Type Members

1.  class InvalidNucleotideException extends Exception

   Thrown when we encounter a letter in the sequence input that we do not expect to see

2.  abstract class KmerTable extends IndexedSeq[Array[Long]]

   A k-mer table is a collection of k-mers, stored in column-major format.

   A k-mer table is a collection of k-mers, stored in column-major format. The first k-mer is stored in kmers(0)(0), kmers(1)(0), ... kmers(n)(0); the second in kmers(0)(1), kmers(1)(1)... kmers(n)(1) and so on. This layout enables fast radix sort. The KmerTable is optionally sorted by construction (by KmerTableBuilder). Each k-mer may contain additional annotation data ("tags") in longs following the sequence data itself.

3.  final class KmerTable1 extends KmerTable

   Specialized KmerTable for n = 1 (k <= 32)

4.  final class KmerTable2 extends KmerTable

   Specialized KmerTable for n = 2 (k <= 64)

5.  final class KmerTable3 extends KmerTable

   Specialized KmerTable for n = 3 (k <= 96)

6.  final class KmerTable4 extends KmerTable

   Specialized KmerTable for n = 4 (k <= 128)

7.  class KmerTableBuilder extends AnyRef

   Builder for k-mer tables.

   Builder for k-mer tables. K-mers are built by gradually adding longs in order. The builder is not reusable.

8.  final class KmerTableBuilder1 extends KmerTableBuilder

   A KmerTableBuilder where each row is 1 Long.

   A KmerTableBuilder where each row is 1 Long. This subclass optimizes addRow() to avoid a loop.

9.  final class KmerTableBuilder2 extends KmerTableBuilder

   A KmerTableBuilder where each row is 2 Longs.

   A KmerTableBuilder where each row is 2 Longs. This subclass optimizes addRow() to avoid a loop.

10.  final class KmerTableBuilder3 extends KmerTableBuilder

    A KmerTableBuilder where each row is 3 Longs.

    A KmerTableBuilder where each row is 3 Longs. This subclass optimizes addRow() to avoid a loop.

11.  final class KmerTableN extends KmerTable

    General KmerTable for any value of n

12.  trait KmerVisitor extends AnyRef
13.  final case class NTBitArray(data: Array[Long], size: Int) extends Ordered[NTBitArray] with Product with Serializable

    A bit-packed sequence of nucleotides, where each letter is represented by two bits.

    A bit-packed sequence of nucleotides, where each letter is represented by two bits. Some operations mutate this object, and others return a new object instead. A new copy can always be obtained with clone(). No operations can change the size of the contained sequence.

    data

    the encoded data. Array of longs, each storing up to 32 nts, with optional padding at the end. The data is left-aligned inside the long, starting from MSB.

    size

    the size of this data represented (in NTs)

14.  final class NTBitArrayBuilder extends AnyRef

    A builder for NTBitArrays.

    A builder for NTBitArrays. It is the user's responsibility to ensure that they do not write past the end of the array. The array is built from the left to the right end.

15.  class NTBitDecoder extends AnyRef

    Methods for decoding NT sequences with reusable buffers.

16.  class NestedRowTagProvider extends RowTagProvider

    Wrap a TagProvider into a RowTagProvider by fixing the row

17.  trait RowTagProvider extends AnyRef

    Source of tags for a single row (super-mer) of k-mers

18.  trait TagProvider extends AnyRef

    Source of tags for a set of k-mers arranged in two dimensions, where the row identifies a super-mer and the col identifies a k-mer position in the super-mer