JavaADAMContext

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. val ac: ADAMContext

   

5. final def asInstanceOf[T0]: T0

   

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6. def clone(): AnyRef

   

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

   

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8. def equals(arg0: Any): Boolean

   

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9. def finalize(): Unit

   

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

    

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11. def getSparkContext: JavaSparkContext

    
    returns

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

12. def hashCode(): Int

    

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13. final def isInstanceOf[T0]: Boolean

    

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14. 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.

15. def loadFeatures(filePath: String): FeatureRDD

    

    Loads in features.

    Loads in features.

    filePath

    The path to load the file from.

    returns

    Returns a FeatureRDD.

16. 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.

17. def loadGenotypes(filePath: String): GenotypeRDD

    

    Loads in genotypes.

    Loads in genotypes.

    filePath

    The path to load the file from.

    returns

    Returns a GenotypeRDD.

18. 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.

19. def loadVariantAnnotations(filePath: String): DatabaseVariantAnnotationRDD

    

    Loads in variant annotations.

    Loads in variant annotations.

    filePath

    The path to load the file from.

    returns

    Returns a DatabaseVariantAnnotationRDD.

20. def loadVariants(filePath: String): VariantRDD

    

    Loads in variants.

    Loads in variants.

    filePath

    The path to load the file from.

    returns

    Returns a VariantRDD.

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

    

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22. final def notify(): Unit

    

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23. final def notifyAll(): Unit

    

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

    

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25. def toString(): String

    

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26. final def wait(): Unit

    

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

    

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

    

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