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org.bdgenomics.cannoli.Cannoli

CannoliReadDataset

implicit class CannoliReadDataset extends AnyRef

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Instance Constructors

  1. new CannoliReadDataset(reads: ReadDataset)

Value Members

  1. final def !=(arg0: Any): Boolean
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  4. def alignWithBowtie2(args: SingleEndBowtie2Args): AlignmentDataset

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

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

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

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

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

    args

    Minimap2 function arguments.

    returns

    AlignmentDataset.

  8. def alignWithStar(args: SingleEndStarArgs): AlignmentDataset

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

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

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

    args

    Unimap function arguments.

    returns

    AlignmentDataset.

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