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. val GENBANK_TAG: String

7. val REFSEQ_TAG: String

8. def apply(name: String, length: Long, md5: CharSequence = null, url: CharSequence = null, refseq: CharSequence = null, genbank: CharSequence = null, assembly: CharSequence = null, species: CharSequence = null): SequenceRecord

9. final def asInstanceOf[T0]: T0

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10. def clone(): AnyRef

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

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12. def equals(arg0: Any): Boolean

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13. def finalize(): Unit

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14. def fromADAMContig(contig: ADAMContig): SequenceRecord

15. def fromADAMContigFragment(fragment: ADAMNucleotideContigFragment): SequenceRecord

16. def fromADAMRecord(rec: ADAMRecord): Set[SequenceRecord]

    Convert an ADAMRecord into one or more SequenceRecords.

    Convert an ADAMRecord into one or more SequenceRecords. The reason that we can't simply use the "fromSpecificRecord" method, below, is that each ADAMRecord 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 ADAMRecord from which to extract the SequenceRecord entries

    returns

    a list of all SequenceRecord entries derivable from this record.

17. def fromSAMSequenceRecord(record: SAMSequenceRecord): SequenceRecord

18. def fromSpecificRecord(rec: SpecificRecord): SequenceRecord

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

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20. def hashCode(): Int

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21. final def isInstanceOf[T0]: Boolean

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

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23. final def notify(): Unit

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24. final def notifyAll(): Unit

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

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26. def toADAMContig(record: SequenceRecord): ADAMContig

27. def toSAMSequenceRecord(record: SequenceRecord): SAMSequenceRecord

28. def toString(): String

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29. final def wait(): Unit

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

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

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