Class

org.bdgenomics.adam.util

IndexedFastaFile

Related Doc: package util

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case class IndexedFastaFile(sc: SparkContext, filePath: String, stringency: ValidationStringency = ValidationStringency.STRICT) 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 = ValidationStringency.STRICT)

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    filePath

    path to fasta or fa index

Value Members

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

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    Definition Classes
    AnyRef → Any

  2. final def ##(): Int

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

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    AnyRef → Any

  4. final def asInstanceOf[T0]: T0

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  5. def clone(): AnyRef

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    Attributes
    protected[java.lang]
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  6. def debug(mkr: Marker, msg: ⇒ Any, t: ⇒ Throwable): Unit

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    Attributes
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    Logging

  7. def debug(msg: ⇒ Any, t: ⇒ Throwable): Unit

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  8. def debug(msg: ⇒ Any): Unit

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

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    Definition Classes
    AnyRef

  10. def error(mkr: Marker, msg: ⇒ Any, t: ⇒ Throwable): Unit

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  11. def error(msg: ⇒ Any, t: ⇒ Throwable): Unit

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  12. def error(msg: ⇒ Any): Unit

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  13. def extract(region: ReferenceRegion): String

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    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

  14. val filePath: String

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    path to fasta or fa index

  15. def finalize(): Unit

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    protected[java.lang]
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    @throws( classOf[java.lang.Throwable] )

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

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  17. def info(mkr: Marker, msg: ⇒ Any, t: ⇒ Throwable): Unit

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  18. def info(msg: ⇒ Any, t: ⇒ Throwable): Unit

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  19. def info(msg: ⇒ Any): Unit

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  20. def isDebugEnabled: Boolean

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  21. def isErrorEnabled: Boolean

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  22. def isInfoEnabled: Boolean

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  23. final def isInstanceOf[T0]: Boolean

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  24. def isTraceEnabled: Boolean

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    Logging

  25. def isWarnEnabled: Boolean

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  26. def logger: Logger

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  27. def loggerName: String

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

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  29. final def notify(): Unit

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  30. final def notifyAll(): Unit

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    Definition Classes
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  31. val sc: SparkContext

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  32. val sequences: SequenceDictionary

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    Definition Classes
    IndexedFastaFile → ReferenceFile

  33. val stringency: ValidationStringency

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

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    Definition Classes
    AnyRef

  35. def trace(mkr: Marker, msg: ⇒ Any, t: ⇒ Throwable): Unit

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  36. def trace(msg: ⇒ Any, t: ⇒ Throwable): Unit

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  37. def trace(msg: ⇒ Any): Unit

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  38. final def wait(): Unit

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

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

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  41. def warn(mkr: Marker, msg: ⇒ Any, t: ⇒ Throwable): Unit

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    Logging

  42. def warn(msg: ⇒ Any, t: ⇒ Throwable): Unit

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  43. def warn(msg: ⇒ Any): Unit

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Inherited from Product

Inherited from Equals

Inherited from Logging

Inherited from ReferenceFile

Inherited from Serializable

Inherited from Serializable

Inherited from AnyRef

Inherited from Any

Ungrouped