package cannoli
- Alphabetic
- Public
- All
Type Members
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class
BcftoolsCall extends CannoliFn[VariantContextDataset, VariantContextDataset]
Bcftools call wrapper as a function VariantContextDataset → VariantContextDataset, for use in cannoli-shell or notebooks.
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class
BcftoolsCallArgs extends Args4jBase
Bcftools call function arguments.
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class
BcftoolsMpileup extends CannoliFn[AlignmentDataset, VariantContextDataset]
Bcftools mpileup wrapper as a function AlignmentDataset → VariantContextDataset, for use in cannoli-shell or notebooks.
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class
BcftoolsMpileupArgs extends Args4jBase
Bcftools mpileup function arguments.
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class
BcftoolsNorm extends CannoliFn[VariantContextDataset, VariantContextDataset]
Bcftools norm wrapper as a function VariantContextDataset → VariantContextDataset, for use in cannoli-shell or notebooks.
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class
BcftoolsNormArgs extends Args4jBase
Bcftools norm function arguments.
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class
BedtoolsIntersect extends CannoliFn[FeatureDataset, FeatureDataset]
Bedtools intersect wrapper as a function FeatureDataset → FeatureDataset, for use in cannoli-shell or notebooks.
Bedtools intersect wrapper as a function FeatureDataset → FeatureDataset, for use in cannoli-shell or notebooks.
val args = new BedtoolsIntersectFnArgs() args.b = "foo.bed" args.useDocker = true val features = ... val pipedFeatures = new BedtoolsIntersectFn(args, sc).apply(features)
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class
BedtoolsIntersectArgs extends Args4jBase
Bedtools intersect function arguments.
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class
Blastn extends CannoliFn[SequenceDataset, AlignmentDataset]
Blastn wrapper as a function SequenceDataset → AlignmentDataset, for use in cannoli-shell or notebooks.
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class
BlastnArgs extends Args4jBase
Blastn function arguments.
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class
Bowtie extends CannoliFn[FragmentDataset, AlignmentDataset]
Bowtie wrapper as a function FragmentDataset → AlignmentDataset, for use in cannoli-shell or notebooks.
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class
Bowtie2 extends CannoliFn[FragmentDataset, AlignmentDataset]
Bowtie 2 wrapper as a function FragmentDataset → AlignmentDataset, for use in cannoli-shell or notebooks.
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class
Bowtie2Args extends Args4jBase
Bowtie 2 function arguments.
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class
BowtieArgs extends Args4jBase
Bowtie function arguments.
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class
BwaMem extends CannoliFn[FragmentDataset, AlignmentDataset]
Bwa mem wrapper as a function FragmentDataset → AlignmentDataset, for use in cannoli-shell or notebooks.
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class
BwaMem2 extends CannoliFn[FragmentDataset, AlignmentDataset]
Bwa-mem2 wrapper as a function FragmentDataset → AlignmentDataset, for use in cannoli-shell or notebooks.
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class
BwaMem2Args extends ReadGroupArgs
Bwa-mem2 function arguments.
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class
BwaMemArgs extends ReadGroupArgs
Bwa mem function arguments.
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abstract
class
CannoliFn[X, Y] extends (X) ⇒ Y with Logging
Cannoli function.
Cannoli function.
- X
Cannoli function argument type parameter.
- Y
Cannoli function result type parameter.
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class
Freebayes extends CannoliFn[AlignmentDataset, VariantContextDataset]
Freebayes wrapper as a function AlignmentDataset → VariantContextDataset, for use in cannoli-shell or notebooks.
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class
FreebayesArgs extends Args4jBase
Freebayes function arguments.
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class
Gem extends CannoliFn[FragmentDataset, AlignmentDataset]
GEM-Mapper wrapper as a function FragmentDataset → AlignmentDataset, for use in cannoli-shell or notebooks.
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class
GemArgs extends Args4jBase
GEM-Mapper function arguments.
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class
LongMinimap2 extends CannoliFn[SequenceDataset, AlignmentDataset]
Minimap2 wrapper as a function SequenceDataset → AlignmentDataset, for use in cannoli-shell or notebooks.
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class
LongUnimap extends CannoliFn[SequenceDataset, AlignmentDataset]
Unimap wrapper as a function SequenceDataset → AlignmentDataset, for use in cannoli-shell or notebooks.
