org.bdgenomics.adam.util

PhredUtils

object PhredUtils extends Serializable

Helper singleton for converting Phred scores to/from probabilities.

As a reminder, given an error probability \epsilon, the Phred score q is:

q = -10 log_{10} \epsilon

Linear Supertypes
Serializable, Serializable, AnyRef, Any
Ordering
  1. Alphabetic
  2. By inheritance
Inherited
  1. PhredUtils
  2. Serializable
  3. Serializable
  4. AnyRef
  5. Any
  1. Hide All
  2. Show all
Learn more about member selection
Visibility
  1. Public
  2. All

Value Members

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

    Definition Classes
    AnyRef

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

    Definition Classes
    Any

  3. final def ##(): Int

    Definition Classes
    AnyRef → Any

  4. final def ==(arg0: AnyRef): Boolean

    Definition Classes
    AnyRef

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

    Definition Classes
    Any

  6. final def asInstanceOf[T0]: T0

    Definition Classes
    Any

  7. def clone(): AnyRef

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

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

    Definition Classes
    AnyRef

  9. def equals(arg0: Any): Boolean

    Definition Classes
    AnyRef → Any

  10. def errorProbabilityToPhred(p: Double): Int

    p

    An error probability to convert to phred.

    returns

    The input probability as a phred score, rounded to the nearest int.

  11. def finalize(): Unit

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

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

    Definition Classes
    AnyRef → Any

  13. def hashCode(): Int

    Definition Classes
    AnyRef → Any

  14. final def isInstanceOf[T0]: Boolean

    Definition Classes
    Any

  15. def logProbabilityToPhred(p: Float): Int

    p

    A log-scaled success probability to conver to phred.

    returns

    Returns this probability as a Phred score. If the log value is 0.0, we clip the phred score to 256.

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

    Definition Classes
    AnyRef

  17. final def notify(): Unit

    Definition Classes
    AnyRef

  18. final def notifyAll(): Unit

    Definition Classes
    AnyRef

  19. def phredToErrorProbability(phred: Int): Double

    phred

    The phred score to convert.

    returns

    The input phred score as an error probability. If the phred score is above 255, we clip to 255.

  20. def phredToLogProbability(phred: Int): Float

    phred

    The phred score to convert.

    returns

    The input phred score as a log success probability.

  21. def phredToSuccessProbability(phred: Int): Double

    phred

    The phred score to convert.

    returns

    The input phred score as a success probability. If the phred score is above 255, we clip to 255.

  22. def successProbabilityToPhred(p: Double): Int

    p

    A success probability to convert to phred.

    returns

    One minus the input probability as a phred score, rounded to the nearest int.

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

    Definition Classes
    AnyRef

  24. def toString(): String

    Definition Classes
    AnyRef → Any

  25. final def wait(): Unit

    Definition Classes
    AnyRef
    Annotations
    @throws( ... )

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

    Definition Classes
    AnyRef
    Annotations
    @throws( ... )

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

    Definition Classes
    AnyRef
    Annotations
    @throws( ... )

Inherited from Serializable

Inherited from Serializable

Inherited from AnyRef

Inherited from Any

Ungrouped