case class
ErrorRateByReadPositionMetric(read_number: Int, position: Int, bases_total: Count, errors: Count, 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
Instance Constructors
-
new
ErrorRateByReadPositionMetric(read_number: Int, position: Int, bases_total: Count, errors: Count, 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)
Value Members
-
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](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_to_c_error_rate: Double
-
val
a_to_g_error_rate: Double
-
val
a_to_t_error_rate: Double
-
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
-
final
def
asInstanceOf[T0]: T0
-
val
bases_total: Count
-
val
c_to_a_error_rate: Double
-
val
c_to_g_error_rate: Double
-
val
c_to_t_error_rate: Double
-
def
canEqual(that: Any): Boolean
-
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
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)]
-
-
-
-
-
-
val
error_rate: Double
-
val
errors: Count
-
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)]
-
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
-
def
formatted(fmtstr: String): String
-
def
genericBuilder[B]: Builder[B, Iterable[B]]
-
def
get(name: String): Option[String]
-
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)]
-
-
-
final
def
isInstanceOf[T0]: Boolean
-
final
def
isTraversableAgain: Boolean
-
def
iterator: Iterator[(String, String)]
-
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
-
def
names: Seq[String]
-
-
def
newBuilder: Builder[(String, String), Iterable[(String, String)]]
-
-
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
position: Int
-
def
product[B >: (String, String)](implicit num: Numeric[B]): B
-
val
read_number: Int
-
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]
-
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
-
def
tail: 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]
-
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
-
Deprecated Value Members
-
def
formatValues(value: Any): String
Inherited from Iterable[(String, String)]
Inherited from Parallelizable[(String, String), ParIterable[(String, String)]]
Inherited from HasNewBuilder[(String, String), Iterable[(String, String)] @scala.annotation.unchecked.uncheckedVariance]
Metrics produced by
ErrorRateByReadPosition
describing the number of base observations and substitution errors at each position within each sequencing read. Error rates are given for the overall substitution error rate and also for each kind of substitution separately. Instead of reporting 12 substitution rates, 6 are reported where complementary substitutions are grouped together, e.g.T>G
substitutions are reported asA>C
.The read number (0 for fragments, 1 for first of pair, 2 for second of pair).
The position or cycle within the read (1-based).
The total number of bases observed at this position.
The total number of errors or non-reference basecalls observed at this position.
The overall error rate at position.
The rate of
A>C
(andT>G
) errors at the position.The rate of
A>G
(andT>C
) errors at the position.The rate of
A>T
(andT>A
) errors at the position.The rate of
C>A
(andG>T
) errors at the position.The rate of
C>G
(andG>C
) errors at the position.The rate of
C>T
(andG>A
) errors at the position.