case class VanillaConsensusRead(id: String, bases: Array[Byte], quals: Array[Byte], depths: Array[Short], errors: Array[Short]) extends SimpleRead with Product with Serializable
Stores information about a consensus read. All four arrays are of equal length.
Depths and errors that have values exceeding Short.MaxValue (32767) will be called to Short.MaxValue.
- bases
the base calls of the consensus read
- quals
the calculated phred-scaled quality scores of the bases
- depths
the number of raw reads that contributed to the consensus call at each position
- errors
the number of contributing raw reads that disagree with the final consensus base at each position
Linear Supertypes
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Implicitly
- by any2stringadd
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Instance Constructors
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new
VanillaConsensusRead(id: String, bases: Array[Byte], quals: Array[Byte], depths: Array[Short], errors: Array[Short])
- bases
the base calls of the consensus read
- quals
the calculated phred-scaled quality scores of the bases
- depths
the number of raw reads that contributed to the consensus call at each position
- errors
the number of contributing raw reads that disagree with the final consensus base at each position
Value Members
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final
def
!=(arg0: Any): Boolean
- Definition Classes
- AnyRef → Any
-
final
def
##(): Int
- Definition Classes
- AnyRef → Any
-
def
+(other: String): String
- Implicit
- This member is added by an implicit conversion from VanillaConsensusRead to any2stringadd[VanillaConsensusRead] performed by method any2stringadd in scala.Predef.
- Definition Classes
- any2stringadd
-
def
->[B](y: B): (VanillaConsensusRead, B)
- Implicit
- This member is added by an implicit conversion from VanillaConsensusRead to ArrowAssoc[VanillaConsensusRead] performed by method ArrowAssoc in scala.Predef.
- Definition Classes
- ArrowAssoc
- Annotations
- @inline()
-
final
def
==(arg0: Any): Boolean
- Definition Classes
- AnyRef → Any
-
final
def
asInstanceOf[T0]: T0
- Definition Classes
- Any
-
def
baseString: String
Returns the consensus read a String - mostly useful for testing.
Returns the consensus read a String - mostly useful for testing.
- Definition Classes
- SimpleRead
-
val
bases: Array[Byte]
- Definition Classes
- VanillaConsensusRead → SimpleRead
-
def
clone(): AnyRef
- Attributes
- protected[java.lang]
- Definition Classes
- AnyRef
- Annotations
- @throws( ... )
- val depths: Array[Short]
-
def
ensuring(cond: (VanillaConsensusRead) ⇒ Boolean, msg: ⇒ Any): VanillaConsensusRead
- Implicit
- This member is added by an implicit conversion from VanillaConsensusRead to Ensuring[VanillaConsensusRead] performed by method Ensuring in scala.Predef.
- Definition Classes
- Ensuring
-
def
ensuring(cond: (VanillaConsensusRead) ⇒ Boolean): VanillaConsensusRead
- Implicit
- This member is added by an implicit conversion from VanillaConsensusRead to Ensuring[VanillaConsensusRead] performed by method Ensuring in scala.Predef.
- Definition Classes
- Ensuring
-
def
ensuring(cond: Boolean, msg: ⇒ Any): VanillaConsensusRead
- Implicit
- This member is added by an implicit conversion from VanillaConsensusRead to Ensuring[VanillaConsensusRead] performed by method Ensuring in scala.Predef.
- Definition Classes
- Ensuring
-
def
ensuring(cond: Boolean): VanillaConsensusRead
- Implicit
- This member is added by an implicit conversion from VanillaConsensusRead to Ensuring[VanillaConsensusRead] performed by method Ensuring in scala.Predef.
- Definition Classes
- Ensuring
-
final
def
eq(arg0: AnyRef): Boolean
- Definition Classes
- AnyRef
- val errors: Array[Short]
-
def
finalize(): Unit
- Attributes
- protected[java.lang]
- Definition Classes
- AnyRef
- Annotations
- @throws( classOf[java.lang.Throwable] )
-
def
formatted(fmtstr: String): String
- Implicit
- This member is added by an implicit conversion from VanillaConsensusRead to StringFormat[VanillaConsensusRead] performed by method StringFormat in scala.Predef.
- Definition Classes
- StringFormat
- Annotations
- @inline()
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final
def
getClass(): Class[_]
- Definition Classes
- AnyRef → Any
-
val
id: String
- Definition Classes
- VanillaConsensusRead → SimpleRead
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final
def
isInstanceOf[T0]: Boolean
- Definition Classes
- Any
-
def
length: Int
Gets the length of the consensus read.
Gets the length of the consensus read.
- Definition Classes
- SimpleRead
-
final
def
ne(arg0: AnyRef): Boolean
- Definition Classes
- AnyRef
-
final
def
notify(): Unit
- Definition Classes
- AnyRef
-
final
def
notifyAll(): Unit
- Definition Classes
- AnyRef
-
def
qualString: String
Retrieves the quals as a phred+33/fastq ascii String.
Retrieves the quals as a phred+33/fastq ascii String.
- Definition Classes
- SimpleRead
-
val
quals: Array[Byte]
- Definition Classes
- VanillaConsensusRead → SimpleRead
-
final
def
synchronized[T0](arg0: ⇒ T0): T0
- Definition Classes
- AnyRef
-
def
truncate(len: Int): VanillaConsensusRead
Truncates the read to the given length.
Truncates the read to the given length. If len > current length, the read is returned at current length.
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final
def
wait(): Unit
- Definition Classes
- AnyRef
- Annotations
- @throws( ... )
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final
def
wait(arg0: Long, arg1: Int): Unit
- Definition Classes
- AnyRef
- Annotations
- @throws( ... )
-
final
def
wait(arg0: Long): Unit
- Definition Classes
- AnyRef
- Annotations
- @throws( ... )
-
def
→[B](y: B): (VanillaConsensusRead, B)
- Implicit
- This member is added by an implicit conversion from VanillaConsensusRead to ArrowAssoc[VanillaConsensusRead] performed by method ArrowAssoc in scala.Predef.
- Definition Classes
- ArrowAssoc