cannoli

Type Members

class BcftoolsCall extends CannoliFn[VariantContextDataset, VariantContextDataset]

Bcftools call wrapper as a function VariantContextDataset → VariantContextDataset, for use in cannoli-shell or notebooks.
class BcftoolsCallArgs extends Args4jBase

Bcftools call function arguments.
class BcftoolsMpileup extends CannoliFn[AlignmentDataset, VariantContextDataset]

Bcftools mpileup wrapper as a function AlignmentDataset → VariantContextDataset, for use in cannoli-shell or notebooks.
class BcftoolsMpileupArgs extends Args4jBase

Bcftools mpileup function arguments.
class BcftoolsNorm extends CannoliFn[VariantContextDataset, VariantContextDataset]

Bcftools norm wrapper as a function VariantContextDataset → VariantContextDataset, for use in cannoli-shell or notebooks.
class BcftoolsNormArgs extends Args4jBase

Bcftools norm function arguments.
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)
class BedtoolsIntersectArgs extends Args4jBase

Bedtools intersect function arguments.
class Blastn extends CannoliFn[SequenceDataset, AlignmentDataset]

Blastn wrapper as a function SequenceDataset → AlignmentDataset, for use in cannoli-shell or notebooks.
class BlastnArgs extends Args4jBase

Blastn function arguments.
class Bowtie extends CannoliFn[FragmentDataset, AlignmentDataset]

Bowtie wrapper as a function FragmentDataset → AlignmentDataset, for use in cannoli-shell or notebooks.
class Bowtie2 extends CannoliFn[FragmentDataset, AlignmentDataset]

Bowtie 2 wrapper as a function FragmentDataset → AlignmentDataset, for use in cannoli-shell or notebooks.
class Bowtie2Args extends Args4jBase

Bowtie 2 function arguments.
class BowtieArgs extends Args4jBase

Bowtie function arguments.
class BwaMem extends CannoliFn[FragmentDataset, AlignmentDataset]

Bwa mem wrapper as a function FragmentDataset → AlignmentDataset, for use in cannoli-shell or notebooks.
class BwaMem2 extends CannoliFn[FragmentDataset, AlignmentDataset]

BwaMem2 wrapper as a function FragmentDataset → AlignmentDataset, for use in cannoli-shell or notebooks.
class BwaMem2Args extends ReadGroupArgs

BwaMem2 function arguments.
class BwaMemArgs extends ReadGroupArgs

Bwa mem function arguments.
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.
class Freebayes extends CannoliFn[AlignmentDataset, VariantContextDataset]

Freebayes wrapper as a function AlignmentDataset → VariantContextDataset, for use in cannoli-shell or notebooks.
class FreebayesArgs extends Args4jBase

Freebayes function arguments.
class Gem extends CannoliFn[FragmentDataset, AlignmentDataset]

GEM-Mapper wrapper as a function FragmentDataset → AlignmentDataset, for use in cannoli-shell or notebooks.
class GemArgs extends Args4jBase

GEM-Mapper function arguments.
class MagicBlast extends CannoliFn[FragmentDataset, AlignmentDataset]

Magic-BLAST wrapper as a function FragmentDataset → AlignmentDataset, for use in cannoli-shell or notebooks.
class MagicBlastArgs extends Args4jBase

Magic-BLAST function arguments.
class Minimap2 extends CannoliFn[FragmentDataset, AlignmentDataset]

Minimap2 wrapper as a function FragmentDataset → AlignmentDataset, for use in cannoli-shell or notebooks.
class Minimap2Args extends Args4jBase

Minimap2 function arguments.
class SamtoolsMpileup extends CannoliFn[AlignmentDataset, VariantContextDataset]

Samtools mpileup wrapper as a function AlignmentDataset → VariantContextDataset, for use in cannoli-shell or notebooks.
class SamtoolsMpileupArgs extends Args4jBase

Samtools mpileup function arguments.
class SingleEndBowtie2 extends CannoliFn[AlignmentDataset, AlignmentDataset]

Single-end read Bowtie 2 wrapper as a function AlignmentDataset → AlignmentDataset, for use in cannoli-shell or notebooks.
class SingleEndBowtie2Args extends Args4jBase

Single-end read Bowtie 2 function arguments.
class SingleEndStar extends CannoliFn[AlignmentDataset, AlignmentDataset]

Single-end read STAR-Mapper wrapper as a function AlignmentDataset → AlignmentDataset, for use in cannoli-shell or notebooks.
class SingleEndStarArgs extends Args4jBase

