FilterBam

Instance Constructors

new FilterBam(in: PathToBam, out: PathToBam, intervals: Option[PathToIntervals])

Value Members

final def !=(arg0: Any): Boolean

Definition Classes
AnyRef → Any
def !=>(other: MultiTask): other.type

Definition Classes
Task → Dependable
def !=>(other: Task): other.type

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 FilterBam to any2stringadd[FilterBam] performed by method any2stringadd in scala.Predef.
Definition Classes
any2stringadd
def ->[B](y: B): (FilterBam, B)

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

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

Definition Classes
AnyRef → Any
def ==>(other: MultiTask): other.type

Definition Classes
Task → Dependable
def ==>(other: Task): other.type

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

Definition Classes
FilterBam → JeanLucTask
final def addPicardArgs(buffer: ListBuffer[Any]): Unit

Override to "hide" the addPicardArgs being addJeanLucArgs.
Override to "hide" the addPicardArgs being addJeanLucArgs.

Attributes
protected
Definition Classes
JeanLucTask → PicardTask
def applyResources(resources: ResourceSet): Unit

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

Definition Classes
PicardTask → 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
var bufferSize: Option[Int]

the buffer size for the samjdk.
the buffer size for the samjdk.

Definition Classes
PicardTask
def clone(): AnyRef

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

Definition Classes
ConfigurationLike
def commandName: String

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

Definition Classes
PicardTask
var compressionLevel: Option[Int]

the compress level to use.
the compress level to use.

Definition Classes
PicardTask
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): Path

Definition Classes
ConfigurationLike
var createIndex: Option[Boolean]

true if we are to create an index, false otherwise.
true if we are to create an index, false otherwise.

Definition Classes
PicardTask
var createMd5File: Option[Boolean]

true if we are to create an Md5 file, false otherwise.
true if we are to create an Md5 file, false otherwise.

Definition Classes
PicardTask
def ensuring(cond: (FilterBam) ⇒ Boolean, msg: ⇒ Any): FilterBam

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

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

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

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

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

Definition Classes
UnitTask → Task
def hashCode(): Int

Definition Classes
AnyRef → Any
val in: PathToBam
val intervals: Option[PathToIntervals]
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
def jarPath: Path

Override to return the path to the JeanLuc jar.
Override to return the path to the JeanLuc jar.

Definition Classes
JeanLucTask → PicardTask
var jvmArgs: List[String]

a list of arguments to the JVM.
a list of arguments to the JVM.

Definition Classes
PicardTask
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: PathToBam
def pickResources(availableResources: ResourceSet): Option[ResourceSet]

Definition Classes
FixedResources → Schedulable
def removeDependency(task: Task): Boolean

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

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

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

Definition Classes
FixedResources
def resources: ResourceSet

Definition Classes
ScheduleWithEmptyDefaultResources
def retry(taskInfo: TaskExecutionInfo, failedOnComplete: Boolean): Option[Task]

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

Definition Classes
AnyRef
def systemPath: Seq[Path]

Attributes
protected
Definition Classes
ConfigurationLike
def toString(): String

Definition Classes
ProcessTask → AnyRef → Any
var useAdvancedGcOptions: Boolean

use advanced garbage collection parameters.
use advanced garbage collection parameters.

Definition Classes
PicardTask
var useAsyncIo: Boolean

true if we are to use asynchronous IO, false otherwise.
true if we are to use asynchronous IO, false otherwise.

Definition Classes
PicardTask
var validationStringency: Option[ValidationStringency]

set the default validation stringency for Picard.
set the default validation stringency for Picard.

Definition Classes
PicardTask
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 withAsyncIo(async: Boolean = true): FilterBam.this.type

Sets asynchronous IO on or off.
Sets asynchronous IO on or off.

Definition Classes
PicardTask
def withCompression(i: Int): FilterBam.this.type

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

Definition Classes
PicardTask
def withIndexing(indexing: Boolean = true): FilterBam.this.type

Sets asynchronous IO on or off.
Sets asynchronous IO on or off.

Definition Classes
PicardTask
def withName(name: String): FilterBam.this.type

Definition Classes
Task
def →[B](y: B): (FilterBam, B)

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

Inherited from JeanLucTask

Inherited from PicardTask

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 FilterBam to any2stringadd[FilterBam]

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

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

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

Ungrouped

Related Doc: package jeanluc

class FilterBam extends JeanLucTask

Instance Constructors

new FilterBam(in: PathToBam, out: PathToBam, intervals: Option[PathToIntervals])

Value Members

final def !=(arg0: Any): Boolean

def !=>(other: MultiTask): other.type

def !=>(other: Task): other.type

final def ##(): Int

def +(other: String): String

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

def ::(other: Task): MultiTask

final def ==(arg0: Any): Boolean

def ==>(other: MultiTask): other.type

def ==>(other: Task): other.type

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

final def addPicardArgs(buffer: ListBuffer[Any]): Unit

def applyResources(resources: ResourceSet): Unit

def args: Seq[Any]

final def asInstanceOf[T0]: T0

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

var bufferSize: Option[Int]

def clone(): AnyRef

def commandLineName: String

def 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): Path

var createIndex: Option[Boolean]

var createMd5File: Option[Boolean]

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

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

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

def ensuring(cond: Boolean): FilterBam

final def eq(arg0: AnyRef): Boolean

def equals(arg0: Any): Boolean

def finalize(): Unit

def formatted(fmtstr: String): String

final def getClass(): Class[_]

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

def hashCode(): Int

val in: PathToBam

val intervals: Option[PathToIntervals]

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]

def jarPath: Path

var jvmArgs: 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: PathToBam

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

def removeDependency(task: Task): Boolean

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

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

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

def resources: ResourceSet

def retry(taskInfo: TaskExecutionInfo, failedOnComplete: Boolean): Option[Task]

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

def systemPath: Seq[Path]

def toString(): String

var useAdvancedGcOptions: Boolean

var useAsyncIo: Boolean

var validationStringency: Option[ValidationStringency]

final def wait(): Unit

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

final def wait(arg0: Long): Unit

def withAsyncIo(async: Boolean = true): FilterBam.this.type

def withCompression(i: Int): FilterBam.this.type

def withIndexing(indexing: Boolean = true): FilterBam.this.type

def withName(name: String): FilterBam.this.type

def →[B](y: B): (FilterBam, B)