org.bdgenomics.adam.apis.java

# JavaADAMContext

#### class JavaADAMContext extends Serializable

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### Instance Constructors

1. #### 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. #### 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 getSparkContext: JavaSparkContext

    returns

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

14. #### def hashCode(): Int

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15. #### final def isInstanceOf[T0]: Boolean

    Definition Classes
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16. #### def loadAlignments(filePath: String): AlignmentRecordRDD

    Loads in an ADAM read file.

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

    filePath

      Path to load the file from.

    returns

      Returns a read RDD.

17. #### def loadCoverage(filePath: String): CoverageRDD

    Loads in a coverage file.

    Loads in a coverage file. This method can load BED, NarrowPeak, GFF3, GTF/GFF2, IntervalList and ADAM files.

    filePath

      Path to load the file from.

    returns

      Returns a Coverage RDD.

18. #### def loadFeatures(filePath: String): FeatureRDD

    Loads in features.

    Loads in features.

    filePath

      The path to load the file from.

    returns

      Returns a FeatureRDD.

19. #### def loadFragments(filePath: String): FragmentRDD

    Loads in read pairs as fragments.

    Loads in read pairs as fragments.

    filePath

      The path to load the file from.

    returns

      Returns a FragmentRDD.

20. #### def loadGenotypes(filePath: String): GenotypeRDD

    Loads in genotypes.

    Loads in genotypes.

    filePath

      The path to load the file from.

    returns

      Returns a GenotypeRDD.

21. #### def loadSequences(filePath: String): NucleotideContigFragmentRDD

    Loads in sequence fragments.

    Loads in sequence fragments.

    Can load from FASTA or from Parquet encoded NucleotideContigFragments.

    filePath

      Path to load the file from.

    returns

      Returns a NucleotideContigFragment RDD.

22. #### def loadVariants(filePath: String): VariantRDD

    Loads in variants.

    Loads in variants.

    filePath

      The path to load the file from.

    returns

      Returns a VariantRDD.

23. #### final def ne(arg0: AnyRef): Boolean

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24. #### final def notify(): Unit

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25. #### final def notifyAll(): Unit

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

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27. #### def toString(): String

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28. #### final def wait(): Unit

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

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30. #### final def wait(arg0: Long): Unit

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