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. val GENBANK_TAG: String

   

5. val REFSEQ_TAG: String

   

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

   

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

    

13. def fromADAMContigFragment(fragment: NucleotideContigFragment): SequenceRecord

    

14. def fromADAMRecord(rec: AlignmentRecord): Set[SequenceRecord]

    

    Convert an Read into one or more SequenceRecords.

    Convert an Read into one or more SequenceRecords. The reason that we can't simply use the "fromSpecificRecord" method, below, is that each Read can (through the fact that it could be a pair of reads) contain 1 or 2 possible SequenceRecord entries for the SequenceDictionary itself. Both have to be extracted, separately.

    rec

    The Read from which to extract the SequenceRecord entries

    returns

    a list of all SequenceRecord entries derivable from this record.

15. def fromSAMSequenceRecord(record: SAMSequenceRecord): SequenceRecord

    

16. def fromSpecificRecord(rec: IndexedRecord): SequenceRecord

    

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

    

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18. def hashCode(): Int

    

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19. final def isInstanceOf[T0]: Boolean

    

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

    

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21. final def notify(): Unit

    

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22. final def notifyAll(): Unit

    

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

    

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24. def toADAMContig(record: SequenceRecord): Contig

    

25. def toSAMSequenceRecord(record: SequenceRecord): SAMSequenceRecord

    

26. def toString(): String

    

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27. final def wait(): Unit

    

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

    

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

    

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