class QualityEncodingDetector extends AnyRef
Class to detect the quality encoding in use in FASTQ files.
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Instance Constructors
- new QualityEncodingDetector()
Value Members
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final
def
!=(arg0: Any): Boolean
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final
def
##(): Int
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def
+(other: String): String
- Implicit
- This member is added by an implicit conversion from QualityEncodingDetector to any2stringadd[QualityEncodingDetector] performed by method any2stringadd in scala.Predef.
- Definition Classes
- any2stringadd
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def
->[B](y: B): (QualityEncodingDetector, B)
- Implicit
- This member is added by an implicit conversion from QualityEncodingDetector to ArrowAssoc[QualityEncodingDetector] performed by method ArrowAssoc in scala.Predef.
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final
def
==(arg0: Any): Boolean
- Definition Classes
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def
add(chs: String): Unit
Adds a String of ascii quality characters to the evidence.
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def
add(ch: Char): Unit
Adds an ascii quality character to the set of evidence.
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final
def
asInstanceOf[T0]: T0
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def
clone(): AnyRef
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- protected[java.lang]
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- @throws( ... )
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def
compatibleEncodings: List[QualityEncoding]
Returns the set of quality formats that are compatible with the qualities seen thus far.
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def
ensuring(cond: (QualityEncodingDetector) ⇒ Boolean, msg: ⇒ Any): QualityEncodingDetector
- Implicit
- This member is added by an implicit conversion from QualityEncodingDetector to Ensuring[QualityEncodingDetector] performed by method Ensuring in scala.Predef.
- Definition Classes
- Ensuring
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def
ensuring(cond: (QualityEncodingDetector) ⇒ Boolean): QualityEncodingDetector
- Implicit
- This member is added by an implicit conversion from QualityEncodingDetector to Ensuring[QualityEncodingDetector] performed by method Ensuring in scala.Predef.
- Definition Classes
- Ensuring
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def
ensuring(cond: Boolean, msg: ⇒ Any): QualityEncodingDetector
- Implicit
- This member is added by an implicit conversion from QualityEncodingDetector to Ensuring[QualityEncodingDetector] performed by method Ensuring in scala.Predef.
- Definition Classes
- Ensuring
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def
ensuring(cond: Boolean): QualityEncodingDetector
- Implicit
- This member is added by an implicit conversion from QualityEncodingDetector to Ensuring[QualityEncodingDetector] performed by method Ensuring in scala.Predef.
- Definition Classes
- Ensuring
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final
def
eq(arg0: AnyRef): Boolean
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def
equals(arg0: Any): Boolean
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def
finalize(): Unit
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def
formatted(fmtstr: String): String
- Implicit
- This member is added by an implicit conversion from QualityEncodingDetector to StringFormat[QualityEncodingDetector] performed by method StringFormat in scala.Predef.
- Definition Classes
- StringFormat
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- @inline()
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final
def
getClass(): Class[_]
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def
hashCode(): Int
- Definition Classes
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def
isAmbiguous: Boolean
Returns true if more than one quality encoding is compatible given the evidence so far.
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def
isCompatible(encoding: QualityEncoding): Boolean
Returns true if the observed qualities are compatible with the encoding, false otherwise.
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final
def
isInstanceOf[T0]: Boolean
- Definition Classes
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final
def
ne(arg0: AnyRef): Boolean
- Definition Classes
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final
def
notify(): Unit
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final
def
notifyAll(): Unit
- Definition Classes
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def
rankedCompatibleEncodings(q: Int): List[QualityEncoding]
Returns the set of compatible encodings ranked by how close the mean value is to Q under each encoding.
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def
sample(ss: Iterator[String], count: Int = 100000): Unit
Samples strings from the iterator until at least
count
qualities have been sampled.Samples strings from the iterator until at least
count
qualities have been sampled.- ss
an iterator of Strings where each string is an ascii string of quality scores
- count
the number of quality scores (not strings!) to attempt to sample
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final
def
synchronized[T0](arg0: ⇒ T0): T0
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def
toString(): String
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final
def
wait(): Unit
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final
def
wait(arg0: Long, arg1: Int): Unit
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final
def
wait(arg0: Long): Unit
- Definition Classes
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- @throws( ... )
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def
→[B](y: B): (QualityEncodingDetector, B)
- Implicit
- This member is added by an implicit conversion from QualityEncodingDetector to ArrowAssoc[QualityEncodingDetector] performed by method ArrowAssoc in scala.Predef.
- Definition Classes
- ArrowAssoc