case class ErrorRateByReadPositionMetric(read_number: Int, position: Int, bases_total: Long, errors: Long, error_rate: Double, a_to_c_error_rate: Double, a_to_g_error_rate: Double, a_to_t_error_rate: Double, c_to_a_error_rate: Double, c_to_g_error_rate: Double, c_to_t_error_rate: Double) extends Metric with Product with Serializable

Gives the error rate and total number of bases observed for each position within the read.

read_number

the read number (ex. 0 for fragments, 1 for read one of a pair, 2 for read two of a pair)

position

the position or cycle within the read (1-based).

bases_total

the total number of bases observed at this position.

errors

the total number of errors or non-reference basecalls observed at this position

error_rate

the overall error rate at position

a_to_c_error_rate

the rate of A>C (and T>G) error at the position

a_to_g_error_rate

the rate of A>G (and T>C) error at the position

a_to_t_error_rate

the rate of A>T (and T>A) error at the position

c_to_a_error_rate

the rate of C>A (and G>T) error at the position

c_to_g_error_rate

the rate of C>G (and G>C) error at the position

c_to_t_error_rate

the rate of C>T (and G>A) error at the position

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  1. ErrorRateByReadPositionMetric
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  8. Any
Implicitly
  1. by any2stringadd
  2. by StringFormat
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Instance Constructors

  1. new ErrorRateByReadPositionMetric(read_number: Int, position: Int, bases_total: Long, errors: Long, error_rate: Double, a_to_c_error_rate: Double, a_to_g_error_rate: Double, a_to_t_error_rate: Double, c_to_a_error_rate: Double, c_to_g_error_rate: Double, c_to_t_error_rate: Double)

    read_number

    the read number (ex. 0 for fragments, 1 for read one of a pair, 2 for read two of a pair)

    position

    the position or cycle within the read (1-based).

    bases_total

    the total number of bases observed at this position.

