case class Template(r1: Option[SAMRecord], r2: Option[SAMRecord], r1Supplementals: Seq[SAMRecord] = Nil, r2Supplementals: Seq[SAMRecord] = Nil, r1Secondaries: Seq[SAMRecord] = Nil, r2Secondaries: Seq[SAMRecord] = Nil) extends Product with Serializable

Class that represents all reads from a template within a BAM file.

Linear Supertypes
Serializable, Serializable, Product, Equals, AnyRef, Any
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Inherited
  1. Template
  2. Serializable
  3. Serializable
  4. Product
  5. Equals
  6. AnyRef
  7. 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 Template(r1: Option[SAMRecord], r2: Option[SAMRecord], r1Supplementals: Seq[SAMRecord] = Nil, r2Supplementals: Seq[SAMRecord] = Nil, r1Secondaries: Seq[SAMRecord] = Nil, r2Secondaries: Seq[SAMRecord] = Nil)

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 Template to any2stringadd[Template] performed by method any2stringadd in scala.Predef.
    Definition Classes
    any2stringadd
  4. def ->[B](y: B): (Template, B)
    Implicit
    This member is added by an implicit conversion from Template to ArrowAssoc[Template] performed by method ArrowAssoc in scala.Predef.
    Definition Classes
    ArrowAssoc
    Annotations
    @inline()
  5. final def ==(arg0: Any): Boolean
    Definition Classes
    AnyRef → Any
  6. def allReads: Iterator[SAMRecord]

    Returns an iterator of all reads for the template.

  7. def allSupplementaryAndSecondary: Iterator[SAMRecord]

    Returns an iterator over all records that are not the primary r1 and r2.

  8. final def asInstanceOf[T0]: T0
    Definition Classes
    Any
  9. def clone(): AnyRef
    Attributes
    protected[java.lang]
    Definition Classes
    AnyRef
    Annotations
    @throws( ... )
  10. def ensuring(cond: (Template) ⇒ Boolean, msg: ⇒ Any): Template
    Implicit
    This member is added by an implicit conversion from Template to Ensuring[Template] performed by method Ensuring in scala.Predef.
    Definition Classes
    Ensuring
  11. def ensuring(cond: (Template) ⇒ Boolean): Template
    Implicit
    This member is added by an implicit conversion from Template to Ensuring[Template] performed by method Ensuring in scala.Predef.
    Definition Classes
    Ensuring
  12. def ensuring(cond: Boolean, msg: ⇒ Any): Template
    Implicit
    This member is added by an implicit conversion from Template to Ensuring[Template] performed by method Ensuring in scala.Predef.
    Definition Classes
    Ensuring
  13. def ensuring(cond: Boolean): Template
    Implicit
    This member is added by an implicit conversion from Template to Ensuring[Template] performed by method Ensuring in scala.Predef.
    Definition Classes
    Ensuring
  14. final def eq(arg0: AnyRef): Boolean
    Definition Classes
    AnyRef
  15. def finalize(): Unit
    Attributes
    protected[java.lang]
    Definition Classes
    AnyRef
    Annotations
    @throws( classOf[java.lang.Throwable] )
  16. def formatted(fmtstr: String): String
    Implicit
    This member is added by an implicit conversion from Template to StringFormat[Template] performed by method StringFormat in scala.Predef.
    Definition Classes
    StringFormat
    Annotations
    @inline()
  17. final def getClass(): Class[_]
    Definition Classes
    AnyRef → Any
  18. final def isInstanceOf[T0]: Boolean
    Definition Classes
    Any
  19. val name: String

    Gets the query name of the template (assumes all records have the same read name).

  20. final def ne(arg0: AnyRef): Boolean
    Definition Classes
    AnyRef
  21. final def notify(): Unit
    Definition Classes
    AnyRef
  22. final def notifyAll(): Unit
    Definition Classes
    AnyRef
  23. val r1: Option[SAMRecord]
  24. val r1Secondaries: Seq[SAMRecord]
  25. val r1Supplementals: Seq[SAMRecord]
  26. val r2: Option[SAMRecord]
  27. val r2Secondaries: Seq[SAMRecord]
  28. val r2Supplementals: Seq[SAMRecord]
  29. lazy val readCount: Int

    The total count of records for the template.

  30. final def synchronized[T0](arg0: ⇒ T0): T0
    Definition Classes
    AnyRef
  31. final def wait(): Unit
    Definition Classes
    AnyRef
    Annotations
    @throws( ... )
  32. final def wait(arg0: Long, arg1: Int): Unit
    Definition Classes
    AnyRef
    Annotations
    @throws( ... )
  33. final def wait(arg0: Long): Unit
    Definition Classes
    AnyRef
    Annotations
    @throws( ... )
  34. def →[B](y: B): (Template, B)
    Implicit
    This member is added by an implicit conversion from Template to ArrowAssoc[Template] performed by method ArrowAssoc in scala.Predef.
    Definition Classes
    ArrowAssoc

Inherited from Serializable

Inherited from Serializable

Inherited from Product

Inherited from Equals

Inherited from AnyRef

Inherited from Any

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

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

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

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

Ungrouped