cli

Type Members

class ADAM2Fasta extends BDGSparkCommand[ADAM2FastaArgs] with Logging
class ADAM2FastaArgs extends Args4jBase
class ADAM2Fastq extends BDGSparkCommand[ADAM2FastqArgs]
class ADAM2FastqArgs extends Args4jBase
class ADAMMain extends Logging
class ADAMModule extends AbstractModule with ScalaModule
final class About extends AnyRef
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
class Fasta2ADAM extends BDGSparkCommand[Fasta2ADAMArgs] with Logging
class Fasta2ADAMArgs extends Args4jBase with ParquetSaveArgs
class FlagStat extends BDGSparkCommand[FlagStatArgs]
class FlagStatArgs extends Args4jBase
class MergeShards extends BDGSparkCommand[MergeShardsArgs]

A command to merge sharded files.
A command to merge sharded files.
This needs to be a Spark command in order to pull in the Hadoop Config via Spark. Also, this allows us to benefit from Spark's YARN/Mesos submission bits, etc.
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 TransformAlignments extends BDGSparkCommand[TransformAlignmentsArgs] with Logging
class TransformAlignmentsArgs extends Args4jBase with ADAMSaveAnyArgs with ParquetArgs
class TransformFeatures extends BDGSparkCommand[TransformFeaturesArgs]
class TransformFeaturesArgs extends Args4jBase with ParquetSaveArgs
class TransformFragments extends BDGSparkCommand[TransformFragmentsArgs] with Logging
class TransformFragmentsArgs extends Args4jBase with ADAMSaveAnyArgs with ParquetArgs
class TransformGenotypes extends BDGSparkCommand[TransformGenotypesArgs]

Convert a file with genotypes into corresponding ADAM format and vice versa.
class TransformGenotypesArgs extends Args4jBase with ADAMSaveAnyArgs with ParquetArgs
class TransformVariants extends BDGSparkCommand[TransformVariantsArgs]

Convert a file with variants into corresponding ADAM format and vice versa.
class TransformVariantsArgs extends Args4jBase with ADAMSaveAnyArgs with ParquetArgs
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

Value Members

object ADAM2Fasta extends BDGCommandCompanion
object ADAM2Fastq extends BDGCommandCompanion
object ADAMMain
object CountContigKmers extends BDGCommandCompanion
object CountReadKmers extends BDGCommandCompanion
object Fasta2ADAM extends BDGCommandCompanion
object FlagStat 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.
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. Optional arguments are only_negative_strands, only_positive_strands and collapse. only_negative_strands and only_positive_strands save coverage computed from only negative and positive strands, respectively. Collapse specifies whether saved coverage should merge neighboring coverage with the same counts to one record.
object TransformAlignments extends BDGCommandCompanion
object TransformFeatures extends BDGCommandCompanion
object TransformFragments extends BDGCommandCompanion
object TransformGenotypes extends BDGCommandCompanion
object TransformVariants extends BDGCommandCompanion
object View extends BDGCommandCompanion

package cli

Type Members

class ADAM2Fasta extends BDGSparkCommand[ADAM2FastaArgs] with Logging

class ADAM2FastaArgs extends Args4jBase

class ADAM2Fastq extends BDGSparkCommand[ADAM2FastqArgs]

class ADAM2FastqArgs extends Args4jBase

class ADAMMain extends Logging

class ADAMModule extends AbstractModule with ScalaModule

final class About extends AnyRef

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

class Fasta2ADAM extends BDGSparkCommand[Fasta2ADAMArgs] with Logging

class Fasta2ADAMArgs extends Args4jBase with ParquetSaveArgs

class FlagStat extends BDGSparkCommand[FlagStatArgs]

class FlagStatArgs extends Args4jBase

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 TransformAlignments extends BDGSparkCommand[TransformAlignmentsArgs] with Logging

class TransformAlignmentsArgs extends Args4jBase with ADAMSaveAnyArgs with ParquetArgs

class TransformFeatures extends BDGSparkCommand[TransformFeaturesArgs]

class TransformFeaturesArgs extends Args4jBase with ParquetSaveArgs

class TransformFragments extends BDGSparkCommand[TransformFragmentsArgs] with Logging

class TransformFragmentsArgs extends Args4jBase with ADAMSaveAnyArgs with ParquetArgs

class TransformGenotypes extends BDGSparkCommand[TransformGenotypesArgs]

class TransformGenotypesArgs extends Args4jBase with ADAMSaveAnyArgs with ParquetArgs

class TransformVariants extends BDGSparkCommand[TransformVariantsArgs]

class TransformVariantsArgs extends Args4jBase with ADAMSaveAnyArgs with ParquetArgs

class View extends BDGSparkCommand[ViewArgs]

class ViewArgs extends Args4jBase with ParquetArgs with ADAMSaveAnyArgs

Value Members

object ADAM2Fasta extends BDGCommandCompanion

object ADAM2Fastq extends BDGCommandCompanion

object ADAMMain

object CountContigKmers extends BDGCommandCompanion

object CountReadKmers extends BDGCommandCompanion

object Fasta2ADAM extends BDGCommandCompanion

object FlagStat extends BDGCommandCompanion

object MergeShards extends BDGCommandCompanion

object PrintADAM extends BDGCommandCompanion

object Reads2Coverage extends BDGCommandCompanion

object TransformAlignments extends BDGCommandCompanion

object TransformFeatures extends BDGCommandCompanion

object TransformFragments extends BDGCommandCompanion

object TransformGenotypes extends BDGCommandCompanion

object TransformVariants extends BDGCommandCompanion

object View extends BDGCommandCompanion

Ungrouped