    errors

    the total number of errors or non-reference basecalls observed at this position

    error_rate

    the overall error rate at position

    a_to_c_error_rate

    the rate of A>C (and T>G) error at the position

    a_to_g_error_rate

    the rate of A>G (and T>C) error at the position

    a_to_t_error_rate

    the rate of A>T (and T>A) error at the position

    c_to_a_error_rate

    the rate of C>A (and G>T) error at the position

    c_to_g_error_rate

    the rate of C>G (and G>C) error at the position

    c_to_t_error_rate

    the rate of C>T (and G>A) error at the position

Value Members

  1. final def !=(arg0: Any): Boolean
    Definition Classes
    AnyRef → Any
  2. final def ##(): Int
    Definition Classes
    AnyRef → Any
  3. def +(other: String): String
    Implicit
    This member is added by an implicit conversion from ErrorRateByReadPositionMetric to any2stringadd[ErrorRateByReadPositionMetric] performed by method any2stringadd in scala.Predef.
    Definition Classes
    any2stringadd
  4. def ->[B](y: B): (ErrorRateByReadPositionMetric, B)
    Implicit
    This member is added by an implicit conversion from ErrorRateByReadPositionMetric to ArrowAssoc[ErrorRateByReadPositionMetric] performed by method ArrowAssoc in scala.Predef.
    Definition Classes
    ArrowAssoc
    Annotations
    @inline()
  5. final def ==(arg0: Any): Boolean
    Definition Classes
    AnyRef → Any
  6. val a_to_c_error_rate: Double
  7. val a_to_g_error_rate: Double
  8. val a_to_t_error_rate: Double
  9. final def asInstanceOf[T0]: T0
    Definition Classes
    Any
  10. val bases_total: Long
  11. val c_to_a_error_rate: Double
  12. val c_to_g_error_rate: Double
  13. val c_to_t_error_rate: Double
  14. def clone(): AnyRef
    Attributes
    protected[java.lang]
    Definition Classes
    AnyRef
    Annotations
    @throws( ... )
  15. def ensuring(cond: (ErrorRateByReadPositionMetric) ⇒ Boolean, msg: ⇒ Any): ErrorRateByReadPositionMetric
    Implicit
    This member is added by an implicit conversion from ErrorRateByReadPositionMetric to Ensuring[ErrorRateByReadPositionMetric] performed by method Ensuring in scala.Predef.
    Definition Classes
    Ensuring
  16. def ensuring(cond: (ErrorRateByReadPositionMetric) ⇒ Boolean): ErrorRateByReadPositionMetric
    Implicit
    This member is added by an implicit conversion from ErrorRateByReadPositionMetric to Ensuring[ErrorRateByReadPositionMetric] performed by method Ensuring in scala.Predef.
    Definition Classes
    Ensuring
  17. def ensuring(cond: Boolean, msg: ⇒ Any): ErrorRateByReadPositionMetric
    Implicit
    This member is added by an implicit conversion from ErrorRateByReadPositionMetric to Ensuring[ErrorRateByReadPositionMetric] performed by method Ensuring in scala.Predef.
    Definition Classes
    Ensuring
  18. def ensuring(cond: Boolean): ErrorRateByReadPositionMetric
    Implicit
    This member is added by an implicit conversion from ErrorRateByReadPositionMetric to Ensuring[ErrorRateByReadPositionMetric] performed by method Ensuring in scala.Predef.
    Definition Classes
    Ensuring
  19. final def eq(arg0: AnyRef): Boolean
    Definition Classes
    AnyRef
  20. val error_rate: Double
  21. val errors: Long
  22. def finalize(): Unit
    Attributes
    protected[java.lang]
    Definition Classes
    AnyRef
    Annotations
    @throws( classOf[java.lang.Throwable] )
  23. def formatValues(value: Any): String

    Override this method to customize how values are formatted.

    Override this method to customize how values are formatted.

    Attributes
    protected
    Definition Classes
    Metric
  24. def formatted(fmtstr: String): String
    Implicit
    This member is added by an implicit conversion from ErrorRateByReadPositionMetric to StringFormat[ErrorRateByReadPositionMetric] performed by method StringFormat in scala.Predef.
    Definition Classes
    StringFormat
    Annotations
    @inline()
  25. final def getClass(): Class[_]
    Definition Classes
    AnyRef → Any
  26. final def isInstanceOf[T0]: Boolean
    Definition Classes
    Any
  27. def names: Seq[String]

    Get the names of the arguments in the order they were defined.

    Get the names of the arguments in the order they were defined.

    Definition Classes
    Metric
  28. final def ne(arg0: AnyRef): Boolean
    Definition Classes
    AnyRef
  29. final def notify(): Unit
    Definition Classes
    AnyRef
  30. final def notifyAll(): Unit
    Definition Classes
    AnyRef
  31. val position: Int
  32. val read_number: Int
  33. final def synchronized[T0](arg0: ⇒ T0): T0
    Definition Classes
    AnyRef
  34. def toString(): String
    Definition Classes
    Metric → AnyRef → Any
  35. def values: Seq[String]

    Get the values of the arguments in the order they were defined.

    Get the values of the arguments in the order they were defined.

    Definition Classes
    Metric
  36. final def wait(): Unit
    Definition Classes
    AnyRef
    Annotations
    @throws( ... )
  37. final def wait(arg0: Long, arg1: Int): Unit
    Definition Classes
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    Annotations
    @throws( ... )
  38. final def wait(arg0: Long): Unit
    Definition Classes
    AnyRef
    Annotations
    @throws( ... )
  39. def →[B](y: B): (ErrorRateByReadPositionMetric, B)
    Implicit
    This member is added by an implicit conversion from ErrorRateByReadPositionMetric to ArrowAssoc[ErrorRateByReadPositionMetric] performed by method ArrowAssoc in scala.Predef.
    Definition Classes
    ArrowAssoc

Inherited from Serializable

Inherited from Serializable

Inherited from Metric

Inherited from Product

Inherited from Equals

Inherited from AnyRef

Inherited from Any

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

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

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

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

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