Cannoli_2.12: CLI 0.14.0 API < Back
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# Packages

-  package root
  Definition Classes
    root
-  package org
  Definition Classes
    root
-  package bdgenomics
  Definition Classes
    org
-  package cannoli
  Definition Classes
    bdgenomics
-  package cli
  Definition Classes
    cannoli
- About
- BcftoolsCall
- BcftoolsCallArgs
- BcftoolsMpileup
- BcftoolsMpileupArgs
- BcftoolsNorm
- BcftoolsNormArgs
- BedtoolsIntersect
- BedtoolsIntersectArgs
- Blastn
- BlastnArgs
- Bowtie
- Bowtie2
- Bowtie2Args
- BowtieArgs
- BwaMem
- BwaMem2
- BwaMem2Args
- BwaMemArgs
- Cannoli
- CannoliModule
- Freebayes
- FreebayesArgs
- Gem
- GemArgs
- InterleaveFastq
- InterleaveFastqArgs
- LongMinimap2
- LongMinimap2Args
- LongUnimap
- LongUnimapArgs
- MagicBlast
- MagicBlastArgs
- Minimap2
- Minimap2Args
- SampleReads
- SampleReadsArgs
- SamtoolsMpileup
- SamtoolsMpileupArgs
- SingleEndBowtie2
- SingleEndBowtie2Args
- SingleEndMinimap2
- SingleEndMinimap2Args
- SingleEndStar
- SingleEndStarArgs
- SingleEndUnimap
- SingleEndUnimapArgs
- Snap
- SnapArgs
- SnpEff
- SnpEffArgs
- Star
- StarArgs
- Unimap
- UnimapArgs
- Vep
- VepArgs
- VtNormalize
- VtNormalizeArgs

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org.bdgenomics.cannoli

# cli 

#### package cli

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Ordering

1. Alphabetic

Visibility

1. Public
2. All

### 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 SingleEndMinimap2 extends BDGSparkCommand[SingleEndMinimap2Args] with Logging

    Single-end read Minimap2 command line wrapper.

43.  class SingleEndMinimap2Args extends cannoli.Minimap2Args with ADAMSaveAnyArgs with CramArgs with ParquetArgs

    Single-end read Minimap2 command line arguments.

44.  class SingleEndStar extends BDGSparkCommand[SingleEndStarArgs] with Logging

    Single-end read STAR-Mapper command line wrapper.

45.  class SingleEndStarArgs extends cannoli.SingleEndStarArgs with ADAMSaveAnyArgs with CramArgs with ParquetArgs

    Single-end read STAR-Mapper command line arguments.

46.  class SingleEndUnimap extends BDGSparkCommand[SingleEndUnimapArgs] with Logging

    Single-end read Unimap command line wrapper.

47.  class SingleEndUnimapArgs extends cannoli.UnimapArgs with ADAMSaveAnyArgs with CramArgs with ParquetArgs

    Single-end read Unimap command line arguments.

48.  class Snap extends BDGSparkCommand[SnapArgs] with Logging

    Scalable Nucleotide Alignment Program (SNAP) command line wrapper.

49.  class SnapArgs extends cannoli.SnapArgs with ADAMSaveAnyArgs with CramArgs with ParquetArgs

    Scalable Nucleotide Alignment Program (SNAP) command line arguments.

50.  class SnpEff extends BDGSparkCommand[SnpEffArgs] with Logging

    SnpEff command line wrapper.

51.  class SnpEffArgs extends cannoli.SnpEffArgs with ADAMSaveAnyArgs with ParquetArgs

    SnpEff command line arguments.

52.  class Star extends BDGSparkCommand[StarArgs] with Logging

    STAR-Mapper command line wrapper.

53.  class StarArgs extends cannoli.StarArgs with ADAMSaveAnyArgs with CramArgs with ParquetArgs

    STAR-Mapper command line arguments.

54.  class Unimap extends BDGSparkCommand[UnimapArgs] with Logging

    Unimap command line wrapper.

55.  class UnimapArgs extends cannoli.UnimapArgs with ADAMSaveAnyArgs with CramArgs with ParquetArgs

    Unimap command line arguments.

56.  class Vep extends BDGSparkCommand[VepArgs] with Logging

    Vep command line wrapper.

57.  class VepArgs extends cannoli.VepArgs with ADAMSaveAnyArgs with ParquetArgs

    Vep command line arguments.

58.  class VtNormalize extends BDGSparkCommand[VtNormalizeArgs] with Logging

    Vt normalize command line wrapper.

59.  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 SingleEndMinimap2 extends BDGCommandCompanion
22.  object SingleEndStar extends BDGCommandCompanion
23.  object SingleEndUnimap extends BDGCommandCompanion
24.  object Snap extends BDGCommandCompanion
25.  object SnpEff extends BDGCommandCompanion
26.  object Star extends BDGCommandCompanion
27.  object Unimap extends BDGCommandCompanion
28.  object Vep extends BDGCommandCompanion
29.  object VtNormalize extends BDGCommandCompanion

### Ungrouped