Class

dagr.tasks.fgbio

TrimPrimers

Related Doc: package fgbio

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class TrimPrimers extends FgBioTask

Linear Supertypes
FgBioTask, Configuration, ConfigurationLike, FixedResources, ScheduleWithEmptyDefaultResources, JarTask, ProcessTask, UnitTask, Schedulable, LazyLogging, Task, Dependable, AnyRef, Any
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  2. By Inheritance
Inherited
  1. TrimPrimers
  2. FgBioTask
  3. Configuration
  4. ConfigurationLike
  5. FixedResources
  6. ScheduleWithEmptyDefaultResources
  7. JarTask
  8. ProcessTask
  9. UnitTask
  10. Schedulable
  11. LazyLogging
  12. Task
  13. Dependable
  14. AnyRef
  15. Any
Implicitly
  1. by any2stringadd
  2. by StringFormat
  3. by Ensuring
  4. by ArrowAssoc
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Visibility
  1. Public
  2. All

Instance Constructors

  1. new TrimPrimers(in: com.fulcrumgenomics.commons.CommonsDef.PathToBam, out: com.fulcrumgenomics.commons.CommonsDef.PathToBam, primers: com.fulcrumgenomics.commons.CommonsDef.FilePath, ref: Option[com.fulcrumgenomics.commons.CommonsDef.PathToFasta], slop: Option[Int] = None, hardClip: Option[Boolean] = None, sortOrder: Option[SortOrder] = None)

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Value Members

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

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    Definition Classes
    AnyRef → Any
  2. def !=>(other: Dependable): Unit

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    Definition Classes
    Task → Dependable
  3. final def ##(): Int

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    Definition Classes
    AnyRef → Any
  4. def +(other: String): String

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    Implicit information
    This member is added by an implicit conversion from TrimPrimers to any2stringadd[TrimPrimers] performed by method any2stringadd in scala.Predef.
    Definition Classes
    any2stringadd
  5. def ->[B](y: B): (TrimPrimers, B)

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    Implicit information
    This member is added by an implicit conversion from TrimPrimers to ArrowAssoc[TrimPrimers] performed by method ArrowAssoc in scala.Predef.
    Definition Classes
    ArrowAssoc
    Annotations
    @inline()
  6. def ::(other: Option[Dependable]): Dependable

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    Definition Classes
    Dependable
  7. def ::(other: Dependable): Dependable

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    Definition Classes
    Dependable
  8. final def ==(arg0: Any): Boolean

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    Definition Classes
    AnyRef → Any
  9. final def ==>(other: Option[Dependable]): Dependable

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    Definition Classes
    Dependable
  10. final def ==>(other: Dependable): Dependable

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    Definition Classes
    Dependable
  11. def addDependent(dependent: Dependable): Unit

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    Definition Classes
    Task → Dependable
  12. def addFgBioArgs(buffer: ListBuffer[Any]): Unit

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    Implement this to add the tool-specific arguments

    Implement this to add the tool-specific arguments

    Attributes
    protected
    Definition Classes
    TrimPrimersFgBioTask
  13. def allTasks: Traversable[Task]

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    Definition Classes
    Task → Dependable
  14. def applyResources(resources: ResourceSet): Unit

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    Definition Classes
    UnitTask → Schedulable
  15. final def args: Seq[Any]

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    Definition Classes
    FgBioTask → ProcessTask
  16. final def asInstanceOf[T0]: T0

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    Definition Classes
    Any
  17. def asType[T](path: String)(implicit arg0: scala.reflect.api.JavaUniverse.TypeTag[T]): T

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    Attributes
    protected
    Definition Classes
    ConfigurationLike
  18. def clone(): AnyRef

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    Attributes
    protected[java.lang]
    Definition Classes
    AnyRef
    Annotations
    @throws( ... )
  19. def commandLineName(name: String): String

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    Definition Classes
    ConfigurationLike
  20. lazy val commandName: String

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    Looks up the first super class that does not have "$anon$" in its name.

    Looks up the first super class that does not have "$anon$" in its name.

