class EstimatePoolingFractions extends FgBioTool with LazyLogging
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- @ClpAnnotation()
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Instance Constructors
- new EstimatePoolingFractions(vcf: FgBioDef.PathToVcf, bam: FgBioDef.PathToBam, output: FgBioDef.FilePath, intervals: Seq[FgBioDef.PathToIntervals] = Seq.empty, samples: Seq[String] = Seq.empty, nonAutosomes: Seq[String] = ..., minGenotypeQuality: Int = 30, minMeanSampleCoverage: Int = 6, minMappingQuality: Int = 20, minBaseQuality: Int = 5)
Type Members
Value Members
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final
def
!=(arg0: Any): Boolean
- Definition Classes
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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 EstimatePoolingFractions to any2stringadd[EstimatePoolingFractions] performed by method any2stringadd in scala.Predef.
- Definition Classes
- any2stringadd
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def
->[B](y: B): (EstimatePoolingFractions, B)
- Implicit
- This member is added by an implicit conversion from EstimatePoolingFractions to ArrowAssoc[EstimatePoolingFractions] performed by method ArrowAssoc in scala.Predef.
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- ArrowAssoc
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- @inline()
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final
def
==(arg0: Any): Boolean
- Definition Classes
- AnyRef → Any
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final
def
asInstanceOf[T0]: T0
- Definition Classes
- Any
- val bam: FgBioDef.PathToBam
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def
clone(): AnyRef
- Attributes
- protected[java.lang]
- Definition Classes
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- @throws( ... )
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def
constructBamIterator(loci: Traversable[Locus]): Iterator[LocusInfo]
Constructs a SamLocusIterator that will visit every locus in the input.
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def
constructVcfIterator(in: VCFFileReader, intervals: Option[IntervalList], samples: Array[String]): Iterator[VariantContext]
Generates an iterator over non-filtered bi-allelic SNPs where all the required samples are genotyped.
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def
ensuring(cond: (EstimatePoolingFractions) ⇒ Boolean, msg: ⇒ Any): EstimatePoolingFractions
- Implicit
- This member is added by an implicit conversion from EstimatePoolingFractions to Ensuring[EstimatePoolingFractions] performed by method Ensuring in scala.Predef.
- Definition Classes
- Ensuring
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def
ensuring(cond: (EstimatePoolingFractions) ⇒ Boolean): EstimatePoolingFractions
- Implicit
- This member is added by an implicit conversion from EstimatePoolingFractions to Ensuring[EstimatePoolingFractions] performed by method Ensuring in scala.Predef.
- Definition Classes
- Ensuring
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def
ensuring(cond: Boolean, msg: ⇒ Any): EstimatePoolingFractions
- Implicit
- This member is added by an implicit conversion from EstimatePoolingFractions to Ensuring[EstimatePoolingFractions] performed by method Ensuring in scala.Predef.
- Definition Classes
- Ensuring
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def
ensuring(cond: Boolean): EstimatePoolingFractions
- Implicit
- This member is added by an implicit conversion from EstimatePoolingFractions to Ensuring[EstimatePoolingFractions] performed by method Ensuring in scala.Predef.
- Definition Classes
- Ensuring
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final
def
eq(arg0: AnyRef): Boolean
- Definition Classes
- AnyRef
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def
equals(arg0: Any): Boolean
- Definition Classes
- AnyRef → Any
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def
execute(): Unit
- Definition Classes
- EstimatePoolingFractions → FgBioTool
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def
fail(exit: Int, message: String): Nothing
Fail with a specific error code and message.
Fail with a specific error code and message.
- Definition Classes
- FgBioTool
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def
fail(message: String): Nothing
Fail with the default exit code and a message.
Fail with the default exit code and a message.
- Definition Classes
- FgBioTool
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def
fail(exit: Int): Nothing
Fail with just an exit code.
Fail with just an exit code.
- Definition Classes
- FgBioTool
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def
fillObserveredFractionAndFilter(loci: Array[Locus], minCoverage: Int): Array[Locus]
Fills in the observedFraction field for each locus that meets coverage and then returns the subset of loci that met coverage.
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def
finalize(): Unit
- Attributes
- protected[java.lang]
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- @throws( classOf[java.lang.Throwable] )
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def
formatted(fmtstr: String): String
- Implicit
- This member is added by an implicit conversion from EstimatePoolingFractions to StringFormat[EstimatePoolingFractions] performed by method StringFormat in scala.Predef.
- Definition Classes
- StringFormat
- Annotations
- @inline()
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final
def
getClass(): Class[_]
- Definition Classes
- AnyRef → Any
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def
hashCode(): Int
- Definition Classes
- AnyRef → Any
- val intervals: Seq[FgBioDef.PathToIntervals]
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def
invalid(message: String): Nothing
Generates a new validation exception with the given message.
Generates a new validation exception with the given message.
- Definition Classes
- FgBioTool
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final
def
isInstanceOf[T0]: Boolean
- Definition Classes
- Any
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lazy val
logger: Logger
- Attributes
- protected
- Definition Classes
- LazyLogging
- val minBaseQuality: Int
- val minGenotypeQuality: Int
- val minMappingQuality: Int
- val minMeanSampleCoverage: Int
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final
def
ne(arg0: AnyRef): Boolean
- Definition Classes
- AnyRef
- val nonAutosomes: Seq[String]
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final
def
notify(): Unit
- Definition Classes
- AnyRef
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final
def
notifyAll(): Unit
- Definition Classes
- AnyRef
- val output: FgBioDef.FilePath
- val samples: Seq[String]
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final
def
synchronized[T0](arg0: ⇒ T0): T0
- Definition Classes
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def
toString(): String
- Definition Classes
- AnyRef → Any
-
def
validate(test: Boolean, message: ⇒ String): Unit
Generates a validation exception if the test value is false.
Generates a validation exception if the test value is false.
- Definition Classes
- FgBioTool
- val vcf: FgBioDef.PathToVcf
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final
def
wait(): Unit
- Definition Classes
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- @throws( ... )
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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): (EstimatePoolingFractions, B)
- Implicit
- This member is added by an implicit conversion from EstimatePoolingFractions to ArrowAssoc[EstimatePoolingFractions] performed by method ArrowAssoc in scala.Predef.
- Definition Classes
- ArrowAssoc