kmerutils 0.0.14

Kmer counting, hashing, sequence sketching
Documentation 
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/// try to guess an upper bound for nb kmer encountered in large seq or files (tens of gb bases)
///
use crate::base::sequence::Sequence;

// We need a guess to allocate HashMap used with Kmer Generation
// for very long sequence we must avoid nb_kmer to sequence length! Find a  good heuristic
pub(crate) fn get_nbkmer_guess(seq: &Sequence) -> usize {
    let nb = 100_000_000 * (1usize + seq.size().ilog2() as usize);

    seq.size().min(nb)
} // end of get_nbkmer_guess

// We need a guess to allocate HashMap used with Kmer Generation
// for vector of sequenc coming from a non concatnated file, we must avoid nb_kmer to sequence length! Find a  good heuristic
pub(crate) fn get_nbkmer_guess_seqs(vseq: &[&Sequence]) -> usize {
    let total_nb_base = vseq.iter().fold(0, |acc, seq| acc + seq.size());
    // for small files do not forget upperbound by size of file (or seq list)

    total_nb_base.min(10_000_000 * (1usize + total_nb_base.ilog2() as usize))
} // end of get_nbkmer_guess_seqs