AlignmentRecordContext

Instance Constructors

new AlignmentRecordContext(sc: SparkContext)

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 adamFastqLoad(firstPairPath: String, secondPairPath: String, fixPairs: Boolean = false, validationStringency: ValidationStringency = ValidationStringency.LENIENT): RDD[AlignmentRecord]

Load AlignmentRecords from two paired-end FASTQ files.
Load AlignmentRecords from two paired-end FASTQ files.
firstPairPath
Path to read first-mates from
secondPairPath
Path to read second-mates from
fixPairs
Iff true, joins the first- and second-reads around their read name (minus the /1 or /2 suffix)
final def asInstanceOf[T0]: T0

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def clone(): AnyRef

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@throws( ... )
final def eq(arg0: AnyRef): Boolean

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def equals(arg0: Any): Boolean

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def finalize(): Unit

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final def getClass(): Class[_]

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def hashCode(): Int

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final def isInstanceOf[T0]: Boolean

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def isTraceEnabled(): Boolean

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protected
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Logging
def loadADAMFromPaths(paths: Seq[Path]): RDD[AlignmentRecord]

Takes a sequence of Path objects (e.
Takes a sequence of Path objects (e.g. the return value of findFiles). Treats each path as corresponding to a Read set -- loads each Read set, converts each set to use the same SequenceDictionary, and returns the union of the RDDs.
(GenomeBridge is using this to load BAMs that have been split into multiple files per sample, for example, one-BAM-per-chromosome.)
paths
The locations of the parquet files to load
returns
a single RDD[Read] that contains the union of the AlignmentRecords in the argument paths.
def log: Logger

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def logDebug(msg: ⇒ String, throwable: Throwable): Unit

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def logDebug(msg: ⇒ String): Unit

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def logError(msg: ⇒ String, throwable: Throwable): Unit

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def logError(msg: ⇒ String): Unit

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def logInfo(msg: ⇒ String, throwable: Throwable): Unit

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def logInfo(msg: ⇒ String): Unit

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def logName: String

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def logTrace(msg: ⇒ String, throwable: Throwable): Unit

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def logTrace(msg: ⇒ String): Unit

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def logWarning(msg: ⇒ String, throwable: Throwable): Unit

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def logWarning(msg: ⇒ String): Unit

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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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val sc: SparkContext
final def synchronized[T0](arg0: ⇒ T0): T0

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def toString(): String

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final def wait(): Unit

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

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final def wait(arg0: Long): Unit

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class AlignmentRecordContext extends Serializable with Logging

Instance Constructors

new AlignmentRecordContext(sc: SparkContext)

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 adamFastqLoad(firstPairPath: String, secondPairPath: String, fixPairs: Boolean = false, validationStringency: ValidationStringency = ValidationStringency.LENIENT): RDD[AlignmentRecord]

final def asInstanceOf[T0]: T0

def clone(): AnyRef

final def eq(arg0: AnyRef): Boolean

def equals(arg0: Any): Boolean

def finalize(): Unit

final def getClass(): Class[_]

def hashCode(): Int

final def isInstanceOf[T0]: Boolean

def isTraceEnabled(): Boolean

def loadADAMFromPaths(paths: Seq[Path]): RDD[AlignmentRecord]

def log: Logger

def logDebug(msg: ⇒ String, throwable: Throwable): Unit

def logDebug(msg: ⇒ String): Unit

def logError(msg: ⇒ String, throwable: Throwable): Unit

def logError(msg: ⇒ String): Unit

def logInfo(msg: ⇒ String, throwable: Throwable): Unit

def logInfo(msg: ⇒ String): Unit

def logName: String

def logTrace(msg: ⇒ String, throwable: Throwable): Unit

def logTrace(msg: ⇒ String): Unit

def logWarning(msg: ⇒ String, throwable: Throwable): Unit

def logWarning(msg: ⇒ String): Unit

final def ne(arg0: AnyRef): Boolean

final def notify(): Unit

final def notifyAll(): Unit

val sc: SparkContext

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

Inherited from Logging

Inherited from Serializable

Inherited from Serializable

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