final case class MinSplitter[+P <: MinimizerPriorities](priorities: P, k: Int) extends Product with Serializable
Split reads into superkmers by ranked motifs (minimizers). Such superkmers can be bucketed by the corresponding minimizer.
- priorities
Minimizer ordering to use for splitting
- k
k-mer length
- Alphabetic
- By Inheritance
- MinSplitter
- Serializable
- Serializable
- Product
- Equals
- AnyRef
- Any
- Hide All
- Show All
- Public
- All
Instance Constructors
-
new
MinSplitter(priorities: P, k: Int)
- priorities
Minimizer ordering to use for splitting
- k
k-mer length
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
-
def
clone(): AnyRef
- Attributes
- protected[lang]
- Definition Classes
- AnyRef
- Annotations
- @throws( ... ) @native()
-
final
def
eq(arg0: AnyRef): Boolean
- Definition Classes
- AnyRef
-
def
finalize(): Unit
- Attributes
- protected[lang]
- Definition Classes
- AnyRef
- Annotations
- @throws( classOf[java.lang.Throwable] )
-
final
def
getClass(): Class[_]
- Definition Classes
- AnyRef → Any
- Annotations
- @native()
-
def
humanReadable(id: BucketId): NTSeq
Compute a human-readable form of the bucket ID.
-
final
def
isInstanceOf[T0]: Boolean
- Definition Classes
- Any
- val k: Int
-
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()
- val priorities: P
-
lazy val
scanner: ShiftScanner
A ShiftScanner associated with this splitter's MinTable
A ShiftScanner associated with this splitter's MinTable
- Annotations
- @transient()
-
def
splitEncode(read: NTSeq, addRC: Boolean = false): Iterator[(Int, Long, ZeroNTBitArray, SeqLocation)]
Split a read into superkmers.
Split a read into superkmers.
- read
the read to split
- addRC
whether to add the reverse complement read on the fly
- returns
an iterator of (position in read, rank (hash/minimizer ID), encoded superkmer, location in sequence if available)
-
def
splitEncodeLocation(read: InputFragment, sequenceIDs: Map[SeqTitle, SeqID]): Iterator[SplitSegment]
Split a read into super-mers, efficiently encoding them in binary form in the process, also preserving sequence ID and location.
Split a read into super-mers, efficiently encoding them in binary form in the process, also preserving sequence ID and location.
- read
The read to split
- sequenceIDs
IDs for each sequence title, to be preserved in the result
- returns
an iterator of superkmers with sequence ID and location populated
-
def
splitRead(encoded: ZeroNTBitArray, matches: Array[Long]): Iterator[(Int, Long, ZeroNTBitArray, SeqLocation)]
Split a read into superkmers, and return them together with the corresponding minimizer.
Split a read into superkmers, and return them together with the corresponding minimizer.
- encoded
the read to split
- matches
discovered motif ranks in the superkmer
- returns
an iterator of (position in read, rank (hash/minimizer ID), encoded superkmer, location in sequence if available)
-
def
splitRead(encoded: ZeroNTBitArray, reverseComplement: Boolean = false): Iterator[(Int, Long, ZeroNTBitArray, SeqLocation)]
Split an encoded read into superkmers.
Split an encoded read into superkmers.
- encoded
the read to split
- returns
an iterator of (position of minimizer in sequence, rank (hash/minimizer ID), encoded superkmer, position of superkmer start in sequence)
-
final
def
synchronized[T0](arg0: ⇒ T0): T0
- Definition Classes
- AnyRef
-
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( ... ) @native()