mirror of
https://github.com/metabarcoding/obitools4.git
synced 2026-11-09 09:24:41 +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.
47 lines
1.5 KiB
Go
47 lines
1.5 KiB
Go
package obisimilarity
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// A block stores the 4-mer tables of a few sequences, transposed: the counter
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// of the word w for the lane j is data[w*width+j]. A vector instruction then
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// handles the same word for all the sequences of the block, and only the words
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// that a sequence contains (a hundred for a short amplicon, out of 256) need
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// to be visited to compare it with all the sequences of the block.
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type tableBlock struct {
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data []uint8
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}
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func newTableBlock(width int) tableBlock {
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return tableBlock{data: make([]uint8, 256*width)}
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}
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// set stores the table t as the lane `lane` of the block.
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func (b *tableBlock) set(width, lane int, t *Table4) {
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for w := range t.Count {
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b.data[w*width+lane] = t.Count[w]
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}
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}
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// common computes the sums of the minima of the counters of the sequence
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// given by its words with every lane of the block (see blockCommon).
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func (b *tableBlock) common(width int, words []uint16, out []uint8) {
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blockCommon(b.data, width, words, out)
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}
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// SparseWords lists the words of a table as w<<8|count, so that the visit of
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// a block only goes through the words present in the sequence. nil is
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// returned when the counters add up to more than 255, which would overflow the
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// 8-bit sums of the blocks.
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func SparseWords(t *Table4) []uint16 {
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words := make([]uint16, 0, 128)
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mass := 0
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for w, c := range t.Count {
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if c > 0 {
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words = append(words, uint16(w)<<8|uint16(c))
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mass += int(c)
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}
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}
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if mass > 255 {
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return nil
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}
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return words
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}
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