package cli
- Alphabetic
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- All
Type Members
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final
class
About extends AnyRef
About.
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class
BcftoolsCall extends BDGSparkCommand[BcftoolsCallArgs] with Logging
Bcftools call command line wrapper.
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class
BcftoolsCallArgs extends cannoli.BcftoolsCallArgs with ADAMSaveAnyArgs with ParquetArgs
Bcftools call command line arguments.
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class
BcftoolsMpileup extends BDGSparkCommand[BcftoolsMpileupArgs] with Logging
Bcftools mpileup command line wrapper.
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class
BcftoolsMpileupArgs extends cannoli.BcftoolsMpileupArgs with ADAMSaveAnyArgs with ParquetArgs
Bcftools mpileup command line arguments.
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class
BcftoolsNorm extends BDGSparkCommand[BcftoolsNormArgs] with Logging
Bcftools norm command line wrapper.
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class
BcftoolsNormArgs extends cannoli.BcftoolsNormArgs with ADAMSaveAnyArgs with ParquetArgs
Bcftools norm command line arguments.
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class
BedtoolsIntersect extends BDGSparkCommand[BedtoolsIntersectArgs] with Logging
Bedtools intersect command line wrapper.
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class
BedtoolsIntersectArgs extends cannoli.BedtoolsIntersectArgs with ADAMSaveAnyArgs with ParquetArgs
Bedtools intersect command line arguments.
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class
Blastn extends BDGSparkCommand[BlastnArgs] with Logging
Blastn command line wrapper.
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class
BlastnArgs extends cannoli.BlastnArgs with ADAMSaveAnyArgs with ParquetArgs
Blastn command line arguments.
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class
Bowtie extends BDGSparkCommand[BowtieArgs] with Logging
Bowtie command line wrapper.
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class
Bowtie2 extends BDGSparkCommand[Bowtie2Args] with Logging
Bowtie 2 command line wrapper.
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class
Bowtie2Args extends cannoli.Bowtie2Args with ADAMSaveAnyArgs with CramArgs with ParquetArgs
Bowtie 2 command line arguments.
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class
BowtieArgs extends cannoli.BowtieArgs with ADAMSaveAnyArgs with CramArgs with ParquetArgs
Bowtie command line arguments.
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class
BwaMem extends BDGSparkCommand[BwaMemArgs] with Logging
Bwa mem command line wrapper.
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class
BwaMem2 extends BDGSparkCommand[BwaMem2Args] with Logging
Bwa-mem2 command line wrapper.
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class
BwaMem2Args extends cannoli.BwaMem2Args with ADAMSaveAnyArgs with CramArgs with ParquetArgs
Bwa-mem2 command line arguments.
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class
BwaMemArgs extends cannoli.BwaMemArgs with ADAMSaveAnyArgs with CramArgs with ParquetArgs
Bwa mem command line arguments.
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class
Cannoli extends Logging
Cannoli main.
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class
CannoliModule extends AbstractModule with ScalaModule
Cannoli module, binds the default list of command groups.
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class
Freebayes extends BDGSparkCommand[FreebayesArgs] with Logging
Freebayes command line wrapper.
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class
FreebayesArgs extends cannoli.FreebayesArgs with ADAMSaveAnyArgs with CramArgs with ParquetArgs
Freebayes command line arguments.
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class
Gem extends BDGSparkCommand[GemArgs] with Logging
GEM-Mapper command line wrapper.
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class
GemArgs extends cannoli.GemArgs with ADAMSaveAnyArgs with CramArgs with ParquetArgs
GEM-Mapper command line arguments.
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class
InterleaveFastq extends BDGSparkCommand[InterleaveFastqArgs] with Logging
Interleaves two FASTQ files.
- class InterleaveFastqArgs extends Args4jBase
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class
LongMinimap2 extends BDGSparkCommand[LongMinimap2Args] with Logging
Long read Minimap2 command line wrapper.
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class
LongMinimap2Args extends cannoli.Minimap2Args with ADAMSaveAnyArgs with ParquetArgs
Long read Minimap2 command line arguments.
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class
LongUnimap extends BDGSparkCommand[LongUnimapArgs] with Logging
Long read Unimap command line wrapper.
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class
LongUnimapArgs extends cannoli.UnimapArgs with ADAMSaveAnyArgs with ParquetArgs
Long read Unimap command line arguments.
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class
MagicBlast extends BDGSparkCommand[MagicBlastArgs] with Logging
MagicBlast command line wrapper.
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class
MagicBlastArgs extends cannoli.MagicBlastArgs with ADAMSaveAnyArgs with CramArgs with ParquetArgs
Magic-BLAST command line arguments.
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class
Minimap2 extends BDGSparkCommand[Minimap2Args] with Logging
Minimap2 command line wrapper.
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class
Minimap2Args extends cannoli.Minimap2Args with ADAMSaveAnyArgs with CramArgs with ParquetArgs
Minimap2 command line arguments.
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class
SampleReads extends BDGSparkCommand[SampleReadsArgs] with Logging
Sample reads from interleaved FASTQ format.
- class SampleReadsArgs extends Args4jBase with ADAMSaveAnyArgs with CramArgs with ParquetArgs
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class
SamtoolsMpileup extends BDGSparkCommand[SamtoolsMpileupArgs] with Logging
Samtools mpileup command line wrapper.
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class
SamtoolsMpileupArgs extends cannoli.SamtoolsMpileupArgs with ADAMSaveAnyArgs with CramArgs with ParquetArgs
Samtools mpileup command line arguments.
