Type Members

1.  type BucketId = Long

   Type of a compacted hash (minimizer)

2.  final case class InputFragment(header: SeqTitle, location: SeqLocation, nucleotides: NTSeq) extends Product with Serializable

   A sequence fragment with a controlled maximum size.

   A sequence fragment with a controlled maximum size. Does not contain whitespace.

   header

   Title/header of the sequence

   location

   1-based location in the source sequence

   nucleotides

   Nucleotides in the source sequence

3.  final case class MinSplitter[+P <: MinimizerPriorities](priorities: P, k: Int) extends Product with Serializable

   Split reads into superkmers by ranked motifs (minimizers).

   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

4.  final case class MinTable(byPriority: ArrayBuffer[NTSeq], largeBuckets: ArrayBuffer[NTSeq] = ArrayBuffer.empty) extends MinimizerPriorities with Product with Serializable

   A table of minimizers with relative priorities (minimizer ordering).

   A table of minimizers with relative priorities (minimizer ordering).

   byPriority

   Minimizers ordered from high priority to low. The position in the array is the rank, and also the unique ID in this table, of the corresponding minimizer. All minimizers must be of equal length.

   largeBuckets

   A subset of byPriority, indicating the motifs that have been found to correspond to large buckets, if any.

5.  trait MinimizerPriorities extends Serializable

   Defines a reversible mapping between encoded minimizers and their priorities.

6.  final class PosRankWindow extends AnyRef

   Tracks Motifs in a moving window, such that the top priority item can always be obtained efficiently.

   Tracks Motifs in a moving window, such that the top priority item can always be obtained efficiently. Mutates the array. Can only be used once. This class looks like an Iterator[Int], but to avoid boxing of integers, does not extend that trait.

   Invariants: the leftmost position has the highest priority (minimal rank). Priority decreases (i.e. rank increases) monotonically going left to right. Motifs are sorted by position. The minimizer of the current k-length window is always the first motif in the list.

7.  final case class RandomXOR(width: Int, xorMask: Long, canonical: Boolean) extends MinimizerPriorities with Product with Serializable

   Compute minimizer priority by XORing with a random mask

8.  final case class SampledFrequencies(table: MinTable, counts: Array[(Long, Int)]) extends Product with Serializable

   Sampled motif frequencies that may be used to construct a new minimizer ordering.

   Sampled motif frequencies that may be used to construct a new minimizer ordering.

   table

   Template table, whose ordering of motifs will be refined based on counted frequencies.

   counts

   Pairs of (minimizer rank, frequency). The minimizers should be a subset of those from the given template MinTable.

9.  final case class ShiftScanner(priorities: MinimizerPriorities) extends Product with Serializable

   Bit-shift scanner for fixed width motifs.

   Bit-shift scanner for fixed width motifs. Identifies all valid (according to some MinimizerPriorities) motifs/minimizers in a sequence.

   priorities

   The minimizer ordering to scan for motifs of

10.  final case class SplitSegment(hash: BucketId, sequence: SeqID, location: SeqLocation, nucleotides: ZeroNTBitArray) extends Product with Serializable

    A hashed segment (i.e.

    A hashed segment (i.e. a superkmer, where every k-mer shares the same minimizer) with minimizer, sequence ID, and 1-based sequence location

    hash

    hash (minimizer)

    sequence

    Sequence ID/header

    location

    Sequence location (1-based) if available

    nucleotides

    Encoded nucleotides of this segment