RefflatParser

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. final def asInstanceOf[T0]: T0

   

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5. def clone(): AnyRef

   

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

   

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7. def equals(arg0: Any): Boolean

   

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8. def finalize(): Unit

   

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

   

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10. def getGenes(refFlatFile: File, sequenceDictionary: SAMSequenceDictionary): List[Gene]

    

    (the load() method)

    (the load() method)

    This method is used instead of the GeneAnnotationReader.loadRefFlat method from Picard, since this method ignores genes which overlap exactly with another gene (only one of the two is returned).

    Reads the refFlat file and does some sanity/formatting checks.

11. def hashCode(): Int

    

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12. final def isInstanceOf[T0]: Boolean

    

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13. def makeGeneFromRefFlatLines(transcriptLines: List[Row]): Gene

    

    This method needed to be copied because it was private and, thus, couldn't be imported.

    This method needed to be copied because it was private and, thus, couldn't be imported.

    This method constructs a Gene object from a set of refFlat rows.

14. def makeTranscriptFromRefFlatLine(gene: Gene, row: Row): Transcript

    

    This method needed to be copied because it was private and, thus, couldn't be imported.

    This method needed to be copied because it was private and, thus, couldn't be imported.

    This method constructs a Transcript object from a refFlat line, which gets added to gene.

    Original comment: Conversion from 0-based half-open to 1-based inclusive intervals is done here.

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

    

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16. final def notify(): Unit

    

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17. final def notifyAll(): Unit

    

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

    

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19. def toString(): String

    

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20. final def wait(): Unit

    

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

    

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

    

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