Module 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=3 Kmers

K4

Marker trait for generating K=4 Kmers

K5

Marker trait for generating K=5 Kmers

K6

Marker trait for generating K=6 Kmers

K7

Marker trait for generating K=7 Kmers

K9

Marker trait for generating K=9 Kmers

K10

Marker trait for generating K=10 Kmers

K11

Marker trait for generating K=11 Kmers

K12

Marker trait for generating K=12 Kmers

K13

Marker trait for generating K=13 Kmers

K14

Marker trait for generating K=14 Kmers

K15

Marker trait for generating K=15 Kmers

K17

Marker trait for generating K=17 Kmers

K18

Marker trait for generating K=18 Kmers

K19

Marker trait for generating K=19 Kmers

K20

Marker trait for generating K=20 Kmers

K21

Marker trait for generating K=21 Kmers

K22

Marker trait for generating K=22 Kmers

K23

Marker trait for generating K=23 Kmers

K24

Marker trait for generating K=24 Kmers

K25

Marker trait for generating K=25 Kmers

K26

Marker trait for generating K=26 Kmers

K27

Marker trait for generating K=27 Kmers

K28

Marker trait for generating K=28 Kmers

K29

Marker trait for generating K=29 Kmers

K30

Marker trait for generating K=30 Kmers

K31

Marker trait for generating K=31 Kmers

K33

Marker trait for generating K=33 Kmers

K34

Marker trait for generating K=34 Kmers

K35

Marker trait for generating K=35 Kmers

K36

Marker trait for generating K=36 Kmers

K37

Marker trait for generating K=37 Kmers

K38

Marker trait for generating K=38 Kmers

K39

Marker trait for generating K=39 Kmers

K40

Marker trait for generating K=40 Kmers

K41

Marker trait for generating K=41 Kmers

K42

Marker trait for generating K=42 Kmers

K43

Marker trait for generating K=43 Kmers

K44

Marker trait for generating K=44 Kmers

K45

Marker trait for generating K=45 Kmers

K46

Marker trait for generating K=46 Kmers

K47

Marker trait for generating K=47 Kmers

K48

Marker struct for generating K=48 Kmers

K49

Marker struct for generating K=49 Kmers

K50

Marker struct for generating K=50 Kmers

K51

Marker struct for generating K=51 Kmers

K52

Marker struct for generating K=52 Kmers

K53

Marker struct for generating K=53 Kmers

K54

Marker struct for generating K=54 Kmers

K55

Marker struct for generating K=55 Kmers

K56

Marker struct for generating K=56 Kmers

K57

Marker struct for generating K=57 Kmers

K58

Marker struct for generating K=58 Kmers

K59

Marker struct for generating K=59 Kmers

K60

Marker struct for generating K=60 Kmers

K61

Marker struct for generating K=61 Kmers

K62

Marker struct for generating K=62 Kmers

K63

Marker struct for generating K=63 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 Aliases

Kmer2

2-base kmer, backed by a single u8

Kmer3

3-base kmer, backed by a single u8

Kmer4

4-base kmer, backed by a single u8

Kmer5

5-base kmer, backed by a single u16

Kmer6

6-base kmer, backed by a single u16

Kmer7

7-base kmer, backed by a single u16

Kmer8

8-base kmer, backed by a single u16

Kmer9

9-base kmer, backed by a single u32

Kmer10

10-base kmer, backed by a single u32

Kmer11

11-base kmer, backed by a single u32

Kmer12

12-base kmer, backed by a single u32

Kmer13

13-base kmer, backed by a single u32

Kmer14

14-base kmer, backed by a single u32

Kmer15

15-base kmer, backed by a single u32

Kmer16

16-base kmer, backed by a single u32

Kmer17

17-base kmer, backed by a single u64

Kmer18

18-base kmer, backed by a single u64

Kmer19

19-base kmer, backed by a single u64

Kmer20

20-base kmer, backed by a single u64

Kmer21

21-base kmer, backed by a single u64

Kmer22

22-base kmer, backed by a single u64

Kmer23

23-base kmer, backed by a single u64

Kmer24

24-base kmer, backed by a single u64

Kmer25

25-base kmer, backed by a single u64

Kmer26

25-base kmer, backed by a single u64

Kmer27

27-base kmer, backed by a single u64

Kmer28

28-base kmer, backed by a single u64

Kmer29

29-base kmer, backed by a single u64

Kmer30

30-base kmer, backed by a single u64

Kmer31

31-base kmer, backed by a single u64

Kmer32

32-base kmer, backed by a single u64

Kmer33

33-base kmer, backed by a single u128

Kmer34

34-base kmer, backed by a single u128

Kmer35

35-base kmer, backed by a single u128

Kmer36

36-base kmer, backed by a single u128

Kmer37

37-base kmer, backed by a single u128

Kmer38

38-base kmer, backed by a single u128

Kmer39

39-base kmer, backed by a single u128

Kmer40

40-base kmer, backed by a single u128

Kmer41

41-base kmer, backed by a single u128

Kmer42

42-base kmer, backed by a single u128

Kmer43

43-base kmer, backed by a single u128

Kmer44

44-base kmer, backed by a single u128

Kmer45

45-base kmer, backed by a single u128

Kmer46

46-base kmer, backed by a single u128

Kmer47

47-base kmer, backed by a single u128

Kmer48

48-base kmer, backed by a single u128

Kmer49

49-base kmer, backed by a single u128

Kmer50

50-base kmer, backed by a single u128

Kmer51

51-base kmer, backed by a single u128

Kmer52

52-base kmer, backed by a single u128

Kmer53

53-base kmer, backed by a single u128

Kmer54

54-base kmer, backed by a single u128

Kmer55

55-base kmer, backed by a single u128

Kmer56

56-base kmer, backed by a single u128

Kmer57

57-base kmer, backed by a single u128

Kmer58

58-base kmer, backed by a single u128

Kmer59

59-base kmer, backed by a single u128

Kmer60

60-base kmer, backed by a single u128

Kmer61

61-base kmer, backed by a single u128

Kmer62

62-base kmer, backed by a single u128

Kmer63

63-base kmer, backed by a single u128

Kmer64

64-base kmer, backed by a single u128