ExtractUmisFromBam

Instance Constructors

new ExtractUmisFromBam(in: com.fulcrumgenomics.commons.CommonsDef.PathToBam, out: com.fulcrumgenomics.commons.CommonsDef.PathToBam, readStructures: Seq[String], umiTags: Seq[String], annotateNames: Boolean = true, clippingAttribute: Option[String] = None)

Value Members

final def !=(arg0: Any): Boolean

Definition Classes
AnyRef → Any
def !=>(other: Dependable): Unit

Definition Classes
Task → Dependable
final def ##(): Int

Definition Classes
AnyRef → Any
def +(other: String): String

Implicit information
This member is added by an implicit conversion from ExtractUmisFromBam to any2stringadd[ExtractUmisFromBam] performed by method any2stringadd in scala.Predef.
Definition Classes
any2stringadd
def ->[B](y: B): (ExtractUmisFromBam, B)

Implicit information
This member is added by an implicit conversion from ExtractUmisFromBam to ArrowAssoc[ExtractUmisFromBam] performed by method ArrowAssoc in scala.Predef.
Definition Classes
ArrowAssoc
Annotations
@inline()
def ::(other: Option[Dependable]): Dependable

Definition Classes
Dependable
def ::(other: Dependable): Dependable

Definition Classes
Dependable
final def ==(arg0: Any): Boolean

Definition Classes
AnyRef → Any
final def ==>(other: Option[Dependable]): Dependable

Definition Classes
Dependable
final def ==>(other: Dependable): Dependable

Definition Classes
Dependable
def >(path: Path): Pipe[SamOrBam, Void]

Definition Classes
Pipe
def >!(path: Path): Pipe[SamOrBam, SamOrBam]

Definition Classes
Pipe
def >>(path: Path): Pipe[SamOrBam, Void]

Definition Classes
Pipe
def >>!(path: Path): Pipe[SamOrBam, SamOrBam]

Definition Classes
Pipe
def addDependent(dependent: Dependable): Unit

Definition Classes
Task → Dependable
def addFgBioArgs(buffer: ListBuffer[Any]): Unit

Implement this to add the tool-specific arguments
Implement this to add the tool-specific arguments

Attributes
protected
Definition Classes
ExtractUmisFromBam → FgBioTask
def allTasks: Traversable[Task]

Definition Classes
Task → Dependable
val annotateNames: Boolean
def applyResources(resources: ResourceSet): Unit

Definition Classes
UnitTask → Schedulable
final def args: Seq[Any]

Definition Classes
FgBioTask → ProcessTask
final def asInstanceOf[T0]: T0

Definition Classes
Any
def asType[T](path: String)(implicit arg0: scala.reflect.api.JavaUniverse.TypeTag[T]): T

Attributes
protected
Definition Classes
ConfigurationLike
val clippingAttribute: Option[String]
def clone(): AnyRef

Attributes
protected[java.lang]
Definition Classes
AnyRef
Annotations
@throws( ... )
def commandLineName(name: String): String

Definition Classes
ConfigurationLike
lazy val commandName: String

Looks up the first super class that does not have "$anon$" in its name.
Looks up the first super class that does not have "$anon$" in its name.

Definition Classes
FgBioTask
var compressionLevel: Option[Int]

the compress level to use for HTSJDK.
the compress level to use for HTSJDK.

Definition Classes
FgBioTask
def config: Config

Attributes
protected
Definition Classes
Configuration → ConfigurationLike
def configure[T](path: String, defaultValue: T)(implicit arg0: scala.reflect.api.JavaUniverse.TypeTag[T]): T

Definition Classes
ConfigurationLike
def configure[T](path: String)(implicit arg0: scala.reflect.api.JavaUniverse.TypeTag[T]): T

Definition Classes
ConfigurationLike
def configureExecutable(path: String, executable: String): Path

Definition Classes
ConfigurationLike
def configureExecutableFromBinDirectory(binPath: String, executable: String, subDir: Option[Path]): Path

Definition Classes
ConfigurationLike
def discardError(): Pipe[SamOrBam, SamOrBam]

Definition Classes
Pipe
def ensuring(cond: (ExtractUmisFromBam) ⇒ Boolean, msg: ⇒ Any): ExtractUmisFromBam

Implicit information
This member is added by an implicit conversion from ExtractUmisFromBam to Ensuring[ExtractUmisFromBam] performed by method Ensuring in scala.Predef.
Definition Classes
Ensuring
def ensuring(cond: (ExtractUmisFromBam) ⇒ Boolean): ExtractUmisFromBam

Implicit information
This member is added by an implicit conversion from ExtractUmisFromBam to Ensuring[ExtractUmisFromBam] performed by method Ensuring in scala.Predef.
Definition Classes
Ensuring
def ensuring(cond: Boolean, msg: ⇒ Any): ExtractUmisFromBam

Implicit information
This member is added by an implicit conversion from ExtractUmisFromBam to Ensuring[ExtractUmisFromBam] performed by method Ensuring in scala.Predef.
Definition Classes
Ensuring
def ensuring(cond: Boolean): ExtractUmisFromBam

Implicit information
This member is added by an implicit conversion from ExtractUmisFromBam to Ensuring[ExtractUmisFromBam] 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 fgBioJar: Path

Can be overridden to use a specific FgBio jar.
Can be overridden to use a specific FgBio jar.

