Crate kmers_rs

K-mers and associated operations.

This library provides functionality for extracting k-mers from sequences, and manipulating them in useful ways. The underlying representation is 64-bit integers (u64), so k > 32 is not supported by this library.

K-mers (or q-grams in some computer science contexts) are k-length sequences of DNA/RNA “letters” represented as unsigned integers. Following usual practice,

• “A” -> b00
• “C” -> b01
• “G” -> b10
• “T” or “U” -> b11

which has the nice property that the complementary bases are bitwise complements.

Structs

• BigSparseAccumulator
  A sparse k-mer accumulator for large set of k-mers.
• CompressedKmerFrequencyList
  A compressed representation for a sorted list of k-mer and count pairs.
• CompressedKmerFrequencyListIterator
  Iterate over a compressed k-mer list
• CompressedKmerList
  A compressed representation for a sorted list of k-mers.
• CompressedKmerListIterator
  Iterate over a compressed k-mer list
• CountingIterator
  Take a sorted iterator and yield k-mer frequencies.
• DenseAccumulator
  Accumulate k-mer frequencies for small to medium k.
• IteratorReadAdaptor
  Convert an iterator over bytes to a Read.
• Kmer
  A k-length nucleotide sequence represented as a 64-bit integer.
• KmerFrequencyIterator
  An iterator producing k-mer frequencies.
• KmerIterator
  An iterator over the k-mers drawn from a sequence.
• MergeIterator
  Merge two k-mer frequency iterators.
• SimpleSparseAccumulator
  A simple sparse accumulator
• Unique
  An iterator producing k-mer frequencies.

Functions

• counting_kmer_frequency_iterator
  Take a sorted iterator and yield k-mer frequencies.
• dot
  Compute the dot product between two k-mer frequency spectra.
• frequency_vector_iter
  Construct a k-mer frequency iterator from an iterator over frequencies.
• jaccard
  Compute the Jaccard cooeficient from two sets of k-mers.
• merge
  Merge two iterators
• unique
  An adaptor that coverts an iterator over k-mers into a k-mer frequency iterator