ADAMRecordRDDFunctions

Instance Constructors

new ADAMRecordRDDFunctions(rdd: RDD[ADAMRecord])

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

Definition Classes
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def adamBQSR(knownSnps: Broadcast[SnpTable]): RDD[ADAMRecord]
def adamCharacterizeTagValues(tag: String): Map[Any, Long]

Calculates the set of unique attribute values that occur for the given tag, and the number of time each value occurs.
Calculates the set of unique attribute values that occur for the given tag, and the number of time each value occurs.
tag
The name of the optional field whose values are to be counted.
returns
A Map whose keys are the values of the tag, and whose values are the number of time each tag-value occurs.
def adamCharacterizeTags(): RDD[(String, Long)]

Converts a set of records into an RDD containing the pairs of all unique tagStrings within the records, along with the count (number of records) which have that particular attribute.
Converts a set of records into an RDD containing the pairs of all unique tagStrings within the records, along with the count (number of records) which have that particular attribute.
returns
An RDD of attribute name / count pairs.
def adamFilterRecordsWithTag(tagName: String): RDD[ADAMRecord]

Returns the subset of the ADAMRecords which have an attribute with the given name.
Returns the subset of the ADAMRecords which have an attribute with the given name.
tagName
The name of the attribute to filter on (should be length 2)
returns
An RDD[ADAMRecord] containing the subset of records with a tag that matches the given name.
def adamFlagStat(): (FlagStatMetrics, FlagStatMetrics)
def adamGetSequenceDictionary(): SequenceDictionary

Aggregates together a sequence dictionary from the different individual reference sequences used in this dataset.
Aggregates together a sequence dictionary from the different individual reference sequences used in this dataset.
returns
A sequence dictionary describing the reference contigs in this dataset.

Definition Classes
ADAMSequenceDictionaryRDDAggregator
def adamMarkDuplicates(): RDD[ADAMRecord]
def adamRealignIndels(): RDD[ADAMRecord]
def adamRecords2Pileup(secondaryAlignments: Boolean = false): RDD[ADAMPileup]

Groups all reads by reference position and returns a non-aggregated pileup RDD.
Groups all reads by reference position and returns a non-aggregated pileup RDD.
secondaryAlignments
Creates pileups for non-primary aligned reads. Default is false.
returns
ADAMPileup without aggregation
def adamRecords2Rods(bucketSize: Int = 1000, secondaryAlignments: Boolean = false): RDD[ADAMRod]

Groups all reads by reference position, with all reference position bases grouped into a rod.
Groups all reads by reference position, with all reference position bases grouped into a rod.
bucketSize
Size in basepairs of buckets. Larger buckets take more time per bucket to convert, but have lower skew. Default is 1000.
secondaryAlignments
Creates rods for non-primary aligned reads. Default is false.
returns
RDD of ADAMRods.
def adamSingleReadBuckets(): RDD[SingleReadBucket]

Groups all reads by record group and read name
Groups all reads by record group and read name
returns
SingleReadBuckets with primary, secondary and unmapped reads
def adamSortReadsByReferencePosition(): RDD[ADAMRecord]
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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protected[java.lang]
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@throws( classOf[java.lang.Throwable] )
final def getClass(): Class[_]

Definition Classes
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def getSequenceRecordsFromElement(elem: ADAMRecord): Set[SequenceRecord]

For a single RDD element, returns 0+ sequence record elements.
For a single RDD element, returns 0+ sequence record elements.
elem
Element from which to extract sequence records.
returns
A seq of sequence records.

Definition Classes
ADAMRecordRDDFunctions → ADAMSequenceDictionaryRDDAggregator
def hashCode(): Int

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final def isInstanceOf[T0]: Boolean

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def isTraceEnabled(): Boolean

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protected
Definition Classes
Logging
def log: Logger

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protected
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Logging
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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protected
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Logging
def logError(msg: ⇒ String): Unit

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

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protected
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Logging
def logInfo(msg: ⇒ String): Unit

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

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protected
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def logTrace(msg: ⇒ String): Unit

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

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protected
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Logging
def logWarning(msg: ⇒ String): Unit

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

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

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class ADAMRecordRDDFunctions extends ADAMSequenceDictionaryRDDAggregator[ADAMRecord]

Instance Constructors

new ADAMRecordRDDFunctions(rdd: RDD[ADAMRecord])

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 adamBQSR(knownSnps: Broadcast[SnpTable]): RDD[ADAMRecord]

def adamCharacterizeTagValues(tag: String): Map[Any, Long]

def adamCharacterizeTags(): RDD[(String, Long)]

def adamFilterRecordsWithTag(tagName: String): RDD[ADAMRecord]

def adamFlagStat(): (FlagStatMetrics, FlagStatMetrics)

def adamGetSequenceDictionary(): SequenceDictionary

def adamMarkDuplicates(): RDD[ADAMRecord]

def adamRealignIndels(): RDD[ADAMRecord]

def adamRecords2Pileup(secondaryAlignments: Boolean = false): RDD[ADAMPileup]

def adamRecords2Rods(bucketSize: Int = 1000, secondaryAlignments: Boolean = false): RDD[ADAMRod]

def adamSingleReadBuckets(): RDD[SingleReadBucket]

def adamSortReadsByReferencePosition(): RDD[ADAMRecord]

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 getSequenceRecordsFromElement(elem: ADAMRecord): Set[SequenceRecord]

def hashCode(): Int

final def isInstanceOf[T0]: Boolean

def isTraceEnabled(): Boolean

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 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

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 ADAMSequenceDictionaryRDDAggregator[ADAMRecord]

Inherited from Logging

Inherited from Serializable

Inherited from Serializable

Inherited from AnyRef

Inherited from Any

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