Value Members

1.  final def !=(arg0: Any): Boolean

   Definition Classes

   AnyRef → Any

2.  final def ##(): Int

   Definition Classes

   AnyRef → Any

3.  def +(other: String): String

   Implicit

   This member is added by an implicit conversion from TrimPrimers to any2stringadd[TrimPrimers] performed by method any2stringadd in scala.Predef.

   Definition Classes

   any2stringadd

4.  def ->[B](y: B): (TrimPrimers, B)

   Implicit

   This member is added by an implicit conversion from TrimPrimers to ArrowAssoc[TrimPrimers] performed by method ArrowAssoc in scala.Predef.

   Definition Classes

   ArrowAssoc

   Annotations

   @inline()

5.  final def ==(arg0: Any): Boolean

   Definition Classes

   AnyRef → Any

6.  final def asInstanceOf[T0]: T0

   Definition Classes

   Any

7.  val autoTrimAttributes: Boolean
8.  def clone(): AnyRef

   Attributes

   protected[java.lang]

   Definition Classes

   AnyRef

   Annotations

   @throws( ... )

9.  def ensuring(cond: (TrimPrimers) ⇒ Boolean, msg: ⇒ Any): TrimPrimers

   Implicit

   This member is added by an implicit conversion from TrimPrimers to Ensuring[TrimPrimers] performed by method Ensuring in scala.Predef.

   Definition Classes

   Ensuring

10.  def ensuring(cond: (TrimPrimers) ⇒ Boolean): TrimPrimers

    Implicit

    This member is added by an implicit conversion from TrimPrimers to Ensuring[TrimPrimers] performed by method Ensuring in scala.Predef.

    Definition Classes

    Ensuring

11.  def ensuring(cond: Boolean, msg: ⇒ Any): TrimPrimers

    Implicit

    This member is added by an implicit conversion from TrimPrimers to Ensuring[TrimPrimers] performed by method Ensuring in scala.Predef.

    Definition Classes

    Ensuring

12.  def ensuring(cond: Boolean): TrimPrimers

    Implicit

    This member is added by an implicit conversion from TrimPrimers to Ensuring[TrimPrimers] performed by method Ensuring in scala.Predef.

    Definition Classes

    Ensuring

13.  final def eq(arg0: AnyRef): Boolean

    Definition Classes

    AnyRef

14.  def equals(arg0: Any): Boolean

    Definition Classes

    AnyRef → Any

15.  def execute(): Unit

    Definition Classes

    TrimPrimers → FgBioTool

16.  def fail(exit: Int, message: String): Nothing

    Fail with a specific error code and message.

    Fail with a specific error code and message.

    Definition Classes

    FgBioTool

17.  def fail(message: String): Nothing

    Fail with the default exit code and a message.

    Fail with the default exit code and a message.

    Definition Classes

    FgBioTool

18.  def fail(exit: Int): Nothing

    Fail with just an exit code.

    Fail with just an exit code.

    Definition Classes

    FgBioTool

19.  def finalize(): Unit

    Attributes

    protected[java.lang]

    Definition Classes

    AnyRef

    Annotations

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

20.  def formatted(fmtstr: String): String

    Implicit

    This member is added by an implicit conversion from TrimPrimers to StringFormat[TrimPrimers] performed by method StringFormat in scala.Predef.

    Definition Classes

    StringFormat

    Annotations

    @inline()

21.  final def getClass(): Class[_]

    Definition Classes

    AnyRef → Any

22.  val hardClip: Boolean
23.  def hashCode(): Int

    Definition Classes

    AnyRef → Any

24.  val input: FgBioDef.PathToBam
25.  def invalid(message: String): Nothing

    Generates a new validation exception with the given message.

    Generates a new validation exception with the given message.

    Definition Classes

    FgBioTool

26.  final def isInstanceOf[T0]: Boolean

    Definition Classes

    Any

27.  lazy val logger: Logger

    Attributes

    protected

    Definition Classes

    LazyLogging

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

    Definition Classes

    AnyRef

29.  final def notify(): Unit

    Definition Classes

    AnyRef

30.  final def notifyAll(): Unit

    Definition Classes

    AnyRef

31.  val output: FgBioDef.PathToBam
32.  val primers: FgBioDef.FilePath
33.  def recalculateTags(rec: SAMRecord, walker: ReferenceSequenceFileWalker): Unit

    Recalculates the MD, NM, and UQ tags on aligned records.

34.  val ref: Option[FgBioDef.PathToFasta]
35.  val slop: Int
36.  val sortOrder: Option[SortOrder]
37.  final def synchronized[T0](arg0: ⇒ T0): T0

    Definition Classes

    AnyRef

38.  val tmp: Option[FgBioDef.DirPath]
39.  def toString(): String

    Definition Classes

    AnyRef → Any

40.  def trimReadsForTemplate(detector: OverlapDetector[Amplicon], maxPrimerLength: Int, reads: Seq[SAMRecord]): Unit

    Trims all the reads for a given template.

41.  def validate(test: Boolean, message: ⇒ String): Unit

    Generates a validation exception if the test value is false.

    Generates a validation exception if the test value is false.

    Definition Classes

    FgBioTool

42.  final def wait(): Unit

    Definition Classes

    AnyRef

    Annotations

    @throws( ... )

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

    Definition Classes

    AnyRef

    Annotations

    @throws( ... )

44.  final def wait(arg0: Long): Unit

    Definition Classes

    AnyRef

    Annotations

    @throws( ... )

45.  def →[B](y: B): (TrimPrimers, B)

    Implicit

    This member is added by an implicit conversion from TrimPrimers to ArrowAssoc[TrimPrimers] performed by method ArrowAssoc in scala.Predef.

    Definition Classes

    ArrowAssoc