Attributes
protected
Definition Classes
FgBioTask
def finalize(): Unit

Attributes
protected[java.lang]
Definition Classes
AnyRef
Annotations
@throws( classOf[java.lang.Throwable] )
def formatted(fmtstr: String): String

Implicit information
This member is added by an implicit conversion from ExtractUmisFromBam to StringFormat[ExtractUmisFromBam] performed by method StringFormat in scala.Predef.
Definition Classes
StringFormat
Annotations
@inline()
final def getClass(): Class[_]

Definition Classes
AnyRef → Any
final def getTasks: Traversable[_ <: ExtractUmisFromBam.this.type]

Definition Classes
UnitTask → Task
def hashCode(): Int

Definition Classes
AnyRef → Any
def headTasks: Traversable[Task]

Definition Classes
Task → Dependable
val in: com.fulcrumgenomics.commons.CommonsDef.PathToBam
final def isInstanceOf[T0]: Boolean

Definition Classes
Any
def jarArgs(jarPath: Path, jvmArgs: Traversable[String] = Nil, jvmProperties: Map[String, String] = Map.empty, jvmMemory: Memory, useAdvancedGcOptions: Boolean = true): List[String]

Attributes
protected
Definition Classes
JarTask
lazy val logger: Logger

Attributes
protected
Definition Classes
LazyLogging
var name: String

Definition Classes
Task
final def ne(arg0: AnyRef): Boolean

Definition Classes
AnyRef
final def notify(): Unit

Definition Classes
AnyRef
final def notifyAll(): Unit

Definition Classes
AnyRef
def onComplete(exitCode: Int): Boolean

Definition Classes
Task
def optionallyConfigure[T](path: String)(implicit arg0: scala.reflect.api.JavaUniverse.TypeTag[T]): Option[T]

Definition Classes
ConfigurationLike
val out: com.fulcrumgenomics.commons.CommonsDef.PathToBam
def pickResources(availableResources: ResourceSet): Option[ResourceSet]

Definition Classes
FixedResources → Schedulable
var quoteIfNecessary: Boolean

Attributes
protected
Definition Classes
ProcessTask
val readStructures: Seq[String]
def removeDependency(task: Task): Boolean

Definition Classes
Task
def requires(cores: Double, memory: String): ExtractUmisFromBam.this.type

Definition Classes
FixedResources
def requires(cores: Cores, memory: Memory): ExtractUmisFromBam.this.type

Definition Classes
FixedResources
def requires(resources: ResourceSet): ExtractUmisFromBam.this.type

Definition Classes
FixedResources
def resources: ResourceSet

Definition Classes
ScheduleWithEmptyDefaultResources
final def synchronized[T0](arg0: ⇒ T0): T0

Definition Classes
AnyRef
def systemPath: Seq[Path]

Attributes
protected
Definition Classes
ConfigurationLike
def tailTasks: Traversable[Task]

Definition Classes
Task → Dependable
def tasksDependedOn: Traversable[Task]

Attributes
protected[dagr.core]
Definition Classes
Task
def tasksDependingOnThisTask: Traversable[Task]

Attributes
protected[dagr.core]
Definition Classes
Task
def toString(): String

Definition Classes
ProcessTask → AnyRef → Any
val umiTags: Seq[String]
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 withCompression(i: Int): ExtractUmisFromBam.this.type

Sets the compression level to a specific value.
Sets the compression level to a specific value.

Definition Classes
FgBioTask
def withName(name: String): ExtractUmisFromBam.this.type

Definition Classes
Task
def |[In2 >: SamOrBam, Out2](next: Pipe[In2, Out2]): Pipe[SamOrBam, Out2]

Definition Classes
Pipe
def →[B](y: B): (ExtractUmisFromBam, B)

Implicit information
This member is added by an implicit conversion from ExtractUmisFromBam to ArrowAssoc[ExtractUmisFromBam] performed by method ArrowAssoc in scala.Predef.
Definition Classes
ArrowAssoc

Inherited from Pipe[SamOrBam, SamOrBam]