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class
SingleEndBowtie2 extends BDGSparkCommand[SingleEndBowtie2Args] with Logging
Single-end read Bowtie 2 command line wrapper.
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class
SingleEndBowtie2Args extends cannoli.SingleEndBowtie2Args with ADAMSaveAnyArgs with CramArgs with ParquetArgs
Single-end read Bowtie 2 command line arguments.
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class
SingleEndBwaMem extends BDGSparkCommand[SingleEndBwaMemArgs] with Logging
Single-end read BwaMem command line wrapper.
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class
SingleEndBwaMem2 extends BDGSparkCommand[SingleEndBwaMem2Args] with Logging
Single-end read Bwa-mem2 command line wrapper.
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class
SingleEndBwaMem2Args extends cannoli.BwaMem2Args with ADAMSaveAnyArgs with CramArgs with ParquetArgs
Single-end read Bwa-mem2 command line arguments.
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class
SingleEndBwaMemArgs extends cannoli.BwaMemArgs with ADAMSaveAnyArgs with CramArgs with ParquetArgs
Single-end read Bwa mem command line arguments.
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class
SingleEndMinimap2 extends BDGSparkCommand[SingleEndMinimap2Args] with Logging
Single-end read Minimap2 command line wrapper.
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class
SingleEndMinimap2Args extends cannoli.Minimap2Args with ADAMSaveAnyArgs with CramArgs with ParquetArgs
Single-end read Minimap2 command line arguments.
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class
SingleEndStar extends BDGSparkCommand[SingleEndStarArgs] with Logging
Single-end read STAR-Mapper command line wrapper.
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class
SingleEndStarArgs extends cannoli.SingleEndStarArgs with ADAMSaveAnyArgs with CramArgs with ParquetArgs
Single-end read STAR-Mapper command line arguments.
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class
SingleEndUnimap extends BDGSparkCommand[SingleEndUnimapArgs] with Logging
Single-end read Unimap command line wrapper.
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class
SingleEndUnimapArgs extends cannoli.UnimapArgs with ADAMSaveAnyArgs with CramArgs with ParquetArgs
Single-end read Unimap command line arguments.
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class
Snap extends BDGSparkCommand[SnapArgs] with Logging
Scalable Nucleotide Alignment Program (SNAP) command line wrapper.
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class
SnapArgs extends cannoli.SnapArgs with ADAMSaveAnyArgs with CramArgs with ParquetArgs
Scalable Nucleotide Alignment Program (SNAP) command line arguments.
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class
SnpEff extends BDGSparkCommand[SnpEffArgs] with Logging
SnpEff command line wrapper.
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class
SnpEffArgs extends cannoli.SnpEffArgs with ADAMSaveAnyArgs with ParquetArgs
SnpEff command line arguments.
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class
Star extends BDGSparkCommand[StarArgs] with Logging
STAR-Mapper command line wrapper.
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class
StarArgs extends cannoli.StarArgs with ADAMSaveAnyArgs with CramArgs with ParquetArgs
STAR-Mapper command line arguments.
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class
Unimap extends BDGSparkCommand[UnimapArgs] with Logging
Unimap command line wrapper.
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class
UnimapArgs extends cannoli.UnimapArgs with ADAMSaveAnyArgs with CramArgs with ParquetArgs
Unimap command line arguments.
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class
Vep extends BDGSparkCommand[VepArgs] with Logging
Vep command line wrapper.
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class
VepArgs extends cannoli.VepArgs with ADAMSaveAnyArgs with ParquetArgs
Vep command line arguments.
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class
VtNormalize extends BDGSparkCommand[VtNormalizeArgs] with Logging
Vt normalize command line wrapper.
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class
VtNormalizeArgs extends cannoli.VtNormalizeArgs with ADAMSaveAnyArgs with ParquetArgs
Vt normalize command line arguments.
Value Members
- object BcftoolsCall extends BDGCommandCompanion
- object BcftoolsMpileup extends BDGCommandCompanion
- object BcftoolsNorm extends BDGCommandCompanion
- object BedtoolsIntersect extends BDGCommandCompanion
- object Blastn extends BDGCommandCompanion
- object Bowtie extends BDGCommandCompanion
- object Bowtie2 extends BDGCommandCompanion
- object BwaMem extends BDGCommandCompanion
- object BwaMem2 extends BDGCommandCompanion
- object Cannoli
- object Freebayes extends BDGCommandCompanion
- object Gem extends BDGCommandCompanion
- object InterleaveFastq extends BDGCommandCompanion
- object LongMinimap2 extends BDGCommandCompanion
- object LongUnimap extends BDGCommandCompanion
- object MagicBlast extends BDGCommandCompanion
- object Minimap2 extends BDGCommandCompanion
- object SampleReads extends BDGCommandCompanion
- object SamtoolsMpileup extends BDGCommandCompanion
- object SingleEndBowtie2 extends BDGCommandCompanion
- object SingleEndBwaMem extends BDGCommandCompanion
- object SingleEndBwaMem2 extends BDGCommandCompanion
- object SingleEndMinimap2 extends BDGCommandCompanion
- object SingleEndStar extends BDGCommandCompanion
- object SingleEndUnimap extends BDGCommandCompanion
- object Snap extends BDGCommandCompanion
- object SnpEff extends BDGCommandCompanion
- object Star extends BDGCommandCompanion
- object Unimap extends BDGCommandCompanion
- object Vep extends BDGCommandCompanion
- object VtNormalize extends BDGCommandCompanion