org.bdgenomics.adam.apis.java

JavaADAMContext

class JavaADAMContext extends Serializable

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Instance Constructors

  1. new JavaADAMContext(sc: SparkContext)

    Builds this Java ADAM Context using an existing Spark Context.

    Builds this Java ADAM Context using an existing Spark Context.

    sc

    Spark Context to use to build this ADAM Context.

    returns

    A new Java ADAM Context.

  2. new JavaADAMContext(jsc: JavaSparkContext)

    Builds this Java ADAM Context using an existing Java Spark Context.

    Builds this Java ADAM Context using an existing Java Spark Context.

    jsc

    Java Spark Context to use to build this ADAM Context.

    returns

    A new Java ADAM Context.

  3. new JavaADAMContext(name: String, master: String)

    Builds this Java ADAM Context by creating a new Spark Context.

    Builds this Java ADAM Context by creating a new Spark Context.

    name

    Name of the Spark Context to create.

    master

    The URI of the Spark master.

    returns

    Returns a new Java ADAM Context, built on a new Spark Context.

  4. new JavaADAMContext(name: String, master: String, sparkHome: String, sparkJars: List[String], sparkEnvVars: Map[String, String], sparkAddStatsListener: Boolean, sparkKryoBufferSize: Integer, sparkMetricsListener: ADAMMetricsListener, loadSystemValues: Boolean, sparkDriverPort: Integer)

    Builds this Java ADAM Context by creating a new Spark Context.

    Builds this Java ADAM Context by creating a new Spark Context.

    name

    Name of the Spark Context to create.

    master

    The URI of the Spark master.

    sparkHome

    Path to the Spark home directory.

    sparkJars

    JAR files to include.

    sparkEnvVars

    A map containing envars and their settings.

    sparkAddStatsListener

    Whether or not to include a stats listener.

    sparkKryoBufferSize

    The size of the kryo serialization buffer in MB.

    sparkMetricsListener

    A metrics listener to attach. Can be null.

    loadSystemValues

    Whether to load system values or not.

    sparkDriverPort

    The port mapping for the Spark driver. Can be null.

    returns

    Returns a new Java ADAM Context, built on a new Spark Context.

  5. new JavaADAMContext(ac: ADAMContext)

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 ac: ADAMContext

  7. def adamRecordLoad[U <: ADAMPredicate[AlignmentRecord]](filePath: String): JavaAlignmentRecordRDD

    Loads in an ADAM read file.

    Loads in an ADAM read file. This method can load SAM, BAM, and ADAM files.

    U

    A predicate to apply on the load.

    filePath

    Path to load the file from.

    returns

    Returns a read RDD.

  8. final def asInstanceOf[T0]: T0

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  9. def clone(): AnyRef

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

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  11. def equals(arg0: Any): Boolean

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  12. def finalize(): Unit

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

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  14. def getSparkContext: JavaSparkContext

    returns

    Returns the Java Spark Context associated with this Java ADAM Context.

  15. def hashCode(): Int

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  16. final def isInstanceOf[T0]: Boolean

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

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  18. final def notify(): Unit

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  19. final def notifyAll(): Unit

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

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  21. def toString(): String

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  22. final def wait(): Unit

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

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

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