Class/Object

au.csiro.variantspark.cli

GenerateFamilyCmd

Related Docs: object GenerateFamilyCmd | package cli

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class GenerateFamilyCmd extends ArgsApp with SparkApp with HailArgs with Logging with TestArgs with Echoable

Generates specification of a synthetic population based on provided pedigree and recombination map. The recombination map defines the genome build to use (at least to the extend that it defined the contigs and their lengths) Optionally it also generates mutations based on provided VCF file as a source of mutation variants. The file needs to use the build (contig spec as the genomic map) Currently only autosomes are supported.

Linear Supertypes
Echoable, TestArgs, HailArgs, SparkApp, Logging, ArgsApp, CmdApp, AnyRef, Any
Ordering
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  2. By Inheritance
Inherited
  1. GenerateFamilyCmd
  2. Echoable
  3. TestArgs
  4. HailArgs
  5. SparkApp
  6. Logging
  7. ArgsApp
  8. CmdApp
  9. AnyRef
  10. Any
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Visibility
  1. Public
  2. All

Instance Constructors

  1. new GenerateFamilyCmd()

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Value Members

  1. final def !=(arg0: Any): Boolean

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    Definition Classes
    AnyRef → Any

  2. final def ##(): Int

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    Definition Classes
    AnyRef → Any

  3. final def ==(arg0: Any): Boolean

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    Definition Classes
    AnyRef → Any

  4. lazy val actualMinPartitions: Int

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    Definition Classes
    HailArgs

  5. final def asInstanceOf[T0]: T0

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    Definition Classes
    Any

  6. val beSilent: Boolean

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    Definition Classes
    Echoable

  7. val beVerbose: Boolean

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    Definition Classes
    Echoable

  8. val bedFile: String

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  9. def clone(): AnyRef

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    Attributes
    protected[java.lang]
    Definition Classes
    AnyRef
    Annotations
    @throws( ... )

  10. lazy val conf: SparkConf

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    Definition Classes
    SparkApp

  11. def createConf: SparkConf

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    Definition Classes
    HailArgs → SparkApp

  12. def defaultMasterUrl: String

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    Definition Classes
    SparkApp

  13. def echo(msg: ⇒ String): Unit

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    Definition Classes
    Echoable

  14. final def eq(arg0: AnyRef): Boolean

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    Definition Classes
    AnyRef

  15. def equals(arg0: Any): Boolean

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    Definition Classes
    AnyRef → Any

  16. def finalize(): Unit

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    Attributes
    protected[java.lang]
    Definition Classes
    AnyRef
    Annotations
    @throws( classOf[java.lang.Throwable] )

  17. final def getClass(): Class[_]

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    Definition Classes
    AnyRef → Any

  18. def hashCode(): Int

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    Definition Classes
    AnyRef → Any

  19. lazy val hc: HailContext

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    Definition Classes
    HailArgs

  20. def isEcho: Boolean

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    Definition Classes
    Echoable

  21. final def isInstanceOf[T0]: Boolean

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    Definition Classes
    Any

  22. def isSilent: Boolean

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    Definition Classes
    Echoable

  23. def isTraceEnabled(): Boolean

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    Attributes
    protected
    Definition Classes
    Logging

  24. def isVerbose: Boolean

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    Definition Classes
    Echoable

  25. def loadMutationsFactory(contigSet: ContigSet)(inputFile: String): DatasetMutationFactory

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  26. def log: Logger

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    Attributes
    protected
    Definition Classes
    Logging

  27. def logDebug(msg: ⇒ String, throwable: Throwable): Unit

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    Attributes
    protected
    Definition Classes
    Logging

  28. def logDebug(msg: ⇒ String): Unit

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    Attributes
    protected
    Definition Classes
    Logging

  29. def logError(msg: ⇒ String, throwable: Throwable): Unit

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    Attributes
    protected
    Definition Classes
    Logging

  30. def logError(msg: ⇒ String): Unit

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    Attributes
    protected
    Definition Classes
    Logging

  31. def logInfo(msg: ⇒ String, throwable: Throwable): Unit

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    Attributes
    protected
    Definition Classes
    Logging

  32. def logInfo(msg: ⇒ String): Unit

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    Attributes
    protected
    Definition Classes
    Logging

  33. def logName: String

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    Attributes
    protected
    Definition Classes
    Logging

  34. def logTrace(msg: ⇒ String, throwable: Throwable): Unit

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    Attributes
    protected
    Definition Classes
    Logging

  35. def logTrace(msg: ⇒ String): Unit

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    Attributes
    protected
    Definition Classes
    Logging

  36. def logWarning(msg: ⇒ String, throwable: Throwable): Unit

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    Attributes
    protected
    Definition Classes
    Logging

  37. def logWarning(msg: ⇒ String): Unit

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    Attributes
    protected
    Definition Classes
    Logging

  38. val minPartitions: Int

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    Definition Classes
    HailArgs

  39. val mutationRate: Double

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  40. final def ne(arg0: AnyRef): Boolean

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    Definition Classes
    AnyRef

  41. final def notify(): Unit

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    Definition Classes
    AnyRef

  42. final def notifyAll(): Unit

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    Definition Classes
    AnyRef

  43. val outputFile: String

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  44. val pedFile: String

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  45. val randomSeed: Long

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  46. def run(): Unit

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    Definition Classes
    GenerateFamilyCmd → ArgsApp
    Annotations
    @Override()

  47. def run(args: Array[String]): Unit

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    Attributes
    protected[au.csiro.sparkle.common.args4j]
    Definition Classes
    ArgsApp → CmdApp

  48. def runApp(args: Array[String]): Unit

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    Attributes
    protected[au.csiro.sparkle.cmd]
    Definition Classes
    CmdApp

  49. implicit lazy val spark: SparkSession

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    Definition Classes
    SparkApp

  50. final def synchronized[T0](arg0: ⇒ T0): T0

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    Definition Classes
    AnyRef

  51. def testArgs: Array[String]

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    Definition Classes
    GenerateFamilyCmd → TestArgs
    Annotations
    @Override()

  52. def toString(): String

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    Definition Classes
    AnyRef → Any

  53. def usage(): Unit

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    Attributes
    protected[au.csiro.sparkle.common.args4j]
    Definition Classes
    ArgsApp → CmdApp

  54. val variantFile: String

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  55. def verbose(msg: ⇒ String): Unit

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    Definition Classes
    Echoable

  56. final def wait(): Unit

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    Definition Classes
    AnyRef
    Annotations
    @throws( ... )

  57. final def wait(arg0: Long, arg1: Int): Unit

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    Definition Classes
    AnyRef
    Annotations
    @throws( ... )

  58. final def wait(arg0: Long): Unit

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    Definition Classes
    AnyRef
    Annotations
    @throws( ... )

  59. def warn(msg: ⇒ String): Unit

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    Definition Classes
    Echoable

Deprecated Value Members

  1. implicit lazy val sc: SparkContext

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    Definition Classes
    SparkApp
    Annotations
    @deprecated
    Deprecated

  2. lazy val sqlContext: SQLContext

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    Definition Classes
    SparkApp
    Annotations
    @deprecated
    Deprecated

Inherited from Echoable

Inherited from TestArgs

Inherited from HailArgs

Inherited from SparkApp

Inherited from Logging

Inherited from ArgsApp

Inherited from CmdApp

Inherited from AnyRef

Inherited from Any

Ungrouped