org.bdgenomics.adam.rdd.fragment

# FragmentDataset

###
Related Docs: class FragmentDataset | package fragment

#### object FragmentDataset

Helper singleton object for building FragmentDatasets.

Linear Supertypes
AnyRef, Any
Ordering

1. Alphabetic
2. By Inheritance

Inherited

1. FragmentDataset
2. AnyRef
3. Any

1. Hide All
2. Show All

Visibility

1. Public
2. All

### 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. #### val WRITE_ORIGINAL_QUALITIES: String

   Hadoop configuration path to check for a boolean value indicating whether the current or original read qualities should be written.

   Hadoop configuration path to check for a boolean value indicating whether the current or original read qualities should be written. True indicates to write the original qualities. The default is false.

5. #### val WRITE_SUFFIXES: String

   Hadoop configuration path to check for a boolean value indicating whether to write the "/1" "/2" suffixes to the read name that indicate whether a read is first or second in a pair.

   Hadoop configuration path to check for a boolean value indicating whether to write the "/1" "/2" suffixes to the read name that indicate whether a read is first or second in a pair. Default is false (no suffixes).

6. #### def apply(ds: Dataset[Fragment], sequences: SequenceDictionary, readGroups: ReadGroupDictionary, processingSteps: Seq[ProcessingStep]): FragmentDataset

   A genomic dataset that supports Datasets of Fragments.

   A genomic dataset that supports Datasets of Fragments.

   ds

     The underlying Dataset of Fragment data.

   sequences

     The genomic sequences this data was aligned to, if any.

   readGroups

     The read groups these Fragments came from.

   processingSteps

     The processing steps that have been applied to this data.

   returns

     A new FragmentDataset.

7. #### def apply(ds: Dataset[Fragment]): FragmentDataset

   A genomic dataset that supports Datasets of Fragments.

   A genomic dataset that supports Datasets of Fragments.

   ds

     The underlying Dataset of Fragment data.

   returns

     A new FragmentDataset.

8. #### def apply(rdd: RDD[Fragment], sequences: SequenceDictionary, readGroups: ReadGroupDictionary, processingSteps: Seq[ProcessingStep]): FragmentDataset

   Builds a FragmentDataset without a partition map.

   Builds a FragmentDataset without a partition map.

   rdd

     The underlying Fragment RDD.

   sequences

     The sequence dictionary for the genomic dataset.

   readGroups

     The read group dictionary for the genomic dataset.

   processingSteps

     The processing steps that have been applied to this data.

   returns

     A new FragmentDataset.

9. #### final def asInstanceOf[T0]: T0

   Definition Classes
     Any

10. #### def clone(): AnyRef

    Attributes
      protected[java.lang]
    Definition Classes
      AnyRef
    Annotations
      @throws( ... )

11. #### final def eq(arg0: AnyRef): Boolean

    Definition Classes
      AnyRef

12. #### def equals(arg0: Any): Boolean

    Definition Classes
      AnyRef → Any

13. #### def finalize(): Unit

    Attributes
      protected[java.lang]
    Definition Classes
      AnyRef
    Annotations
      @throws( classOf[java.lang.Throwable] )

14. #### final def getClass(): Class[_]

    Definition Classes
      AnyRef → Any

15. #### def hashCode(): Int

    Definition Classes
      AnyRef → Any

16. #### final def isInstanceOf[T0]: Boolean

    Definition Classes
      Any

17. #### final def ne(arg0: AnyRef): Boolean

    Definition Classes
      AnyRef

18. #### final def notify(): Unit

    Definition Classes
      AnyRef

19. #### final def notifyAll(): Unit

    Definition Classes
      AnyRef

20. #### final def synchronized[T0](arg0: ⇒ T0): T0

    Definition Classes
      AnyRef

21. #### def toString(): String

    Definition Classes
      AnyRef → Any

22. #### final def wait(): Unit

    Definition Classes
      AnyRef
    Annotations
      @throws( ... )

23. #### final def wait(arg0: Long, arg1: Int): Unit

    Definition Classes
      AnyRef
    Annotations
      @throws( ... )

24. #### final def wait(arg0: Long): Unit

    Definition Classes
      AnyRef
    Annotations
      @throws( ... )

### Inherited from AnyRef

### Inherited from Any

### Ungrouped