Class/Object

org.hammerlab.bam.check.eager

Checker

Related Docs: object Checker | package eager

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case class Checker(uncompressedStream: SeekableUncompressedBytes, contigLengths: ContigLengths, readsToCheck: ReadsToCheck) extends PosChecker[Boolean] with ReadStartFinder with Product with Serializable

check.Checker implementation that emits a Boolean at each org.hammerlab.bgzf.Pos indicating whether it is a read-record boundary.

Linear Supertypes
Serializable, Serializable, Product, Equals, ReadStartFinder, PosChecker[Boolean], check.Checker[Boolean], AnyRef, Any
Ordering
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  2. By Inheritance
Inherited
  1. Checker
  2. Serializable
  3. Serializable
  4. Product
  5. Equals
  6. ReadStartFinder
  7. PosChecker
  8. Checker
  9. AnyRef
  10. Any
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Visibility
  1. Public
  2. All

Instance Constructors

  1. new Checker(uncompressedStream: SeekableUncompressedBytes, contigLengths: ContigLengths, readsToCheck: ReadsToCheck)

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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. def apply(startPos: Long)(implicit successfulReads: SuccessfulReads): Boolean

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    Attributes
    protected
    Definition Classes
    Checker → PosChecker

  5. def apply(pos: Pos): Boolean

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    Main record-checking entry-point

    Main record-checking entry-point

    Definition Classes
    PosChecker → Checker

  6. final def asInstanceOf[T0]: T0

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    Definition Classes
    Any

  7. val buf: ByteBuffer

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    Definition Classes
    PosChecker

  8. def clone(): AnyRef

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

  9. val contigLengths: ContigLengths

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    Definition Classes
    Checker → PosChecker

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

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    Definition Classes
    AnyRef

  11. def finalize(): Unit

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

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

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    Definition Classes
    AnyRef → Any

  13. def getRefPosError(): Option[RefPosError]

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    Reusable logic for fetching a reference-sequence index and reference-position

    Reusable logic for fetching a reference-sequence index and reference-position

    Definition Classes
    PosChecker

  14. final def isInstanceOf[T0]: Boolean

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    Definition Classes
    Any

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

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    Definition Classes
    AnyRef

  16. def nextReadStart(start: Pos)(implicit maxReadSize: MaxReadSize): Option[Pos]

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    Definition Classes
    Checker → ReadStartFinder

  17. def nextReadStartWithDelta(start: Pos)(implicit maxReadSize: MaxReadSize): Option[(Pos, Int)]

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  18. final def notify(): Unit

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    Definition Classes
    AnyRef

  19. final def notifyAll(): Unit

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    Definition Classes
    AnyRef

  20. val readNameBuffer: ByteBuffer

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    Definition Classes
    PosChecker

  21. val readsToCheck: ReadsToCheck

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    Definition Classes
    Checker → PosChecker

  22. def seek(pos: Pos): Unit

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    Definition Classes
    PosChecker

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

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    Definition Classes
    AnyRef

  24. lazy val uncompressedBytes: ByteChannel

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    Definition Classes
    PosChecker

  25. val uncompressedStream: SeekableUncompressedBytes

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    Definition Classes
    Checker → PosChecker

  26. final def wait(): Unit

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    Definition Classes
    AnyRef
    Annotations
    @throws( ... )

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

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    Definition Classes
    AnyRef
    Annotations
    @throws( ... )

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

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    Definition Classes
    AnyRef
    Annotations
    @throws( ... )

Inherited from Serializable

Inherited from Serializable

Inherited from Product

Inherited from Equals

Inherited from ReadStartFinder

Inherited from PosChecker[Boolean]

Inherited from check.Checker[Boolean]

Inherited from AnyRef

Inherited from Any

Ungrouped