AlleleAtLocus

Value Members

1. final def !=(arg0: AnyRef): Boolean

   Definition Classes

   AnyRef

2. final def !=(arg0: Any): Boolean

   Definition Classes

   Any

3. final def ##(): Int

   Definition Classes

   AnyRef → Any

4. final def ==(arg0: AnyRef): Boolean

   Definition Classes

   AnyRef

5. final def ==(arg0: Any): Boolean

   Definition Classes

   Any

6. final def asInstanceOf[T0]: T0

   Definition Classes

   Any

7. def clone(): AnyRef

   Attributes

   protected[java.lang]

   Definition Classes

   AnyRef

   Annotations

   @throws( ... )

8. final def eq(arg0: AnyRef): Boolean

   Definition Classes

   AnyRef

9. def equals(arg0: Any): Boolean

   Definition Classes

   AnyRef → Any

10. def finalize(): Unit

    Attributes

    protected[java.lang]

    Definition Classes

    AnyRef

    Annotations

    @throws( classOf[java.lang.Throwable] )

11. final def getClass(): Class[_]

    Definition Classes

    AnyRef → Any

12. def hashCode(): Int

    Definition Classes

    AnyRef → Any

13. final def isInstanceOf[T0]: Boolean

    Definition Classes

    Any

14. final def ne(arg0: AnyRef): Boolean

    Definition Classes

    AnyRef

15. final def notify(): Unit

    Definition Classes

    AnyRef

16. final def notifyAll(): Unit

    Definition Classes

    AnyRef

17. final def synchronized[T0](arg0: ⇒ T0): T0

    Definition Classes

    AnyRef

18. def toString(): String

    Definition Classes

    AnyRef → Any

19. def variantAlleles(pileups: PerSample[Pileup], anyAlleleMinSupportingReads: Int, anyAlleleMinSupportingPercent: Double, maxAlleles: Option[Int] = None, atLeastOneAllele: Boolean = false, onlyStandardBases: Boolean = true): Vector[AlleleAtLocus]

    Given one or more pileups, return a sequence of AlleleAtLocus instances giving the possible variant alleles at the *next site* in the pileups.

    Given one or more pileups, return a sequence of AlleleAtLocus instances giving the possible variant alleles at the *next site* in the pileups.

    Pileup elements whose *current* position is a variant are ignored here. The alleles returned start at the subsequent reference base and continue as long the bases do not match the reference. This is a pattern used throughout the joint caller: given a pileup at locus X we call variants that start at locus X + 1. This is done to avoid calling variants in the middle of longer variants.

    pileups

    one or more pileups

    anyAlleleMinSupportingReads

    minimum number of reads in a single sample an allele must have

    anyAlleleMinSupportingPercent

    minimum percent of reads (i.e. between 0 and 100) an allele must have

    maxAlleles

    if not None, return at most this many alleles

    atLeastOneAllele

    if true, then always return at least one allele (useful for force calling). If no alleles meet the minimum number of reads criteria, then the allele with the most reads (even though it doesn't meet the threshold) will be returned. If there are no alternate alleles at all, then the allele "N" is returned.

    onlyStandardBases

    only include alleles made entirely of standard bases (no N's)

    returns

    the alleles sequenced at this site

20. final def wait(): Unit

    Definition Classes

    AnyRef

    Annotations

    @throws( ... )

21. final def wait(arg0: Long, arg1: Int): Unit

    Definition Classes

    AnyRef

    Annotations

    @throws( ... )

22. final def wait(arg0: Long): Unit

    Definition Classes

    AnyRef

    Annotations

    @throws( ... )