Module pattern 

Pattern matching algorithms for biological sequences.

Provides exact and approximate string matching on &[u8] slices, suitable for DNA, RNA, and protein sequences alike.

Exact matchers

• horspool — Boyer-Moore-Horspool with bad-character shift table, O(n/m) average
• kmp — Knuth-Morris-Pratt with failure function, O(n+m)
• shift_and — Shift-And bitparallel (pattern <= 64)
• bndm — Backward Nondeterministic DAWG Matching, bitparallel (pattern <= 64)
• bom — Backward Oracle Matching with factor oracle

Approximate matchers

• myers_bitparallel — Myers bit-parallel edit distance (pattern <= 64)
• ukkonen — Ukkonen cut-off approximate matching via bounded DP

Functions

bndm

Backward Nondeterministic DAWG Matching (BNDM) exact pattern matching.

bom

Backward Oracle Matching (BOM) exact pattern matching.

horspool

Boyer-Moore-Horspool exact pattern matching.

kmp

Knuth-Morris-Pratt exact pattern matching.

myers_bitparallel

Myers bit-parallel approximate matching.

shift_and

Shift-And bitparallel exact pattern matching.

ukkonen

Ukkonen cut-off approximate matching via bounded dynamic programming.