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introduce obidefault

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This commit is contained in:
Eric Coissac
2025-01-27 17:12:45 +01:00
parent 0a567f621c
commit 7c4042df6b
69 changed files with 505 additions and 479 deletions
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8
pkg/obitools/obitagpcr/pcrtag.go
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@@ -4,8 +4,8 @@ import (
log "github.com/sirupsen/logrus"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obialign"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obidefault"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiiter"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obioptions"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiseq"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obitools/obiconvert"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obitools/obimultiplex"
@@ -44,7 +44,7 @@ func IPCRTagPESequencesBatch(iterator obiiter.IBioSequence,
log.Fatalln("Sequence data must be paired")
}
nworkers := obioptions.CLIParallelWorkers()
nworkers := obidefault.ParallelWorkers()
ngsfilter, err := obimultiplex.CLINGSFIlter()
if err != nil {
@@ -180,14 +180,14 @@ func IPCRTagPESequencesBatch(iterator obiiter.IBioSequence,
if !obimultiplex.CLIConservedErrors() {
log.Println("Discards unassigned sequences")
iout = iout.FilterOn(obiseq.HasAttribute("obimultiplex_error").Not(), obioptions.CLIBatchSize())
iout = iout.FilterOn(obiseq.HasAttribute("obimultiplex_error").Not(), obidefault.BatchSize())
}
var unidentified obiiter.IBioSequence
if obimultiplex.CLIUnidentifiedFileName() != "" {
log.Printf("Unassigned sequences saved in file: %s\n", obimultiplex.CLIUnidentifiedFileName())
unidentified, iout = iout.DivideOn(obiseq.HasAttribute("obimultiplex_error"),
obioptions.CLIBatchSize())
obidefault.BatchSize())
go func() {
_, err := obiconvert.CLIWriteBioSequences(unidentified,