Package

org.bdgenomics.cannoli

cli

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package cli

Visibility
  1. Public
  2. All

Type Members

  1. final class About extends AnyRef

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  2. class BcftoolsMpileup extends BDGSparkCommand[BcftoolsMpileupArgs] with Logging

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    Bcftools mpileup command line wrapper.

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

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    Bcftools mpileup command line arguments.

  4. class BcftoolsNorm extends BDGSparkCommand[BcftoolsNormArgs] with Logging

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    Bcftools norm command line wrapper.

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

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    Bcftools norm command line arguments.

  6. class BedtoolsIntersect extends BDGSparkCommand[BedtoolsIntersectArgs] with Logging

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    Bedtools intersect command line wrapper.

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

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    Bedtools intersect command line arguments.

  8. class Bowtie extends BDGSparkCommand[BowtieArgs] with Logging

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    Bowtie command line wrapper.

  9. class Bowtie2 extends BDGSparkCommand[Bowtie2Args] with Logging

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    Bowtie 2 command line wrapper.

  10. class Bowtie2Args extends cannoli.Bowtie2Args with ADAMSaveAnyArgs with ParquetArgs

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    Bowtie 2 command line arguments.

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

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    Bowtie command line arguments.

  12. class Bwa extends BDGSparkCommand[BwaArgs] with Logging

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    Bwa command line wrapper.

  13. class BwaArgs extends cannoli.BwaArgs with ADAMSaveAnyArgs with ParquetArgs

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    Bwa command line arguments.

  14. class Cannoli extends Logging

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    Cannoli main.

  15. class CannoliModule extends AbstractModule with ScalaModule

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    Cannoli module, binds the default list of command groups.

  16. class Freebayes extends BDGSparkCommand[FreebayesArgs] with Logging

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    Freebayes command line wrapper.

  17. class FreebayesArgs extends cannoli.FreebayesArgs with ADAMSaveAnyArgs with ParquetArgs

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    Freebayes command line arguments.

  18. class Gem extends BDGSparkCommand[GemArgs] with Logging

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    GEM-Mapper command line wrapper.

  19. class GemArgs extends cannoli.GemArgs with ADAMSaveAnyArgs with ParquetArgs

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    GEM-Mapper command line arguments.

  20. class InterleaveFastq extends BDGSparkCommand[InterleaveFastqArgs] with Logging

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    Interleaves two FASTQ files.

  21. class InterleaveFastqArgs extends Args4jBase

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  22. class Minimap2 extends BDGSparkCommand[Minimap2Args] with Logging

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    Minimap2 command line wrapper.

  23. class Minimap2Args extends cannoli.Minimap2Args with ADAMSaveAnyArgs with ParquetArgs

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    Minimap2 command line arguments.

  24. class SampleReads extends BDGSparkCommand[SampleReadsArgs] with Logging

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    Sample reads from interleaved FASTQ format.

  25. class SampleReadsArgs extends Args4jBase with ADAMSaveAnyArgs with ParquetArgs

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  26. class SamtoolsMpileup extends BDGSparkCommand[SamtoolsMpileupArgs] with Logging

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    Samtools mpileup command line wrapper.

  27. class SamtoolsMpileupArgs extends cannoli.SamtoolsMpileupArgs with ADAMSaveAnyArgs with ParquetArgs

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    Samtools mpileup command line arguments.

  28. class SnpEff extends BDGSparkCommand[SnpEffArgs] with Logging

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    SnpEff command line wrapper.

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

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    SnpEff command line arguments.

  30. class Vep extends BDGSparkCommand[VepArgs] with Logging

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    Vep command line wrapper.

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

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    Vep command line arguments.

  32. class VtNormalize extends BDGSparkCommand[VtNormalizeArgs] with Logging

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    Vt normalize command line wrapper.

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

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    Vt normalize command line arguments.

Value Members

  1. object BcftoolsMpileup extends BDGCommandCompanion

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  2. object BcftoolsNorm extends BDGCommandCompanion

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  3. object BedtoolsIntersect extends BDGCommandCompanion

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  4. object Bowtie extends BDGCommandCompanion

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  5. object Bowtie2 extends BDGCommandCompanion

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  6. object Bwa extends BDGCommandCompanion

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  7. object Cannoli

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  8. object Freebayes extends BDGCommandCompanion

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  9. object Gem extends BDGCommandCompanion

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  10. object InterleaveFastq extends BDGCommandCompanion

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  11. object Minimap2 extends BDGCommandCompanion

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  12. object SampleReads extends BDGCommandCompanion

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  13. object SamtoolsMpileup extends BDGCommandCompanion

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  14. object SnpEff extends BDGCommandCompanion

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  15. object Vep extends BDGCommandCompanion

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  16. object VtNormalize extends BDGCommandCompanion

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