RichAlignmentRecord

Value Members

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

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

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3. final def ##(): Int

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

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

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6. val CIGAR_CODEC: TextCigarCodec

7. val ILLUMINA_READNAME_REGEX: Regex

8. def apply(record: AlignmentRecord): RichAlignmentRecord

9. final def asInstanceOf[T0]: T0

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10. val cigarPattern: Pattern

11. def clone(): AnyRef

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    protected[java.lang]

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

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13. def equals(arg0: Any): Boolean

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14. def finalize(): Unit

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    protected[java.lang]

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

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

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16. def hashCode(): Int

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17. final def isInstanceOf[T0]: Boolean

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

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19. final def notify(): Unit

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20. final def notifyAll(): Unit

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21. implicit def recordToRichRecord(record: AlignmentRecord): RichAlignmentRecord

22. def referenceLengthFromCigar(cigar: String): Int

    Parses a CIGAR string, and returns the aligned length with respect to the reference genome (i.

    Parses a CIGAR string, and returns the aligned length with respect to the reference genome (i.e. skipping clipping, padding, and insertion operators)

    cigar

    The CIGAR string whose reference length is to be measured

    returns

    A non-negative integer, the sum of the MDNX= operators in the CIGAR string.

23. implicit def richRecordToRecord(record: RichAlignmentRecord): AlignmentRecord

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

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25. def toString(): String

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26. final def wait(): Unit

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    @throws( ... )

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

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

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