Packages

c

org.bdgenomics.cannoli.Cannoli

CannoliFragmentDataset

implicit class CannoliFragmentDataset extends AnyRef

Linear Supertypes
AnyRef, Any
Ordering
  1. Alphabetic
  2. By Inheritance
Inherited
  1. CannoliFragmentDataset
  2. AnyRef
  3. Any
  1. Hide All
  2. Show All
Visibility
  1. Public
  2. All

Instance Constructors

  1. new CannoliFragmentDataset(fragments: FragmentDataset)

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. def alignWithBowtie(args: BowtieArgs): AlignmentDataset

    Align the paired-end reads in this FragmentDataset with Bowtie via Cannoli.

    Align the paired-end reads in this FragmentDataset with Bowtie via Cannoli.

    args

    Bowtie function arguments.

    returns

    AlignmentDataset.

  5. def alignWithBowtie2(args: Bowtie2Args): AlignmentDataset

    Align the paired-end reads in this FragmentDataset with Bowtie 2 via Cannoli.

    Align the paired-end reads in this FragmentDataset with Bowtie 2 via Cannoli.

    args

    Bowtie2 function arguments.

    returns

    AlignmentDataset.

  6. def alignWithBwaMem(args: BwaMemArgs): AlignmentDataset

    Align the paired-end reads in this FragmentDataset with bwa mem via Cannoli.

    Align the paired-end reads in this FragmentDataset with bwa mem via Cannoli.

    args

    Bwa mem function arguments.

    returns

    AlignmentDataset.

  7. def alignWithBwaMem2(args: BwaMem2Args): AlignmentDataset

    Align the paired-end reads in this FragmentDataset with Bwa-mem2 via Cannoli.

    Align the paired-end reads in this FragmentDataset with Bwa-mem2 via Cannoli.

    args

    BwaMem2 function arguments.

    returns

    AlignmentDataset.

  8. def alignWithGem(args: GemArgs): AlignmentDataset

    Align the paired-end reads in this FragmentDataset with GEM-Mapper via Cannoli.

    Align the paired-end reads in this FragmentDataset with GEM-Mapper via Cannoli.

    args

    GEM-Mapper function arguments.

    returns

    AlignmentDataset.

  9. def alignWithMagicBlast(args: MagicBlastArgs): AlignmentDataset

    Align the paired-end reads in this FragmentDataset with Magic-BLAST via Cannoli.

    Align the paired-end reads in this FragmentDataset with Magic-BLAST via Cannoli.

    args

    Magic-BLAST function arguments.

    returns

    AlignmentDataset.

  10. def alignWithMinimap2(args: Minimap2Args): AlignmentDataset

    Align the paired-end reads in this FragmentDataset with Minimap2 via Cannoli.

    Align the paired-end reads in this FragmentDataset with Minimap2 via Cannoli.

    args

    Minimap2 function arguments.

    returns

    AlignmentDataset.

  11. def alignWithSnap(args: SnapArgs): AlignmentDataset

    Align the paired-end reads in this FragmentDataset with SNAP via Cannoli.

    Align the paired-end reads in this FragmentDataset with SNAP via Cannoli.

    args

    SNAP function arguments.

    returns

    AlignmentDataset.

  12. def alignWithStar(args: StarArgs): AlignmentDataset

    Align the paired-end reads in this FragmentDataset with STAR via Cannoli.

    Align the paired-end reads in this FragmentDataset with STAR via Cannoli.

    args

    STAR function arguments.

    returns

    AlignmentDataset.

  13. def alignWithUnimap(args: UnimapArgs): AlignmentDataset

    Align the paired-end reads in this FragmentDataset with Unimap via Cannoli.

    Align the paired-end reads in this FragmentDataset with Unimap via Cannoli.

    args

    Unimap function arguments.

    returns

    AlignmentDataset.

  14. final def asInstanceOf[T0]: T0
    Definition Classes
    Any
  15. def clone(): AnyRef
    Attributes
    protected[lang]
    Definition Classes
    AnyRef
    Annotations
    @throws( ... ) @native()
  16. final def eq(arg0: AnyRef): Boolean
    Definition Classes
    AnyRef
  17. def equals(arg0: Any): Boolean
    Definition Classes
    AnyRef → Any
  18. def finalize(): Unit
    Attributes
    protected[lang]
    Definition Classes
    AnyRef
    Annotations
    @throws( classOf[java.lang.Throwable] )
  19. final def getClass(): Class[_]
    Definition Classes
    AnyRef → Any
    Annotations
    @native()
  20. def hashCode(): Int
    Definition Classes
    AnyRef → Any
    Annotations
    @native()
  21. final def isInstanceOf[T0]: Boolean
    Definition Classes
    Any
  22. final def ne(arg0: AnyRef): Boolean
    Definition Classes
    AnyRef
  23. final def notify(): Unit
    Definition Classes
    AnyRef
    Annotations
    @native()
  24. final def notifyAll(): Unit
    Definition Classes
    AnyRef
    Annotations
    @native()
  25. final def synchronized[T0](arg0: ⇒ T0): T0
    Definition Classes
    AnyRef
  26. def toString(): String
    Definition Classes
    AnyRef → Any
  27. final def wait(): Unit
    Definition Classes
    AnyRef
    Annotations
    @throws( ... )
  28. final def wait(arg0: Long, arg1: Int): Unit
    Definition Classes
    AnyRef
    Annotations
    @throws( ... )
  29. final def wait(arg0: Long): Unit
    Definition Classes
    AnyRef
    Annotations
    @throws( ... ) @native()

Inherited from AnyRef

Inherited from Any

Ungrouped