cli

Type Members

class ADAM2Vcf extends ADAMSparkCommand[ADAM2VcfArgs] with DictionaryCommand with Logging
class ADAM2VcfArgs extends Args4jBase with ParquetArgs with SparkArgs
trait ADAMCommand extends Runnable
trait ADAMCommandCompanion extends AnyRef
trait ADAMSparkCommand[A <: Args4jBase with SparkArgs] extends ADAMCommand with SparkCommand
class Args4jBase extends AnyRef
class Bam2ADAM extends ADAMCommand
class Bam2ADAMArgs extends Args4jBase with ParquetArgs
class BuildInformation extends ADAMCommand
class CalculateDepth extends ADAMSparkCommand[CalculateDepthArgs]
class CalculateDepthArgs extends Args4jBase with SparkArgs with ParquetArgs
class CompareADAM extends ADAMSparkCommand[CompareADAMArgs] with Serializable
class CompareADAMArgs extends Args4jBase with SparkArgs with ParquetArgs with Serializable
trait DictionaryCommand extends AnyRef
class Fasta2ADAM extends ADAMSparkCommand[Fasta2ADAMArgs] with Logging
class Fasta2ADAMArgs extends Args4jBase with ParquetArgs with SparkArgs
class FindReads extends ADAMSparkCommand[FindReadsArgs] with Serializable
class FindReadsArgs extends Args4jBase with SparkArgs with ParquetArgs with Serializable
class FlagStat extends ADAMSparkCommand[FlagStatArgs]
class FlagStatArgs extends Args4jBase with SparkArgs with ParquetArgs
class GenotypeConcordance extends ADAMSparkCommand[GenotypeConcordanceArgs] with Logging
class GenotypeConcordanceArgs extends Args4jBase with ParquetArgs with SparkArgs
class ListDict extends ADAMSparkCommand[ListDictArgs]
class ListDictArgs extends Args4jBase with SparkArgs with ParquetArgs
class MpileupArgs extends Args4jBase with SparkArgs
class MpileupCommand extends ADAMSparkCommand[MpileupArgs] with Logging
trait ParquetArgs extends Args4jBase
class PileupAggregator extends ADAMSparkCommand[PileupAggregatorArgs]
class PileupAggregatorArgs extends Args4jBase with SparkArgs with ParquetArgs
class PluginExecutor extends ADAMSparkCommand[PluginExecutorArgs]
class PluginExecutorArgs extends Args4jBase with SparkArgs with ParquetArgs
class PrintADAM extends ADAMSparkCommand[PrintADAMArgs]
class PrintADAMArgs extends Args4jBase with SparkArgs
class PrintTags extends ADAMSparkCommand[PrintTagsArgs]
class PrintTagsArgs extends Args4jBase with SparkArgs with ParquetArgs
class Reads2Ref extends ADAMSparkCommand[Reads2RefArgs]
class Reads2RefArgs extends Args4jBase with ParquetArgs with SparkArgs
trait SparkArgs extends Args4jBase
trait SparkCommand extends ADAMCommand
class SummarizeGenotypes extends ADAMSparkCommand[SummarizeGenotypesArgs] with Logging
class SummarizeGenotypesArgs extends Args4jBase with ParquetArgs with SparkArgs
class Transform extends ADAMSparkCommand[TransformArgs] with Logging
class TransformArgs extends Args4jBase with ParquetArgs with SparkArgs
class Vcf2ADAM extends ADAMSparkCommand[Vcf2ADAMArgs] with DictionaryCommand with Logging
class Vcf2ADAMArgs extends Args4jBase with ParquetArgs with SparkArgs
class Vcf2FlatGenotype extends ADAMCommand
class Vcf2FlatGenotypeArgs extends Args4jBase with ParquetArgs
class VcfAnnotation2ADAM extends ADAMSparkCommand[VcfAnnotation2ADAMArgs] with Logging
class VcfAnnotation2ADAMArgs extends Args4jBase with ParquetArgs with SparkArgs

Value Members

object ADAM2Vcf extends ADAMCommandCompanion
object ADAMMain extends Logging
object Args4j
object Bam2ADAM extends ADAMCommandCompanion
object BuildInformation extends ADAMCommandCompanion
object CalculateDepth extends ADAMCommandCompanion

CalculateDepth (accessible as the command 'depth' through the CLI) takes two arguments, an ADAMRecord file and a VCF (or equivalent) file, and calculates the number of reads (the 'depth') from the ADAMRecord file which overlap each of the variants given by the VCF.
object CompareADAM extends ADAMCommandCompanion with Serializable

CompareADAM is a tool for pairwise comparison of ADAM files (or merged sets of ADAM files, see the note on the -recurse{1,2} optional parameters, below).
object Fasta2ADAM extends ADAMCommandCompanion
object FindReads extends ADAMCommandCompanion with Serializable

FindReads is an auxiliary command to CompareADAM -- whereas CompareADAM takes two ADAM files (which presumably contain the same reads, processed differently), joins them based on read-name, and computes aggregates of one or more metrics (BucketComparisons) across those joined reads -- FindReads performs the same join-and-metric-computation, but takes a second argument as well: a boolean condition on the value(s) of the metric(s) computed.
object FlagStat extends ADAMCommandCompanion
object GenotypeConcordance extends ADAMCommandCompanion
object ListDict extends ADAMCommandCompanion
object MpileupCommand extends ADAMCommandCompanion
object PileupAggregator extends ADAMCommandCompanion
object PluginExecutor extends ADAMCommandCompanion

This set of classes executes a plugin along with the associated input location.
object PrintADAM extends ADAMCommandCompanion
object PrintTags extends ADAMCommandCompanion

