Packages

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_QUALITY_SCORES: String

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

    Hadoop configuration path to check for a boolean value indicating whether the current or original read quality scores should be written. True indicates to write the original quality scores. 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
    @native() @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
    Annotations
    @native()
  15. def hashCode(): Int
    Definition Classes
    AnyRef → Any
    Annotations
    @native()
  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
    Annotations
    @native()
  19. final def notifyAll(): Unit
    Definition Classes
    AnyRef
    Annotations
    @native()
  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
    @native() @throws( ... )

Inherited from AnyRef

Inherited from Any

Ungrouped