2Args extends cannoli.BwaMem2Args with ADAMSaveAnyArgs with CramArgs with ParquetArgs

    Bwa-mem2 command line arguments.

  19. class BwaMemArgs extends cannoli.BwaMemArgs with ADAMSaveAnyArgs with CramArgs with ParquetArgs

    Bwa mem command line arguments.

  20. class Cannoli extends Logging

    Cannoli main.

  21. class CannoliModule extends AbstractModule with ScalaModule

    Cannoli module, binds the default list of command groups.

  22. class Freebayes extends BDGSparkCommand[FreebayesArgs] with Logging

    Freebayes command line wrapper.

  23. class FreebayesArgs extends cannoli.FreebayesArgs with ADAMSaveAnyArgs with CramArgs with ParquetArgs

    Freebayes command line arguments.

  24. class Gem extends BDGSparkCommand[GemArgs] with Logging

    GEM-Mapper command line wrapper.

  25. class GemArgs extends cannoli.GemArgs with ADAMSaveAnyArgs with CramArgs with ParquetArgs

    GEM-Mapper command line arguments.

  26. class InterleaveFastq extends BDGSparkCommand[InterleaveFastqArgs] with Logging

    Interleaves two FASTQ files.

  27. class InterleaveFastqArgs extends Args4jBase
  28. class LongMinimap2 extends BDGSparkCommand[LongMinimap2Args] with Logging

    Long read Minimap2 command line wrapper.

  29. class LongMinimap2Args extends cannoli.Minimap2Args with ADAMSaveAnyArgs with ParquetArgs

    Long read Minimap2 command line arguments.

  30. class LongUnimap extends BDGSparkCommand[LongUnimapArgs] with Logging

    Long read Unimap command line wrapper.

  31. class LongUnimapArgs extends cannoli.UnimapArgs with ADAMSaveAnyArgs with ParquetArgs

    Long read Unimap command line arguments.

  32. class MagicBlast extends BDGSparkCommand[MagicBlastArgs] with Logging

    MagicBlast command line wrapper.

  33. class MagicBlastArgs extends cannoli.MagicBlastArgs with ADAMSaveAnyArgs with CramArgs with ParquetArgs

    Magic-BLAST command line arguments.

  34. class Minimap2 extends BDGSparkCommand[Minimap2Args] with Logging

    Minimap2 command line wrapper.

  35. class Minimap2Args extends cannoli.Minimap2Args with ADAMSaveAnyArgs with CramArgs with ParquetArgs

    Minimap2 command line arguments.

  36. class SampleReads extends BDGSparkCommand[SampleReadsArgs] with Logging

    Sample reads from interleaved FASTQ format.

  37. class SampleReadsArgs extends Args4jBase with ADAMSaveAnyArgs with CramArgs with ParquetArgs
  38. class SamtoolsMpileup extends BDGSparkCommand[SamtoolsMpileupArgs] with Logging

    Samtools mpileup command line wrapper.

  39. class SamtoolsMpileupArgs extends cannoli.SamtoolsMpileupArgs with ADAMSaveAnyArgs with CramArgs with ParquetArgs

    Samtools mpileup command line arguments.

  40. class SingleEndBowtie2 extends BDGSparkCommand[SingleEndBowtie2Args] with Logging

    Single-end read Bowtie 2 command line wrapper.

  41. class SingleEndBowtie2Args extends cannoli.SingleEndBowtie2Args with ADAMSaveAnyArgs with CramArgs with ParquetArgs

    Single-end read Bowtie 2 command line arguments.

  42. class SingleEndBwaMem extends BDGSparkCommand[SingleEndBwaMemArgs] with Logging

    Single-end read BwaMem command line wrapper.

  43. class SingleEndBwaMem2 extends BDGSparkCommand[SingleEndBwaMem2Args] with Logging

    Single-end read Bwa-mem2 command line wrapper.

  44. class SingleEndBwaMem2Args extends cannoli.BwaMem2Args with ADAMSaveAnyArgs with CramArgs with ParquetArgs

    Single-end read Bwa-mem2 command line arguments.

  45. class SingleEndBwaMemArgs extends cannoli.BwaMemArgs with ADAMSaveAnyArgs with CramArgs with ParquetArgs

    Single-end read Bwa mem command line arguments.

  46. class SingleEndMinimap2 extends BDGSparkCommand[SingleEndMinimap2Args] with Logging

    Single-end read Minimap2 command line wrapper.

