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

org.bdgenomics.cannoli.Cannoli

# CannoliAlignmentDataset

###
Related Doc: package Cannoli

#### implicit class CannoliAlignmentDataset extends AnyRef

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### Instance Constructors

1. #### new CannoliAlignmentDataset(alignments: AlignmentDataset)

### 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 alignWithBowtie2(args: SingleEndBowtie2Args): AlignmentDataset

   Align the unaligned single-end reads in this AlignmentDataset with Bowtie 2 via Cannoli.

   Align the unaligned single-end reads in this AlignmentDataset with Bowtie 2 via Cannoli.

   args

     Bowtie 2 function arguments.

   returns

     AlignmentDataset.

5. #### def alignWithStar(args: SingleEndStarArgs): AlignmentDataset

   Align the unaligned single-end reads in this AlignmentDataset with STAR-Mapper via Cannoli.

   Align the unaligned single-end reads in this AlignmentDataset with STAR-Mapper via Cannoli.

   args

     STAR-Mapper function arguments.

   returns

     AlignmentDataset.

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

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7. #### def callVariantsWithBcftoolsMpileup(args: BcftoolsMpileupArgs, stringency: ValidationStringency = ValidationStringency.LENIENT): VariantContextDataset

   Call variants from the alignments in this AlignmentDataset with bcftools mpileup via Cannoli.

   Call variants from the alignments in this AlignmentDataset with bcftools mpileup via Cannoli.

   args

     Bcftools mpileup function arguments.

   stringency

     Validation stringency. Defaults to ValidationStringency.LENIENT.

   returns

     VariantContextDataset.

8. #### def callVariantsWithFreebayes(args: FreebayesArgs, stringency: ValidationStringency = ValidationStringency.LENIENT): VariantContextDataset

   Call variants from the alignments in this AlignmentDataset with Freebayes via Cannoli.

   Call variants from the alignments in this AlignmentDataset with Freebayes via Cannoli.

   args

     Freebayes function arguments.

   stringency

     Validation stringency. Defaults to ValidationStringency.LENIENT.

   returns

     VariantContextDataset.

9. #### def callVariantsWithSamtoolsMpileup(args: SamtoolsMpileupArgs, stringency: ValidationStringency = ValidationStringency.LENIENT): VariantContextDataset

   Call variants from the alignments in this AlignmentDataset with samtools mpileup via Cannoli.

   Call variants from the alignments in this AlignmentDataset with samtools mpileup via Cannoli.

   args

     Samtools mpileup function arguments.

   stringency

     Validation stringency. Defaults to ValidationStringency.LENIENT.

   returns

     VariantContextDataset.

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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### Inherited from AnyRef

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