package util
Routines and classes for managing sequence and k-mer representations.
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Type Members
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class
InvalidNucleotideException extends Exception
Thrown when we encounter a letter in the sequence input that we do not expect to see
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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.
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final
class
KmerTable1 extends KmerTable
Specialized KmerTable for n = 1 (k <= 32)
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final
class
KmerTable2 extends KmerTable
Specialized KmerTable for n = 2 (k <= 64)
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final
class
KmerTable3 extends KmerTable
Specialized KmerTable for n = 3 (k <= 96)
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final
class
KmerTable4 extends KmerTable
Specialized KmerTable for n = 4 (k <= 128)
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final
class
KmerTableBuilder extends AnyRef
Builder for k-mer tables.
Builder for k-mer tables. K-mers are built by gradually adding longs in order.
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final
class
KmerTableN extends KmerTable
General KmerTable for any value of n
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trait
NTBitArray extends AnyRef
A bit-packed array of nucleotides, where each letter is represented by two bits.
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class
NTBitDecoder extends AnyRef
Methods for decoding NT sequences of a fixed length, with reusable buffers.
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class
NestedRowTagProvider extends RowTagProvider
Wrap a TagProvider into a RowTagProvider by fixing the row
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final
case class
OffsetNTBitArray(data: Array[Long], offset: Int, size: Int) extends NTBitArray with Product with Serializable
An NTBitArray that begins at some offset in its binary data
An NTBitArray that begins at some offset in its binary data
- data
the encoded data
- offset
the offset where this sequence starts
- size
the size of this data
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trait
RowTagProvider extends AnyRef
Source of tags for a single row (super-mer) of k-mers
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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
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final
case class
ZeroNTBitArray(data: Array[Long], size: Int) extends NTBitArray with Product with Serializable
An NTBitArray that begins at offset zero in its binary data
An NTBitArray that begins at offset zero in its binary data
- data
the encoded data
- size
the size of this data
Value Members
- object Arrays
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object
BitRepresentation
Helper functions for working with a low level bit representation of nucleotide sequences.
- object DNAHelpers
- object EmptyRowTagProvider extends RowTagProvider
- object KmerTable
- object NTBitArray