case class SequenceRecord(name: String, length: Long, url: Option[String], md5: Option[String], refseq: Option[String], genbank: Option[String], assembly: Option[String], species: Option[String], index: Option[Int]) extends Serializable with Product

Metadata about a single reference sequence.

name

The name of this reference in the assembly.

length

The length of the sequence for this reference.

url

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

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).

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.

Linear Supertypes
Product, Equals, Serializable, Serializable, AnyRef, Any
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  1. SequenceRecord
  2. Product
  3. Equals
  4. Serializable
  5. Serializable
  6. AnyRef
  7. Any
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Instance Constructors

  1. new SequenceRecord(name: String, length: Long, url: Option[String], md5: Option[String], refseq: Option[String], genbank: Option[String], assembly: Option[String], species: Option[String], index: Option[Int])

    name

    The name of this reference in the assembly.

    length

    The length of the sequence for this reference.

    url

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

    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).

    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.

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
    AnyRef → Any
  4. final def asInstanceOf[T0]: T0
    Definition Classes
    Any
  5. val assembly: Option[String]
  6. def clone(): AnyRef
    Attributes
    protected[lang]
    Definition Classes
    AnyRef
    Annotations
    @throws( ... ) @native() @HotSpotIntrinsicCandidate()
  7. final def eq(arg0: AnyRef): Boolean
    Definition Classes
    AnyRef
  8. def equals(o: Any): Boolean
    Definition Classes
    SequenceRecord → Equals → AnyRef → Any
  9. val genbank: Option[String]
  10. final def getClass(): Class[_]
    Definition Classes
    AnyRef → Any
    Annotations
    @native() @HotSpotIntrinsicCandidate()
  11. val index: Option[Int]
  12. final def isInstanceOf[T0]: Boolean
    Definition Classes
    Any
  13. val length: Long
  14. val md5: Option[String]
  15. val name: String
  16. final def ne(arg0: AnyRef): Boolean
    Definition Classes
    AnyRef
  17. final def notify(): Unit
    Definition Classes
    AnyRef
    Annotations
    @native() @HotSpotIntrinsicCandidate()
  18. final def notifyAll(): Unit
    Definition Classes
    AnyRef
    Annotations
    @native() @HotSpotIntrinsicCandidate()
  19. val refseq: Option[String]
  20. val species: Option[String]
  21. def stripIndex: SequenceRecord

    returns

    Returns a new sequence record with the index unset.

  22. final def synchronized[T0](arg0: ⇒ T0): T0
    Definition Classes
    AnyRef
  23. def toADAMReference: Reference

    returns

    Builds an Avro Reference representation from this record.

  24. def toSAMSequenceRecord: SAMSequenceRecord

    Converts this sequence record into a SAM sequence record.

    Converts this sequence record into a SAM sequence record.

    returns

    A SAM formatted sequence record.

  25. def toString(): String
    Definition Classes
    SequenceRecord → AnyRef → Any
  26. val url: Option[String]
  27. final def wait(arg0: Long, arg1: Int): Unit
    Definition Classes
    AnyRef
    Annotations
    @throws( ... )
  28. final def wait(arg0: Long): Unit
    Definition Classes
    AnyRef
    Annotations
    @throws( ... ) @native()
  29. final def wait(): Unit
    Definition Classes
    AnyRef
    Annotations
    @throws( ... )

Deprecated Value Members

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

Inherited from Product

Inherited from Equals

Inherited from Serializable

Inherited from Serializable

Inherited from AnyRef

Inherited from Any

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