cli

Type Members

class ADAM2Fasta extends BDGSparkCommand[ADAM2FastaArgs] with Logging
class ADAM2FastaArgs extends Args4jBase with ParquetLoadSaveArgs
class ADAM2Fastq extends BDGSparkCommand[ADAM2FastqArgs]
class ADAM2FastqArgs extends Args4jBase with ParquetLoadSaveArgs
class ADAM2Vcf extends BDGSparkCommand[ADAM2VcfArgs] with DictionaryCommand with Logging
class ADAM2VcfArgs extends Args4jBase with ParquetArgs
class ADAMMain extends Logging
class ADAMModule extends AbstractModule with ScalaModule
final class About extends AnyRef
class AlleleCount extends BDGSparkCommand[AlleleCountArgs] with Logging
class AlleleCountArgs extends Args4jBase with ParquetArgs
class CalculateDepth extends BDGSparkCommand[CalculateDepthArgs]
class CalculateDepthArgs extends Args4jBase with ParquetArgs
case class CommandGroup(name: String, commands: List[BDGCommandCompanion]) extends Product with Serializable
class CountContigKmers extends BDGSparkCommand[CountContigKmersArgs] with Logging
class CountContigKmersArgs extends Args4jBase with ParquetArgs
class CountReadKmers extends BDGSparkCommand[CountReadKmersArgs] with Logging
class CountReadKmersArgs extends Args4jBase with ParquetArgs
trait DictionaryCommand extends AnyRef
class Fasta2ADAM extends BDGSparkCommand[Fasta2ADAMArgs] with Logging
class Fasta2ADAMArgs extends Args4jBase with ParquetSaveArgs
class FlagStat extends BDGSparkCommand[FlagStatArgs]
class FlagStatArgs extends Args4jBase with ParquetArgs
class Flatten extends BDGSparkCommand[FlattenArgs] with Logging
class FlattenArgs extends Args4jBase with ParquetSaveArgs
class Fragments2Reads extends BDGSparkCommand[Fragments2ReadsArgs] with Logging
class Fragments2ReadsArgs extends Args4jBase with ADAMSaveAnyArgs with ParquetArgs
class ListDict extends BDGSparkCommand[ListDictArgs]
class ListDictArgs extends Args4jBase with ParquetArgs
class MergeShards extends BDGSparkCommand[MergeShardsArgs]

A command to merge sharded files.
class MergeShardsArgs extends Args4jBase
class PrintADAM extends BDGSparkCommand[PrintADAMArgs]
class PrintADAMArgs extends Args4jBase
class Reads2Coverage extends BDGSparkCommand[Reads2CoverageArgs]
class Reads2CoverageArgs extends Args4jBase with ParquetArgs
class Reads2Fragments extends BDGSparkCommand[Reads2FragmentsArgs] with Logging
class Reads2FragmentsArgs extends Args4jBase with ADAMSaveAnyArgs with ParquetArgs
class Transform extends BDGSparkCommand[TransformArgs] with Logging
class TransformArgs extends Args4jBase with ADAMSaveAnyArgs with ParquetArgs
class TransformFeatures extends BDGSparkCommand[TransformFeaturesArgs]
class TransformFeaturesArgs extends Args4jBase with ParquetSaveArgs
class Vcf2ADAM extends BDGSparkCommand[Vcf2ADAMArgs] with DictionaryCommand with Logging
class Vcf2ADAMArgs extends Args4jBase with ParquetSaveArgs
class VcfAnnotation2ADAM extends BDGSparkCommand[VcfAnnotation2ADAMArgs] with Logging
class VcfAnnotation2ADAMArgs extends Args4jBase with ParquetSaveArgs
class View extends BDGSparkCommand[ViewArgs]

The adam view command implements some of the functionality of samtools view, specifically the -f, -F, -c, and -o options, in an optionally distributed fashion.
class ViewArgs extends Args4jBase with ParquetArgs with ADAMSaveAnyArgs
class Wig2BedArgs extends Args4jBase
class WigFix2Bed extends BDGCommand

Value Members

object ADAM2Fasta extends BDGCommandCompanion
object ADAM2Fastq extends BDGCommandCompanion
object ADAM2Vcf extends BDGCommandCompanion
object ADAMMain
object AlleleCount extends BDGCommandCompanion
object AlleleCountHelper extends Serializable
object CalculateDepth extends BDGCommandCompanion

CalculateDepth (accessible as the command 'depth' through the CLI) takes two arguments, an Read file and a VCF (or equivalent) file, and calculates the number of reads (the 'depth') from the Read file which overlap each of the variants given by the VCF.
object CountContigKmers extends BDGCommandCompanion
object CountReadKmers extends BDGCommandCompanion
object Fasta2ADAM extends BDGCommandCompanion
object FlagStat extends BDGCommandCompanion
object Flatten extends BDGCommandCompanion
object Fragments2Reads extends BDGCommandCompanion
object ListDict extends BDGCommandCompanion
object MergeShards extends BDGCommandCompanion
object PrintADAM extends BDGCommandCompanion
object Reads2Coverage extends BDGCommandCompanion

Reads2Coverage (accessible as the command 'reads2coverage' through the CLI) takes two arguments, an INPUT and OUTPUT, and calculates the number of reads from INPUT at every location in the file.
object Reads2Fragments extends BDGCommandCompanion
object Transform extends BDGCommandCompanion
object TransformFeatures extends BDGCommandCompanion
object Vcf2ADAM extends BDGCommandCompanion
object VcfAnnotation2ADAM extends BDGCommandCompanion
object View extends BDGCommandCompanion
object WigFix2Bed extends BDGCommandCompanion

