c

com.fulcrumgenomics.util

AmpliconLabeller

class AmpliconLabeller extends AnyRef

Labels (add SAM tags) to records based on assigned amplicons.

The output will have the following tags added: - ap: the assigned primer coordinates (ex. chr1:1010873-1010894) - am: the mate's assigned primer coordinates (ex. chr1:1011118-1011137) - ip: the assigned amplicon id - im: the mate's assigned amplicon id (or = if the same as the assigned amplicon)

If not primer/amplicon was found, then no tag will be written.

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Implicitly
  1. by any2stringadd
  2. by StringFormat
  3. by Ensuring
  4. by ArrowAssoc
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Instance Constructors

  1. new AmpliconLabeller(amplicons: Iterator[Amplicon] = Iterator.empty, primerCoordinatesTag: String = AssignPrimers.PrimerCoordinateTag, matePrimerCoordinatesTag: String = ..., ampliconIdentifierTag: String = AssignPrimers.AmpliconIdentifierTag, mateAmpliconIdentifierTag: String = ...)

    amplicons

    the amplicons used to collect metrics, may be empty

    primerCoordinatesTag

    the SAM tag to store the primer genomic coordinates for the read

    matePrimerCoordinatesTag

    the SAM tag to store the primer genomic coordinates for the read's mate

    ampliconIdentifierTag

    the SAM tag to store the amplicon identifier for the read

    mateAmpliconIdentifierTag

    the SAM tag to store the amplicon identifier for the read's mate

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 AmpliconLabeller to any2stringadd[AmpliconLabeller] performed by method any2stringadd in scala.Predef.
    Definition Classes
    any2stringadd
  4. def ->[B](y: B): (AmpliconLabeller, B)
    Implicit
    This member is added by an implicit conversion from AmpliconLabeller to ArrowAssoc[AmpliconLabeller] performed by method ArrowAssoc in scala.Predef.
    Definition Classes
    ArrowAssoc
    Annotations
    @inline()
  5. final def ==(arg0: Any): Boolean
    Definition Classes
    AnyRef → Any
  6. val ampliconIdentifierTag: String
  7. val amplicons: Iterator[Amplicon]
  8. final def asInstanceOf[T0]: T0
    Definition Classes
    Any
  9. def clone(): AnyRef
    Attributes
    protected[lang]
    Definition Classes
    AnyRef
    Annotations
    @throws( ... ) @native()
  10. def ensuring(cond: (AmpliconLabeller) ⇒ Boolean, msg: ⇒ Any): AmpliconLabeller
    Implicit
    This member is added by an implicit conversion from AmpliconLabeller to Ensuring[AmpliconLabeller] performed by method Ensuring in scala.Predef.
    Definition Classes
    Ensuring
  11. def ensuring(cond: (AmpliconLabeller) ⇒ Boolean): AmpliconLabeller
    Implicit
    This member is added by an implicit conversion from AmpliconLabeller to Ensuring[AmpliconLabeller] performed by method Ensuring in scala.Predef.
    Definition Classes
    Ensuring
  12. def ensuring(cond: Boolean, msg: ⇒ Any): AmpliconLabeller
    Implicit
    This member is added by an implicit conversion from AmpliconLabeller to Ensuring[AmpliconLabeller] performed by method Ensuring in scala.Predef.
    Definition Classes
    Ensuring
  13. def ensuring(cond: Boolean): AmpliconLabeller
    Implicit
    This member is added by an implicit conversion from AmpliconLabeller to Ensuring[AmpliconLabeller] performed by method Ensuring in scala.Predef.
    Definition Classes
    Ensuring
  14. final def eq(arg0: AnyRef): Boolean
    Definition Classes
    AnyRef
  15. def equals(arg0: Any): Boolean
    Definition Classes
    AnyRef → Any
  16. def finalize(): Unit
    Attributes
    protected[lang]
    Definition Classes
    AnyRef
    Annotations
    @throws( classOf[java.lang.Throwable] )
  17. def formatted(fmtstr: String): String
    Implicit
    This member is added by an implicit conversion from AmpliconLabeller to StringFormat[AmpliconLabeller] performed by method StringFormat in scala.Predef.
    Definition Classes
    StringFormat
    Annotations
    @inline()
  18. final def getClass(): Class[_]
    Definition Classes
    AnyRef → Any
    Annotations
    @native()
  19. def hashCode(): Int
    Definition Classes
    AnyRef → Any
    Annotations
    @native()
  20. final def isInstanceOf[T0]: Boolean
    Definition Classes
    Any
  21. def label(r1: SamRecord, r2: SamRecord, recAmplicon: Option[Amplicon], mateAmplicon: Option[Amplicon]): Unit

    Labels (adds SAM tags) to a read pair based on the assigned amplicon(s) for itself and potentially its mate.

    Labels (adds SAM tags) to a read pair based on the assigned amplicon(s) for itself and potentially its mate.

    r1

    the first of pair

    r2

    the second of pair

    recAmplicon

    the assigned amplicon for the record

    mateAmplicon

    the assigned amplicon fo the record's mate (if paired)

  22. def label(rec: SamRecord, recAmplicon: Option[Amplicon] = None, mateAmplicon: Option[Amplicon] = None): Unit

    Labels (adds SAM tags) to a record based on the assigned amplicon(s) for itself and potentially its mate.

    Labels (adds SAM tags) to a record based on the assigned amplicon(s) for itself and potentially its mate.

    rec

    the record to label

    recAmplicon

    the assigned amplicon for the record

    mateAmplicon

    the assigned amplicon fo the record's mate (if paired)

  23. val mateAmpliconIdentifierTag: String
  24. val matePrimerCoordinatesTag: String
  25. val metrics: Map[Amplicon, AssignPrimersMetric]
  26. final def ne(arg0: AnyRef): Boolean
    Definition Classes
    AnyRef
  27. final def notify(): Unit
    Definition Classes
    AnyRef
    Annotations
    @native()
  28. final def notifyAll(): Unit
    Definition Classes
    AnyRef
    Annotations
    @native()
  29. val primerCoordinatesTag: String
  30. final def synchronized[T0](arg0: ⇒ T0): T0
    Definition Classes
    AnyRef
  31. def toString(): String
    Definition Classes
    AnyRef → Any
  32. final def wait(): Unit
    Definition Classes
    AnyRef
    Annotations
    @throws( ... )
  33. final def wait(arg0: Long, arg1: Int): Unit
    Definition Classes
    AnyRef
    Annotations
    @throws( ... )
  34. final def wait(arg0: Long): Unit
    Definition Classes
    AnyRef
    Annotations
    @throws( ... ) @native()
  35. def →[B](y: B): (AmpliconLabeller, B)
    Implicit
    This member is added by an implicit conversion from AmpliconLabeller to ArrowAssoc[AmpliconLabeller] performed by method ArrowAssoc in scala.Predef.
    Definition Classes
    ArrowAssoc

Inherited from AnyRef

Inherited from Any

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

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

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

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

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