Packages

c

com.fulcrumgenomics.umi.CorrectUmis

UmiCorrectionMetrics

case class UmiCorrectionMetrics(umi: String, total_matches: Long = 0, perfect_matches: Long = 0, one_mismatch_matches: Long = 0, two_mismatch_matches: Long = 0, other_matches: Long = 0, fraction_of_matches: Double = 0, representation: Double = 0) extends Metric with Product with Serializable

Metrics for the correction of UMI sequences to a fixed set of known UMIs.

umi

the corrected UMI sequence (or all Ns for unmatched)

total_matches

the number of UMI sequences that matched/were corrected to this UMI

perfect_matches

the number of UMI sequences that were perfect matches to this UMI

one_mismatch_matches

the number of UMI sequences that matched with a single mismatch

two_mismatch_matches

the number of UMI sequences that matched with two mismatches

other_matches

the number of UMI sequences that matched with > 2 mismatches

fraction_of_matches

the fraction of all UMIs that matched or were corrected to this UMI

representation

the total_matches for this UMI divided by the mean total_matches for all UMIs

Linear Supertypes
Serializable, Serializable, Metric, Product, Equals, AnyRef, Any
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Inherited
  1. UmiCorrectionMetrics
  2. Serializable
  3. Serializable
  4. Metric
  5. Product
  6. Equals
  7. AnyRef
  8. Any
Implicitly
  1. by any2stringadd
  2. by StringFormat
  3. by Ensuring
  4. by ArrowAssoc
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Visibility
  1. Public
  2. All

Instance Constructors

  1. new UmiCorrectionMetrics(umi: String, total_matches: Long = 0, perfect_matches: Long = 0, one_mismatch_matches: Long = 0, two_mismatch_matches: Long = 0, other_matches: Long = 0, fraction_of_matches: Double = 0, representation: Double = 0)

    umi

    the corrected UMI sequence (or all Ns for unmatched)

    total_matches

    the number of UMI sequences that matched/were corrected to this UMI

    perfect_matches

    the number of UMI sequences that were perfect matches to this UMI

    one_mismatch_matches

    the number of UMI sequences that matched with a single mismatch

    two_mismatch_matches

    the number of UMI sequences that matched with two mismatches

    other_matches

    the number of UMI sequences that matched with > 2 mismatches

    fraction_of_matches

    the fraction of all UMIs that matched or were corrected to this UMI

    representation

    the total_matches for this UMI divided by the mean total_matches for all UMIs

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 UmiCorrectionMetrics to any2stringadd[UmiCorrectionMetrics] performed by method any2stringadd in scala.Predef.
    Definition Classes
    any2stringadd
  4. def ->[B](y: B): (UmiCorrectionMetrics, B)
    Implicit
    This member is added by an implicit conversion from UmiCorrectionMetrics to ArrowAssoc[UmiCorrectionMetrics] performed by method ArrowAssoc in scala.Predef.
    Definition Classes
    ArrowAssoc
    Annotations
    @inline()
  5. final def ==(arg0: Any): Boolean
    Definition Classes
    AnyRef → Any
  6. final def asInstanceOf[T0]: T0
    Definition Classes
    Any
  7. def clone(): AnyRef
    Attributes
    protected[java.lang]
    Definition Classes
    AnyRef
    Annotations
    @throws( ... )
  8. def ensuring(cond: (UmiCorrectionMetrics) ⇒ Boolean, msg: ⇒ Any): UmiCorrectionMetrics
    Implicit
    This member is added by an implicit conversion from UmiCorrectionMetrics to Ensuring[UmiCorrectionMetrics] performed by method Ensuring in scala.Predef.
    Definition Classes
    Ensuring
  9. def ensuring(cond: (UmiCorrectionMetrics) ⇒ Boolean): UmiCorrectionMetrics
    Implicit
    This member is added by an implicit conversion from UmiCorrectionMetrics to Ensuring[UmiCorrectionMetrics] performed by method Ensuring in scala.Predef.
    Definition Classes
    Ensuring
  10. def ensuring(cond: Boolean, msg: ⇒ Any): UmiCorrectionMetrics
    Implicit
    This member is added by an implicit conversion from UmiCorrectionMetrics to Ensuring[UmiCorrectionMetrics] performed by method Ensuring in scala.Predef.
    Definition Classes
    Ensuring
  11. def ensuring(cond: Boolean): UmiCorrectionMetrics
    Implicit
    This member is added by an implicit conversion from UmiCorrectionMetrics to Ensuring[UmiCorrectionMetrics] performed by method Ensuring in scala.Predef.
    Definition Classes
    Ensuring
  12. final def eq(arg0: AnyRef): Boolean
    Definition Classes
    AnyRef
  13. def finalize(): Unit
    Attributes
    protected[java.lang]
    Definition Classes
    AnyRef
    Annotations
    @throws( classOf[java.lang.Throwable] )
  14. 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
  15. def formatted(fmtstr: String): String
    Implicit
    This member is added by an implicit conversion from UmiCorrectionMetrics to StringFormat[UmiCorrectionMetrics] performed by method StringFormat in scala.Predef.
    Definition Classes
    StringFormat
    Annotations
    @inline()
  16. var fraction_of_matches: Double
  17. final def getClass(): Class[_]
    Definition Classes
    AnyRef → Any
  18. final def isInstanceOf[T0]: Boolean
    Definition Classes
    Any
  19. 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
  20. final def ne(arg0: AnyRef): Boolean
    Definition Classes
    AnyRef
  21. final def notify(): Unit
    Definition Classes
    AnyRef
  22. final def notifyAll(): Unit
    Definition Classes
    AnyRef
  23. var one_mismatch_matches: Long
  24. var other_matches: Long
  25. var perfect_matches: Long
  26. var representation: Double
  27. final def synchronized[T0](arg0: ⇒ T0): T0
    Definition Classes
    AnyRef
  28. def toString(): String
    Definition Classes
    Metric → AnyRef → Any
  29. var total_matches: Long
  30. var two_mismatch_matches: Long
  31. val umi: String
  32. 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
  33. final def wait(): Unit
    Definition Classes
    AnyRef
    Annotations
    @throws( ... )
  34. final def wait(arg0: Long, arg1: Int): Unit
    Definition Classes
    AnyRef
    Annotations
    @throws( ... )
  35. final def wait(arg0: Long): Unit
    Definition Classes
    AnyRef
    Annotations
    @throws( ... )
  36. def →[B](y: B): (UmiCorrectionMetrics, B)
    Implicit
    This member is added by an implicit conversion from UmiCorrectionMetrics to ArrowAssoc[UmiCorrectionMetrics] 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 UmiCorrectionMetrics to any2stringadd[UmiCorrectionMetrics]

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

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

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

Ungrouped