class GroupReadsByUmi extends FgBioTool with LazyLogging
- Annotations
- @ClpAnnotation()
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Inherited
- GroupReadsByUmi
- LazyLogging
- FgBioTool
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Implicitly
- by any2stringadd
- by StringFormat
- by Ensuring
- by ArrowAssoc
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Visibility
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Instance Constructors
- new GroupReadsByUmi(input: FgBioDef.PathToBam = Io.StdIn, output: FgBioDef.PathToBam = Io.StdOut, familySizeHistogram: Option[FgBioDef.FilePath] = None, rawTag: String = "RX", assignTag: String = "MI", minMapQ: Int = 30, includeNonPfReads: Boolean = false, strategy: String, edits: Int = 1, tmpDir: FgBioDef.DirPath = ...)
Type Members
- type ReadPair = (SAMRecord, SAMRecord)
Value Members
-
final
def
!=(arg0: Any): Boolean
- Definition Classes
- AnyRef → Any
-
final
def
##(): Int
- Definition Classes
- AnyRef → Any
-
def
+(other: String): String
- Implicit
- This member is added by an implicit conversion from GroupReadsByUmi to any2stringadd[GroupReadsByUmi] performed by method any2stringadd in scala.Predef.
- Definition Classes
- any2stringadd
-
def
->[B](y: B): (GroupReadsByUmi, B)
- Implicit
- This member is added by an implicit conversion from GroupReadsByUmi to ArrowAssoc[GroupReadsByUmi] performed by method ArrowAssoc in scala.Predef.
- Definition Classes
- ArrowAssoc
- Annotations
- @inline()
-
final
def
==(arg0: Any): Boolean
- Definition Classes
- AnyRef → Any
-
final
def
asInstanceOf[T0]: T0
- Definition Classes
- Any
- val assignTag: String
-
def
assignUmiGroups(pairs: Seq[ReadPair]): Unit
Takes in pairs of reads and writes an attribute (specified by
assignTag) denoting sub-grouping into UMI groups by original molecule. -
def
clone(): AnyRef
- Attributes
- protected[java.lang]
- Definition Classes
- AnyRef
- Annotations
- @throws( ... )
- val edits: Int
-
def
ensuring(cond: (GroupReadsByUmi) ⇒ Boolean, msg: ⇒ Any): GroupReadsByUmi
- Implicit
- This member is added by an implicit conversion from GroupReadsByUmi to Ensuring[GroupReadsByUmi] performed by method Ensuring in scala.Predef.
- Definition Classes
- Ensuring
-
def
ensuring(cond: (GroupReadsByUmi) ⇒ Boolean): GroupReadsByUmi
- Implicit
- This member is added by an implicit conversion from GroupReadsByUmi to Ensuring[GroupReadsByUmi] performed by method Ensuring in scala.Predef.
- Definition Classes
- Ensuring
-
def
ensuring(cond: Boolean, msg: ⇒ Any): GroupReadsByUmi
- Implicit
- This member is added by an implicit conversion from GroupReadsByUmi to Ensuring[GroupReadsByUmi] performed by method Ensuring in scala.Predef.
- Definition Classes
- Ensuring
-
def
ensuring(cond: Boolean): GroupReadsByUmi
- Implicit
- This member is added by an implicit conversion from GroupReadsByUmi to Ensuring[GroupReadsByUmi] performed by method Ensuring in scala.Predef.
- Definition Classes
- Ensuring
-
final
def
eq(arg0: AnyRef): Boolean
- Definition Classes
- AnyRef
-
def
equals(arg0: Any): Boolean
- Definition Classes
- AnyRef → Any
-
def
execute(): Unit
- Definition Classes
- GroupReadsByUmi → FgBioTool
-
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
-
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
-
def
fail(exit: Int): Nothing
Fail with just an exit code.
Fail with just an exit code.
- Definition Classes
- FgBioTool
- val familySizeHistogram: Option[FgBioDef.FilePath]
-
def
finalize(): Unit
- Attributes
- protected[java.lang]
- Definition Classes
- AnyRef
- Annotations
- @throws( classOf[java.lang.Throwable] )
-
def
formatted(fmtstr: String): String
- Implicit
- This member is added by an implicit conversion from GroupReadsByUmi to StringFormat[GroupReadsByUmi] performed by method StringFormat in scala.Predef.
- Definition Classes
- StringFormat
- Annotations
- @inline()
-
final
def
getClass(): Class[_]
- Definition Classes
- AnyRef → Any
-
def
hashCode(): Int
- Definition Classes
- AnyRef → Any
- val includeNonPfReads: Boolean
- val input: FgBioDef.PathToBam
-
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
-
final
def
isInstanceOf[T0]: Boolean
- Definition Classes
- Any
-
lazy val
logger: Logger
- Attributes
- protected
- Definition Classes
- LazyLogging
- val minMapQ: Int
-
final
def
ne(arg0: AnyRef): Boolean
- Definition Classes
- AnyRef
-
final
def
notify(): Unit
- Definition Classes
- AnyRef
-
final
def
notifyAll(): Unit
- Definition Classes
- AnyRef
- val output: FgBioDef.PathToBam
- val rawTag: String
- val strategy: String
-
final
def
synchronized[T0](arg0: ⇒ T0): T0
- Definition Classes
- AnyRef
-
def
takeNextGroup(iterator: BufferedIterator[ReadPair]): Seq[ReadPair]
Consumes the next group of pairs with all matching end positions and returns them.
- val tmpDir: FgBioDef.DirPath
-
def
toString(): String
- Definition Classes
- AnyRef → Any
-
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
-
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): (GroupReadsByUmi, B)
- Implicit
- This member is added by an implicit conversion from GroupReadsByUmi to ArrowAssoc[GroupReadsByUmi] performed by method ArrowAssoc in scala.Predef.
- Definition Classes
- ArrowAssoc