Struct debruijn::filter::CountFilter

pub struct CountFilter { /* fields omitted */ }

A simple KmerSummarizer that only accepts kmers that are observed at least a given number of times. The metadata returned about a Kmer is the number of times it was observed, capped at 2^16.

Methods

impl CountFilter

pub fn new(min_kmer_obs: usize) -> CountFilter

Construct a CountFilter KmerSummarizer only accepts kmers that are observed at least min_kmer_obs times.

Trait Implementations

impl<D> KmerSummarizer<D, u16> for CountFilter

fn summarize<K, F: Iterator<Item = (K, Exts, D)>>(
    &self,
    items: F
) -> (bool, Exts, u16)

The input items is an iterator over kmer observations. Input observation is a tuple of (kmer, extensions, data). The summarize function inspects the data and returns a tuple indicating: * whether this kmer passes the filtering criteria (e.g. is there a sufficient number of observation) * the accumulated Exts of the kmer * a summary data object of type DO that will be used as a color annotation in the DeBruijn graph.