WigFix2Bed (accessible as the command "wigfix2bed" through the CLI) takes fixed wiggle file and converts it to a BED formatted file.

package cli

Type Members

class ADAM2Fasta extends BDGSparkCommand[ADAM2FastaArgs] with Logging

class ADAM2FastaArgs extends Args4jBase with ParquetLoadSaveArgs

class ADAM2Fastq extends BDGSparkCommand[ADAM2FastqArgs]

class ADAM2FastqArgs extends Args4jBase with ParquetLoadSaveArgs

class ADAM2Vcf extends BDGSparkCommand[ADAM2VcfArgs] with DictionaryCommand with Logging

class ADAM2VcfArgs extends Args4jBase with ParquetArgs

class ADAMMain extends Logging

class ADAMModule extends AbstractModule with ScalaModule

final class About extends AnyRef

class AlleleCount extends BDGSparkCommand[AlleleCountArgs] with Logging

class AlleleCountArgs extends Args4jBase with ParquetArgs

class CalculateDepth extends BDGSparkCommand[CalculateDepthArgs]

class CalculateDepthArgs extends Args4jBase with ParquetArgs

case class CommandGroup(name: String, commands: List[BDGCommandCompanion]) extends Product with Serializable

class CountContigKmers extends BDGSparkCommand[CountContigKmersArgs] with Logging

class CountContigKmersArgs extends Args4jBase with ParquetArgs

class CountReadKmers extends BDGSparkCommand[CountReadKmersArgs] with Logging

class CountReadKmersArgs extends Args4jBase with ParquetArgs

trait DictionaryCommand extends AnyRef

class Fasta2ADAM extends BDGSparkCommand[Fasta2ADAMArgs] with Logging

class Fasta2ADAMArgs extends Args4jBase with ParquetSaveArgs

class FlagStat extends BDGSparkCommand[FlagStatArgs]

class FlagStatArgs extends Args4jBase with ParquetArgs

class Flatten extends BDGSparkCommand[FlattenArgs] with Logging

class FlattenArgs extends Args4jBase with ParquetSaveArgs

class Fragments2Reads extends BDGSparkCommand[Fragments2ReadsArgs] with Logging

class Fragments2ReadsArgs extends Args4jBase with ADAMSaveAnyArgs with ParquetArgs

class ListDict extends BDGSparkCommand[ListDictArgs]

class ListDictArgs extends Args4jBase with ParquetArgs

class MergeShards extends BDGSparkCommand[MergeShardsArgs]

class MergeShardsArgs extends Args4jBase

class PrintADAM extends BDGSparkCommand[PrintADAMArgs]

class PrintADAMArgs extends Args4jBase

class Reads2Coverage extends BDGSparkCommand[Reads2CoverageArgs]

class Reads2CoverageArgs extends Args4jBase with ParquetArgs

class Reads2Fragments extends BDGSparkCommand[Reads2FragmentsArgs] with Logging

class Reads2FragmentsArgs extends Args4jBase with ADAMSaveAnyArgs with ParquetArgs

class Transform extends BDGSparkCommand[TransformArgs] with Logging

class TransformArgs extends Args4jBase with ADAMSaveAnyArgs with ParquetArgs

class TransformFeatures extends BDGSparkCommand[TransformFeaturesArgs]

class TransformFeaturesArgs extends Args4jBase with ParquetSaveArgs

class Vcf2ADAM extends BDGSparkCommand[Vcf2ADAMArgs] with DictionaryCommand with Logging

class Vcf2ADAMArgs extends Args4jBase with ParquetSaveArgs

class VcfAnnotation2ADAM extends BDGSparkCommand[VcfAnnotation2ADAMArgs] with Logging

class VcfAnnotation2ADAMArgs extends Args4jBase with ParquetSaveArgs

class View extends BDGSparkCommand[ViewArgs]

class ViewArgs extends Args4jBase with ParquetArgs with ADAMSaveAnyArgs

class Wig2BedArgs extends Args4jBase

class WigFix2Bed extends BDGCommand

Value Members

object ADAM2Fasta extends BDGCommandCompanion

object ADAM2Fastq extends BDGCommandCompanion

object ADAM2Vcf extends BDGCommandCompanion

object ADAMMain

object AlleleCount extends BDGCommandCompanion

object AlleleCountHelper extends Serializable

object CalculateDepth extends BDGCommandCompanion

object CountContigKmers extends BDGCommandCompanion

object CountReadKmers extends BDGCommandCompanion

object Fasta2ADAM extends BDGCommandCompanion

object FlagStat extends BDGCommandCompanion

object Flatten extends BDGCommandCompanion

object Fragments2Reads extends BDGCommandCompanion

object ListDict extends BDGCommandCompanion

object MergeShards extends BDGCommandCompanion

object PrintADAM extends BDGCommandCompanion

object Reads2Coverage extends BDGCommandCompanion

object Reads2Fragments extends BDGCommandCompanion

object Transform extends BDGCommandCompanion

object TransformFeatures extends BDGCommandCompanion

object Vcf2ADAM extends BDGCommandCompanion

object VcfAnnotation2ADAM extends BDGCommandCompanion

object View extends BDGCommandCompanion

object WigFix2Bed extends BDGCommandCompanion

Ungrouped