cli

Type Members

class ADAM2Vcf extends ADAMSparkCommand[ADAM2VcfArgs] with DictionaryCommand with Logging
class ADAM2VcfArgs extends Args4jBase with ParquetArgs
trait ADAMCommand extends Runnable
trait ADAMCommandCompanion extends AnyRef
trait ADAMSparkCommand[A <: Args4jBase] extends ADAMCommand with Logging
class Adam2Fastq extends ADAMSparkCommand[Adam2FastqArgs]
class Adam2FastqArgs extends Args4jBase with ParquetLoadSaveArgs
class AlleleCount extends ADAMSparkCommand[AlleleCountArgs] with Logging
class AlleleCountArgs extends Args4jBase with ParquetArgs
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 ParquetArgs
class CompareADAM extends ADAMSparkCommand[CompareADAMArgs] with Serializable
class CompareADAMArgs extends Args4jBase with ParquetArgs with Serializable
class CountKmers extends ADAMSparkCommand[CountKmersArgs] with Logging
class CountKmersArgs extends Args4jBase with ParquetArgs
trait DictionaryCommand extends AnyRef
class Fasta2ADAM extends ADAMSparkCommand[Fasta2ADAMArgs] with Logging
class Fasta2ADAMArgs extends Args4jBase with ParquetSaveArgs
class Features2ADAM extends ADAMSparkCommand[Features2ADAMArgs]
class Features2ADAMArgs extends Args4jBase with ParquetSaveArgs
class FindReads extends ADAMSparkCommand[FindReadsArgs] with Serializable
class FindReadsArgs extends Args4jBase with ParquetArgs with Serializable
class FlagStat extends ADAMSparkCommand[FlagStatArgs]
class FlagStatArgs extends Args4jBase with ParquetArgs
case class FreqJson(base: Long, freq: Long) extends Product with Serializable
class GenotypeConcordance extends ADAMSparkCommand[GenotypeConcordanceArgs] with Logging
class GenotypeConcordanceArgs extends Args4jBase with ParquetArgs
class ListDict extends ADAMSparkCommand[ListDictArgs]
class ListDictArgs extends Args4jBase with ParquetArgs
trait LoadFileArgs extends AnyRef
class MpileupArgs extends Args4jBase
class MpileupCommand extends ADAMSparkCommand[MpileupArgs] with Logging
trait ParquetArgs extends Args4jBase with ADAMParquetArgs
trait ParquetLoadSaveArgs extends Args4jBase with ParquetSaveArgs with LoadFileArgs with SaveFileArgs
trait ParquetSaveArgs extends Args4jBase with ParquetArgs with ADAMSaveArgs
class PluginExecutor extends ADAMSparkCommand[PluginExecutorArgs]
class PluginExecutorArgs extends Args4jBase with ParquetArgs
class PrintADAM extends ADAMSparkCommand[PrintADAMArgs]
class PrintADAMArgs extends Args4jBase
class PrintGenes extends ADAMSparkCommand[PrintGenesArgs] with Serializable
class PrintGenesArgs extends Args4jBase with ParquetArgs with Serializable
class PrintTags extends ADAMSparkCommand[PrintTagsArgs]
class PrintTagsArgs extends Args4jBase with ParquetArgs
class Reads2Ref extends ADAMSparkCommand[Reads2RefArgs]
class Reads2RefArgs extends Args4jBase with ParquetSaveArgs
trait SaveFileArgs extends AnyRef
class SummarizeGenotypes extends ADAMSparkCommand[SummarizeGenotypesArgs] with Logging
class SummarizeGenotypesArgs extends Args4jBase with ParquetArgs
case class TrackJson(readName: String, start: Long, end: Long, track: Long) extends Product with Serializable
class Transform extends ADAMSparkCommand[TransformArgs] with Logging
class TransformArgs extends Args4jBase with ADAMSaveAnyArgs with ParquetArgs
case class VariationJson(contigName: String, alleles: String, start: Long, end: Long, track: Long) extends Product with Serializable
class Vcf2ADAM extends ADAMSparkCommand[Vcf2ADAMArgs] with DictionaryCommand with Logging
class Vcf2ADAMArgs extends Args4jBase with ParquetSaveArgs
class VcfAnnotation2ADAM extends ADAMSparkCommand[VcfAnnotation2ADAMArgs] with Logging
class VcfAnnotation2ADAMArgs extends Args4jBase with ParquetSaveArgs
class View extends ADAMSparkCommand[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 ADAMSaveArgs
class VizReads extends ADAMSparkCommand[VizReadsArgs]
class VizReadsArgs extends Args4jBase with ParquetArgs
class VizServlet extends ScalatraServlet with JacksonJsonSupport
class Wig2BedArgs extends Args4jBase
class WigFix2Bed extends ADAMCommand

Value Members

object ADAM2Vcf extends ADAMCommandCompanion
object ADAMMain extends Logging
object Adam2Fastq extends ADAMCommandCompanion
object AlleleCount extends ADAMCommandCompanion
object AlleleCountHelper extends Serializable
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 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 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 CountKmers extends ADAMCommandCompanion
object Fasta2ADAM extends ADAMCommandCompanion
object Features2ADAM 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 PluginExecutor extends ADAMCommandCompanion

This set of classes executes a plugin along with the associated input location.
object PrintADAM extends ADAMCommandCompanion
object PrintGenes extends ADAMCommandCompanion with Serializable
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 SummarizeGenotypes extends ADAMCommandCompanion
object Transform extends ADAMCommandCompanion
object Vcf2ADAM extends ADAMCommandCompanion
object VcfAnnotation2ADAM extends ADAMCommandCompanion
object View extends ADAMCommandCompanion
object VizReads extends ADAMCommandCompanion
object WigFix2Bed extends ADAMCommandCompanion

