Class/Object

org.bdgenomics.adam.models

SnpTable

Related Docs: object SnpTable | package models

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class SnpTable extends Serializable with Logging

A table containing all of the SNPs in a known variation dataset.

Linear Supertypes
Logging, Serializable, Serializable, AnyRef, Any
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Inherited
  1. SnpTable
  2. Logging
  3. Serializable
  4. Serializable
  5. AnyRef
  6. Any
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Visibility
  1. Public
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Instance Constructors

  1. new SnpTable(table: Map[String, Set[Long]])

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    table

    A map between a contig name and a set containing all coordinates where a point variant is known to exist.

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. final def asInstanceOf[T0]: T0

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    Definition Classes
    Any

  5. def clone(): AnyRef

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

  6. def contains(location: ReferencePosition): Boolean

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    Is there a known SNP at the given reference location?

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

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    Definition Classes
    AnyRef

  8. def equals(arg0: Any): Boolean

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    Definition Classes
    AnyRef → Any

  9. def finalize(): Unit

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

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

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    Definition Classes
    AnyRef → Any

  11. def hashCode(): Int

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    Definition Classes
    AnyRef → Any

  12. final def isInstanceOf[T0]: Boolean

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    Definition Classes
    Any

  13. def isMasked(residue: Residue): Boolean

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    Is there a known SNP at the reference location of this Residue?

  14. def isTraceEnabled(): Boolean

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    Attributes
    protected
    Definition Classes
    Logging

  15. def log: Logger

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    Attributes
    protected
    Definition Classes
    Logging

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

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    Attributes
    protected
    Definition Classes
    Logging

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

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    Attributes
    protected
    Definition Classes
    Logging

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

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    Attributes
    protected
    Definition Classes
    Logging

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

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    Attributes
    protected
    Definition Classes
    Logging

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

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    Attributes
    protected
    Definition Classes
    Logging

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

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    Attributes
    protected
    Definition Classes
    Logging

  22. def logName: String

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    Attributes
    protected
    Definition Classes
    Logging

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

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    Attributes
    protected
    Definition Classes
    Logging

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

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    Attributes
    protected
    Definition Classes
    Logging

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

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    Attributes
    protected
    Definition Classes
    Logging

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

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    Attributes
    protected
    Definition Classes
    Logging

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

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    Definition Classes
    AnyRef

  28. final def notify(): Unit

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    Definition Classes
    AnyRef

  29. final def notifyAll(): Unit

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    Definition Classes
    AnyRef

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

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    Definition Classes
    AnyRef

  31. def toString(): String

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    Definition Classes
    AnyRef → Any

  32. final def wait(): Unit

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    Definition Classes
    AnyRef
    Annotations
    @throws( ... )

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

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    Definition Classes
    AnyRef
    Annotations
    @throws( ... )

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

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    Definition Classes
    AnyRef
    Annotations
    @throws( ... )

Inherited from Logging

Inherited from Serializable

Inherited from Serializable

Inherited from AnyRef

Inherited from Any

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