Module debruijn::kmer

Represent kmers with statically know length in compact integer types

A kmer is a DNA sequence with statically-known length K. The sequence is stored the smallest possible integer type Efficient methods for reverse complement and shifting new bases into the left or right of a sequence are provided. Kmers implement Eq to test if two kmers represent the same string. Kmers implement Ord, which corresponds to the natural lexicographic ordering.

use debruijn::*;
use debruijn::kmer::*;

let k1 = Kmer16::from_ascii(b"ACGTACGTACGTACGT");

// Reverse complement
let rc_k1 = k1.rc();

// Double reverse complement
let k1_copy = rc_k1.rc();
assert_eq!(k1, k1_copy);

// Push one base onto the left
assert_eq!(k1.extend_left(base_to_bits(b'T')), Kmer16::from_ascii(b"TACGTACGTACGTACG"));

// Generate a set of kmers from a string, then sort
let mut all_kmers = Kmer16::kmers_from_ascii(b"TACGTACGTACGTACGTT");
all_kmers.sort();
assert_eq!(all_kmers,
    vec![
        Kmer16::from_ascii(b"ACGTACGTACGTACGT"),
        Kmer16::from_ascii(b"CGTACGTACGTACGTT"),
        Kmer16::from_ascii(b"TACGTACGTACGTACG")
    ]);

Structs

IntKmer	A Kmer sequence with a statically know K. K will fill the underlying integer type.
K2	Marker trait for generating K=6 Kmers
K3	Marker trait for generating K=6 Kmers
K4	Marker trait for generating K=6 Kmers
K5	Marker trait for generating K=6 Kmers
K6	Marker trait for generating K=6 Kmers
K12	Marker trait for generating K=12 Kmers
K14	Marker trait for generating K=14 Kmers
K20	Marker trait for generating K=20 Kmers
K24	Marker trait for generating K=24 Kmers
K30	Marker trait for generating K=30 Kmers
K31	Marker trait for generating K=31 Kmers
K40	Marker trait for generating K=40 Kmers
K48	Marker struct for generating K=48 Kmers
VarIntKmer	A fixed-length Kmer sequence that may not fill the bits of T

Traits

IntHelp	Trait for specialized integer operations used in DeBruijn Graph
KmerSize	Helper trait for declaring the K value of a Kmer. Will be removed when const generics are available

Type Definitions

Kmer2
Kmer3
Kmer4
Kmer5
Kmer6
Kmer8	8-base kmer, backed by a single u16
Kmer12	12-base kmer, backed by a single u32
Kmer14	14-base kmer, backed by a single u32
Kmer16	16-base kmer, backed by a single u32
Kmer20	20-base kmer, backed by a single u64
Kmer24	24-base kmer, backed by a single u64
Kmer30	30-base kmer, backed by a single u64
Kmer32	32-base kmer, backed by a single u64
Kmer40	40-base kmer, backed by a single u128
Kmer48	48-base kmer, backed by a single u128
Kmer64	64-base kmer, backed by a single u128