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com.fulcrumgenomics.umi.ReviewConsensusVariants

ConsensusVariantReviewInfo

case class ConsensusVariantReviewInfo(chrom: String, pos: Int, ref: String, genotype: String, filters: String, A: Int, C: Int, G: Int, T: Int, N: Int, consensus_read: String, consensus_insert: String, consensus_call: String, consensus_qual: Int, a: Int, c: Int, g: Int, t: Int, n: Int) extends Metric with Product with Serializable

Metric class that is used to output detailed information on each consensus read that carries a variant allele

chrom

the chromosome on which the variant exists

pos

the position of the variant

ref

the reference allele at the position

genotype

the genotype of the sample in question

filters

the set of filters applied to the variant in the VCF

A

the count of A observations at the variant locus

C

the count of C observations at the variant locus

G

the count of G observations at the variant locus

T

the count of T observations at the variant locus

N

the count of N observations at the variant locus

consensus_read

the consensus read name for which the following fields contain values

consensus_insert

a description of the insert that generated the consensus read

consensus_call

the base call from the consensus read

consensus_qual

the quality score from the consensus read

a

the number of As in raw-reads contributing to the consensus base call at the variant site

c

the number of Cs in raw-reads contributing to the consensus base call at the variant site

g

the number of Gs in raw-reads contributing to the consensus base call at the variant site

t

the number of Ts in raw-reads contributing to the consensus base call at the variant site

n

the number of Ns in raw-reads contributing to the consensus base call at the variant site

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  1. ConsensusVariantReviewInfo
  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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Instance Constructors

  1. new ConsensusVariantReviewInfo(chrom: String, pos: Int, ref: String, genotype: String, filters: String, A: Int, C: Int, G: Int, T: Int, N: Int, consensus_read: String, consensus_insert: String, consensus_call: String, consensus_qual: Int, a: Int, c: Int, g: Int, t: Int, n: Int)

    chrom

    the chromosome on which the variant exists

    pos

    the position of the variant

    ref

    the reference allele at the position

    genotype

    the genotype of the sample in question

    filters

    the set of filters applied to the variant in the VCF

    A

    the count of A observations at the variant locus

    C

    the count of C observations at the variant locus

    G

    the count of G observations at the variant locus

    T

    the count of T observations at the variant locus

    N

    the count of N observations at the variant locus

    consensus_read

    the consensus read name for which the following fields contain values

    consensus_insert

    a description of the insert that generated the consensus read

    consensus_call

    the base call from the consensus read

    consensus_qual

    the quality score from the consensus read

    a

    the number of As in raw-reads contributing to the consensus base call at the variant site

    c

    the number of Cs in raw-reads contributing to the consensus base call at the variant site

    g

    the number of Gs in raw-reads contributing to the consensus base call at the variant site

    t

    the number of Ts in raw-reads contributing to the consensus base call at the variant site

    n

    the number of Ns in raw-reads contributing to the consensus base call at the variant site

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 ConsensusVariantReviewInfo to any2stringadd[ConsensusVariantReviewInfo] performed by method any2stringadd in scala.Predef.
    Definition Classes
    any2stringadd
  4. def ->[B](y: B): (ConsensusVariantReviewInfo, B)
    Implicit
    This member is added by an implicit conversion from ConsensusVariantReviewInfo to ArrowAssoc[ConsensusVariantReviewInfo] 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: Int
  7. val C: Int
  8. val G: Int
  9. val N: Int
  10. val T: Int
  11. val a: Int
  12. final def asInstanceOf[T0]: T0
    Definition Classes
    Any
  13. val c: Int
  14. val chrom: String
  15. def clone(): AnyRef
    Attributes
    protected[java.lang]
    Definition Classes
    AnyRef
    Annotations
    @throws( ... )
  16. val consensus_call: String
  17. val consensus_insert: String
  18. val consensus_qual: Int
  19. val consensus_read: String
  20. def ensuring(cond: (ConsensusVariantReviewInfo) ⇒ Boolean, msg: ⇒ Any): ConsensusVariantReviewInfo
    Implicit
    This member is added by an implicit conversion from ConsensusVariantReviewInfo to Ensuring[ConsensusVariantReviewInfo] performed by method Ensuring in scala.Predef.
    Definition Classes
    Ensuring
  21. def ensuring(cond: (ConsensusVariantReviewInfo) ⇒ Boolean): ConsensusVariantReviewInfo
    Implicit
    This member is added by an implicit conversion from ConsensusVariantReviewInfo to Ensuring[ConsensusVariantReviewInfo] performed by method Ensuring in scala.Predef.
    Definition Classes
    Ensuring
  22. def ensuring(cond: Boolean, msg: ⇒ Any): ConsensusVariantReviewInfo
    Implicit
    This member is added by an implicit conversion from ConsensusVariantReviewInfo to Ensuring[ConsensusVariantReviewInfo] performed by method Ensuring in scala.Predef.
    Definition Classes
    Ensuring
  23. def ensuring(cond: Boolean): ConsensusVariantReviewInfo
    Implicit
    This member is added by an implicit conversion from ConsensusVariantReviewInfo to Ensuring[ConsensusVariantReviewInfo] performed by method Ensuring in scala.Predef.
    Definition Classes
    Ensuring
  24. final def eq(arg0: AnyRef): Boolean
    Definition Classes
    AnyRef
  25. val filters: String
  26. def finalize(): Unit
    Attributes
    protected[java.lang]
    Definition Classes
    AnyRef
    Annotations
    @throws( classOf[java.lang.Throwable] )
  27. 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
  28. def formatted(fmtstr: String): String
    Implicit
    This member is added by an implicit conversion from ConsensusVariantReviewInfo to StringFormat[ConsensusVariantReviewInfo] performed by method StringFormat in scala.Predef.
    Definition Classes
    StringFormat
    Annotations
    @inline()
  29. val g: Int
  30. val genotype: String
  31. final def getClass(): Class[_]
    Definition Classes
    AnyRef → Any
  32. final def isInstanceOf[T0]: Boolean
    Definition Classes
    Any
  33. val n: Int
  34. 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
  35. final def ne(arg0: AnyRef): Boolean
    Definition Classes
    AnyRef
  36. final def notify(): Unit
    Definition Classes
    AnyRef
  37. final def notifyAll(): Unit
    Definition Classes
    AnyRef
  38. val pos: Int
  39. val ref: String
  40. final def synchronized[T0](arg0: ⇒ T0): T0
    Definition Classes
    AnyRef
  41. val t: Int
  42. def toString(): String
    Definition Classes
    Metric → AnyRef → Any
  43. 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
  44. final def wait(): Unit
    Definition Classes
    AnyRef
    Annotations
    @throws( ... )
  45. final def wait(arg0: Long, arg1: Int): Unit
    Definition Classes
    AnyRef
    Annotations
    @throws( ... )
  46. final def wait(arg0: Long): Unit
    Definition Classes
    AnyRef
    Annotations
    @throws( ... )
  47. def [B](y: B): (ConsensusVariantReviewInfo, B)
    Implicit
    This member is added by an implicit conversion from ConsensusVariantReviewInfo to ArrowAssoc[ConsensusVariantReviewInfo] 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 ConsensusVariantReviewInfo to any2stringadd[ConsensusVariantReviewInfo]

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

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

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

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