    Definition Classes
    FgBioTask
  21. var compressionLevel: Option[Int]

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    the compress level to use for HTSJDK.

    the compress level to use for HTSJDK.

    Definition Classes
    FgBioTask
  22. def config: Config

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    Attributes
    protected
    Definition Classes
    Configuration → ConfigurationLike
  23. def configure[T](path: String, defaultValue: T)(implicit arg0: scala.reflect.api.JavaUniverse.TypeTag[T]): T

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    Definition Classes
    ConfigurationLike
  24. def configure[T](path: String)(implicit arg0: scala.reflect.api.JavaUniverse.TypeTag[T]): T

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    Definition Classes
    ConfigurationLike
  25. def configureExecutable(path: String, executable: String): Path

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    Definition Classes
    ConfigurationLike
  26. def configureExecutableFromBinDirectory(binPath: String, executable: String, subDir: Option[Path]): Path

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    Definition Classes
    ConfigurationLike
  27. def ensuring(cond: (TrimPrimers) ⇒ Boolean, msg: ⇒ Any): TrimPrimers

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    Implicit information
    This member is added by an implicit conversion from TrimPrimers to Ensuring[TrimPrimers] performed by method Ensuring in scala.Predef.
    Definition Classes
    Ensuring
  28. def ensuring(cond: (TrimPrimers) ⇒ Boolean): TrimPrimers

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    Implicit information
    This member is added by an implicit conversion from TrimPrimers to Ensuring[TrimPrimers] performed by method Ensuring in scala.Predef.
    Definition Classes
    Ensuring
  29. def ensuring(cond: Boolean, msg: ⇒ Any): TrimPrimers

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    Implicit information
    This member is added by an implicit conversion from TrimPrimers to Ensuring[TrimPrimers] performed by method Ensuring in scala.Predef.
    Definition Classes
    Ensuring
  30. def ensuring(cond: Boolean): TrimPrimers

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    Implicit information
    This member is added by an implicit conversion from TrimPrimers to Ensuring[TrimPrimers] performed by method Ensuring in scala.Predef.
    Definition Classes
    Ensuring
  31. final def eq(arg0: AnyRef): Boolean

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    Definition Classes
    AnyRef
  32. def equals(arg0: Any): Boolean

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    Definition Classes
    AnyRef → Any
  33. def fgBioJar: Path

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    Can be overridden to use a specific FgBio jar.

    Can be overridden to use a specific FgBio jar.

    Attributes
    protected
    Definition Classes
    FgBioTask
  34. def finalize(): Unit

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    Attributes
    protected[java.lang]
    Definition Classes
    AnyRef
    Annotations
    @throws( classOf[java.lang.Throwable] )
  35. def formatted(fmtstr: String): String

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    Implicit information
    This member is added by an implicit conversion from TrimPrimers to StringFormat[TrimPrimers] performed by method StringFormat in scala.Predef.
    Definition Classes
    StringFormat
    Annotations
    @inline()
  36. final def getClass(): Class[_]

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    Definition Classes
    AnyRef → Any
  37. final def getTasks: Traversable[_ <: TrimPrimers.this.type]

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    Definition Classes
    UnitTask → Task
  38. val hardClip: Option[Boolean]

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  39. def hashCode(): Int

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    Definition Classes
    AnyRef → Any
  40. def headTasks: Traversable[Task]

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    Definition Classes
    Task → Dependable
  41. val in: com.fulcrumgenomics.commons.CommonsDef.PathToBam

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  42. final def isInstanceOf[T0]: Boolean

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    Definition Classes
    Any
  43. def jarArgs(jarPath: Path, jvmArgs: Traversable[String] = Nil, jvmProperties: Map[String, String] = Map.empty, jvmMemory: Memory, useAdvancedGcOptions: Boolean = true): List[String]

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    Attributes
    protected
    Definition Classes
    JarTask
  44. lazy val logger: Logger

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    Attributes
    protected
    Definition Classes
    LazyLogging
  45. var name: String

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    Definition Classes
    Task
  46. final def ne(arg0: AnyRef): Boolean

