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

c

org.bdgenomics.cannoli.cli

# BcftoolsNormArgs 

###

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

Bcftools norm command line arguments.

Linear Supertypes
ParquetArgs, ADAMSaveAnyArgs, SaveArgs, ParquetRDDArgs, cannoli.BcftoolsNormArgs, Args4jBase, AnyRef, Any
 
Ordering

1. Alphabetic
2. By Inheritance

Inherited

1. BcftoolsNormArgs
2. ParquetArgs
3. ADAMSaveAnyArgs
4. SaveArgs
5. ParquetRDDArgs
6. BcftoolsNormArgs
7. Args4jBase
8. AnyRef
9. Any

1. Hide All
2. Show All

Visibility

1. Public
2. All

### Instance Constructors

1.  new BcftoolsNormArgs()

### Value Members

1.  final def !=(arg0: Any): Boolean
   Definition Classes
     AnyRef → Any
2.  final def ##(): Int
   Definition Classes
     AnyRef → Any
3.  final def ==(arg0: Any): Boolean
   Definition Classes
     AnyRef → Any
4.  var addFiles: Boolean
   Definition Classes
     BcftoolsNormArgs
5.  final def asInstanceOf[T0]: T0
   Definition Classes
     Any
6.  var asSingleFile: Boolean
   Definition Classes
     BcftoolsNormArgs → ADAMSaveAnyArgs
7.  val blockSize: Int
   Definition Classes
     ParquetArgs → ParquetRDDArgs
   Annotations
     @Option()
8.  def clone(): AnyRef
   Attributes
     protected[lang]
   Definition Classes
     AnyRef
   Annotations
     @throws( ... ) @native() @HotSpotIntrinsicCandidate()
9.  val compressionCodec: CompressionCodecName
   Definition Classes
     ParquetArgs → ParquetRDDArgs
   Annotations
     @Option()
10.  var deferMerging: Boolean
    Definition Classes
      BcftoolsNormArgs → ADAMSaveAnyArgs
11.  val disableDictionaryEncoding: Boolean
    Definition Classes
      ParquetArgs → ParquetRDDArgs
    Annotations
      @Option()
12.  var disableFastConcat: Boolean
    Definition Classes
      BcftoolsNormArgs → ADAMSaveAnyArgs
13.  var doPrintUsage: Boolean
    Definition Classes
      Args4jBase
14.  final def eq(arg0: AnyRef): Boolean
    Definition Classes
      AnyRef
15.  def equals(arg0: Any): Boolean
    Definition Classes
      AnyRef → Any
16.  var executable: String
    Definition Classes
      BcftoolsNormArgs
17.  final def getClass(): Class[_]
    Definition Classes
      AnyRef → Any
    Annotations
      @native() @HotSpotIntrinsicCandidate()
18.  def hashCode(): Int
    Definition Classes
      AnyRef → Any
    Annotations
      @native() @HotSpotIntrinsicCandidate()
19.  var image: String
    Definition Classes
      BcftoolsNormArgs
20.  var inputPath: String
21.  final def isInstanceOf[T0]: Boolean
    Definition Classes
      Any
22.  val logLevel: String
    Definition Classes
      ParquetArgs
    Annotations
      @Option()
23.  final def ne(arg0: AnyRef): Boolean
    Definition Classes
      AnyRef
24.  final def notify(): Unit
    Definition Classes
      AnyRef
    Annotations
      @native() @HotSpotIntrinsicCandidate()
25.  final def notifyAll(): Unit
    Definition Classes
      AnyRef
    Annotations
      @native() @HotSpotIntrinsicCandidate()
26.  var outputPath: String
    Definition Classes
      BcftoolsNormArgs → SaveArgs
27.  val pageSize: Int
    Definition Classes
      ParquetArgs → ParquetRDDArgs
    Annotations
      @Option()
28.  var referencePath: String
    Definition Classes
      BcftoolsNormArgs
29.  var sortFastqOutput: Boolean
    Definition Classes
      BcftoolsNormArgs → ADAMSaveAnyArgs
30.  var stringency: String
31.  var sudo: Boolean
    Definition Classes
      BcftoolsNormArgs
32.  final def synchronized[T0](arg0: ⇒ T0): T0
    Definition Classes
      AnyRef
33.  def toString(): String
    Definition Classes
      AnyRef → Any
34.  var useDocker: Boolean
    Definition Classes
      BcftoolsNormArgs
35.  var useSingularity: Boolean
    Definition Classes
      BcftoolsNormArgs
36.  final def wait(arg0: Long, arg1: Int): Unit
    Definition Classes
      AnyRef
    Annotations
      @throws( ... )
37.  final def wait(arg0: Long): Unit
    Definition Classes
      AnyRef
    Annotations
      @throws( ... ) @native()
38.  final def wait(): Unit
    Definition Classes
      AnyRef
    Annotations
      @throws( ... )

### Deprecated Value Members

1.  def finalize(): Unit
   Attributes
     protected[lang]
   Definition Classes
     AnyRef
   Annotations
     @throws( classOf[java.lang.Throwable] ) @Deprecated @deprecated
   Deprecated

     (Since version ) see corresponding Javadoc for more information.

### Inherited from ParquetArgs

### Inherited from ADAMSaveAnyArgs

### Inherited from SaveArgs

### Inherited from ParquetRDDArgs

### Inherited from cannoli.BcftoolsNormArgs

### Inherited from Args4jBase

### Inherited from AnyRef

### Inherited from Any

### Ungrouped