ConsensusVariantReviewInfo

final def !=(arg0: Any): Boolean

final def ##(): Int

def +(other: String): String

def ++[B >: (String, String), That](that: GenTraversableOnce[B])(implicit bf: CanBuildFrom[Iterable[(String, String)], B, That]): That

def ++:[B >: (String, String), That](that: Traversable[B])(implicit bf: CanBuildFrom[Iterable[(String, String)], B, That]): That

def ++:[B >: (String, String), That](that: TraversableOnce[B])(implicit bf: CanBuildFrom[Iterable[(String, String)], B, That]): That

def ->[B](y: B): (ConsensusVariantReviewInfo, B)

def /:[B](z: B)(op: (B, (String, String)) ⇒ B): B

def :\[B](z: B)(op: ((String, String), B) ⇒ B): B

final def ==(arg0: Any): Boolean

val A: Int

The count of A observations at the variant locus across all consensus reads.

val C: Int

The count of C observations at the variant locus across all consensus reads.

val G: Int

The count of G observations at the variant locus across all consensus reads.

val N: Int

The count of N observations at the variant locus across all consensus reads.

val T: Int

The count of T observations at the variant locus across all consensus reads.

val a: Int

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

def addString(b: StringBuilder): StringBuilder

def addString(b: StringBuilder, sep: String): StringBuilder

def addString(b: StringBuilder, start: String, sep: String, end: String): StringBuilder

def aggregate[B](z: ⇒ B)(seqop: (B, (String, String)) ⇒ B, combop: (B, B) ⇒ B): B

def apply(name: String): String

Gets the value of the field by name.

final def asInstanceOf[T0]: T0

val c: Int

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

def canEqual(that: Any): Boolean

val chrom: String

The chromosome on which the variant exists.

def clone(): AnyRef

def collect[B, That](pf: PartialFunction[(String, String), B])(implicit bf: CanBuildFrom[Iterable[(String, String)], B, That]): That

def collectFirst[B](pf: PartialFunction[(String, String), B]): Option[B]

def companion: GenericCompanion[Iterable]

val consensus_call: Char

The base call from the consensus read.

val consensus_insert: String

A description of the insert that generated the consensus read.

val consensus_qual: Int

The quality score from the consensus read.

val consensus_read: String

The consensus read name for which the following fields contain values.

def copyToArray[B >: (String, String)](xs: Array[B], start: Int, len: Int): Unit

def copyToArray[B >: (String, String)](xs: Array[B]): Unit

def copyToArray[B >: (String, String)](xs: Array[B], start: Int): Unit

def copyToBuffer[B >: (String, String)](dest: Buffer[B]): Unit

def count(p: ((String, String)) ⇒ Boolean): Int

def drop(n: Int): Iterable[(String, String)]

def dropRight(n: Int): Iterable[(String, String)]

def dropWhile(p: ((String, String)) ⇒ Boolean): Iterable[(String, String)]

def ensuring(cond: (ConsensusVariantReviewInfo) ⇒ Boolean, msg: ⇒ Any): ConsensusVariantReviewInfo

def ensuring(cond: (ConsensusVariantReviewInfo) ⇒ Boolean): ConsensusVariantReviewInfo

def ensuring(cond: Boolean, msg: ⇒ Any): ConsensusVariantReviewInfo

def ensuring(cond: Boolean): ConsensusVariantReviewInfo

final def eq(arg0: AnyRef): Boolean

def exists(p: ((String, String)) ⇒ Boolean): Boolean

def filter(p: ((String, String)) ⇒ Boolean): Iterable[(String, String)]

def filterNot(p: ((String, String)) ⇒ Boolean): Iterable[(String, String)]

val filters: String

The set of filters applied to the variant in the VCF.

