c

org.bdgenomics.adam.util

IndexedFastaFile

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
Ordering
  1. Alphabetic
  2. By Inheritance
Inherited
  1. IndexedFastaFile
  2. Product
  3. Equals
  4. Logging
  5. ReferenceFile
  6. Serializable
  7. Serializable
  8. AnyRef
  9. Any
  1. Hide All
  2. Show All
Visibility
  1. Public
  2. All

Instance Constructors

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

    filePath

    path to fasta or fa index

Value Members

  1. final def !=(arg0: Any): Boolean
    Definition Classes
    AnyRef → Any
  2. final def ##(): Int
    Definition Classes
    AnyRef → Any
  3. final def ==(arg0: Any): Boolean
    Definition Classes
    AnyRef → Any
  4. final def asInstanceOf[T0]: T0
    Definition Classes
    Any
  5. def clone(): AnyRef
    Attributes
    protected[lang]
    Definition Classes
    AnyRef
    Annotations
    @throws( ... ) @native() @HotSpotIntrinsicCandidate()
  6. def debug(mkr: Marker, msg: ⇒ Any, t: ⇒ Throwable): Unit
    Attributes
    protected
    Definition Classes
    Logging
  7. def debug(msg: ⇒ Any, t: ⇒ Throwable): Unit
    Attributes
    protected
    Definition Classes
    Logging
  8. def debug(msg: ⇒ Any): Unit
    Attributes
    protected
    Definition Classes
    Logging
  9. final def eq(arg0: AnyRef): Boolean
    Definition Classes
    AnyRef
  10. def error(mkr: Marker, msg: ⇒ Any, t: ⇒ Throwable): Unit
    Attributes
    protected
    Definition Classes
    Logging
  11. def error(msg: ⇒ Any, t: ⇒ Throwable): Unit
    Attributes
    protected
    Definition Classes
    Logging
  12. def error(msg: ⇒ Any): Unit
    Attributes
    protected
    Definition Classes
    Logging
  13. 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
    IndexedFastaFileReferenceFile
  14. val filePath: String
  15. final def getClass(): Class[_]
    Definition Classes
    AnyRef → Any
    Annotations
    @native() @HotSpotIntrinsicCandidate()
  16. def info(mkr: Marker, msg: ⇒ Any, t: ⇒ Throwable): Unit
    Attributes
    protected
    Definition Classes
    Logging
  17. def info(msg: ⇒ Any, t: ⇒ Throwable): Unit
    Attributes
    protected
    Definition Classes
    Logging
  18. def info(msg: ⇒ Any): Unit
    Attributes
    protected
    Definition Classes
    Logging
  19. def isDebugEnabled: Boolean
    Attributes
    protected
    Definition Classes
    Logging
  20. def isErrorEnabled: Boolean
    Attributes
    protected
    Definition Classes
    Logging
  21. def isInfoEnabled: Boolean
    Attributes
    protected
    Definition Classes
    Logging
  22. final def isInstanceOf[T0]: Boolean
    Definition Classes
    Any
  23. def isTraceEnabled: Boolean
    Attributes
    protected
    Definition Classes
    Logging
  24. def isWarnEnabled: Boolean
    Attributes
    protected
    Definition Classes
    Logging
  25. def logger: Logger
    Attributes
    protected
    Definition Classes
    Logging
  26. def loggerName: String
    Attributes
    protected
    Definition Classes
    Logging
  27. final def ne(arg0: AnyRef): Boolean
    Definition Classes
    AnyRef
  28. final def notify(): Unit
    Definition Classes
    AnyRef
    Annotations
    @native() @HotSpotIntrinsicCandidate()
  29. final def notifyAll(): Unit
    Definition Classes
    AnyRef
    Annotations
    @native() @HotSpotIntrinsicCandidate()
  30. val references: SequenceDictionary
    Definition Classes
    IndexedFastaFileReferenceFile
  31. val sc: SparkContext
  32. val stringency: ValidationStringency
  33. final def synchronized[T0](arg0: ⇒ T0): T0
    Definition Classes
    AnyRef
  34. def trace(mkr: Marker, msg: ⇒ Any, t: ⇒ Throwable): Unit
    Attributes
    protected
    Definition Classes
    Logging
  35. def trace(msg: ⇒ Any, t: ⇒ Throwable): Unit
    Attributes
    protected
    Definition Classes
    Logging
  36. def trace(msg: ⇒ Any): Unit
    Attributes
    protected
    Definition Classes
    Logging
  37. final def wait(arg0: Long, arg1: Int): Unit
    Definition Classes
    AnyRef
    Annotations
    @throws( ... )
  38. final def wait(arg0: Long): Unit
    Definition Classes
    AnyRef
    Annotations
    @throws( ... ) @native()
  39. final def wait(): Unit
    Definition Classes
    AnyRef
    Annotations
    @throws( ... )
  40. def warn(mkr: Marker, msg: ⇒ Any, t: ⇒ Throwable): Unit
    Attributes
    protected
    Definition Classes
    Logging
  41. def warn(msg: ⇒ Any, t: ⇒ Throwable): Unit
    Attributes
    protected
    Definition Classes
    Logging
  42. def warn(msg: ⇒ Any): Unit
    Attributes
    protected
    Definition Classes
    Logging

Deprecated Value Members

  1. def finalize(): Unit
    Attributes
    protected[lang]
    Definition Classes
    AnyRef
    Annotations
    @throws( classOf[java.lang.Throwable] ) @Deprecated
    Deprecated

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