o

org.bdgenomics.adam.util

FileExtensions

object FileExtensions

Match path names to file extensions.

Linear Supertypes
AnyRef, Any
Ordering
  1. Alphabetic
  2. By Inheritance
Inherited
  1. FileExtensions
  2. AnyRef
  3. Any
  1. Hide All
  2. Show All
Visibility
  1. Public
  2. All

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. final def eq(arg0: AnyRef): Boolean
    Definition Classes
    AnyRef
  7. def equals(arg0: Any): Boolean
    Definition Classes
    AnyRef → Any
  8. final def getClass(): Class[_]
    Definition Classes
    AnyRef → Any
    Annotations
    @native() @HotSpotIntrinsicCandidate()
  9. def hashCode(): Int
    Definition Classes
    AnyRef → Any
    Annotations
    @native() @HotSpotIntrinsicCandidate()
  10. def is2BitExt(pathName: String): Boolean

    pathName

    The path name to match.

    returns

    Returns true if the path name matches a 2bit format file extension.

  11. def isBamExt(pathName: String): Boolean

    pathName

    The path name to match.

    returns

    Returns true if the path name matches a BAM/CRAM/SAM format file extension.

  12. def isBedExt(pathName: String): Boolean

    pathName

    The path name to match.

    returns

    Returns true if the path name matches a BED6/12 format file extension.

  13. def isDictExt(pathName: String): Boolean

    pathName

    The path name to match.

    returns

    Returns true if the path name matches an HTSJDK sequence dictionary (.dict) extension.

  14. def isFastaExt(pathName: String): Boolean

    pathName

    The path name to match.

    returns

    Returns true if the path name matches a FASTA format file extension.

  15. def isFastqExt(pathName: String): Boolean

    pathName

    The path name to match.

    returns

    Returns true if the path name matches a FASTQ format file extension.

  16. def isGenomeExt(pathName: String): Boolean

    pathName

    The path name to match.

    returns

    Returns true if the path name matches a Bedtools genome file (.genome) extension.

  17. def isGff3Ext(pathName: String): Boolean

    pathName

    The path name to match.

    returns

    Returns true if the path name matches a GFF3 format file extension.

  18. def isGtfExt(pathName: String): Boolean

    pathName

    The path name to match.

    returns

    Returns true if the path name matches a GFF2/GTF format file extension.

  19. def isGzip(pathName: String): Boolean

    pathName

    The path name to match.

    returns

    Returns true if the path name matches a GZIP format file extension.

  20. final def isInstanceOf[T0]: Boolean
    Definition Classes
    Any
  21. def isInterleavedFastqExt(pathName: String): Boolean

    pathName

    The path name to match.

    returns

    Returns true if the path name matches an interleaved FASTQ format file extension.

  22. def isIntervalListExt(pathName: String): Boolean

    pathName

    The path name to match.

    returns

    Returns true if the path name matches an IntervalList format file extension.

  23. def isNarrowPeakExt(pathName: String): Boolean

    pathName

    The path name to match.

    returns

    Returns true if the path name matches a NarrowPeak format file extension.

  24. def isTextExt(pathName: String): Boolean

    pathName

    The path name to match.

    returns

    Returns true if the path name matches a text file (.txt) extension.

  25. def isVcfExt(pathName: String): Boolean

    pathName

    The path name to match.

    returns

    Returns true if the path name matches a VCF format file extension.

  26. final def ne(arg0: AnyRef): Boolean
    Definition Classes
    AnyRef
  27. final def notify(): Unit
    Definition Classes
    AnyRef
    Annotations
    @native() @HotSpotIntrinsicCandidate()
  28. final def notifyAll(): Unit
    Definition Classes
    AnyRef
    Annotations
    @native() @HotSpotIntrinsicCandidate()
  29. final def synchronized[T0](arg0: ⇒ T0): T0
    Definition Classes
    AnyRef
  30. def toString(): String
    Definition Classes
    AnyRef → Any
  31. final def wait(arg0: Long, arg1: Int): Unit
    Definition Classes
    AnyRef
    Annotations
    @throws( ... )
  32. final def wait(arg0: Long): Unit
    Definition Classes
    AnyRef
    Annotations
    @throws( ... ) @native()
  33. final def wait(): Unit
    Definition Classes
    AnyRef
    Annotations
    @throws( ... )

Deprecated Value Members

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

Inherited from AnyRef

Inherited from Any

Ungrouped