org.bdgenomics.adam.util

IndexedFastaFile

case class IndexedFastaFile(sc: SparkContext, filePath: String, stringency: ValidationStringency = ...) extends ReferenceFile with Logging with Product with Serializable

Loads and extracts sequences directly from indexed fasta or fa files. filePath requires fai index in the same directory with same naming convention.

filePath

path to fasta or fa index

Linear Supertypes
Product, Equals, Logging, ReferenceFile, Serializable, Serializable, AnyRef, Any
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Inherited
  1. IndexedFastaFile
  2. Product
  3. Equals
  4. Logging
  5. ReferenceFile
  6. Serializable
  7. Serializable
  8. AnyRef
  9. Any
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Instance Constructors

  1. new IndexedFastaFile(sc: SparkContext, filePath: String, stringency: ValidationStringency = ...)

    filePath

    path to fasta or fa index

Value Members

  1. final def !=(arg0: AnyRef): Boolean

    Definition Classes
    AnyRef

  2. final def !=(arg0: Any): Boolean

    Definition Classes
    Any

  3. final def ##(): Int

    Definition Classes
    AnyRef → Any

  4. final def ==(arg0: AnyRef): Boolean

    Definition Classes
    AnyRef

  5. final def ==(arg0: Any): Boolean

    Definition Classes
    Any

  6. final def asInstanceOf[T0]: T0

    Definition Classes
    Any

  7. def clone(): AnyRef

    Attributes
    protected[java.lang]
    Definition Classes
    AnyRef
    Annotations
    @throws( ... )

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

    Definition Classes
    AnyRef

  9. def extract(region: ReferenceRegion): String

    Extracts base sequence from FastaSequenceIndex

    Extracts base sequence from FastaSequenceIndex

    region

    The desired ReferenceRegion to extract.

    returns

    The reference sequence at the desired locus.

    Definition Classes
    IndexedFastaFile → ReferenceFile

  10. val filePath: String

    path to fasta or fa index

  11. def finalize(): Unit

    Attributes
    protected[java.lang]
    Definition Classes
    AnyRef
    Annotations
    @throws( classOf[java.lang.Throwable] )

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

    Definition Classes
    AnyRef → Any

  13. final def isInstanceOf[T0]: Boolean

    Definition Classes
    Any

  14. def isTraceEnabled(): Boolean

    Attributes
    protected
    Definition Classes
    Logging

  15. def log: Logger

    Attributes
    protected
    Definition Classes
    Logging

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

    Attributes
    protected
    Definition Classes
    Logging

  17. def logDebug(msg: ⇒ String): Unit

    Attributes
    protected
    Definition Classes
    Logging

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

    Attributes
    protected
    Definition Classes
    Logging

  19. def logError(msg: ⇒ String): Unit

    Attributes
    protected
    Definition Classes
    Logging

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

    Attributes
    protected
    Definition Classes
    Logging

  21. def logInfo(msg: ⇒ String): Unit

    Attributes
    protected
    Definition Classes
    Logging

  22. def logName: String

    Attributes
    protected
    Definition Classes
    Logging

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

    Attributes
    protected
    Definition Classes
    Logging

  24. def logTrace(msg: ⇒ String): Unit

    Attributes
    protected
    Definition Classes
    Logging

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

    Attributes
    protected
    Definition Classes
    Logging

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

    Attributes
    protected
    Definition Classes
    Logging

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

    Definition Classes
    AnyRef

  28. final def notify(): Unit

    Definition Classes
    AnyRef

  29. final def notifyAll(): Unit

    Definition Classes
    AnyRef

  30. val sc: SparkContext

  31. val sequences: SequenceDictionary

    Definition Classes
    IndexedFastaFile → ReferenceFile

  32. val stringency: ValidationStringency

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

    Definition Classes
    AnyRef

  34. final def wait(): Unit

    Definition Classes
    AnyRef
    Annotations
    @throws( ... )

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

    Definition Classes
    AnyRef
    Annotations
    @throws( ... )

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

    Definition Classes
    AnyRef
    Annotations
    @throws( ... )

Inherited from Product

Inherited from Equals

Inherited from Logging

Inherited from ReferenceFile

Inherited from Serializable

Inherited from Serializable

Inherited from AnyRef

Inherited from Any

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