cli

Type Members

class ADAM2Fasta extends BDGSparkCommand[ADAM2FastaArgs] with Logging
class ADAM2FastaArgs 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
class Adam2Fastq extends BDGSparkCommand[Adam2FastqArgs]
class Adam2FastqArgs extends Args4jBase with ParquetLoadSaveArgs
class AlleleCount extends BDGSparkCommand[AlleleCountArgs] with Logging
class AlleleCountArgs extends Args4jBase with ParquetArgs
class BuildInformation extends BDGCommand
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 Features2ADAM extends BDGSparkCommand[Features2ADAMArgs]
class Features2ADAMArgs 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 PluginExecutor extends BDGSparkCommand[PluginExecutorArgs]
class PluginExecutorArgs extends Args4jBase with ParquetArgs
class PrintADAM extends BDGSparkCommand[PrintADAMArgs]
class PrintADAMArgs extends Args4jBase
class PrintGenes extends BDGSparkCommand[PrintGenesArgs] with Serializable
class PrintGenesArgs extends Args4jBase with ParquetArgs with Serializable
class PrintTags extends BDGSparkCommand[PrintTagsArgs]
class PrintTagsArgs 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 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.
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.
It is agnostic to its input and output being SAM, BAM, or ADAM files; when printing to stdout it prints SAM.
class ViewArgs extends Args4jBase with ParquetArgs with ADAMSaveAnyArgs
class Wig2BedArgs extends Args4jBase
class WigFix2Bed extends BDGCommand

Value Members

object ADAM2Fasta extends BDGCommandCompanion
object ADAM2Vcf extends BDGCommandCompanion
object ADAMMain
object Adam2Fastq extends BDGCommandCompanion
object AlleleCount extends BDGCommandCompanion
object AlleleCountHelper extends Serializable
object BuildInformation extends BDGCommandCompanion
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.
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. It then reports, on standard out, the location and name of each variant along with the calculated depth.
object CountContigKmers extends BDGCommandCompanion
object CountReadKmers extends BDGCommandCompanion
object Fasta2ADAM extends BDGCommandCompanion
object Features2ADAM extends BDGCommandCompanion
object FlagStat extends BDGCommandCompanion
object Flatten extends BDGCommandCompanion
object Fragments2Reads extends BDGCommandCompanion
object ListDict extends BDGCommandCompanion
object PluginExecutor extends BDGCommandCompanion

This set of classes executes a plugin along with the associated input location.
This set of classes executes a plugin along with the associated input location.
Example usage: adam plugin org.bdgenomics.adam.plugins.Take10Plugin reads12.sam
org.bdgenomics.adam.plugins.Take10Plugin is a simple example plugin. The org.bdgenomics.adam.plugins.ADAMPlugin interface defines the class that will run using this command.
object PrintADAM extends BDGCommandCompanion
object PrintGenes extends BDGCommandCompanion with Serializable
object PrintTags extends BDGCommandCompanion

Reads in the tagStrings field of every record, and prints out the set of unique tags found in those fields along with the number of records that have each particular tag.
object Reads2Fragments extends BDGCommandCompanion
object Transform 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.
WigFix2Bed (accessible as the command "wigfix2bed" through the CLI) takes fixed wiggle file and converts it to a BED formatted file. The wiggle file is a text based format that implements run-length encoding, without any guarantees where the sync markers are. This makes it difficult to use as a "splittable" format, and necessitates processing the file locally.

package cli

Type Members

class ADAM2Fasta extends BDGSparkCommand[ADAM2FastaArgs] with Logging

class ADAM2FastaArgs 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

class Adam2Fastq extends BDGSparkCommand[Adam2FastqArgs]

class Adam2FastqArgs extends Args4jBase with ParquetLoadSaveArgs

class AlleleCount extends BDGSparkCommand[AlleleCountArgs] with Logging

class AlleleCountArgs extends Args4jBase with ParquetArgs

class BuildInformation extends BDGCommand

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 Features2ADAM extends BDGSparkCommand[Features2ADAMArgs]

class Features2ADAMArgs 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 PluginExecutor extends BDGSparkCommand[PluginExecutorArgs]

class PluginExecutorArgs extends Args4jBase with ParquetArgs

class PrintADAM extends BDGSparkCommand[PrintADAMArgs]

class PrintADAMArgs extends Args4jBase

class PrintGenes extends BDGSparkCommand[PrintGenesArgs] with Serializable

class PrintGenesArgs extends Args4jBase with ParquetArgs with Serializable

class PrintTags extends BDGSparkCommand[PrintTagsArgs]

class PrintTagsArgs 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 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 ADAM2Vcf extends BDGCommandCompanion

object ADAMMain

object Adam2Fastq extends BDGCommandCompanion

object AlleleCount extends BDGCommandCompanion

object AlleleCountHelper extends Serializable

object BuildInformation extends BDGCommandCompanion

object CalculateDepth extends BDGCommandCompanion

object CountContigKmers extends BDGCommandCompanion

object CountReadKmers extends BDGCommandCompanion

object Fasta2ADAM extends BDGCommandCompanion

object Features2ADAM extends BDGCommandCompanion

object FlagStat extends BDGCommandCompanion

object Flatten extends BDGCommandCompanion

object Fragments2Reads extends BDGCommandCompanion

object ListDict extends BDGCommandCompanion

object PluginExecutor extends BDGCommandCompanion

object PrintADAM extends BDGCommandCompanion

object PrintGenes extends BDGCommandCompanion with Serializable

object PrintTags extends BDGCommandCompanion

object Reads2Fragments extends BDGCommandCompanion

object Transform extends BDGCommandCompanion

object Vcf2ADAM extends BDGCommandCompanion

object VcfAnnotation2ADAM extends BDGCommandCompanion

object View extends BDGCommandCompanion