mirror of
https://github.com/metabarcoding/obitools4.git
synced 2026-11-09 17:24:41 +00:00
Eric Coissac
e511650f5b
Introduces parallel processing for clustering, refines scoring mechanisms, and expands test coverage for the alignment functionality. This change introduces parallel processing capabilities within the clustering logic, updates the core similarity engine with new data structures and scoring methods, and implements a comprehensive test suite for the alignment tool. It also adds new command-line options for configuring alignment parameters and reference lengths.
55 lines
1.6 KiB
Go
55 lines
1.6 KiB
Go
// Package obisimilarity holds what the tools that compare nucleotide sequences
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// by the length of their longest common subsequence (obiclust, obialign) have
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// in common: the scoring of a pair against a threshold, with the lossless
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// 4-mer filter that avoids most of the alignments, and the index that finds
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// the sequences a given one can be similar to.
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//
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// The scoring follows the arithmetic of sumaclust and sumatra (integer
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// truncations, floating point comparisons) so that the same pairs are
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// accepted with the same scores.
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package obisimilarity
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// Table4 is the 4-mer occurrence table of a sequence: one saturating counter
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// per word, and the number of occurrences that did not fit in the counters.
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type Table4 struct {
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Count [256]uint8
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Overflow int
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}
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// NewTable4 counts the 4-mers of a sequence made of the letters a, c, g
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// and t. The 2-bit code of a base is (letter>>1)&3, i.e. a=0, c=1, t=2, g=3.
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func NewTable4(seq []byte) *Table4 {
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t := new(Table4)
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t.Fill(seq)
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return t
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}
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// Fill counts the 4-mers of seq in a zeroed table.
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func (t *Table4) Fill(seq []byte) {
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if len(seq) < 4 {
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return
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}
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w := uint(0)
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for i, c := range seq {
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w = (w<<2 | uint(c>>1)&3) & 0xFF
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if i < 3 {
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continue
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}
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if t.Count[w] < 255 {
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t.Count[w]++
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} else {
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t.Overflow++
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}
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}
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}
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// minCommonWords is the minimum number of 4-mers that two sequences must
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// share when the longest has length reflen and they have a common
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// subsequence of length lcs.
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func minCommonWords(reflen, lcs int) int {
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nbfrag := (reflen-lcs)*2 + 1
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smin := lcs / nbfrag
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r := lcs - smin*nbfrag
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return max(smin-2, 0)*r + max(smin-3, 0)*(nbfrag-r)
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}
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