MarkIlluminaAdapters

Instance Constructors

new MarkIlluminaAdapters(in: PathToBam, out: PathToBam, prefix: Option[Path], fivePrimeAdapter: Option[String] = None, threePrimeAdapter: 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 MarkIlluminaAdapters to any2stringadd[MarkIlluminaAdapters] performed by method any2stringadd in scala.Predef.
Definition Classes
any2stringadd
def ->[B](y: B): (MarkIlluminaAdapters, B)

Implicit information
This member is added by an implicit conversion from MarkIlluminaAdapters to ArrowAssoc[MarkIlluminaAdapters] 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 addPicardArgs(buffer: ListBuffer[Any]): Unit

Attributes
protected
Definition Classes
MarkIlluminaAdapters → PicardTask
def allTasks: Traversable[Task]

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

Definition Classes
UnitTask → Schedulable
final 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(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
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, subDir: Option[Path]): 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 discardError(): Pipe[SamOrBam, SamOrBam]

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

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

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

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

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

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

Definition Classes
UnitTask → Task
def hashCode(): Int

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

Definition Classes
Task → Dependable
val in: PathToBam

The path to the input BAM
The path to the input BAM

Definition Classes
MarkIlluminaAdapters → PicardMetricsTask
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

The path to the JAR to be executed.
The path to the JAR to be executed.

Definition Classes
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
def metricsExtension: String

All Picard metric generating tools should define their own metrics extension.
All Picard metric generating tools should define their own metrics extension.

Definition Classes
MarkIlluminaAdapters → PicardMetricsTask
def metricsFile(extension: String, kind: PicardOutput.Value): Path

Build a path to a metrics file (text of PDF) using the appropriate prefix derived from either the supplied prefix, or the input file name.
Build a path to a metrics file (text of PDF) using the appropriate prefix derived from either the supplied prefix, or the input file name. Useful when a program produces multiple outputs, as in the case of CollectGcBiasMetrics.

Definition Classes
PicardMetricsTask
def metricsFile: Path

Gets the metrics file path, assuming that the program generates a single metrics file with a known extension.
Gets the metrics file path, assuming that the program generates a single metrics file with a known extension.

Definition Classes
PicardMetricsTask
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
def pathPrefix: PathPrefix

Method that should be used to fetch the file prefix, instead of accessing prefix directly.
Method that should be used to fetch the file prefix, instead of accessing prefix directly.

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

Definition Classes
FixedResources → Schedulable
val prefix: Option[Path]

The optional path to the prefix of the metrics file
The optional path to the prefix of the metrics file

Definition Classes
MarkIlluminaAdapters → PicardMetricsTask
var quoteIfNecessary: Boolean

Attributes
protected
Definition Classes
ProcessTask
def removeDependency(task: Task): Boolean

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

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

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

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

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

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

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

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

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

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

Inherited from Pipe[SamOrBam, SamOrBam]

Inherited from PicardMetricsTask

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 MarkIlluminaAdapters to any2stringadd[MarkIlluminaAdapters]

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

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

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

Ungrouped

Related Docs: object MarkIlluminaAdapters | package picard

class MarkIlluminaAdapters extends PicardTask with PicardMetricsTask with Pipe[SamOrBam, SamOrBam]

Instance Constructors

new MarkIlluminaAdapters(in: PathToBam, out: PathToBam, prefix: Option[Path], fivePrimeAdapter: Option[String] = None, threePrimeAdapter: 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): (MarkIlluminaAdapters, 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 addPicardArgs(buffer: ListBuffer[Any]): Unit

def allTasks: Traversable[Task]

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

var bufferSize: Option[Int]

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

var createIndex: Option[Boolean]

var createMd5File: Option[Boolean]

def discardError(): Pipe[SamOrBam, SamOrBam]

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

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

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

def ensuring(cond: Boolean): MarkIlluminaAdapters

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[_ <: MarkIlluminaAdapters.this.type]

def hashCode(): Int

def headTasks: Traversable[Task]

val in: 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]

def jarPath: Path

var jvmArgs: List[String]

lazy val logger: Logger

def metricsExtension: String

def metricsFile(extension: String, kind: PicardOutput.Value): Path

def metricsFile: Path

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]

def pathPrefix: PathPrefix

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

val prefix: Option[Path]

var quoteIfNecessary: Boolean

def removeDependency(task: Task): Boolean

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

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

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

def resources: ResourceSet

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

def systemPath: Seq[Path]

def tailTasks: Traversable[Task]

def tasksDependedOn: Traversable[Task]