# CannoliFragmentDataset - Cannoli_2.11: Core 0.8.0 API - org.bdgenomics.cannoli.Cannoli.CannoliFragmentDataset
CannoliFragmentDataset - Cannoli 2.11 Core 0.8.0 API - org.bdgenomics.cannoli.Cannoli.CannoliFragmentDataset
Keywords: CannoliFragmentDataset Cannoli 2.11 Core 0.8.0 API org.bdgenomics.cannoli.Cannoli.CannoliFragmentDataset

org.bdgenomics.cannoli.Cannoli

# CannoliFragmentDataset

###
Related Doc: package Cannoli

#### implicit class CannoliFragmentDataset extends AnyRef

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### Instance Constructors

1. #### new CannoliFragmentDataset(fragments: FragmentDataset)

### Value Members

1. #### final def !=(arg0: Any): Boolean

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2. #### final def ##(): Int

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3. #### final def ==(arg0: Any): Boolean

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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 alignWithBwa(args: BwaArgs): AlignmentDataset

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

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

   args

     Bwa function arguments.

   returns

     AlignmentDataset.

7. #### 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.

8. #### 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.

9. #### 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.

10. #### 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.

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

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

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

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

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

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

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

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

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

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

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

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

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