sealed trait SamOrder extends Product
Trait for specifying BAM orderings.
Linear Supertypes
Known Subclasses
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Inherited
- SamOrder
- Product
- Equals
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Implicitly
- by any2stringadd
- by StringFormat
- by Ensuring
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Visibility
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Abstract Value Members
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abstract
def
canEqual(that: Any): Boolean
- Definition Classes
- Equals
-
abstract
def
groupOrder: GroupOrder
Returns the group order that should be set in the SAM header.
Returns the group order that should be set in the SAM header. None will cause GO to be unset.
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abstract
def
productArity: Int
- Definition Classes
- Product
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abstract
def
productElement(n: Int): Any
- Definition Classes
- Product
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abstract
def
sortOrder: SortOrder
Returns the sort order that should be set in the SAM header.
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abstract
def
sortkey: (SamRecord) ⇒ A
Function to generate the sort key for sorting records into this ordering.
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abstract
def
subSort: Option[String]
The subsort string to be placed *after* the sort order in the SS tag.
Concrete Value Members
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final
def
!=(arg0: Any): Boolean
- Definition Classes
- AnyRef → Any
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final
def
##(): Int
- Definition Classes
- AnyRef → Any
- def +(other: String): String
- def ->[B](y: B): (SamOrder, B)
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final
def
==(arg0: Any): Boolean
- Definition Classes
- AnyRef → Any
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def
applyTo(header: SAMFileHeader): SAMFileHeader
Sets the appropriate fields in the SAM header for the order.
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final
def
asInstanceOf[T0]: T0
- Definition Classes
- Any
-
def
clone(): AnyRef
- Attributes
- protected[java.lang]
- Definition Classes
- AnyRef
- Annotations
- @throws( ... )
- def ensuring(cond: (SamOrder) ⇒ Boolean, msg: ⇒ Any): SamOrder
- def ensuring(cond: (SamOrder) ⇒ Boolean): SamOrder
- def ensuring(cond: Boolean, msg: ⇒ Any): SamOrder
- def ensuring(cond: Boolean): SamOrder
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final
def
eq(arg0: AnyRef): Boolean
- Definition Classes
- AnyRef
-
def
equals(arg0: Any): Boolean
- Definition Classes
- AnyRef → Any
-
def
finalize(): Unit
- Attributes
- protected[java.lang]
- Definition Classes
- AnyRef
- Annotations
- @throws( classOf[java.lang.Throwable] )
- def formatted(fmtstr: String): String
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final
def
getClass(): Class[_]
- Definition Classes
- AnyRef → Any
-
def
hashCode(): Int
- Definition Classes
- AnyRef → Any
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final
def
isInstanceOf[T0]: Boolean
- Definition Classes
- Any
-
def
name: String
Returns the order's name.
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final
def
ne(arg0: AnyRef): Boolean
- Definition Classes
- AnyRef
-
final
def
notify(): Unit
- Definition Classes
- AnyRef
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final
def
notifyAll(): Unit
- Definition Classes
- AnyRef
-
def
productIterator: Iterator[Any]
- Definition Classes
- Product
-
def
productPrefix: String
- Definition Classes
- Product
-
final
def
synchronized[T0](arg0: ⇒ T0): T0
- Definition Classes
- AnyRef
-
def
toString(): String
- Definition Classes
- AnyRef → Any
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final
def
wait(): Unit
- Definition Classes
- AnyRef
- Annotations
- @throws( ... )
-
final
def
wait(arg0: Long, arg1: Int): Unit
- Definition Classes
- AnyRef
- Annotations
- @throws( ... )
-
final
def
wait(arg0: Long): Unit
- Definition Classes
- AnyRef
- Annotations
- @throws( ... )
- def →[B](y: B): (SamOrder, B)