def finalize(): Unit

def find(p: ((String, String)) ⇒ Boolean): Option[(String, String)]

def flatMap[B, That](f: ((String, String)) ⇒ GenTraversableOnce[B])(implicit bf: CanBuildFrom[Iterable[(String, String)], B, That]): That

def flatten[B](implicit asTraversable: ((String, String)) ⇒ GenTraversableOnce[B]): Iterable[B]

def fold[A1 >: (String, String)](z: A1)(op: (A1, A1) ⇒ A1): A1

def foldLeft[B](z: B)(op: (B, (String, String)) ⇒ B): B

def foldRight[B](z: B)(op: ((String, String), B) ⇒ B): B

def forall(p: ((String, String)) ⇒ Boolean): Boolean

def foreach[U](f: ((String, String)) ⇒ U): Unit

def formatValue(value: Any): String

Override this method to customize how values are formatted.

def formatted(fmtstr: String): String

val g: Int

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

def genericBuilder[B]: Builder[B, Iterable[B]]

val genotype: String

The genotype of the sample in question.

def get(name: String): Option[String]

Gets the value of the field by name, returns None if it does not exist.

final def getClass(): Class[_]

def groupBy[K](f: ((String, String)) ⇒ K): Map[K, Iterable[(String, String)]]

def grouped(size: Int): Iterator[Iterable[(String, String)]]

def hasDefiniteSize: Boolean

def head: (String, String)

def headOption: Option[(String, String)]

def init: Iterable[(String, String)]

def inits: Iterator[Iterable[(String, String)]]

def isEmpty: Boolean

final def isInstanceOf[T0]: Boolean

final def isTraversableAgain: Boolean

def iterator: Iterator[(String, String)]

Gets an iterator over the fields of this metric in the order they were defined.

def last: (String, String)

def lastOption: Option[(String, String)]

def map[B, That](f: ((String, String)) ⇒ B)(implicit bf: CanBuildFrom[Iterable[(String, String)], B, That]): That

def max[B >: (String, String)](implicit cmp: Ordering[B]): (String, String)

def maxBy[B](f: ((String, String)) ⇒ B)(implicit cmp: Ordering[B]): (String, String)

def min[B >: (String, String)](implicit cmp: Ordering[B]): (String, String)

def minBy[B](f: ((String, String)) ⇒ B)(implicit cmp: Ordering[B]): (String, String)

def mkString: String

def mkString(sep: String): String

def mkString(start: String, sep: String, end: String): String

val n: Int

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

def names: Seq[String]

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

final def ne(arg0: AnyRef): Boolean

def newBuilder: Builder[(String, String), Iterable[(String, String)]]

def nonEmpty: Boolean

final def notify(): Unit

final def notifyAll(): Unit

def par: ParIterable[(String, String)]

def parCombiner: Combiner[(String, String), ParIterable[(String, String)]]

def partition(p: ((String, String)) ⇒ Boolean): (Iterable[(String, String)], Iterable[(String, String)])

val pos: Int

The position of the variant.

def product[B >: (String, String)](implicit num: Numeric[B]): B

def reduce[A1 >: (String, String)](op: (A1, A1) ⇒ A1): A1

def reduceLeft[B >: (String, String)](op: (B, (String, String)) ⇒ B): B

def reduceLeftOption[B >: (String, String)](op: (B, (String, String)) ⇒ B): Option[B]

def reduceOption[A1 >: (String, String)](op: (A1, A1) ⇒ A1): Option[A1]

def reduceRight[B >: (String, String)](op: ((String, String), B) ⇒ B): B

def reduceRightOption[B >: (String, String)](op: ((String, String), B) ⇒ B): Option[B]

val ref: String

The reference allele at the position.

