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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Instance Constructors
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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
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final
def
!=(arg0: Any): Boolean
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final
def
##(): Int
- Definition Classes
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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
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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.
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- @inline()
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final
def
==(arg0: Any): Boolean
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- AnyRef → Any
- val A: Int
- val C: Int
- val G: Int
- val N: Int
- val T: Int
- val a: Int
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final
def
asInstanceOf[T0]: T0
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- val c: Int
- val chrom: String
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def
clone(): AnyRef
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- protected[java.lang]
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- @throws( ... )
- val consensus_call: String
- val consensus_insert: String
- val consensus_qual: Int
- val consensus_read: String
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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
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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
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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
-
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
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final
def
eq(arg0: AnyRef): Boolean
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- val filters: String
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def
finalize(): Unit
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def
formatValues(value: Any): String
Override this method to customize how values are formatted.
Override this method to customize how values are formatted.
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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.
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- StringFormat
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- @inline()
- val g: Int
- val genotype: String
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final
def
getClass(): Class[_]
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final
def
isInstanceOf[T0]: Boolean
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- val n: Int
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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.
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final
def
ne(arg0: AnyRef): Boolean
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final
def
notify(): Unit
- Definition Classes
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final
def
notifyAll(): Unit
- Definition Classes
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- val pos: Int
- val ref: String
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final
def
synchronized[T0](arg0: ⇒ T0): T0
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- val t: Int
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def
toString(): String
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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.
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final
def
wait(): Unit
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def
wait(arg0: Long, arg1: Int): Unit
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final
def
wait(arg0: Long): Unit
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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