VCFStreamWriter

This internal row -> variant context stream writer maintains a header that is set exactly once. The sample IDs are set by sampleIdInfo if predetermined, or inferred from the first written row otherwise.

If missing sample IDs were used to set the header, sample IDs in all rows to be written will be replaced with those from the header. If all sample IDs are present when setting the header, sample IDs in written rows will not be replaced. Mixed missing/present sample IDs are not permitted.

Linear Supertypes

Serializable, Serializable, GlowLogging, LazyLogging, LazyLogging, Logging, Closeable, AutoCloseable, AnyRef, Any

Instance Constructors

new VCFStreamWriter(stream: OutputStream, headerLineSet: Set[VCFHeaderLine], sampleIdInfo: SampleIdInfo, writeHeader: Boolean)

stream
The stream to write to
headerLineSet
Header lines used to set the VCF header
sampleIdInfo
Sample IDs, which may be predetermined or must be inferred
writeHeader
Whether to write the header in this stream

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 checkInferredSampleIds(vcBuilder: VariantContextBuilder): VariantContextBuilder
def clone(): AnyRef

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

Definition Classes
VCFStreamWriter → Closeable → AutoCloseable
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] )
final def getClass(): Class[_]

Definition Classes
AnyRef → Any
def hashCode(): Int

Definition Classes
AnyRef → Any
var header: VCFHeader
var headerSampleSet: HashSet[String]
final def isInstanceOf[T0]: Boolean

Definition Classes
Any
lazy val logger: Logger

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

Definition Classes
AnyRef
final def notify(): Unit

Definition Classes
AnyRef
final def notifyAll(): Unit

Definition Classes
AnyRef
def replaceMissingSampleIds(vcBuilder: VariantContextBuilder): VariantContextBuilder
var replaceSampleIds: Boolean
def setHeader(vcBuilder: VariantContextBuilder): Unit
final def synchronized[T0](arg0: ⇒ T0): T0

Definition Classes
AnyRef
def toString(): String

Definition Classes
AnyRef → Any
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 write(vc: VariantContext): Unit

Related Doc: package vcf

class VCFStreamWriter extends Closeable with GlowLogging with Serializable

Instance Constructors

new VCFStreamWriter(stream: OutputStream, headerLineSet: Set[VCFHeaderLine], sampleIdInfo: SampleIdInfo, writeHeader: Boolean)

Value Members

final def !=(arg0: Any): Boolean

final def ##(): Int

final def ==(arg0: Any): Boolean

final def asInstanceOf[T0]: T0

def checkInferredSampleIds(vcBuilder: VariantContextBuilder): VariantContextBuilder

def clone(): AnyRef

def close(): Unit

final def eq(arg0: AnyRef): Boolean

def equals(arg0: Any): Boolean

def finalize(): Unit

final def getClass(): Class[_]

def hashCode(): Int

var header: VCFHeader

var headerSampleSet: HashSet[String]

final def isInstanceOf[T0]: Boolean

lazy val logger: Logger

final def ne(arg0: AnyRef): Boolean

final def notify(): Unit

final def notifyAll(): Unit

def replaceMissingSampleIds(vcBuilder: VariantContextBuilder): VariantContextBuilder

var replaceSampleIds: Boolean

def setHeader(vcBuilder: VariantContextBuilder): Unit

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

def toString(): String

final def wait(): Unit

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

final def wait(arg0: Long): Unit

def write(vc: VariantContext): Unit

Inherited from Serializable

Inherited from Serializable

Inherited from GlowLogging

Inherited from LazyLogging

Inherited from LazyLogging

Inherited from Logging

Inherited from Closeable

Inherited from AutoCloseable

Inherited from AnyRef

Inherited from Any

Ungrouped