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

Changes to be committed:

Browse Source 
modified:   cmd/obitools/obitag/main.go
	modified:   cmd/obitools/obitag2/main.go
	modified:   go.mod
	modified:   go.sum
	modified:   pkg/obiformats/ncbitaxdump/read.go
	modified:   pkg/obioptions/version.go
	modified:   pkg/obiseq/attributes.go
	modified:   pkg/obiseq/taxonomy_lca.go
	modified:   pkg/obiseq/taxonomy_methods.go
	modified:   pkg/obiseq/taxonomy_predicate.go
	modified:   pkg/obitax/inner.go
	modified:   pkg/obitax/lca.go
	new file:   pkg/obitax/taxid.go
	modified:   pkg/obitax/taxon.go
	modified:   pkg/obitax/taxonomy.go
	modified:   pkg/obitax/taxonslice.go
	modified:   pkg/obitools/obicleandb/obicleandb.go
	modified:   pkg/obitools/obigrep/options.go
	modified:   pkg/obitools/obilandmark/obilandmark.go
	modified:   pkg/obitools/obilandmark/options.go
	modified:   pkg/obitools/obirefidx/famlilyindexing.go
	modified:   pkg/obitools/obirefidx/geomindexing.go
	modified:   pkg/obitools/obirefidx/obirefidx.go
	modified:   pkg/obitools/obirefidx/options.go
	modified:   pkg/obitools/obitag/obigeomtag.go
	modified:   pkg/obitools/obitag/obitag.go
	modified:   pkg/obitools/obitag/options.go
	modified:   pkg/obiutils/strings.go
This commit is contained in:
Eric Coissac
2024-12-19 13:36:59 +01:00
parent f41a6fbb60
commit 795df34d1a
28 changed files with 590 additions and 280 deletions
Download Patch File Download Diff File Expand all files Collapse all files

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

@ -7,8 +7,8 @@ import (
log "github.com/sirupsen/logrus"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiiter"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obitax"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obitools/obiconvert"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obitools/obifind"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obitools/obitag"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obioptions"
@ -44,9 +44,9 @@ func main() {
fs, err := obiconvert.CLIReadBioSequences(args...)
obiconvert.OpenSequenceDataErrorMessage(args, err)
taxo, error := obifind.CLILoadSelectedTaxonomy()
if error != nil {
log.Panicln(error)
taxo := obitax.DefaultTaxonomy()
if taxo == nil {
log.Panicln("No loaded taxonomy")
}
references := obitag.CLIRefDB()

8
cmd/obitools/obitag2/main.go
View File

@ -7,8 +7,8 @@ import (
log "github.com/sirupsen/logrus"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiiter"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obitax"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obitools/obiconvert"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obitools/obifind"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obitools/obitag"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obitools/obitag2"
@ -45,9 +45,9 @@ func main() {
fs, err := obiconvert.CLIReadBioSequences(args...)
obiconvert.OpenSequenceDataErrorMessage(args, err)
taxo, error := obifind.CLILoadSelectedTaxonomy()
if error != nil {
log.Panicln(error)
taxo := obitax.DefaultTaxonomy()
if taxo == nil {
log.Panicln("No loaded taxonomy")
}
references := obitag.CLIRefDB()