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com.jnpersson.discount.util

KmerTableBuilder

final class KmerTableBuilder extends AnyRef

Builder for k-mer tables. K-mers are built by gradually adding longs in order.

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Instance Constructors

  1. 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

  1. final def !=(arg0: Any): Boolean
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  2. final def ##(): Int
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  3. final def ==(arg0: Any): Boolean
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  4. 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.

  5. def addLongs(xs: Array[Long]): Unit

    Add multiple long values.

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  7. def clone(): AnyRef
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  16. final def notifyAll(): Unit
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  17. 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

  18. final def synchronized[T0](arg0: ⇒ T0): T0
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