SequenceRecord

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(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

   

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6. def clone(): AnyRef

   

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   protected[java.lang]

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

   

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8. def equals(arg0: Any): Boolean

   

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9. def finalize(): Unit

   

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   protected[java.lang]

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   @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[_]

    

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15. def hashCode(): Int

    

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16. final def isInstanceOf[T0]: Boolean

    

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

    

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18. final def notify(): Unit

    

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19. final def notifyAll(): Unit

    

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

    

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21. def toString(): String

    

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22. final def wait(): Unit

    

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    @throws( ... )

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

    

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

    

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