BgenRecordWriter

Instance Constructors

new BgenRecordWriter(outputStream: OutputStream, schema: StructType, writeHeader: Boolean, numVariants: Long, bitsPerProb: Int, maxPloidy: Int, defaultPloidy: Int, defaultPhasing: Boolean)

outputStream
The output stream to write to
schema
Schema of the input rows
writeHeader
If true, write the header
numVariants
Number of variants (for the header)
bitsPerProb
Number of bits used to represent each genotype/haplotype probability value
maxPloidy
If ploidy is missing, it is inferred as some value in [1, maxPloidy]
defaultPloidy
If phasing and ploidy are missing or the inferred ploidy is ambiguous, we assume ploidy is defaultPloidy
defaultPhasing
If phasing is missing and the inferred phasing is ambiguous, we assume phasing is defaultPhasing

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
val buffSize: Int
def clone(): AnyRef

Attributes
protected[java.lang]
Definition Classes
AnyRef
Annotations
@throws( ... )
def close(): Unit
val converter: InternalRowToBgenRowConverter
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 getCompressedGenotypeProbabilityData(row: BgenRow): (Int, Array[Byte])

# Bytes | Description
# Bytes | Description
+
4 | Number of samples ----------------------------------------------------------------------------------------------- 2 | Number of alleles ----------------------------------------------------------------------------------------------- 1 | Minimum ploidy of samples ----------------------------------------------------------------------------------------------- 1 | Maximum ploidy of samples ----------------------------------------------------------------------------------------------- N | The nth byte represents the ploidy and missingness of the nth sample. Ploidy is | encoded in the least significant 6 bits of this value. Missingness is encoded by the | most significant bit (1 if missing). ----------------------------------------------------------------------------------------------- 1 | 1 if phased, 0 if unphased ----------------------------------------------------------------------------------------------- 1 | Number of bits used to store each probability = B ----------------------------------------------------------------------------------------------- X | Probabilities for each possible haplotype (if phased)/genotype (if unphased) -----------------------------------------------------------------------------------------------
def hashCode(): Int

Definition Classes
AnyRef → Any
var headerHasBeenWritten: Boolean
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
val probBlockSizeMap: HashMap[GenotypeCharacteristics, ProbabilityBlockSize]
val probabilityWriter: (Long, LittleEndianDataOutputStream) ⇒ Unit
val stream: LittleEndianDataOutputStream
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(row: InternalRow): Unit

A Bgen file consists of a header followed by M variant data blocks.
A Bgen file consists of a header followed by M variant data blocks. Variant data blocks consist of: - Variant identifying data - Genotype data block
def writeGenotypeDataBlock(row: BgenRow): Unit

# Bytes | Description
# Bytes | Description
+
4 | Total length of the the rest of the data for this variant = C -------------------------------------------------------------------------------------- 4 | Total length of the probability data after decompression = D -------------------------------------------------------------------------------------- C-4 | Genotype probability data for each of the N samples: decompressed to D bytes --------------------------------------------------------------------------------------

Related Docs: object BgenRecordWriter | package bgen

class BgenRecordWriter extends GlowLogging

Instance Constructors

new BgenRecordWriter(outputStream: OutputStream, schema: StructType, writeHeader: Boolean, numVariants: Long, bitsPerProb: Int, maxPloidy: Int, defaultPloidy: Int, defaultPhasing: Boolean)

Value Members

final def !=(arg0: Any): Boolean

final def ##(): Int

final def ==(arg0: Any): Boolean

final def asInstanceOf[T0]: T0

val buffSize: Int

def clone(): AnyRef

def close(): Unit

val converter: InternalRowToBgenRowConverter

final def eq(arg0: AnyRef): Boolean

def equals(arg0: Any): Boolean

def finalize(): Unit

final def getClass(): Class[_]

def getCompressedGenotypeProbabilityData(row: BgenRow): (Int, Array[Byte])

+

def hashCode(): Int

var headerHasBeenWritten: Boolean

final def isInstanceOf[T0]: Boolean

lazy val logger: Logger

final def ne(arg0: AnyRef): Boolean

final def notify(): Unit

final def notifyAll(): Unit

val probBlockSizeMap: HashMap[GenotypeCharacteristics, ProbabilityBlockSize]

val probabilityWriter: (Long, LittleEndianDataOutputStream) ⇒ Unit

val stream: LittleEndianDataOutputStream

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(row: InternalRow): Unit

def writeGenotypeDataBlock(row: BgenRow): Unit

+

Inherited from GlowLogging

Inherited from LazyLogging

Inherited from LazyLogging

Inherited from Logging

Inherited from AnyRef

Inherited from Any

Ungrouped