ADAM_2.12: CLI 0.36.0 API < Back
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# Packages

-  package root
  Definition Classes
    root
-  package org
  Definition Classes
    root
-  package bdgenomics
  Definition Classes
    org
-  package adam
  Definition Classes
    bdgenomics
-  package cli
  Definition Classes
    adam
- ADAM2Fastq
- ADAM2FastqArgs
- ADAMMain
- ADAMModule
- About
- CommandGroup
- CountReadKmers
- CountReadKmersArgs
- CountSliceKmers
- CountSliceKmersArgs
- Coverage
- CoverageArgs
- FlagStat
- FlagStatArgs
- MergeShards
- MergeShardsArgs
- PrintADAM
- PrintADAMArgs
- TransformAlignments
- TransformAlignmentsArgs
- TransformFeatures
- TransformFeaturesArgs
- TransformFragments
- TransformFragmentsArgs
- TransformGenotypes
- TransformGenotypesArgs
- TransformSequences
- TransformSequencesArgs
- TransformSlices
- TransformSlicesArgs
- TransformVariants
- TransformVariantsArgs
- View
- ViewArgs

c

org.bdgenomics.adam.cli

# TransformFragmentsArgs 

###

#### class TransformFragmentsArgs extends Args4jBase with ADAMSaveAnyArgs with ParquetArgs with CramArgs

Linear Supertypes
CramArgs, ParquetArgs, ADAMSaveAnyArgs, SaveArgs, ParquetRDDArgs, Args4jBase, AnyRef, Any
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Ordering

1. Alphabetic
2. By Inheritance

Inherited

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

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Visibility

1. Public
2. All

### Instance Constructors

1.  new TransformFragmentsArgs()

### 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.  final def asInstanceOf[T0]: T0
   Definition Classes
     Any
5.  var asSingleFile: Boolean
   Definition Classes
     TransformFragmentsArgs → ADAMSaveAnyArgs
6.  var binQualityScores: String
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.  def configureCramFormat(sc: SparkContext): Option[Unit]

    Configure CRAM format.

    Configure CRAM format.

    sc

      Spark context to configure

    Definition Classes
      CramArgs
11.  val cramReference: String
    Definition Classes
      CramArgs
    Annotations
      @Option()
12.  var deferMerging: Boolean
    Definition Classes
      TransformFragmentsArgs → ADAMSaveAnyArgs
13.  val disableDictionaryEncoding: Boolean
    Definition Classes
      ParquetArgs → ParquetRDDArgs
    Annotations
      @Option()
14.  var disableFastConcat: Boolean
    Definition Classes
      TransformFragmentsArgs → ADAMSaveAnyArgs
15.  var doPrintUsage: Boolean
    Definition Classes
      Args4jBase
16.  final def eq(arg0: AnyRef): Boolean
    Definition Classes
      AnyRef
17.  def equals(arg0: Any): Boolean
    Definition Classes
      AnyRef → Any
18.  final def getClass(): Class[_]
    Definition Classes
      AnyRef → Any
    Annotations
      @native() @HotSpotIntrinsicCandidate()
19.  def hashCode(): Int
    Definition Classes
      AnyRef → Any
    Annotations
      @native() @HotSpotIntrinsicCandidate()
20.  var inputPath: String
21.  final def isInstanceOf[T0]: Boolean
    Definition Classes
      Any
22.  var loadAsAlignments: Boolean
23.  val logLevel: String
    Definition Classes
      ParquetArgs
    Annotations
      @Option()
24.  var markDuplicates: Boolean
25.  var maxReadLength: Int
26.  final def ne(arg0: AnyRef): Boolean
    Definition Classes
      AnyRef
27.  final def notify(): Unit
    Definition Classes
      AnyRef
    Annotations
      @native() @HotSpotIntrinsicCandidate()
28.  final def notifyAll(): Unit
    Definition Classes
      AnyRef
    Annotations
      @native() @HotSpotIntrinsicCandidate()
29.  var outputPath: String
    Definition Classes
      TransformFragmentsArgs → SaveArgs
30.  val pageSize: Int
    Definition Classes
      ParquetArgs → ParquetRDDArgs
    Annotations
      @Option()
31.  var pairedFastqFile: String
32.  var saveAsAlignments: Boolean
33.  var sortByReadName: Boolean
34.  var sortByReferencePosition: Boolean
35.  var sortByReferencePositionAndIndex: Boolean
36.  var sortFastqOutput: Boolean
    Definition Classes
      TransformFragmentsArgs → ADAMSaveAnyArgs
37.  final def synchronized[T0](arg0: ⇒ T0): T0
    Definition Classes
      AnyRef
38.  def toString(): String
    Definition Classes
      AnyRef → Any
39.  final def wait(arg0: Long, arg1: Int): Unit
    Definition Classes
      AnyRef
    Annotations
      @throws( ... )
40.  final def wait(arg0: Long): Unit
    Definition Classes
      AnyRef
    Annotations
      @throws( ... ) @native()
41.  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 CramArgs

### Inherited from ParquetArgs

### Inherited from ADAMSaveAnyArgs

### Inherited from SaveArgs

### Inherited from ParquetRDDArgs

### Inherited from Args4jBase

### Inherited from AnyRef

### Inherited from Any

### Ungrouped