SequenceRecord

Value Members

1. final def !=(arg0: AnyRef): Boolean

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2. final def !=(arg0: Any): Boolean

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3. final def ##(): Int

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4. final def ==(arg0: AnyRef): Boolean

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5. final def ==(arg0: Any): Boolean

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6. def apply(name: String, length: Long, md5: String = null, url: String = null, refseq: String = null, genbank: String = null, assembly: String = null, species: String = null, referenceIndex: Option[Int] = None): SequenceRecord

   Java friendly apply method that wraps null strings.

   Java friendly apply method that wraps null strings.

   name

   The name of the contig.

   length

   The length of the contig.

   md5

   If available, the MD5 checksum for the contig.

   url

   If available, the URL the contig is accessible from.

   refseq

   If available, the REFSEQ ID for the contig.

   genbank

   If available, the Genbank ID for the contig.

   assembly

   If available, the assembly name for the assembly this contig is from.

   species

   If available, the species this contig was assembled from.

   referenceIndex

   If available, the number of this contig in a set of contigs.

   returns

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

7. final def asInstanceOf[T0]: T0

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8. def clone(): AnyRef

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

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10. def equals(arg0: Any): Boolean

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11. def finalize(): Unit

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12. def fromADAMContig(contig: Contig): SequenceRecord

    Builds a sequence record from an Avro Contig.

    Builds a sequence record from an Avro Contig.

    contig

    Contig record to build from.

    returns

    This Contig record as a SequenceRecord.

13. 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.

14. def fromSAMSequenceRecord(record: SAMSequenceRecord): SequenceRecord

15. final def getClass(): Class[_]

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16. def hashCode(): Int

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17. final def isInstanceOf[T0]: Boolean

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

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19. final def notify(): Unit

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20. final def notifyAll(): Unit

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

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22. def toString(): String

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23. final def wait(): Unit

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

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

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