c

com.fulcrumgenomics.bam

EstimatePoolingFractions

class EstimatePoolingFractions extends FgBioTool with LazyLogging

Annotations
@ClpAnnotation()
Linear Supertypes
LazyLogging, FgBioTool, AnyRef, Any
Ordering
  1. Alphabetic
  2. By Inheritance
Inherited
  1. EstimatePoolingFractions
  2. LazyLogging
  3. FgBioTool
  4. AnyRef
  5. Any
Implicitly
  1. by any2stringadd
  2. by StringFormat
  3. by Ensuring
  4. by ArrowAssoc
  1. Hide All
  2. Show All
Visibility
  1. Public
  2. All

Instance Constructors

  1. 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

  1. case class Locus (chrom: String, pos: Int, ref: Char, alt: Char, expectedSampleFractions: Array[Double], observedFraction: Option[Double] = None) extends Product with Serializable

Value Members

  1. final def !=(arg0: Any): Boolean
    Definition Classes
    AnyRef → Any
  2. final def ##(): Int
    Definition Classes
    AnyRef → Any
  3. 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
  4. 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
    Annotations
    @inline()
  5. final def ==(arg0: Any): Boolean
    Definition Classes
    AnyRef → Any
  6. final def asInstanceOf[T0]: T0
    Definition Classes
    Any
  7. val bam: FgBioDef.PathToBam
  8. def clone(): AnyRef
    Attributes
    protected[java.lang]
    Definition Classes
    AnyRef
    Annotations
    @throws( ... )
  9. def constructBamIterator(loci: Traversable[Locus]): Iterator[LocusInfo]

    Constructs a SamLocusIterator that will visit every locus in the input.

  10. 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.

  11. 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
  12. 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
  13. 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
  14. 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
  15. final def eq(arg0: AnyRef): Boolean
    Definition Classes
    AnyRef
  16. def equals(arg0: Any): Boolean
    Definition Classes
    AnyRef → Any
  17. def execute(): Unit
    Definition Classes
    EstimatePoolingFractions → FgBioTool
  18. 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
  19. 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
  20. def fail(exit: Int): Nothing

    Fail with just an exit code.

    Fail with just an exit code.

    Definition Classes
    FgBioTool
  21. 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.

  22. def finalize(): Unit
    Attributes
    protected[java.lang]
    Definition Classes
    AnyRef
    Annotations
    @throws( classOf[java.lang.Throwable] )
  23. 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()
  24. final def getClass(): Class[_]
    Definition Classes
    AnyRef → Any
  25. def hashCode(): Int
    Definition Classes
    AnyRef → Any
  26. val intervals: Seq[FgBioDef.PathToIntervals]
  27. 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
  28. final def isInstanceOf[T0]: Boolean
    Definition Classes
    Any
  29. lazy val logger: Logger
    Attributes
    protected
    Definition Classes
    LazyLogging
  30. val minBaseQuality: Int
  31. val minGenotypeQuality: Int
  32. val minMappingQuality: Int
  33. val minMeanSampleCoverage: Int
  34. final def ne(arg0: AnyRef): Boolean
    Definition Classes
    AnyRef
  35. val nonAutosomes: Seq[String]
  36. final def notify(): Unit
    Definition Classes
    AnyRef
  37. final def notifyAll(): Unit
    Definition Classes
    AnyRef
  38. val output: FgBioDef.FilePath
  39. val samples: Seq[String]
  40. final def synchronized[T0](arg0: ⇒ T0): T0
    Definition Classes
    AnyRef
  41. def toString(): String
    Definition Classes
    AnyRef → Any
  42. 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
  43. val vcf: FgBioDef.PathToVcf
  44. final def wait(): Unit
    Definition Classes
    AnyRef
    Annotations
    @throws( ... )
  45. final def wait(arg0: Long, arg1: Int): Unit
    Definition Classes
    AnyRef
    Annotations
    @throws( ... )
  46. final def wait(arg0: Long): Unit
    Definition Classes
    AnyRef
    Annotations
    @throws( ... )
  47. 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

Inherited from LazyLogging

Inherited from FgBioTool

Inherited from AnyRef

Inherited from Any

Inherited by implicit conversion any2stringadd from EstimatePoolingFractions to any2stringadd[EstimatePoolingFractions]

Inherited by implicit conversion StringFormat from EstimatePoolingFractions to StringFormat[EstimatePoolingFractions]

Inherited by implicit conversion Ensuring from EstimatePoolingFractions to Ensuring[EstimatePoolingFractions]

Inherited by implicit conversion ArrowAssoc from EstimatePoolingFractions to ArrowAssoc[EstimatePoolingFractions]

Ungrouped