ReferenceBroadcast

Type Members

case class ArrayBackedReferenceSequence(contigName: ContigName, wrapped: Broadcast[Array[Byte]]) extends ContigSequence with Product with Serializable

The standard ContigSequence implementation, which is an Array of bases.
case class MapBackedReferenceSequence(contigName: ContigName, length: NumLoci, wrapped: Broadcast[Map[Int, Byte]]) extends ContigSequence with Product with Serializable

A ContigSequence implementation that uses a Map to store only a subset of bases.

Value Members

final def !=(arg0: AnyRef): Boolean

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final def !=(arg0: Any): Boolean

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final def ##(): Int

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final def ==(arg0: AnyRef): Boolean

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final def ==(arg0: Any): Boolean

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def apply(broadcastedContigs: Map[String, ContigSequence]): ReferenceBroadcast
def apply(fastaPath: String, sc: SparkContext, partialFasta: Boolean = false): ReferenceBroadcast

Load a ReferenceBroadcast, caching the result.
Load a ReferenceBroadcast, caching the result.
fastaPath
Local path to a FASTA file
sc
the spark context
partialFasta
is this a "partial fasta"? Partial fastas are used in tests to load only a subset of the reference. In production runs this will usually be false.
returns
ReferenceBroadcast which maps contig/chromosome names to broadcasted sequences
final def asInstanceOf[T0]: T0

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def clone(): AnyRef

Attributes
protected[java.lang]
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@throws( ... )
def debug(msg: ⇒ Any, t: ⇒ Throwable): Unit

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def debug(msg: ⇒ Any): Unit

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final def eq(arg0: AnyRef): Boolean

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def equals(arg0: Any): Boolean

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

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protected
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Logging
def error(msg: ⇒ Any): Unit

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protected
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def finalize(): Unit

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protected[java.lang]
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@throws( classOf[java.lang.Throwable] )
final def getClass(): Class[_]

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def hashCode(): Int

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

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protected
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Logging
def info(msg: ⇒ Any): Unit

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Logging
def isDebugEnabled: Boolean

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Logging
def isErrorEnabled: Boolean

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Logging
def isInfoEnabled: Boolean

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final def isInstanceOf[T0]: Boolean

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def isTraceEnabled: Boolean

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def isWarnEnabled: Boolean

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def logger: Logger

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def loggerName: String

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final def ne(arg0: AnyRef): Boolean

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final def notify(): Unit

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final def notifyAll(): Unit

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def readFasta(fastaPath: String, sc: SparkContext): ReferenceBroadcast

Read a regular fasta file
Read a regular fasta file
fastaPath
local path to fasta
sc
the spark context
returns
a ReferenceBroadcast instance containing ArrayBackedReferenceSequence objects.
def readPartialFasta(fastaPath: String, sc: SparkContext): ReferenceBroadcast

Read a "partial fasta" from the given path.
Read a "partial fasta" from the given path.
A "partial fasta" is a fasta file where the reference names look like "chr1:9242255-9242454/249250621". That gives the contig name, the start and end locus, and the total contig size. The associated sequence in the file gives the reference sequence for just the sites between start and end.
Partial fastas are used for testing to avoid distributing full reference genomes.
fastaPath
local path to partial fasta
sc
the spark context
returns
a ReferenceBroadcast instance containing MapBackedReferenceSequence objects
final def synchronized[T0](arg0: ⇒ T0): T0

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def toString(): String

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

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protected
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Logging
def trace(msg: ⇒ Any): Unit

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protected
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Logging
final def wait(): Unit

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

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@throws( ... )
final def wait(arg0: Long): Unit

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

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protected
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Logging
def warn(msg: ⇒ Any): Unit

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Logging

object ReferenceBroadcast extends Logging with Serializable

Type Members

case class ArrayBackedReferenceSequence(contigName: ContigName, wrapped: Broadcast[Array[Byte]]) extends ContigSequence with Product with Serializable

case class MapBackedReferenceSequence(contigName: ContigName, length: NumLoci, wrapped: Broadcast[Map[Int, Byte]]) extends ContigSequence with Product with Serializable

Value Members

final def !=(arg0: AnyRef): Boolean

final def !=(arg0: Any): Boolean

final def ##(): Int

final def ==(arg0: AnyRef): Boolean

final def ==(arg0: Any): Boolean

def apply(broadcastedContigs: Map[String, ContigSequence]): ReferenceBroadcast

def apply(fastaPath: String, sc: SparkContext, partialFasta: Boolean = false): ReferenceBroadcast

final def asInstanceOf[T0]: T0

def clone(): AnyRef

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

def debug(msg: ⇒ Any): Unit

final def eq(arg0: AnyRef): Boolean

def equals(arg0: Any): Boolean

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

def error(msg: ⇒ Any): Unit

def finalize(): Unit

final def getClass(): Class[_]

def hashCode(): Int

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

def readFasta(fastaPath: String, sc: SparkContext): ReferenceBroadcast

def readPartialFasta(fastaPath: String, sc: SparkContext): ReferenceBroadcast

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

def toString(): String

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(msg: ⇒ Any, t: ⇒ Throwable): Unit

def warn(msg: ⇒ Any): Unit

Inherited from Serializable

Inherited from Serializable

Inherited from Logging

Inherited from AnyRef

Inherited from Any

Ungrouped