VCFOutFormatter

Instance Constructors

new VCFOutFormatter(conf: Configuration, optHeaderLines: Option[CollectionAccumulator[VCFHeaderLine]])

OutFormatter that reads streaming VCF.
OutFormatter that reads streaming VCF. Defaults to ValidationStringency.LENIENT. Java-friendly constructor.
conf
Hadoop configuration.
optHeaderLines
Optional accumulator for VCF header lines.
new VCFOutFormatter(conf: Configuration, acc: CollectionAccumulator[VCFHeaderLine])

OutFormatter that reads streaming VCF.
OutFormatter that reads streaming VCF. Defaults to ValidationStringency.LENIENT. Java-friendly constructor.
conf
Hadoop configuration.
acc
Accumulator for VCF header lines.
new VCFOutFormatter(conf: Configuration, stringency: ValidationStringency)

OutFormatter that reads streaming VCF.
OutFormatter that reads streaming VCF. Java-friendly constructor.
conf
Hadoop configuration.
new VCFOutFormatter(conf: Configuration)

OutFormatter that reads streaming VCF.
OutFormatter that reads streaming VCF. Defaults to ValidationStringency.LENIENT. Java-friendly no-arg constructor.
conf
Hadoop configuration.
new VCFOutFormatter(conf: Configuration, stringency: ValidationStringency, optHeaderLines: Option[CollectionAccumulator[VCFHeaderLine]])

conf
Hadoop configuration.
stringency
Validation stringency.
optHeaderLines
Optional accumulator for VCF header lines.

Value Members

final def !=(arg0: Any): Boolean

Definition Classes
AnyRef → Any
final def ##(): Int

Definition Classes
AnyRef → Any
final def ==(arg0: Any): Boolean

Definition Classes
AnyRef → Any
final def asInstanceOf[T0]: T0

Definition Classes
Any
def clone(): AnyRef

Attributes
protected[java.lang]
Definition Classes
AnyRef
Annotations
@throws( ... )
val conf: Configuration

Hadoop configuration.
def debug(mkr: Marker, msg: ⇒ Any, t: ⇒ Throwable): Unit

Attributes
protected
Definition Classes
Logging
def debug(msg: ⇒ Any, t: ⇒ Throwable): Unit

Attributes
protected
Definition Classes
Logging
def debug(msg: ⇒ Any): Unit

Attributes
protected
Definition Classes
Logging
final def eq(arg0: AnyRef): Boolean

Definition Classes
AnyRef
def error(mkr: Marker, msg: ⇒ Any, t: ⇒ Throwable): Unit

Attributes
protected
Definition Classes
Logging
def error(msg: ⇒ Any, t: ⇒ Throwable): Unit

Attributes
protected
Definition Classes
Logging
def error(msg: ⇒ Any): Unit

Attributes
protected
Definition Classes
Logging
def finalize(): Unit

Attributes
protected[java.lang]
Definition Classes
AnyRef
Annotations
@throws( classOf[java.lang.Throwable] )
final def getClass(): Class[_]

Definition Classes
AnyRef → Any
def info(mkr: Marker, msg: ⇒ Any, t: ⇒ Throwable): Unit

Attributes
protected
Definition Classes
Logging
def info(msg: ⇒ Any, t: ⇒ Throwable): Unit

Attributes
protected
Definition Classes
Logging
def info(msg: ⇒ Any): Unit

Attributes
protected
Definition Classes
Logging
def isDebugEnabled: Boolean

Attributes
protected
Definition Classes
Logging
def isErrorEnabled: Boolean

Attributes
protected
Definition Classes
Logging
def isInfoEnabled: Boolean

Attributes
protected
Definition Classes
Logging
final def isInstanceOf[T0]: Boolean

Definition Classes
Any
def isTraceEnabled: Boolean

Attributes
protected
Definition Classes
Logging
def isWarnEnabled: Boolean

Attributes
protected
Definition Classes
Logging
def logger: Logger

Attributes
protected
Definition Classes
Logging
def loggerName: String

Attributes
protected
Definition Classes
Logging
final def ne(arg0: AnyRef): Boolean

Definition Classes
AnyRef
final def notify(): Unit

Definition Classes
AnyRef
final def notifyAll(): Unit

Definition Classes
AnyRef
val optHeaderLines: Option[CollectionAccumulator[VCFHeaderLine]]

Optional accumulator for VCF header lines.
def read(is: InputStream): Iterator[VariantContext]

Reads VariantContexts from an input stream.
Reads VariantContexts from an input stream. Autodetects VCF format.
is
An InputStream connected to a process we are piping from.
returns
Returns an iterator of AlignmentRecords read from the stream.

