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.
36 lines
1.1 KiB
Go
36 lines
1.1 KiB
Go
//go:build goexperiment.simd
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package obisimilarity
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import "simd"
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// commonWords is the upper bound used for the number of 4-mers shared by two
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// sequences: the sum of the minima of the counters, plus the minimum of the
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// two overflows.
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//
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// The minima of the 256 counters are computed by vectors of bytes, and summed
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// in 16-bit lanes (at most 256*255 spread over the lanes, the lanes being at
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// least 8 in number, so that none of them overflows).
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func commonWords(t1, t2 *Table4) int {
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var probe simd.Uint8s
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vl := probe.Len()
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acc := simd.BroadcastUint16s(0)
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low := simd.BroadcastUint16s(0x00FF)
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for i := 0; i < len(t1.Count); i += vl {
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m := simd.LoadUint8s(t1.Count[i:]).Min(simd.LoadUint8s(t2.Count[i:])).ReshapeToUint16s()
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acc = acc.Add(m.And(low)).Add(m.ShiftAllRight(8))
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}
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// sum the pairs of 16-bit lanes into 32-bit lanes, then add those up
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wide := acc.ReshapeToUint32s()
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sums := wide.And(simd.BroadcastUint32s(0xFFFF)).Add(wide.ShiftAllRight(16))
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var lanes [32]uint32
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sums.Store(lanes[:])
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total := 0
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for _, v := range lanes[:sums.Len()] {
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total += int(v)
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}
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return total + min(t1.Overflow, t2.Overflow)
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}
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