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    Definition Classes
    AnyRef
  47. final def notify(): Unit

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    Definition Classes
    AnyRef
  48. final def notifyAll(): Unit

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    Definition Classes
    AnyRef
  49. def onComplete(exitCode: Int): Boolean

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    Definition Classes
    Task
  50. def optionallyConfigure[T](path: String)(implicit arg0: scala.reflect.api.JavaUniverse.TypeTag[T]): Option[T]

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    Definition Classes
    ConfigurationLike
  51. val out: com.fulcrumgenomics.commons.CommonsDef.PathToBam

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  52. def pickResources(availableResources: ResourceSet): Option[ResourceSet]

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    Definition Classes
    FixedResources → Schedulable
  53. val primers: com.fulcrumgenomics.commons.CommonsDef.FilePath

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  54. var quoteIfNecessary: Boolean

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    Attributes
    protected
    Definition Classes
    ProcessTask
  55. val ref: Option[com.fulcrumgenomics.commons.CommonsDef.PathToFasta]

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  56. def removeDependency(task: Task): Boolean

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    Definition Classes
    Task
  57. def requires(cores: Double, memory: String): TrimPrimers.this.type

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    Definition Classes
    FixedResources
  58. def requires(cores: Cores, memory: Memory): TrimPrimers.this.type

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    Definition Classes
    FixedResources
  59. def requires(resources: ResourceSet): TrimPrimers.this.type

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    Definition Classes
    FixedResources
  60. def resources: ResourceSet

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    Definition Classes
    ScheduleWithEmptyDefaultResources
  61. val slop: Option[Int]

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  62. val sortOrder: Option[SortOrder]

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

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    Definition Classes
    AnyRef
  64. def systemPath: Seq[Path]

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    Attributes
    protected
    Definition Classes
    ConfigurationLike
  65. def tailTasks: Traversable[Task]

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    Definition Classes
    Task → Dependable
  66. def tasksDependedOn: Traversable[Task]

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    Attributes
    protected[dagr.core]
    Definition Classes
    Task
  67. def tasksDependingOnThisTask: Traversable[Task]

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    Attributes
    protected[dagr.core]
    Definition Classes
    Task
  68. def toString(): String

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    Definition Classes
    ProcessTask → AnyRef → Any
  69. final def wait(): Unit

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    Definition Classes
    AnyRef
    Annotations
    @throws( ... )
  70. final def wait(arg0: Long, arg1: Int): Unit

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    Definition Classes
    AnyRef
    Annotations
    @throws( ... )
  71. final def wait(arg0: Long): Unit

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    Definition Classes
    AnyRef
    Annotations
    @throws( ... )
  72. def withCompression(i: Int): TrimPrimers.this.type

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    Sets the compression level to a specific value.

    Sets the compression level to a specific value.

    Definition Classes
    FgBioTask
  73. def withName(name: String): TrimPrimers.this.type

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    Definition Classes
    Task
  74. def [B](y: B): (TrimPrimers, B)

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    Implicit information
    This member is added by an implicit conversion from TrimPrimers to ArrowAssoc[TrimPrimers] performed by method ArrowAssoc in scala.Predef.
    Definition Classes
    ArrowAssoc

Inherited from FgBioTask

Inherited from Configuration

Inherited from ConfigurationLike

Inherited from FixedResources

Inherited from ScheduleWithEmptyDefaultResources

Inherited from JarTask

Inherited from ProcessTask

Inherited from UnitTask

Inherited from Schedulable

Inherited from LazyLogging

Inherited from Task

Inherited from Dependable

Inherited from AnyRef

Inherited from Any

Inherited by implicit conversion any2stringadd from TrimPrimers to any2stringadd[TrimPrimers]

Inherited by implicit conversion StringFormat from TrimPrimers to StringFormat[TrimPrimers]

Inherited by implicit conversion Ensuring from TrimPrimers to Ensuring[TrimPrimers]

Inherited by implicit conversion ArrowAssoc from TrimPrimers to ArrowAssoc[TrimPrimers]

Ungrouped