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 Reads2Ref extends ADAMCommandCompanion
object Reads2RefArgs
object SummarizeGenotypes extends ADAMCommandCompanion
object Transform extends ADAMCommandCompanion
object Vcf2ADAM extends ADAMCommandCompanion
object Vcf2FlatGenotype extends ADAMCommandCompanion

Vcf2FlatGenotype converts .
object VcfAnnotation2ADAM extends ADAMCommandCompanion

package cli

Type Members

class ADAM2Vcf extends ADAMSparkCommand[ADAM2VcfArgs] with DictionaryCommand with Logging

class ADAM2VcfArgs extends Args4jBase with ParquetArgs with SparkArgs

trait ADAMCommand extends Runnable

trait ADAMCommandCompanion extends AnyRef

trait ADAMSparkCommand[A <: Args4jBase with SparkArgs] extends ADAMCommand with SparkCommand

class Args4jBase extends AnyRef

class Bam2ADAM extends ADAMCommand

class Bam2ADAMArgs extends Args4jBase with ParquetArgs

class BuildInformation extends ADAMCommand

class CalculateDepth extends ADAMSparkCommand[CalculateDepthArgs]

class CalculateDepthArgs extends Args4jBase with SparkArgs with ParquetArgs

class CompareADAM extends ADAMSparkCommand[CompareADAMArgs] with Serializable

class CompareADAMArgs extends Args4jBase with SparkArgs with ParquetArgs with Serializable

trait DictionaryCommand extends AnyRef

class Fasta2ADAM extends ADAMSparkCommand[Fasta2ADAMArgs] with Logging

class Fasta2ADAMArgs extends Args4jBase with ParquetArgs with SparkArgs

class FindReads extends ADAMSparkCommand[FindReadsArgs] with Serializable

class FindReadsArgs extends Args4jBase with SparkArgs with ParquetArgs with Serializable

class FlagStat extends ADAMSparkCommand[FlagStatArgs]

class FlagStatArgs extends Args4jBase with SparkArgs with ParquetArgs

class GenotypeConcordance extends ADAMSparkCommand[GenotypeConcordanceArgs] with Logging

class GenotypeConcordanceArgs extends Args4jBase with ParquetArgs with SparkArgs

class ListDict extends ADAMSparkCommand[ListDictArgs]

class ListDictArgs extends Args4jBase with SparkArgs with ParquetArgs

class MpileupArgs extends Args4jBase with SparkArgs

class MpileupCommand extends ADAMSparkCommand[MpileupArgs] with Logging

trait ParquetArgs extends Args4jBase

class PileupAggregator extends ADAMSparkCommand[PileupAggregatorArgs]

class PileupAggregatorArgs extends Args4jBase with SparkArgs with ParquetArgs

class PluginExecutor extends ADAMSparkCommand[PluginExecutorArgs]

class PluginExecutorArgs extends Args4jBase with SparkArgs with ParquetArgs

class PrintADAM extends ADAMSparkCommand[PrintADAMArgs]

class PrintADAMArgs extends Args4jBase with SparkArgs

class PrintTags extends ADAMSparkCommand[PrintTagsArgs]

class PrintTagsArgs extends Args4jBase with SparkArgs with ParquetArgs

class Reads2Ref extends ADAMSparkCommand[Reads2RefArgs]

class Reads2RefArgs extends Args4jBase with ParquetArgs with SparkArgs

trait SparkArgs extends Args4jBase

trait SparkCommand extends ADAMCommand

class SummarizeGenotypes extends ADAMSparkCommand[SummarizeGenotypesArgs] with Logging

class SummarizeGenotypesArgs extends Args4jBase with ParquetArgs with SparkArgs

class Transform extends ADAMSparkCommand[TransformArgs] with Logging

class TransformArgs extends Args4jBase with ParquetArgs with SparkArgs

class Vcf2ADAM extends ADAMSparkCommand[Vcf2ADAMArgs] with DictionaryCommand with Logging

class Vcf2ADAMArgs extends Args4jBase with ParquetArgs with SparkArgs

class Vcf2FlatGenotype extends ADAMCommand

class Vcf2FlatGenotypeArgs extends Args4jBase with ParquetArgs

class VcfAnnotation2ADAM extends ADAMSparkCommand[VcfAnnotation2ADAMArgs] with Logging

class VcfAnnotation2ADAMArgs extends Args4jBase with ParquetArgs with SparkArgs

Value Members

object ADAM2Vcf extends ADAMCommandCompanion

object ADAMMain extends Logging

object Args4j

object Bam2ADAM extends ADAMCommandCompanion

object BuildInformation extends ADAMCommandCompanion

object CalculateDepth extends ADAMCommandCompanion

object CompareADAM extends ADAMCommandCompanion with Serializable

object Fasta2ADAM extends ADAMCommandCompanion

object FindReads extends ADAMCommandCompanion with Serializable

object FlagStat extends ADAMCommandCompanion

object GenotypeConcordance extends ADAMCommandCompanion

object ListDict extends ADAMCommandCompanion

object MpileupCommand extends ADAMCommandCompanion

object PileupAggregator extends ADAMCommandCompanion

object PluginExecutor extends ADAMCommandCompanion

object PrintADAM extends ADAMCommandCompanion

object PrintTags extends ADAMCommandCompanion

object Reads2Ref extends ADAMCommandCompanion

object Reads2RefArgs

object SummarizeGenotypes extends ADAMCommandCompanion

object Transform extends ADAMCommandCompanion

object Vcf2ADAM extends ADAMCommandCompanion

object Vcf2FlatGenotype extends ADAMCommandCompanion

object VcfAnnotation2ADAM extends ADAMCommandCompanion

Ungrouped