c

com.fulcrumgenomics.umi

CallMolecularConsensusReads

class CallMolecularConsensusReads extends FgBioTool with LazyLogging

Annotations
@ClpAnnotation()
Linear Supertypes
LazyLogging, FgBioTool, AnyRef, Any
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Inherited
  1. CallMolecularConsensusReads
  2. LazyLogging
  3. FgBioTool
  4. AnyRef
  5. Any
Implicitly
  1. by any2stringadd
  2. by StringFormat
  3. by Ensuring
  4. by ArrowAssoc
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Visibility
  1. Public
  2. All

Instance Constructors

  1. new CallMolecularConsensusReads(input: FgBioDef.PathToBam, output: FgBioDef.PathToBam, rejects: Option[FgBioDef.PathToBam] = None, tag: String = DefaultTag, readNamePrefix: Option[String] = None, readGroupId: String = "A", errorRatePreUmi: PhredScore = DefaultErrorRatePreUmi, errorRatePostUmi: PhredScore = DefaultErrorRatePostUmi, minInputBaseQuality: PhredScore = DefaultMinInputBaseQuality, minConsensusBaseQuality: PhredScore = 2.toByte, minReads: Int, maxReads: Option[Int] = None, outputPerBaseTags: Boolean = DefaultProducePerBaseTags, sortOrder: Option[SortOrder] = Some(SortOrder.queryname), debug: Boolean = false)

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 CallMolecularConsensusReads to any2stringadd[CallMolecularConsensusReads] performed by method any2stringadd in scala.Predef.
    Definition Classes
    any2stringadd
  4. def ->[B](y: B): (CallMolecularConsensusReads, B)
    Implicit
    This member is added by an implicit conversion from CallMolecularConsensusReads to ArrowAssoc[CallMolecularConsensusReads] 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. def clone(): AnyRef
    Attributes
    protected[java.lang]
    Definition Classes
    AnyRef
    Annotations
    @throws( ... )
  8. val debug: Boolean
  9. def ensuring(cond: (CallMolecularConsensusReads) ⇒ Boolean, msg: ⇒ Any): CallMolecularConsensusReads
    Implicit
    This member is added by an implicit conversion from CallMolecularConsensusReads to Ensuring[CallMolecularConsensusReads] performed by method Ensuring in scala.Predef.
    Definition Classes
    Ensuring
  10. def ensuring(cond: (CallMolecularConsensusReads) ⇒ Boolean): CallMolecularConsensusReads
    Implicit
    This member is added by an implicit conversion from CallMolecularConsensusReads to Ensuring[CallMolecularConsensusReads] performed by method Ensuring in scala.Predef.
    Definition Classes
    Ensuring
  11. def ensuring(cond: Boolean, msg: ⇒ Any): CallMolecularConsensusReads
    Implicit
    This member is added by an implicit conversion from CallMolecularConsensusReads to Ensuring[CallMolecularConsensusReads] performed by method Ensuring in scala.Predef.
    Definition Classes
    Ensuring
  12. def ensuring(cond: Boolean): CallMolecularConsensusReads
    Implicit
    This member is added by an implicit conversion from CallMolecularConsensusReads to Ensuring[CallMolecularConsensusReads] 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. val errorRatePostUmi: PhredScore
  16. val errorRatePreUmi: PhredScore
  17. def execute(): Unit

    Main method that does the work of reading input files, creating the consensus reads, and writing the output file.

    Main method that does the work of reading input files, creating the consensus reads, and writing the output file.

    Definition Classes
    CallMolecularConsensusReads → FgBioTool
  18. 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
  19. 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
  20. def fail(exit: Int): Nothing

    Fail with just an exit code.

    Fail with just an exit code.

    Definition Classes
    FgBioTool
  21. def finalize(): Unit
    Attributes
    protected[java.lang]
    Definition Classes
    AnyRef
    Annotations
    @throws( classOf[java.lang.Throwable] )
  22. def formatted(fmtstr: String): String
    Implicit
    This member is added by an implicit conversion from CallMolecularConsensusReads to StringFormat[CallMolecularConsensusReads] performed by method StringFormat in scala.Predef.
    Definition Classes
    StringFormat
    Annotations
    @inline()
  23. final def getClass(): Class[_]
    Definition Classes
    AnyRef → Any
  24. def hashCode(): Int
    Definition Classes
    AnyRef → Any
  25. val input: FgBioDef.PathToBam
  26. 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
  27. final def isInstanceOf[T0]: Boolean
    Definition Classes
    Any
  28. lazy val logger: Logger
    Attributes
    protected
    Definition Classes
    LazyLogging
  29. val maxReads: Option[Int]
  30. val minConsensusBaseQuality: PhredScore
  31. val minInputBaseQuality: PhredScore
  32. val minReads: Int
  33. final def ne(arg0: AnyRef): Boolean
    Definition Classes
    AnyRef
  34. final def notify(): Unit
    Definition Classes
    AnyRef
  35. final def notifyAll(): Unit
    Definition Classes
    AnyRef
  36. val output: FgBioDef.PathToBam
  37. val outputPerBaseTags: Boolean
  38. val readGroupId: String
  39. val readNamePrefix: Option[String]
  40. val rejects: Option[FgBioDef.PathToBam]
  41. val sortOrder: Option[SortOrder]
  42. final def synchronized[T0](arg0: ⇒ T0): T0
    Definition Classes
    AnyRef
  43. val tag: String
  44. def toString(): String
    Definition Classes
    AnyRef → Any
  45. 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
  46. final def wait(): Unit
    Definition Classes
    AnyRef
    Annotations
    @throws( ... )
  47. final def wait(arg0: Long, arg1: Int): Unit
    Definition Classes
    AnyRef
    Annotations
    @throws( ... )
  48. final def wait(arg0: Long): Unit
    Definition Classes
    AnyRef
    Annotations
    @throws( ... )
  49. def →[B](y: B): (CallMolecularConsensusReads, B)
    Implicit
    This member is added by an implicit conversion from CallMolecularConsensusReads to ArrowAssoc[CallMolecularConsensusReads] performed by method ArrowAssoc in scala.Predef.
    Definition Classes
    ArrowAssoc

Inherited from LazyLogging

Inherited from FgBioTool

Inherited from AnyRef

Inherited from Any

Inherited by implicit conversion any2stringadd from CallMolecularConsensusReads to any2stringadd[CallMolecularConsensusReads]

Inherited by implicit conversion StringFormat from CallMolecularConsensusReads to StringFormat[CallMolecularConsensusReads]

Inherited by implicit conversion Ensuring from CallMolecularConsensusReads to Ensuring[CallMolecularConsensusReads]

Inherited by implicit conversion ArrowAssoc from CallMolecularConsensusReads to ArrowAssoc[CallMolecularConsensusReads]

Ungrouped