object SequenceRecord extends Serializable

Companion object for creating Sequence Records.

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Value Members

  1. final def !=(arg0: Any): Boolean
    Definition Classes
    AnyRef → Any
  2. final def ##(): Int
    Definition Classes
    AnyRef → Any
  3. final def ==(arg0: Any): Boolean
    Definition Classes
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  4. def apply(name: String, length: Long, md5: String = null, url: String = null, refseq: String = null, genbank: String = null, assembly: String = null, species: String = null, index: Option[Int] = None): SequenceRecord

    Java friendly apply method that wraps null strings.

    Java friendly apply method that wraps null strings.

    name

    The name of this reference in the assembly.

    length

    The length of the sequence for this reference.

    md5

    If available, the MD5 checksum uniquely representing this reference as a lower-case hexadecimal string, calculated as the MD5 of the upper-case sequence excluding all whitespace characters (equivalent to SQ:M5 in SAM).

    url

    If available, the URI from which the reference sequence was obtained.

    refseq

    If available, the REFSEQ ID for the reference.

    genbank

    If available, the Genbank ID for the reference.

    assembly

    If available, the name of the assembly for this reference.

    species

    If available, the species that this reference is for.

    index

    If available, the number of this reference in a set of references.

    returns

    Returns a new SequenceRecord where all strings except for name are wrapped in Options to check for null values.

  5. final def asInstanceOf[T0]: T0
    Definition Classes
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  6. def clone(): AnyRef
    Attributes
    protected[lang]
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    @throws( ... ) @native() @HotSpotIntrinsicCandidate()
  7. final def eq(arg0: AnyRef): Boolean
    Definition Classes
    AnyRef
  8. def equals(arg0: Any): Boolean
    Definition Classes
    AnyRef → Any
  9. def fromADAMReference(reference: Reference): SequenceRecord

    Builds a sequence record from an Avro Reference.

    Builds a sequence record from an Avro Reference.

    reference

    Reference record to build from.

    returns

    This Reference record as a SequenceRecord.

  10. def fromSAMSequenceRecord(record: SAMSequenceRecord): SequenceRecord
  11. def fromSequence(sequence: Sequence): SequenceRecord

    Builds a sequence record from a sequence.

    Builds a sequence record from a sequence.

    sequence

    Sequence to build from.

    returns

    The specified sequence as a SequenceRecord.

  12. def fromSlice(slice: Slice): SequenceRecord

    Builds a sequence record from a slice.

    Builds a sequence record from a slice.

    slice

    Slice to build from.

    returns

    The specified slice as a SequenceRecord.

  13. final def getClass(): Class[_]
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    @native() @HotSpotIntrinsicCandidate()
  14. def hashCode(): Int
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    @native() @HotSpotIntrinsicCandidate()
  15. final def isInstanceOf[T0]: Boolean
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  16. final def ne(arg0: AnyRef): Boolean
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  17. final def notify(): Unit
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    @native() @HotSpotIntrinsicCandidate()
  18. final def notifyAll(): Unit
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    @native() @HotSpotIntrinsicCandidate()
  19. final def synchronized[T0](arg0: ⇒ T0): T0
    Definition Classes
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  20. def toString(): String
    Definition Classes
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  21. final def wait(arg0: Long, arg1: Int): Unit
    Definition Classes
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    @throws( ... )
  22. final def wait(arg0: Long): Unit
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    @throws( ... ) @native()
  23. final def wait(): Unit
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    @throws( ... )

Deprecated Value Members

  1. def finalize(): Unit
    Attributes
    protected[lang]
    Definition Classes
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    @throws( classOf[java.lang.Throwable] ) @Deprecated @deprecated
    Deprecated

    (Since version ) see corresponding Javadoc for more information.

Inherited from Serializable

Inherited from Serializable

Inherited from AnyRef

Inherited from Any

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