Single-end read STAR-Mapper function arguments.
class Snap extends CannoliFn[FragmentDataset, AlignmentDataset]

Scalable Nucleotide Alignment Program (SNAP) wrapper as a function FragmentDataset → AlignmentDataset, for use in cannoli-shell or notebooks.
class SnapArgs extends ReadGroupArgs

Scalable Nucleotide Alignment Program (SNAP) function arguments.
class SnpEff extends CannoliFn[VariantContextDataset, VariantContextDataset]

SnpEff wrapper as a function VariantContextDataset → VariantContextDataset, for use in cannoli-shell or notebooks.
class SnpEffArgs extends Args4jBase

SnpEff function arguments.
class Star extends CannoliFn[FragmentDataset, AlignmentDataset]

STAR-Mapper wrapper as a function FragmentDataset → AlignmentDataset, for use in cannoli-shell or notebooks.
class StarArgs extends Args4jBase

STAR-Mapper function arguments.
class Vep extends CannoliFn[VariantContextDataset, VariantContextDataset]

Vep wrapper as a function VariantContextDataset → VariantContextDataset, for use in cannoli-shell or notebooks.
class VepArgs extends Args4jBase

Vep function arguments.
class VtNormalize extends CannoliFn[VariantContextDataset, VariantContextDataset]

Vt normalize wrapper as a function VariantContextDataset → VariantContextDataset, for use in cannoli-shell or notebooks.
class VtNormalizeArgs extends Args4jBase

Vt normalize function arguments.

Value Members

object Cannoli

Implicits on Cannoli function source data sets.

package cannoli

Type Members

class BcftoolsCall extends CannoliFn[VariantContextDataset, VariantContextDataset]

class BcftoolsCallArgs extends Args4jBase

class BcftoolsMpileup extends CannoliFn[AlignmentDataset, VariantContextDataset]

class BcftoolsMpileupArgs extends Args4jBase

class BcftoolsNorm extends CannoliFn[VariantContextDataset, VariantContextDataset]

class BcftoolsNormArgs extends Args4jBase

class BedtoolsIntersect extends CannoliFn[FeatureDataset, FeatureDataset]

class BedtoolsIntersectArgs extends Args4jBase

class Blastn extends CannoliFn[SequenceDataset, AlignmentDataset]

class BlastnArgs extends Args4jBase

class Bowtie extends CannoliFn[FragmentDataset, AlignmentDataset]

class Bowtie2 extends CannoliFn[FragmentDataset, AlignmentDataset]

class Bowtie2Args extends Args4jBase

class BowtieArgs extends Args4jBase

class BwaMem extends CannoliFn[FragmentDataset, AlignmentDataset]

class BwaMem2 extends CannoliFn[FragmentDataset, AlignmentDataset]

class BwaMem2Args extends ReadGroupArgs

class BwaMemArgs extends ReadGroupArgs

abstract class CannoliFn[X, Y] extends (X) ⇒ Y with Logging

class Freebayes extends CannoliFn[AlignmentDataset, VariantContextDataset]

class FreebayesArgs extends Args4jBase

class Gem extends CannoliFn[FragmentDataset, AlignmentDataset]

class GemArgs extends Args4jBase

class MagicBlast extends CannoliFn[FragmentDataset, AlignmentDataset]

class MagicBlastArgs extends Args4jBase

class Minimap2 extends CannoliFn[FragmentDataset, AlignmentDataset]

class Minimap2Args extends Args4jBase

class SamtoolsMpileup extends CannoliFn[AlignmentDataset, VariantContextDataset]

class SamtoolsMpileupArgs extends Args4jBase

class SingleEndBowtie2 extends CannoliFn[AlignmentDataset, AlignmentDataset]

class SingleEndBowtie2Args extends Args4jBase

class SingleEndStar extends CannoliFn[AlignmentDataset, AlignmentDataset]

class SingleEndStarArgs extends Args4jBase

class Snap extends CannoliFn[FragmentDataset, AlignmentDataset]

class SnapArgs extends ReadGroupArgs

class SnpEff extends CannoliFn[VariantContextDataset, VariantContextDataset]

class SnpEffArgs extends Args4jBase

class Star extends CannoliFn[FragmentDataset, AlignmentDataset]

class StarArgs extends Args4jBase

class Vep extends CannoliFn[VariantContextDataset, VariantContextDataset]

class VepArgs extends Args4jBase

class VtNormalize extends CannoliFn[VariantContextDataset, VariantContextDataset]

class VtNormalizeArgs extends Args4jBase

Value Members

object Cannoli

Ungrouped