AlignmentsRDD

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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 assembleContigAggregates: RDD[ContigAggregate]

   

   Collects "interesting" (read start, stop, ref/nonref counting) events on alignments

   Collects "interesting" (read start, stop, ref/nonref counting) events on alignments

   returns

   distributed collection of PileupRecords

6. def clone(): AnyRef

   

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

   

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8. def finalize(): Unit

   

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

   

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10. def initContigLengths(read: SAMRecord): Map[String, Int]

    

    initializes mapper between contig and its length basing on header values

    initializes mapper between contig and its length basing on header values

    read

    single aligned read (its header contains info about all contigs)

11. final def isInstanceOf[T0]: Boolean

    

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12. val logger: Logger

    

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

    

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14. final def notify(): Unit

    

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15. final def notifyAll(): Unit

    

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16. def prepareOutputAggregates(aggMap: HashMap[String, ContigAggregate], cigarMap: HashMap[String, Int]): Array[ContigAggregate]

    

    transforms map structure of contigEventAggregates, by reducing number of last zeroes in the cov array also adds calculated maxCigar len to output

    transforms map structure of contigEventAggregates, by reducing number of last zeroes in the cov array also adds calculated maxCigar len to output

    aggMap

    mapper between contig and contigEventAggregate

    cigarMap

    mapper between contig and max length of cigar in given

17. val rdd: RDD[SAMRecord]

    

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

    

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19. final def wait(): Unit

    

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

    

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

    

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