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 ADAM2Vcf extends ADAMSparkCommand[ADAM2VcfArgs] with DictionaryCommand with Logging

class ADAM2VcfArgs extends Args4jBase with ParquetArgs

trait ADAMCommand extends Runnable

trait ADAMCommandCompanion extends AnyRef

trait ADAMSparkCommand[A <: Args4jBase] extends ADAMCommand with Logging

class Adam2Fastq extends ADAMSparkCommand[Adam2FastqArgs]

class Adam2FastqArgs extends Args4jBase with ParquetLoadSaveArgs

class AlleleCount extends ADAMSparkCommand[AlleleCountArgs] with Logging

class AlleleCountArgs extends Args4jBase with ParquetArgs

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 ParquetArgs

class CompareADAM extends ADAMSparkCommand[CompareADAMArgs] with Serializable

class CompareADAMArgs extends Args4jBase with ParquetArgs with Serializable

class CountKmers extends ADAMSparkCommand[CountKmersArgs] with Logging

class CountKmersArgs extends Args4jBase with ParquetArgs

trait DictionaryCommand extends AnyRef

class Fasta2ADAM extends ADAMSparkCommand[Fasta2ADAMArgs] with Logging

class Fasta2ADAMArgs extends Args4jBase with ParquetSaveArgs

class Features2ADAM extends ADAMSparkCommand[Features2ADAMArgs]

class Features2ADAMArgs extends Args4jBase with ParquetSaveArgs

class FindReads extends ADAMSparkCommand[FindReadsArgs] with Serializable

class FindReadsArgs extends Args4jBase with ParquetArgs with Serializable

class FlagStat extends ADAMSparkCommand[FlagStatArgs]

class FlagStatArgs extends Args4jBase with ParquetArgs

case class FreqJson(base: Long, freq: Long) extends Product with Serializable

class GenotypeConcordance extends ADAMSparkCommand[GenotypeConcordanceArgs] with Logging

class GenotypeConcordanceArgs extends Args4jBase with ParquetArgs

class ListDict extends ADAMSparkCommand[ListDictArgs]

class ListDictArgs extends Args4jBase with ParquetArgs

trait LoadFileArgs extends AnyRef

class MpileupArgs extends Args4jBase

class MpileupCommand extends ADAMSparkCommand[MpileupArgs] with Logging

trait ParquetArgs extends Args4jBase with ADAMParquetArgs

trait ParquetLoadSaveArgs extends Args4jBase with ParquetSaveArgs with LoadFileArgs with SaveFileArgs

trait ParquetSaveArgs extends Args4jBase with ParquetArgs with ADAMSaveArgs

class PluginExecutor extends ADAMSparkCommand[PluginExecutorArgs]

class PluginExecutorArgs extends Args4jBase with ParquetArgs

class PrintADAM extends ADAMSparkCommand[PrintADAMArgs]

class PrintADAMArgs extends Args4jBase

class PrintGenes extends ADAMSparkCommand[PrintGenesArgs] with Serializable

class PrintGenesArgs extends Args4jBase with ParquetArgs with Serializable

class PrintTags extends ADAMSparkCommand[PrintTagsArgs]

class PrintTagsArgs extends Args4jBase with ParquetArgs

class Reads2Ref extends ADAMSparkCommand[Reads2RefArgs]

class Reads2RefArgs extends Args4jBase with ParquetSaveArgs

trait SaveFileArgs extends AnyRef

class SummarizeGenotypes extends ADAMSparkCommand[SummarizeGenotypesArgs] with Logging

class SummarizeGenotypesArgs extends Args4jBase with ParquetArgs

case class TrackJson(readName: String, start: Long, end: Long, track: Long) extends Product with Serializable

class Transform extends ADAMSparkCommand[TransformArgs] with Logging

class TransformArgs extends Args4jBase with ADAMSaveAnyArgs with ParquetArgs

case class VariationJson(contigName: String, alleles: String, start: Long, end: Long, track: Long) extends Product with Serializable

class Vcf2ADAM extends ADAMSparkCommand[Vcf2ADAMArgs] with DictionaryCommand with Logging

class Vcf2ADAMArgs extends Args4jBase with ParquetSaveArgs

class VcfAnnotation2ADAM extends ADAMSparkCommand[VcfAnnotation2ADAMArgs] with Logging

class VcfAnnotation2ADAMArgs extends Args4jBase with ParquetSaveArgs

class View extends ADAMSparkCommand[ViewArgs]

class ViewArgs extends Args4jBase with ParquetArgs with ADAMSaveArgs

class VizReads extends ADAMSparkCommand[VizReadsArgs]

class VizReadsArgs extends Args4jBase with ParquetArgs

class VizServlet extends ScalatraServlet with JacksonJsonSupport

class Wig2BedArgs extends Args4jBase

class WigFix2Bed extends ADAMCommand

Value Members

object ADAM2Vcf extends ADAMCommandCompanion

object ADAMMain extends Logging

object Adam2Fastq extends ADAMCommandCompanion

object AlleleCount extends ADAMCommandCompanion

object AlleleCountHelper extends Serializable

object Args4j

object Bam2ADAM extends ADAMCommandCompanion

object BuildInformation extends ADAMCommandCompanion

object CalculateDepth extends ADAMCommandCompanion