  47. class SingleEndMinimap2Args extends cannoli.Minimap2Args with ADAMSaveAnyArgs with CramArgs with ParquetArgs

    Single-end read Minimap2 command line arguments.

  48. class SingleEndStar extends BDGSparkCommand[SingleEndStarArgs] with Logging

    Single-end read STAR-Mapper command line wrapper.

  49. class SingleEndStarArgs extends cannoli.SingleEndStarArgs with ADAMSaveAnyArgs with CramArgs with ParquetArgs

    Single-end read STAR-Mapper command line arguments.

  50. class SingleEndUnimap extends BDGSparkCommand[SingleEndUnimapArgs] with Logging

    Single-end read Unimap command line wrapper.

  51. class SingleEndUnimapArgs extends cannoli.UnimapArgs with ADAMSaveAnyArgs with CramArgs with ParquetArgs

    Single-end read Unimap command line arguments.

  52. class Snap extends BDGSparkCommand[SnapArgs] with Logging

    Scalable Nucleotide Alignment Program (SNAP) command line wrapper.

  53. class SnapArgs extends cannoli.SnapArgs with ADAMSaveAnyArgs with CramArgs with ParquetArgs

    Scalable Nucleotide Alignment Program (SNAP) command line arguments.

  54. class SnpEff extends BDGSparkCommand[SnpEffArgs] with Logging

    SnpEff command line wrapper.

  55. class SnpEffArgs extends cannoli.SnpEffArgs with ADAMSaveAnyArgs with ParquetArgs

    SnpEff command line arguments.

  56. class Star extends BDGSparkCommand[StarArgs] with Logging

    STAR-Mapper command line wrapper.

  57. class StarArgs extends cannoli.StarArgs with ADAMSaveAnyArgs with CramArgs with ParquetArgs

    STAR-Mapper command line arguments.

  58. class Unimap extends BDGSparkCommand[UnimapArgs] with Logging

    Unimap command line wrapper.

  59. class UnimapArgs extends cannoli.UnimapArgs with ADAMSaveAnyArgs with CramArgs with ParquetArgs

    Unimap command line arguments.

  60. class Vep extends BDGSparkCommand[VepArgs] with Logging

    Vep command line wrapper.

  61. class VepArgs extends cannoli.VepArgs with ADAMSaveAnyArgs with ParquetArgs

    Vep command line arguments.

  62. class VtNormalize extends BDGSparkCommand[VtNormalizeArgs] with Logging

    Vt normalize command line wrapper.

  63. class VtNormalizeArgs extends cannoli.VtNormalizeArgs with ADAMSaveAnyArgs with ParquetArgs

    Vt normalize command line arguments.

Value Members

  1. object BcftoolsCall extends BDGCommandCompanion
  2. object BcftoolsMpileup extends BDGCommandCompanion
  3. object BcftoolsNorm extends BDGCommandCompanion
  4. object BedtoolsIntersect extends BDGCommandCompanion
  5. object Blastn extends BDGCommandCompanion
  6. object Bowtie extends BDGCommandCompanion
  7. object Bowtie2 extends BDGCommandCompanion
  8. object BwaMem extends BDGCommandCompanion
  9. object BwaMem2 extends BDGCommandCompanion
  10. object Cannoli
  11. object Freebayes extends BDGCommandCompanion
  12. object Gem extends BDGCommandCompanion
  13. object InterleaveFastq extends BDGCommandCompanion
  14. object LongMinimap2 extends BDGCommandCompanion
  15. object LongUnimap extends BDGCommandCompanion
  16. object MagicBlast extends BDGCommandCompanion
  17. object Minimap2 extends BDGCommandCompanion
  18. object SampleReads extends BDGCommandCompanion
  19. object SamtoolsMpileup extends BDGCommandCompanion
  20. object SingleEndBowtie2 extends BDGCommandCompanion
  21. object SingleEndBwaMem extends BDGCommandCompanion
  22. object SingleEndBwaMem2 extends BDGCommandCompanion
  23. object SingleEndMinimap2 extends BDGCommandCompanion
  24. object SingleEndStar extends BDGCommandCompanion
  25. object SingleEndUnimap extends BDGCommandCompanion
  26. object Snap extends BDGCommandCompanion
  27. object SnpEff extends BDGCommandCompanion
  28. object Star extends BDGCommandCompanion
  29. object Unimap extends BDGCommandCompanion
  30. object Vep extends BDGCommandCompanion
  31. object VtNormalize extends BDGCommandCompanion

Ungrouped