SequenceDictionary

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. def apply(recordsIn: SequenceRecord*): SequenceDictionary

7. final def asInstanceOf[T0]: T0

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8. def clone(): AnyRef

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

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10. def equals(arg0: Any): Boolean

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11. def finalize(): Unit

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12. def fromSAMHeader(header: SAMFileHeader): SequenceDictionary

    Extracts a SAM sequence dictionary from a SAM file header and returns an ADAM sequence dictionary.

    Extracts a SAM sequence dictionary from a SAM file header and returns an ADAM sequence dictionary.

    header

    SAM file header.

    returns

    Returns an ADAM style sequence dictionary.

    See also

    fromSAMSequenceDictionary

13. def fromSAMReader(samReader: SAMFileReader): SequenceDictionary

14. def fromSAMSequenceDictionary(samDict: SAMSequenceDictionary): SequenceDictionary

    Converts a picard/samtools SAMSequenceDictionary into an ADAM sequence dictionary.

    Converts a picard/samtools SAMSequenceDictionary into an ADAM sequence dictionary.

    samDict

    SAM style sequence dictionary.

    returns

    Returns an ADAM style sequence dictionary.

    See also

    fromVCFHeader

    fromSAMHeader

15. def fromVCFHeader(header: VCFHeader): SequenceDictionary

    Extracts a SAM sequence dictionary from a VCF header and returns an ADAM sequence dictionary.

    Extracts a SAM sequence dictionary from a VCF header and returns an ADAM sequence dictionary.

    header

    SAM file header.

    returns

    Returns an ADAM style sequence dictionary.

    See also

    fromSAMSequenceDictionary

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

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17. def hashCode(): Int

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18. final def isInstanceOf[T0]: Boolean

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

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20. def nonoverlappingHash(x: CharSequence, conflicts: (Int) ⇒ Boolean): Int

21. final def notify(): Unit

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22. final def notifyAll(): Unit

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

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24. def toString(): String

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25. final def wait(): Unit

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

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

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