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class
MagicBlast extends CannoliFn[FragmentDataset, AlignmentDataset]
Magic-BLAST wrapper as a function FragmentDataset → AlignmentDataset, for use in cannoli-shell or notebooks.
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class
MagicBlastArgs extends Args4jBase
Magic-BLAST function arguments.
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class
Minimap2 extends CannoliFn[FragmentDataset, AlignmentDataset]
Minimap2 wrapper as a function FragmentDataset → AlignmentDataset, for use in cannoli-shell or notebooks.
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class
Minimap2Args extends ReadGroupArgs
Minimap2 function arguments.
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class
SamtoolsMpileup extends CannoliFn[AlignmentDataset, VariantContextDataset]
Samtools mpileup wrapper as a function AlignmentDataset → VariantContextDataset, for use in cannoli-shell or notebooks.
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class
SamtoolsMpileupArgs extends Args4jBase
Samtools mpileup function arguments.
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class
SingleEndBowtie2 extends CannoliFn[AlignmentDataset, AlignmentDataset]
Single-end read Bowtie 2 wrapper as a function AlignmentDataset → AlignmentDataset, for use in cannoli-shell or notebooks.
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class
SingleEndBowtie2Args extends Args4jBase
Single-end read Bowtie 2 function arguments.
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class
SingleEndBwaMem extends CannoliFn[AlignmentDataset, AlignmentDataset]
Bwa mem wrapper as a function AlignmentDataset → AlignmentDataset, for use in cannoli-shell or notebooks.
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class
SingleEndBwaMem2 extends CannoliFn[AlignmentDataset, AlignmentDataset]
Bwa-mem2 wrapper as a function AlignmentDataset → AlignmentDataset, for use in cannoli-shell or notebooks.
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class
SingleEndMinimap2 extends CannoliFn[AlignmentDataset, AlignmentDataset]
Minimap2 wrapper as a function AlignmentDataset → AlignmentDataset, for use in cannoli-shell or notebooks.
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class
SingleEndStar extends CannoliFn[AlignmentDataset, AlignmentDataset]
Single-end read STAR-Mapper wrapper as a function AlignmentDataset → AlignmentDataset, for use in cannoli-shell or notebooks.
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class
SingleEndStarArgs extends Args4jBase
Single-end read STAR-Mapper function arguments.
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class
SingleEndUnimap extends CannoliFn[AlignmentDataset, AlignmentDataset]
Unimap wrapper as a function AlignmentDataset → AlignmentDataset, for use in cannoli-shell or notebooks.
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class
Snap extends CannoliFn[FragmentDataset, AlignmentDataset]
Scalable Nucleotide Alignment Program (SNAP) wrapper as a function FragmentDataset → AlignmentDataset, for use in cannoli-shell or notebooks.
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class
SnapArgs extends ReadGroupArgs
Scalable Nucleotide Alignment Program (SNAP) function arguments.
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class
SnpEff extends CannoliFn[VariantContextDataset, VariantContextDataset]
SnpEff wrapper as a function VariantContextDataset → VariantContextDataset, for use in cannoli-shell or notebooks.
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class
SnpEffArgs extends Args4jBase
SnpEff function arguments.
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class
Star extends CannoliFn[FragmentDataset, AlignmentDataset]
STAR-Mapper wrapper as a function FragmentDataset → AlignmentDataset, for use in cannoli-shell or notebooks.
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class
StarArgs extends Args4jBase
STAR-Mapper function arguments.
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class
Unimap extends CannoliFn[FragmentDataset, AlignmentDataset]
Unimap wrapper as a function FragmentDataset → AlignmentDataset, for use in cannoli-shell or notebooks.
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class
UnimapArgs extends ReadGroupArgs
Unimap function arguments.
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class
Vep extends CannoliFn[VariantContextDataset, VariantContextDataset]
Vep wrapper as a function VariantContextDataset → VariantContextDataset, for use in cannoli-shell or notebooks.
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class
VepArgs extends Args4jBase
Vep function arguments.
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class
VtNormalize extends CannoliFn[VariantContextDataset, VariantContextDataset]
Vt normalize wrapper as a function VariantContextDataset → VariantContextDataset, for use in cannoli-shell or notebooks.
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class
VtNormalizeArgs extends Args4jBase
Vt normalize function arguments.