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Adds some stats in obiparing about fast align results

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Former-commit-id: 44f6d6538e759dd7dc1db068a812957f6b20f50d
This commit is contained in:
Eric Coissac
2023-11-24 10:57:10 +01:00
parent ce66b0af2f
commit ec31ae86b9
2 changed files with 5 additions and 4 deletions
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4
pkg/obialign/pairedendalign.go
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@ -352,7 +352,7 @@ func PERightAlign(seqA, seqB *obiseq.BioSequence, gap float64,
func PEAlign(seqA, seqB *obiseq.BioSequence, func PEAlign(seqA, seqB *obiseq.BioSequence,
gap float64, delta int, gap float64, delta int,
arena PEAlignArena) (int, []int) { arena PEAlignArena) (int, []int, int, int) {
var score, shift int var score, shift int
var startA, startB int var startA, startB int
var partLen, over int var partLen, over int
@ -467,5 +467,5 @@ func PEAlign(seqA, seqB *obiseq.BioSequence,
arena.pointer.path = append(arena.pointer.path, extra3, 0) arena.pointer.path = append(arena.pointer.path, extra3, 0)
} }
return score, arena.pointer.path return score, arena.pointer.path, fastScore, over
} }

5
pkg/obitools/obipairing/pairing.go
View File

@ -108,7 +108,7 @@ func AssemblePESequences(seqA, seqB *obiseq.BioSequence,
inplace bool, inplace bool,
arenaAlign obialign.PEAlignArena) *obiseq.BioSequence { arenaAlign obialign.PEAlignArena) *obiseq.BioSequence {
score, path := obialign.PEAlign(seqA, seqB, gap, delta, arenaAlign) score, path, fastscore, over := obialign.PEAlign(seqA, seqB, gap, delta, arenaAlign)
cons, match := obialign.BuildQualityConsensus(seqA, seqB, path, true) cons, match := obialign.BuildQualityConsensus(seqA, seqB, path, true)
left := path[0] left := path[0]
@ -123,6 +123,8 @@ func AssemblePESequences(seqA, seqB *obiseq.BioSequence,
identity = 0 identity = 0
} }
annot := cons.Annotations() annot := cons.Annotations()
annot["paring_fast_score"] = fastscore
annot["paring_fast_overlap"] = over
if aliLength >= minOverlap && identity >= minIdentity { if aliLength >= minOverlap && identity >= minIdentity {
annot["mode"] = "alignment" annot["mode"] = "alignment"
@ -216,7 +218,6 @@ func IAssemblePESequencesBatch(iterator obiiter.IBioSequence,
nworkers = sizes[0] nworkers = sizes[0]
} }
newIter := obiiter.MakeIBioSequence() newIter := obiiter.MakeIBioSequence()
newIter.Add(nworkers) newIter.Add(nworkers)