implicit class CannoliAlignmentDataset extends AnyRef
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- new CannoliAlignmentDataset(alignments: AlignmentDataset)
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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.
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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.
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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.
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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.
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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.
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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.
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final
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asInstanceOf[T0]: T0
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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.
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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.
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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.
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clone(): AnyRef
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