Definition Classes
VCFOutFormatter → OutFormatter
val stringency: ValidationStringency

Validation stringency.
final def synchronized[T0](arg0: ⇒ T0): T0

Definition Classes
AnyRef
def trace(mkr: Marker, msg: ⇒ Any, t: ⇒ Throwable): Unit

Attributes
protected
Definition Classes
Logging
def trace(msg: ⇒ Any, t: ⇒ Throwable): Unit

Attributes
protected
Definition Classes
Logging
def trace(msg: ⇒ Any): Unit

Attributes
protected
Definition Classes
Logging
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 warn(mkr: Marker, msg: ⇒ Any, t: ⇒ Throwable): Unit

Attributes
protected
Definition Classes
Logging
def warn(msg: ⇒ Any, t: ⇒ Throwable): Unit

Attributes
protected
Definition Classes
Logging
def warn(msg: ⇒ Any): Unit

Attributes
protected
Definition Classes
Logging

Related Doc: package variant

case class VCFOutFormatter(conf: Configuration, stringency: ValidationStringency, optHeaderLines: Option[CollectionAccumulator[VCFHeaderLine]]) extends OutFormatter[VariantContext] with Logging with Product with Serializable

Instance Constructors

new VCFOutFormatter(conf: Configuration, optHeaderLines: Option[CollectionAccumulator[VCFHeaderLine]])

new VCFOutFormatter(conf: Configuration, acc: CollectionAccumulator[VCFHeaderLine])

new VCFOutFormatter(conf: Configuration, stringency: ValidationStringency)

new VCFOutFormatter(conf: Configuration)

new VCFOutFormatter(conf: Configuration, stringency: ValidationStringency, optHeaderLines: Option[CollectionAccumulator[VCFHeaderLine]])

Value Members

final def !=(arg0: Any): Boolean

final def ##(): Int

final def ==(arg0: Any): Boolean

final def asInstanceOf[T0]: T0

def clone(): AnyRef

val conf: Configuration

def debug(mkr: Marker, msg: ⇒ Any, t: ⇒ Throwable): Unit

def debug(msg: ⇒ Any, t: ⇒ Throwable): Unit

def debug(msg: ⇒ Any): Unit

final def eq(arg0: AnyRef): Boolean

def error(mkr: Marker, msg: ⇒ Any, t: ⇒ Throwable): Unit

def error(msg: ⇒ Any, t: ⇒ Throwable): Unit

def error(msg: ⇒ Any): Unit

def finalize(): Unit

final def getClass(): Class[_]

def info(mkr: Marker, msg: ⇒ Any, t: ⇒ Throwable): Unit

def info(msg: ⇒ Any, t: ⇒ Throwable): Unit

def info(msg: ⇒ Any): Unit

def isDebugEnabled: Boolean

def isErrorEnabled: Boolean

def isInfoEnabled: Boolean

final def isInstanceOf[T0]: Boolean

def isTraceEnabled: Boolean

def isWarnEnabled: Boolean

def logger: Logger

def loggerName: String

final def ne(arg0: AnyRef): Boolean

final def notify(): Unit

final def notifyAll(): Unit

val optHeaderLines: Option[CollectionAccumulator[VCFHeaderLine]]

def read(is: InputStream): Iterator[VariantContext]

val stringency: ValidationStringency

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

def trace(mkr: Marker, msg: ⇒ Any, t: ⇒ Throwable): Unit

def trace(msg: ⇒ Any, t: ⇒ Throwable): Unit

def trace(msg: ⇒ Any): Unit

final def wait(): Unit

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

final def wait(arg0: Long): Unit

def warn(mkr: Marker, msg: ⇒ Any, t: ⇒ Throwable): Unit

def warn(msg: ⇒ Any, t: ⇒ Throwable): Unit

def warn(msg: ⇒ Any): Unit

Inherited from Product

Inherited from Equals

Inherited from Logging

Inherited from OutFormatter[VariantContext]

Inherited from Serializable

Inherited from Serializable

Inherited from AnyRef

Inherited from Any

Ungrouped