ADAMAlignmentRecordContext

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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 adamBamLoad(filePath: String): RDD[AlignmentRecord]

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   protected[org.bdgenomics.adam.rdd]

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. final def getClass(): Class[_]

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13. def hashCode(): Int

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14. final def isInstanceOf[T0]: Boolean

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15. def isTraceEnabled(): Boolean

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16. def loadADAMFromPaths(paths: Seq[Path]): RDD[AlignmentRecord]

    Takes a sequence of Path objects (e.

    Takes a sequence of Path objects (e.g. the return value of findFiles). Treats each path as corresponding to a Read set -- loads each Read set, converts each set to use the same SequenceDictionary, and returns the union of the RDDs.

    (GenomeBridge is using this to load BAMs that have been split into multiple files per sample, for example, one-BAM-per-chromosome.)

    paths

    The locations of the parquet files to load

    returns

    a single RDD[Read] that contains the union of the ADAMRecords in the argument paths.

17. def log: Logger

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18. def logDebug(msg: ⇒ String, throwable: Throwable): Unit

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19. def logDebug(msg: ⇒ String): Unit

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20. def logError(msg: ⇒ String, throwable: Throwable): Unit

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21. def logError(msg: ⇒ String): Unit

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22. def logInfo(msg: ⇒ String, throwable: Throwable): Unit

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23. def logInfo(msg: ⇒ String): Unit

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24. def logName: String

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25. def logTrace(msg: ⇒ String, throwable: Throwable): Unit

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26. def logTrace(msg: ⇒ String): Unit

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27. def logWarning(msg: ⇒ String, throwable: Throwable): Unit

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28. def logWarning(msg: ⇒ String): Unit

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

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30. final def notify(): Unit

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31. final def notifyAll(): Unit

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32. val sc: SparkContext

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

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34. def toString(): String

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35. final def wait(): Unit

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

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

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