def repr: Iterable[(String, String)]

def reversed: List[(String, String)]

def sameElements[B >: (String, String)](that: GenIterable[B]): Boolean

def scan[B >: (String, String), That](z: B)(op: (B, B) ⇒ B)(implicit cbf: CanBuildFrom[Iterable[(String, String)], B, That]): That

def scanLeft[B, That](z: B)(op: (B, (String, String)) ⇒ B)(implicit bf: CanBuildFrom[Iterable[(String, String)], B, That]): That

def scanRight[B, That](z: B)(op: ((String, String), B) ⇒ B)(implicit bf: CanBuildFrom[Iterable[(String, String)], B, That]): That

def seq: Iterable[(String, String)]

def size: Int

def slice(from: Int, until: Int): Iterable[(String, String)]

def sliding(size: Int, step: Int): Iterator[Iterable[(String, String)]]

def sliding(size: Int): Iterator[Iterable[(String, String)]]

def span(p: ((String, String)) ⇒ Boolean): (Iterable[(String, String)], Iterable[(String, String)])

def splitAt(n: Int): (Iterable[(String, String)], Iterable[(String, String)])

def stringPrefix: String

def sum[B >: (String, String)](implicit num: Numeric[B]): B

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

val t: Int

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

def tail: Iterable[(String, String)]

def tails: Iterator[Iterable[(String, String)]]

def take(n: Int): Iterable[(String, String)]

def takeRight(n: Int): Iterable[(String, String)]

def takeWhile(p: ((String, String)) ⇒ Boolean): Iterable[(String, String)]

def thisCollection: Iterable[(String, String)]

def to[Col[_]](implicit cbf: CanBuildFrom[Nothing, (String, String), Col[(String, String)]]): Col[(String, String)]

def toArray[B >: (String, String)](implicit arg0: ClassTag[B]): Array[B]

def toBuffer[B >: (String, String)]: Buffer[B]

def toCollection(repr: Iterable[(String, String)]): Iterable[(String, String)]

def toIndexedSeq: IndexedSeq[(String, String)]

def toIterable: Iterable[(String, String)]

def toIterator: Iterator[(String, String)]

def toList: List[(String, String)]

def toMap[T, U](implicit ev: <:<[(String, String), (T, U)]): Map[T, U]

def toParArray: ParArray[T]

def toSeq: Seq[(String, String)]

def toSet[B >: (String, String)]: Set[B]

def toStream: Stream[(String, String)]

def toString(): String

def toTraversable: Traversable[(String, String)]

def toVector: Vector[(String, String)]

def transpose[B](implicit asTraversable: ((String, String)) ⇒ GenTraversableOnce[B]): Iterable[Iterable[B]]

def unzip[A1, A2](implicit asPair: ((String, String)) ⇒ (A1, A2)): (Iterable[A1], Iterable[A2])

def unzip3[A1, A2, A3](implicit asTriple: ((String, String)) ⇒ (A1, A2, A3)): (Iterable[A1], Iterable[A2], Iterable[A3])

def values: Seq[String]

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

def view(from: Int, until: Int): IterableView[(String, String), Iterable[(String, String)]]

def view: IterableView[(String, String), Iterable[(String, String)]]

final def wait(): Unit

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

final def wait(arg0: Long): Unit

def withFilter(p: ((String, String)) ⇒ Boolean): FilterMonadic[(String, String), Iterable[(String, String)]]

def zip[A1 >: (String, String), B, That](that: GenIterable[B])(implicit bf: CanBuildFrom[Iterable[(String, String)], (A1, B), That]): That

def zipAll[B, A1 >: (String, String), That](that: GenIterable[B], thisElem: A1, thatElem: B)(implicit bf: CanBuildFrom[Iterable[(String, String)], (A1, B), That]): That

def zipWithIndex[A1 >: (String, String), That](implicit bf: CanBuildFrom[Iterable[(String, String)], (A1, Int), That]): That

def →[B](y: B): (ConsensusVariantReviewInfo, B)

def filter(p: ((String, String)) ⇒ Boolean): TraversableOnce[(String, String)]

def flatMap[B](f: ((String, String)) ⇒ GenTraversableOnce[B]): TraversableOnce[B]

def map[B](f: ((String, String)) ⇒ B): TraversableOnce[B]

def withFilter(p: ((String, String)) ⇒ Boolean): Iterator[(String, String)]

def formatValues(value: Any): String