object AlignmentRecordDataset extends Serializable
- Alphabetic
- By Inheritance
- AlignmentRecordDataset
- Serializable
- Serializable
- AnyRef
- Any
- Hide All
- Show All
- Public
- All
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
-
val
WRITE_ORIGINAL_QUALITIES: String
Hadoop configuration path to check for a boolean value indicating whether the current or original read qualities should be written.
Hadoop configuration path to check for a boolean value indicating whether the current or original read qualities should be written. True indicates to write the original qualities. The default is false.
-
val
WRITE_SUFFIXES: String
Hadoop configuration path to check for a boolean value indicating whether to write the "/1" "/2" suffixes to the read name that indicate whether a read is first or second in a pair.
Hadoop configuration path to check for a boolean value indicating whether to write the "/1" "/2" suffixes to the read name that indicate whether a read is first or second in a pair. Default is false (no suffixes).
-
def
apply(ds: Dataset[AlignmentRecord], sequences: SequenceDictionary, readGroups: ReadGroupDictionary, processingSteps: Seq[ProcessingStep]): AlignmentRecordDataset
Builds an AlignmentRecordDataset without a partition map from a Dataset.
Builds an AlignmentRecordDataset without a partition map from a Dataset.
- ds
The underlying AlignmentRecord Dataset.
- sequences
The sequence dictionary for the genomic dataset.
- readGroups
The read group dictionary for the genomic dataset.
- returns
A new AlignmentRecordDataset.
-
def
apply(rdd: RDD[AlignmentRecord], sequences: SequenceDictionary, readGroups: ReadGroupDictionary, processingSteps: Seq[ProcessingStep]): AlignmentRecordDataset
Builds an AlignmentRecordDataset without a partition map from an RDD.
Builds an AlignmentRecordDataset without a partition map from an RDD.
- rdd
The underlying AlignmentRecord RDD.
- sequences
The sequence dictionary for the genomic dataset.
- readGroups
The read group dictionary for the genomic dataset.
- returns
A new AlignmentRecordDataset.
-
final
def
asInstanceOf[T0]: T0
- Definition Classes
- Any
-
def
clone(): AnyRef
- Attributes
- protected[java.lang]
- Definition Classes
- AnyRef
- Annotations
- @native() @throws( ... )
-
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
- Annotations
- @native()
-
def
hashCode(): Int
- Definition Classes
- AnyRef → Any
- Annotations
- @native()
-
final
def
isInstanceOf[T0]: Boolean
- Definition Classes
- Any
-
final
def
ne(arg0: AnyRef): Boolean
- Definition Classes
- AnyRef
-
final
def
notify(): Unit
- Definition Classes
- AnyRef
- Annotations
- @native()
-
final
def
notifyAll(): Unit
- Definition Classes
- AnyRef
- Annotations
- @native()
-
final
def
synchronized[T0](arg0: ⇒ T0): T0
- Definition Classes
- AnyRef
-
def
toString(): String
- Definition Classes
- AnyRef → Any
-
def
unaligned(rdd: RDD[AlignmentRecord]): AlignmentRecordDataset
Builds an AlignmentRecordDataset for unaligned reads.
Builds an AlignmentRecordDataset for unaligned reads.
- rdd
The underlying AlignmentRecord RDD.
- returns
A new AlignmentRecordDataset.
-
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
- @native() @throws( ... )