Object/Class

org.bdgenomics.adam.models

SequenceDictionary

Related Docs: class SequenceDictionary | package models

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object SequenceDictionary extends Serializable

SequenceDictionary contains the (bijective) map between Ints (the referenceId) and Strings (the referenceName) from the header of a BAM file, or the combined result of multiple such SequenceDictionaries.

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Value Members

  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. def apply(reader: SamReader): SequenceDictionary

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  5. def apply(header: SAMFileHeader): SequenceDictionary

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  6. def apply(dict: SAMSequenceDictionary): SequenceDictionary

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  7. def apply(records: SequenceRecord*): SequenceDictionary

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  8. final def asInstanceOf[T0]: T0

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  9. def clone(): AnyRef

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    protected[java.lang]
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    @throws( ... )

  10. def empty: SequenceDictionary

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    returns

    Creates a new, empty SequenceDictionary.

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

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  12. def equals(arg0: Any): Boolean

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  13. def finalize(): Unit

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

  14. def fromAvro(contigs: Seq[Contig]): SequenceDictionary

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    Creates a sequence dictionary from a sequence of Avro Contigs.

    Creates a sequence dictionary from a sequence of Avro Contigs.

    contigs

    Seq of Contig records.

    returns

    Returns a sequence dictionary.

  15. def fromSAMHeader(header: SAMFileHeader): SequenceDictionary

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    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

  16. def fromSAMReader(samReader: SamReader): SequenceDictionary

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  17. def fromSAMSequenceDictionary(samDict: SAMSequenceDictionary): SequenceDictionary

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    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

  18. def fromVCFHeader(header: VCFHeader): SequenceDictionary

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    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

    VCF file header.

    returns

    Returns an ADAM style sequence dictionary.

    See also

    fromSAMHeader

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

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  20. def hashCode(): Int

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  21. final def isInstanceOf[T0]: Boolean

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

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  23. final def notify(): Unit

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  24. final def notifyAll(): Unit

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

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    Definition Classes
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  26. def toSAMSequenceDictionary(dictionary: SequenceDictionary): SAMSequenceDictionary

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  27. def toString(): String

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  28. final def wait(): Unit

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    @throws( ... )

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

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

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Inherited from Serializable

Inherited from Serializable

Inherited from AnyRef

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