obitools/obitools4
2
0
Fork 0
mirror of https://github.com/metabarcoding/obitools4.git synced 2025-06-29 16:20:46 +00:00
Code Issues Packages Projects Releases Wiki Activity

Add automatic garbage collection on ApatPattern

Browse Source
This commit is contained in:
Eric Coissac
2022-01-24 17:26:30 +01:00
parent 703eb62819
commit 251d3be923
10 changed files with 119 additions and 92 deletions
Download Patch File Download Diff File Expand all files Collapse all files

6
cmd/obitools/obicount/main.go
View File

@ -49,15 +49,15 @@ func main() {
(&s).Recycle()
}
if obicount.IsPrintingVariantCount() {
if obicount.CLIIsPrintingVariantCount() {
fmt.Printf(" %d", nvariant)
}
if obicount.IsPrintingReadCount() {
if obicount.CLIIsPrintingReadCount() {
fmt.Printf(" %d", nread)
}
if obicount.IsPrintingSymbolCount() {
if obicount.CLIIsPrintingSymbolCount() {
fmt.Printf(" %d", nsymbol)
}

8
cmd/obitools/obifind/main.go
View File

@ -22,13 +22,13 @@ func main() {
}
switch {
case obifind.RequestsPathForTaxid() >= 0:
taxonomy, err := obifind.LoadSelectedTaxonomy()
case obifind.CLIRequestsPathForTaxid() >= 0:
taxonomy, err := obifind.CLILoadSelectedTaxonomy()
if err != nil {
fmt.Printf("%+v", err)
}
taxon, err := taxonomy.Taxon(obifind.RequestsPathForTaxid())
taxon, err := taxonomy.Taxon(obifind.CLIRequestsPathForTaxid())
if err != nil {
fmt.Printf("%+v", err)
@ -44,7 +44,7 @@ func main() {
fmt.Sprintf("path:%d", taxon.Taxid()))
case len(args) == 0:
taxonomy, err := obifind.LoadSelectedTaxonomy()
taxonomy, err := obifind.CLILoadSelectedTaxonomy()
if err != nil {
fmt.Printf("%+v", err)
}

4
cmd/obitools/obipairing/main.go
View File

@ -7,6 +7,7 @@ import (
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obioptions"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obitools/obiconvert"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obitools/obimultiplex"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obitools/obipairing"
)
@ -28,7 +29,7 @@ func main() {
trace.Start(ftrace)
defer trace.Stop()
optionParser := obioptions.GenerateOptionParser(obipairing.OptionSet)
optionParser := obioptions.GenerateOptionParser(obimultiplex.OptionSet)
optionParser(os.Args)
pairs, _ := obipairing.IBatchPairedSequence()
@ -36,6 +37,7 @@ func main() {
obipairing.GapPenality(),
obipairing.Delta(),
obipairing.MinOverlap(),
obipairing.MinIdentity(),
obipairing.WithStats(),
obioptions.ParallelWorkers(),
)