package cli
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Type Members
- class ADAM2Fastq extends BDGSparkCommand[ADAM2FastqArgs]
- class ADAM2FastqArgs extends Args4jBase with CramArgs
- class ADAMMain extends Logging
- class ADAMModule extends AbstractModule with ScalaModule
-
final
class
About extends AnyRef
About.
- case class CommandGroup(name: String, commands: List[BDGCommandCompanion]) extends Product with Serializable
- class CountReadKmers extends BDGSparkCommand[CountReadKmersArgs] with Logging
- class CountReadKmersArgs extends Args4jBase with ParquetArgs with CramArgs
- class CountSliceKmers extends BDGSparkCommand[CountSliceKmersArgs] with Logging
- class CountSliceKmersArgs extends Args4jBase with ParquetArgs
- class Coverage extends BDGSparkCommand[CoverageArgs]
- class CoverageArgs extends Args4jBase with ParquetArgs with CramArgs
- class FlagStat extends BDGSparkCommand[FlagStatArgs]
- class FlagStatArgs extends Args4jBase with CramArgs
-
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 TransformAlignments extends BDGSparkCommand[TransformAlignmentsArgs] with Logging
- class TransformAlignmentsArgs extends Args4jBase with ADAMSaveAnyArgs with ParquetArgs with CramArgs
- 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 with CramArgs
-
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 TransformSequences extends BDGSparkCommand[TransformSequencesArgs]
- class TransformSequencesArgs extends Args4jBase with ParquetSaveArgs
- class TransformSlices extends BDGSparkCommand[TransformSlicesArgs]
- class TransformSlicesArgs extends Args4jBase with ParquetSaveArgs
-
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 ofsamtools view
, specifically the -f, -F, -c, and -o options, in an optionally distributed fashion.The
adam view
command implements some of the functionality ofsamtools 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 with CramArgs
Value Members
- object ADAM2Fastq extends BDGCommandCompanion
- object ADAMMain
- object CountReadKmers extends BDGCommandCompanion
- object CountSliceKmers extends BDGCommandCompanion
-
object
Coverage extends BDGCommandCompanion
Coverage (accessible as the command 'coverage' through the CLI) takes two arguments, an INPUT and OUTPUT, and calculates the number of reads from INPUT at every location in the file.
Coverage (accessible as the command 'coverage' 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 FlagStat extends BDGCommandCompanion
- object MergeShards extends BDGCommandCompanion
- object PrintADAM extends BDGCommandCompanion
- object TransformAlignments extends BDGCommandCompanion
- object TransformFeatures extends BDGCommandCompanion
- object TransformFragments extends BDGCommandCompanion
- object TransformGenotypes extends BDGCommandCompanion
- object TransformSequences extends BDGCommandCompanion
- object TransformSlices extends BDGCommandCompanion
- object TransformVariants extends BDGCommandCompanion
- object View extends BDGCommandCompanion