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

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

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

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

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

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

10. #### def fromADAMContigFragment(fragment: NucleotideContigFragment): SequenceRecord

    Extracts the contig metadata from a nucleotide fragment.

    Extracts the contig metadata from a nucleotide fragment.

    fragment

      The assembly fragment to extract a SequenceRecord from.

    returns

      The sequence record metadata from a single assembly fragment.

11. #### 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.

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

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

    Definition Classes
      AnyRef → Any

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

    Definition Classes
      AnyRef → Any

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

    Definition Classes
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16. #### final def ne(arg0: AnyRef): Boolean

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      AnyRef

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

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

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

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

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

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      @throws( ... )

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

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      @throws( ... )

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

    Definition Classes
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      @throws( ... )

### Inherited from Serializable

### Inherited from AnyRef

### Inherited from Any

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