mirror of
https://github.com/metabarcoding/obitools4.git
synced 2026-11-09 17:24:41 +00:00
Eric Coissac
8cc02aa9c1
This commit introduces significant changes to the sequence processing pipeline, implementing parallel loading, k-mer budget control, explicit memory management, and refined logic for pair evaluation and resolution.
45 lines
1.7 KiB
Go
45 lines
1.7 KiB
Go
package obiprimer
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import (
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"fmt"
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"strings"
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"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiseq"
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)
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// span writes the 1-based GenBank range of the lp bases starting at the 0-based
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// position pos. On a circular sequence a range running over the junction is
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// split in two.
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func span(pos, lp, n int, circular bool) string {
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end := pos + lp
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if end > n && circular {
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return fmt.Sprintf("%d..%d,1..%d", pos+1, n, end-n)
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}
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return fmt.Sprintf("%d..%d", pos+1, end)
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}
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// referenceSites describes an amplicon of a pair on the reference sequence raw.
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//
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// The location lists the two primer sites left to right as join(a..b,c..d),
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// inside complement() when the first primer of the pair (Primer1 once the pair
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// is in string order) binds the reverse strand. The amplicon is the region
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// between the sites, read 5'->3' from the first primer, in lower case.
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//
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// swappedByOrder says whether putting the pair in string order exchanged the
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// two primers of the key.
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func referenceSites(raw []byte, h refHit, p PairParams, swappedByOrder bool) (location, amplicon string) {
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lp, n := p.PrimerLength, len(raw)
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// The key slot 1 is the upstream primer unless the match order was swapped;
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// the exchange due to the string order flips it again.
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firstIsUpstream := h.swapped == swappedByOrder
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location = "join(" + span(int(h.up.pos()), lp, n, p.Circular) + "," + span(int(h.down.pos()), lp, n, p.Circular) + ")"
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region := []byte(strings.ToLower(string(raw[int(h.up.pos())+lp : int(h.down.pos())])))
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if firstIsUpstream {
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return location, string(region)
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}
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rc := obiseq.NewBioSequence("", region, "").ReverseComplement(true)
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return "complement(" + location + ")", string(rc.Sequence())
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}
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