NormalizationUtils

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

   

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2. final def ##(): Int

   

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

   

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4. final def asInstanceOf[T0]: T0

   

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5. def clone(): AnyRef

   

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

   

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7. def equals(arg0: Any): Boolean

   

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8. def finalize(): Unit

   

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

   

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10. def hashCode(): Int

    

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11. final def isInstanceOf[T0]: Boolean

    

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12. def leftAlignIndel(read: AlignmentRecord): Cigar

    

    Given a cigar, returns the cigar with the position of the cigar shifted left.

    Given a cigar, returns the cigar with the position of the cigar shifted left.

    read

    Read whose Cigar should be left align.

    returns

    Cigar fully moved left.

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

    

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14. final def notify(): Unit

    

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15. final def notifyAll(): Unit

    

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16. def numberOfPositionsToShiftIndel(variant: String, preceeding: String): Int

    

    Returns the maximum number of bases that an indel can be shifted left during left normalization.

    Returns the maximum number of bases that an indel can be shifted left during left normalization. Requires that the indel has been trimmed. For an insertion, this should be called on read data

    variant

    Bases of indel variant sequence.

    preceeding

    Bases of sequence to left of variant.

    returns

    The number of bases to shift an indel for it to be left normalized.

17. def shiftIndel(cigar: Cigar, position: Int, shifts: Int): Cigar

    

    Shifts an indel left by n.

    Shifts an indel left by n. Is tail call recursive.

    cigar

    Cigar to shift.

    position

    Position of element to move.

    shifts

    Number of bases to shift element.

    returns

    Cigar that has been shifted as far left as possible.

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

    

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19. def toString(): String

    

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20. final def wait(): Unit

    

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

    

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

    

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