final class KmerTableBuilder extends AnyRef
Builder for k-mer tables. K-mers are built by gradually adding longs in order.
- Alphabetic
- By Inheritance
- KmerTableBuilder
- AnyRef
- Any
- Hide All
- Show All
- Public
- All
Instance Constructors
-
new
KmerTableBuilder(width: Int, tagWidth: Int, sizeEstimate: Int, k: Int)
- width
Width of k-mers (in longs, e.g. ceil(k/32)), including tag data
- tagWidth
With of extra longs used to annotate k-mers with additional information (part of width)
- sizeEstimate
Estimated number of k-mers that will be inserted
- k
k
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
-
def
addLong(x: Long): Unit
Add a single long value.
Add a single long value. Calling this method 'width' times adds a single k-mer to the table.
-
def
addLongs(xs: Array[Long]): Unit
Add multiple long values.
-
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
equals(arg0: Any): Boolean
- Definition Classes
- AnyRef → Any
-
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
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()
-
def
result(sort: Boolean): KmerTable
Construct a k-mer table that contains all the inserted k-mers.
Construct a k-mer table that contains all the inserted k-mers. After calling this method, this builder is invalid and should be discarded.
- sort
Whether the k-mers should be sorted.
- returns
The resulting k-mer table
-
final
def
synchronized[T0](arg0: ⇒ T0): T0
- Definition Classes
- AnyRef
-
def
toString(): String
- Definition Classes
- AnyRef → Any
-
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()