Class

dagr.tasks.gatk

HaplotypeCaller

Related Doc: package gatk

Permalink

class HaplotypeCaller extends GatkTask

Runs the GATK haplotype caller in GVCF mode on a single sample.

Linear Supertypes
GatkTask, Configuration, ConfigurationLike, FixedResources, ScheduleWithEmptyDefaultResources, JarTask, ProcessTask, UnitTask, Schedulable, LazyLogging, Task, Dependable, AnyRef, Any
Ordering
  1. Alphabetic
  2. By Inheritance
Inherited
  1. HaplotypeCaller
  2. GatkTask
  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
  1. Hide All
  2. Show All
Visibility
  1. Public
  2. All

Instance Constructors

  1. new HaplotypeCaller(ref: PathToFasta, intervals: Option[PathToIntervals], bam: PathToBam, vcf: PathToVcf, maxAlternateAlleles: Int = 3, minPruning: Int = 3, contaminationFraction: Double = 0.0, rnaMode: Boolean = false, useNativePairHmm: Boolean = false, maxReadsInRegionPerSample: Option[Int] = None, minReadsPerAlignmentStart: Option[Int] = None)

    Permalink

Value Members

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

    Permalink
    Definition Classes
    AnyRef → Any

  2. def !=>(other: Dependable): Unit

    Permalink
    Definition Classes
    Task → Dependable

  3. final def ##(): Int

    Permalink
    Definition Classes
    AnyRef → Any

  4. def +(other: String): String

    Permalink
    Implicit information
    This member is added by an implicit conversion from HaplotypeCaller to any2stringadd[HaplotypeCaller] performed by method any2stringadd in scala.Predef.
    Definition Classes
    any2stringadd

  5. def ->[B](y: B): (HaplotypeCaller, B)

    Permalink
    Implicit information
    This member is added by an implicit conversion from HaplotypeCaller to ArrowAssoc[HaplotypeCaller] performed by method ArrowAssoc in scala.Predef.
    Definition Classes
    ArrowAssoc
    Annotations
    @inline()

  6. def ::(other: Option[Dependable]): Dependable

    Permalink
    Definition Classes
    Dependable

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

    Permalink
    Definition Classes
    Dependable

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

    Permalink
    Definition Classes
    AnyRef → Any

  9. final def ==>(other: Option[Dependable]): Dependable

    Permalink
    Definition Classes
    Dependable

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

    Permalink
    Definition Classes
    Dependable

  11. def addDependent(dependent: Dependable): Unit

    Permalink
    Definition Classes
    Task → Dependable

  12. def addWalkerArgs(buffer: ListBuffer[Any]): Unit

    Permalink
    Attributes
    protected
    Definition Classes
    HaplotypeCaller → GatkTask

  13. def allTasks: Traversable[Task]

    Permalink
    Definition Classes
    Task → Dependable

  14. def applyResources(resources: ResourceSet): Unit

    Permalink
    Definition Classes
    UnitTask → Schedulable

  15. def args: Seq[Any]

    Permalink
    Definition Classes
    GatkTask → ProcessTask

  16. final def asInstanceOf[T0]: T0

    Permalink
    Definition Classes
    Any

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

    Permalink
    Attributes
    protected
    Definition Classes
    ConfigurationLike

  18. val bam: PathToBam

    Permalink

  19. val bamCompression: Option[Int]

    Permalink
    Definition Classes
    GatkTask

  20. def clone(): AnyRef

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

  21. def commandLineName(name: String): String

    Permalink
    Definition Classes
    ConfigurationLike

  22. def config: Config

    Permalink
    Attributes
    protected
    Definition Classes
    Configuration → ConfigurationLike

  23. def configure[T](path: String, defaultValue: T)(implicit arg0: scala.reflect.api.JavaUniverse.TypeTag[T]): T

    Permalink
    Definition Classes
    ConfigurationLike

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

    Permalink
    Definition Classes
    ConfigurationLike

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

    Permalink
    Definition Classes
    ConfigurationLike

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

    Permalink
    Definition Classes
    ConfigurationLike

  27. val contaminationFraction: Double

    Permalink

  28. def ensuring(cond: (HaplotypeCaller) ⇒ Boolean, msg: ⇒ Any): HaplotypeCaller

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

  29. def ensuring(cond: (HaplotypeCaller) ⇒ Boolean): HaplotypeCaller

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

  30. def ensuring(cond: Boolean, msg: ⇒ Any): HaplotypeCaller

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

  31. def ensuring(cond: Boolean): HaplotypeCaller

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

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

    Permalink
    Definition Classes
    AnyRef

  33. def equals(arg0: Any): Boolean

    Permalink
    Definition Classes
    AnyRef → Any

  34. def finalize(): Unit

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

  35. def formatted(fmtstr: String): String

    Permalink
    Implicit information
    This member is added by an implicit conversion from HaplotypeCaller to StringFormat[HaplotypeCaller] performed by method StringFormat in scala.Predef.
    Definition Classes
    StringFormat
    Annotations
    @inline()

  36. def gatkJar: Path

    Permalink

    Can be overridden to use a specific GATK jar.