Inherited from FgBioTask

Inherited from Configuration

Inherited from ConfigurationLike

Inherited from FixedResources

Inherited from ScheduleWithEmptyDefaultResources

Inherited from JarTask

Inherited from ProcessTask

Inherited from UnitTask

Inherited from Schedulable

Inherited from LazyLogging

Inherited from Task

Inherited from Dependable

Inherited from AnyRef

Inherited from Any

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

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

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

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

Ungrouped

Related Doc: package fgbio

class ExtractUmisFromBam extends FgBioTask with Pipe[SamOrBam, SamOrBam]

Instance Constructors

new ExtractUmisFromBam(in: com.fulcrumgenomics.commons.CommonsDef.PathToBam, out: com.fulcrumgenomics.commons.CommonsDef.PathToBam, readStructures: Seq[String], umiTags: Seq[String], annotateNames: Boolean = true, clippingAttribute: Option[String] = None)

Value Members

final def !=(arg0: Any): Boolean

def !=>(other: Dependable): Unit

final def ##(): Int

def +(other: String): String

def ->[B](y: B): (ExtractUmisFromBam, B)

def ::(other: Option[Dependable]): Dependable

def ::(other: Dependable): Dependable

final def ==(arg0: Any): Boolean

final def ==>(other: Option[Dependable]): Dependable

final def ==>(other: Dependable): Dependable

def >(path: Path): Pipe[SamOrBam, Void]

def >!(path: Path): Pipe[SamOrBam, SamOrBam]

def >>(path: Path): Pipe[SamOrBam, Void]

def >>!(path: Path): Pipe[SamOrBam, SamOrBam]

def addDependent(dependent: Dependable): Unit

def addFgBioArgs(buffer: ListBuffer[Any]): Unit

def allTasks: Traversable[Task]

val annotateNames: Boolean

def applyResources(resources: ResourceSet): Unit

final def args: Seq[Any]

final def asInstanceOf[T0]: T0

def asType[T](path: String)(implicit arg0: scala.reflect.api.JavaUniverse.TypeTag[T]): T

val clippingAttribute: Option[String]

def clone(): AnyRef

def commandLineName(name: String): String

lazy val commandName: String

var compressionLevel: Option[Int]

def config: Config

def configure[T](path: String, defaultValue: T)(implicit arg0: scala.reflect.api.JavaUniverse.TypeTag[T]): T

def configure[T](path: String)(implicit arg0: scala.reflect.api.JavaUniverse.TypeTag[T]): T

def configureExecutable(path: String, executable: String): Path

def configureExecutableFromBinDirectory(binPath: String, executable: String, subDir: Option[Path]): Path

def discardError(): Pipe[SamOrBam, SamOrBam]

def ensuring(cond: (ExtractUmisFromBam) ⇒ Boolean, msg: ⇒ Any): ExtractUmisFromBam

def ensuring(cond: (ExtractUmisFromBam) ⇒ Boolean): ExtractUmisFromBam

def ensuring(cond: Boolean, msg: ⇒ Any): ExtractUmisFromBam

def ensuring(cond: Boolean): ExtractUmisFromBam

final def eq(arg0: AnyRef): Boolean

def equals(arg0: Any): Boolean

def fgBioJar: Path

def finalize(): Unit

def formatted(fmtstr: String): String

final def getClass(): Class[_]

final def getTasks: Traversable[_ <: ExtractUmisFromBam.this.type]

def hashCode(): Int

def headTasks: Traversable[Task]

val in: com.fulcrumgenomics.commons.CommonsDef.PathToBam

final def isInstanceOf[T0]: Boolean

def jarArgs(jarPath: Path, jvmArgs: Traversable[String] = Nil, jvmProperties: Map[String, String] = Map.empty, jvmMemory: Memory, useAdvancedGcOptions: Boolean = true): List[String]

lazy val logger: Logger

var name: String

final def ne(arg0: AnyRef): Boolean

final def notify(): Unit

final def notifyAll(): Unit

def onComplete(exitCode: Int): Boolean

def optionallyConfigure[T](path: String)(implicit arg0: scala.reflect.api.JavaUniverse.TypeTag[T]): Option[T]

val out: com.fulcrumgenomics.commons.CommonsDef.PathToBam

def pickResources(availableResources: ResourceSet): Option[ResourceSet]

var quoteIfNecessary: Boolean

val readStructures: Seq[String]

def removeDependency(task: Task): Boolean

def requires(cores: Double, memory: String): ExtractUmisFromBam.this.type

def requires(cores: Cores, memory: Memory): ExtractUmisFromBam.this.type

def requires(resources: ResourceSet): ExtractUmisFromBam.this.type

def resources: ResourceSet

final def synchronized[T0](arg0: ⇒ T0): T0

def systemPath: Seq[Path]

def tailTasks: Traversable[Task]

def tasksDependedOn: Traversable[Task]

def tasksDependingOnThisTask: Traversable[Task]

def toString(): String

val umiTags: Seq[String]

final def wait(): Unit

final def wait(arg0: Long, arg1: Int): Unit