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org.bdgenomics.cannoli.Cannoli

CannoliAlignmentDataset

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 alignWithBwaMem(args: BwaMemArgs): AlignmentDataset

    Align the unaligned single-end reads in this AlignmentDataset with bwa mem via Cannoli.

    Align the unaligned single-end reads in this AlignmentDataset with bwa mem via Cannoli.

    args

    Bwa mem function arguments.

    returns

    AlignmentDataset.

  6. def alignWithBwaMem2(args: BwaMem2Args): AlignmentDataset

    Align the unaligned single-end reads in this AlignmentDataset with Bwa-mem2 via Cannoli.

    Align the unaligned single-end reads in this AlignmentDataset with Bwa-mem2 via Cannoli.

    args

    Bwa-mem2 function arguments.

    returns

    AlignmentDataset.

  7. def alignWithMinimap2(args: Minimap2Args): AlignmentDataset

    Align the unaligned single-end reads in this AlignmentDataset with Minimap2 via Cannoli.

    Align the unaligned single-end reads in this AlignmentDataset with Minimap2 via Cannoli.

    args

    Minimap2 function arguments.

    returns

    AlignmentDataset.

  8. 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.

  9. def alignWithUnimap(args: UnimapArgs): AlignmentDataset

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

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

    args

    Unimap function arguments.

    returns

    AlignmentDataset.

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

  12. 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.

  13. 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.

  14. def clone(): AnyRef
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