cli

Type Members

final class About extends AnyRef
class Bcftools extends BDGSparkCommand[BcftoolsArgs] with Logging

Bcftools.
class BcftoolsArgs extends Args4jBase with ADAMSaveAnyArgs with ParquetArgs
class Bedtools extends BDGSparkCommand[BedtoolsArgs] with Logging

Bedtools.
class BedtoolsArgs extends Args4jBase with ADAMSaveAnyArgs with ParquetArgs
class Bowtie extends BDGSparkCommand[BowtieArgs] with Logging

Bowtie.
class Bowtie2 extends BDGSparkCommand[Bowtie2Args] with Logging

Bowtie 2.
class Bowtie2Args extends Args4jBase with ADAMSaveAnyArgs with ParquetArgs
class BowtieArgs extends Args4jBase with ADAMSaveAnyArgs with ParquetArgs
class Bwa extends BDGSparkCommand[BwaArgs] with Logging

Bwa.
class BwaArgs extends Args4jBase with ADAMSaveAnyArgs with ParquetArgs
class Cannoli extends Logging

Cannoli main.
class CannoliModule extends AbstractModule with ScalaModule

Cannoli module, binds the default list of command groups.
class Freebayes extends BDGSparkCommand[FreebayesArgs] with Logging

Freebayes.
class FreebayesArgs extends Args4jBase with ADAMSaveAnyArgs with ParquetArgs
class InterleaveFastq extends BDGSparkCommand[InterleaveFastqArgs] with Logging

Interleaves two FASTQ files.
class InterleaveFastqArgs extends Args4jBase
class SampleReads extends BDGSparkCommand[SampleReadsArgs] with Logging

Sample reads from interleaved FASTQ format.
class SampleReadsArgs extends Args4jBase with ADAMSaveAnyArgs with ParquetArgs
class Samtools extends BDGSparkCommand[SamtoolsArgs] with Logging

Samtools.
class SamtoolsArgs extends Args4jBase with ADAMSaveAnyArgs with ParquetArgs
class SnpEff extends BDGSparkCommand[SnpEffArgs] with Logging

SnpEff.
class SnpEffArgs extends Args4jBase with ADAMSaveAnyArgs with ParquetArgs
class Vt extends BDGSparkCommand[VtArgs] with Logging

Vt.
class VtArgs extends Args4jBase with ADAMSaveAnyArgs with ParquetArgs

Value Members

object Bcftools extends BDGCommandCompanion
object Bedtools extends BDGCommandCompanion
object Bowtie extends BDGCommandCompanion
object Bowtie2 extends BDGCommandCompanion
object Bwa extends BDGCommandCompanion
object Cannoli
object Freebayes extends BDGCommandCompanion
object InterleaveFastq extends BDGCommandCompanion
object SampleReads extends BDGCommandCompanion
object Samtools extends BDGCommandCompanion
object SnpEff extends BDGCommandCompanion
object Vt extends BDGCommandCompanion

package cli

Type Members

final class About extends AnyRef

class Bcftools extends BDGSparkCommand[BcftoolsArgs] with Logging

class BcftoolsArgs extends Args4jBase with ADAMSaveAnyArgs with ParquetArgs

class Bedtools extends BDGSparkCommand[BedtoolsArgs] with Logging

class BedtoolsArgs extends Args4jBase with ADAMSaveAnyArgs with ParquetArgs

class Bowtie extends BDGSparkCommand[BowtieArgs] with Logging

class Bowtie2 extends BDGSparkCommand[Bowtie2Args] with Logging

class Bowtie2Args extends Args4jBase with ADAMSaveAnyArgs with ParquetArgs

class BowtieArgs extends Args4jBase with ADAMSaveAnyArgs with ParquetArgs

class Bwa extends BDGSparkCommand[BwaArgs] with Logging

class BwaArgs extends Args4jBase with ADAMSaveAnyArgs with ParquetArgs

class Cannoli extends Logging

class CannoliModule extends AbstractModule with ScalaModule

class Freebayes extends BDGSparkCommand[FreebayesArgs] with Logging

class FreebayesArgs extends Args4jBase with ADAMSaveAnyArgs with ParquetArgs

class InterleaveFastq extends BDGSparkCommand[InterleaveFastqArgs] with Logging

class InterleaveFastqArgs extends Args4jBase

class SampleReads extends BDGSparkCommand[SampleReadsArgs] with Logging

class SampleReadsArgs extends Args4jBase with ADAMSaveAnyArgs with ParquetArgs

class Samtools extends BDGSparkCommand[SamtoolsArgs] with Logging

class SamtoolsArgs extends Args4jBase with ADAMSaveAnyArgs with ParquetArgs

class SnpEff extends BDGSparkCommand[SnpEffArgs] with Logging

class SnpEffArgs extends Args4jBase with ADAMSaveAnyArgs with ParquetArgs

class Vt extends BDGSparkCommand[VtArgs] with Logging

class VtArgs extends Args4jBase with ADAMSaveAnyArgs with ParquetArgs

Value Members

object Bcftools extends BDGCommandCompanion

object Bedtools extends BDGCommandCompanion

object Bowtie extends BDGCommandCompanion

object Bowtie2 extends BDGCommandCompanion

object Bwa extends BDGCommandCompanion

object Cannoli

object Freebayes extends BDGCommandCompanion

object InterleaveFastq extends BDGCommandCompanion

object SampleReads extends BDGCommandCompanion

object Samtools extends BDGCommandCompanion

object SnpEff extends BDGCommandCompanion

object Vt extends BDGCommandCompanion

Ungrouped