    Can be overridden to use a specific GATK jar.

    Attributes
    protected
    Definition Classes
    GatkTask

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

    Permalink
    Definition Classes
    AnyRef → Any

  38. final def getTasks: Traversable[_ <: HaplotypeCaller.this.type]

    Permalink
    Definition Classes
    UnitTask → Task

  39. def hashCode(): Int

    Permalink
    Definition Classes
    AnyRef → Any

  40. def headTasks: Traversable[Task]

    Permalink
    Definition Classes
    Task → Dependable

  41. val intervals: Option[PathToIntervals]

    Permalink
    Definition Classes
    GatkTask

  42. final def isInstanceOf[T0]: Boolean

    Permalink
    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]

    Permalink
    Attributes
    protected
    Definition Classes
    JarTask

  44. lazy val logger: Logger

    Permalink
    Attributes
    protected
    Definition Classes
    LazyLogging

  45. val maxAlternateAlleles: Int

    Permalink

  46. val maxReadsInRegionPerSample: Option[Int]

    Permalink

  47. val minPruning: Int

    Permalink

  48. val minReadsPerAlignmentStart: Option[Int]

    Permalink

  49. var name: String

    Permalink
    Definition Classes
    Task

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

    Permalink
    Definition Classes
    AnyRef

  51. final def notify(): Unit

    Permalink
    Definition Classes
    AnyRef

  52. final def notifyAll(): Unit

    Permalink
    Definition Classes
    AnyRef

  53. def onComplete(exitCode: Int): Boolean

    Permalink
    Definition Classes
    Task

  54. def optionallyConfigure[T](path: String)(implicit arg0: scala.reflect.api.JavaUniverse.TypeTag[T]): Option[T]

    Permalink
    Definition Classes
    ConfigurationLike

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

    Permalink
    Definition Classes
    FixedResources → Schedulable

  56. var quoteIfNecessary: Boolean

    Permalink
    Attributes
    protected
    Definition Classes
    ProcessTask

  57. val ref: PathToFasta

    Permalink
    Definition Classes
    GatkTask

  58. def removeDependency(task: Task): Boolean

    Permalink
    Definition Classes
    Task

  59. def requires(cores: Double, memory: String): HaplotypeCaller.this.type

    Permalink
    Definition Classes
    FixedResources

  60. def requires(cores: Cores, memory: Memory): HaplotypeCaller.this.type

    Permalink
    Definition Classes
    FixedResources

  61. def requires(resources: ResourceSet): HaplotypeCaller.this.type

    Permalink
    Definition Classes
    FixedResources

  62. def resources: ResourceSet

    Permalink
    Definition Classes
    ScheduleWithEmptyDefaultResources

  63. val rnaMode: Boolean

    Permalink

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

    Permalink
    Definition Classes
    AnyRef

  65. def systemPath: Seq[Path]

    Permalink
    Attributes
    protected
    Definition Classes
    ConfigurationLike

  66. def tailTasks: Traversable[Task]

    Permalink
    Definition Classes
    Task → Dependable

  67. def tasksDependedOn: Traversable[Task]

    Permalink
    Attributes
    protected[dagr.core]
    Definition Classes
    Task

  68. def tasksDependingOnThisTask: Traversable[Task]

    Permalink
    Attributes
    protected[dagr.core]
    Definition Classes
    Task

  69. def toString(): String

    Permalink
    Definition Classes
    ProcessTask → AnyRef → Any

  70. val useNativePairHmm: Boolean

    Permalink

  71. val vcf: PathToVcf

    Permalink

  72. final def wait(): Unit

    Permalink
    Definition Classes
    AnyRef
    Annotations
    @throws( ... )

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

    Permalink
    Definition Classes
    AnyRef
    Annotations
    @throws( ... )

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

    Permalink
    Definition Classes
    AnyRef
    Annotations
    @throws( ... )

  75. val walker: String

    Permalink
    Definition Classes
    GatkTask

  76. def withName(name: String): HaplotypeCaller.this.type

    Permalink
    Definition Classes
    Task

  77. def →[B](y: B): (HaplotypeCaller, B)

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

Inherited from GatkTask

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 HaplotypeCaller to any2stringadd[HaplotypeCaller]

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

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

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

Ungrouped