org.bdgenomics.adam.models

# SequenceRecord

###
Related Docs: class SequenceRecord | package models

#### 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
     AnyRef → Any

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
     Any

6. #### def clone(): AnyRef

   Attributes
     protected[java.lang]
   Definition Classes
     AnyRef
   Annotations
     @throws( ... )

7. #### final def eq(arg0: AnyRef): Boolean

   Definition Classes
     AnyRef

8. #### def equals(arg0: Any): Boolean

   Definition Classes
     AnyRef → Any

9. #### def finalize(): Unit

   Attributes
     protected[java.lang]
   Definition Classes
     AnyRef
   Annotations
     @throws( classOf[java.lang.Throwable] )

10. #### def fromADAMReference(reference: Reference): SequenceRecord

    Builds a sequence record from an Avro Contig.

    Builds a sequence record from an Avro Contig.

    returns

      This Contig record as a SequenceRecord.

11. #### def fromSAMSequenceRecord(record: SAMSequenceRecord): SequenceRecord

12. #### 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.

13. #### 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.

14. #### final def getClass(): Class[_]

    Definition Classes
      AnyRef → Any

15. #### def hashCode(): Int

    Definition Classes
      AnyRef → Any

16. #### final def isInstanceOf[T0]: Boolean

    Definition Classes
      Any

17. #### final def ne(arg0: AnyRef): Boolean

    Definition Classes
      AnyRef

18. #### final def notify(): Unit

    Definition Classes
      AnyRef

19. #### final def notifyAll(): Unit

    Definition Classes
      AnyRef

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

    Definition Classes
      AnyRef

21. #### def toString(): String

    Definition Classes
      AnyRef → Any

22. #### final def wait(): Unit

    Definition Classes
      AnyRef
    Annotations
      @throws( ... )

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

    Definition Classes
      AnyRef
    Annotations
      @throws( ... )

24. #### final def wait(arg0: Long): Unit

    Definition Classes
      AnyRef
    Annotations
      @throws( ... )

### Inherited from Serializable

### Inherited from AnyRef

### Inherited from Any

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