diff --git a/cmd/obitools/obitag/main.go b/cmd/obitools/obitag/main.go index ecf5d96..c93e422 100644 --- a/cmd/obitools/obitag/main.go +++ b/cmd/obitools/obitag/main.go @@ -73,10 +73,12 @@ func main() { var identified obiiter.IBioSequence + fsrb := fs.Rebatch(obidefault.BatchSize()) + if obitag.CLIGeometricMode() { - identified = obitag.CLIGeomAssignTaxonomy(fs, references, taxo) + identified = obitag.CLIGeomAssignTaxonomy(fsrb, references, taxo) } else { - identified = obitag.CLIAssignTaxonomy(fs, references, taxo) + identified = obitag.CLIAssignTaxonomy(fsrb, references, taxo) } obiconvert.CLIWriteBioSequences(identified, true) diff --git a/pkg/obioptions/version.go b/pkg/obioptions/version.go index 036e2e8..4c56538 100644 --- a/pkg/obioptions/version.go +++ b/pkg/obioptions/version.go @@ -8,7 +8,7 @@ import ( // corresponds to the last commit, and not the one when the file will be // commited -var _Commit = "8448783" +var _Commit = "8b379d3" var _Version = "Release 4.4.0" // Version returns the version of the obitools package. diff --git a/pkg/obitools/obiclean/chimera.go b/pkg/obitools/obiclean/chimera.go index 04545f7..270af1a 100644 --- a/pkg/obitools/obiclean/chimera.go +++ b/pkg/obitools/obiclean/chimera.go @@ -2,10 +2,12 @@ package obiclean import ( "fmt" + "os" "sort" "git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiseq" "git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiutils" + "github.com/schollz/progressbar/v3" log "github.com/sirupsen/logrus" ) @@ -119,8 +121,20 @@ func AnnotateChimera(samples map[string]*[]*seqPCR) { } + pbopt := make([]progressbar.Option, 0, 5) + pbopt = append(pbopt, + progressbar.OptionSetWriter(os.Stderr), + progressbar.OptionSetWidth(15), + progressbar.OptionShowIts(), + progressbar.OptionSetPredictTime(true), + progressbar.OptionSetDescription("[Chimera detection]"), + ) + + bar := progressbar.NewOptions(len(samples), pbopt...) + for sn, sqs := range samples { w(sn, sqs) + bar.Add(1) } } diff --git a/pkg/obitools/obiconvert/options.go b/pkg/obitools/obiconvert/options.go index 7b4fc28..9b1a94d 100644 --- a/pkg/obitools/obiconvert/options.go +++ b/pkg/obitools/obiconvert/options.go @@ -33,6 +33,7 @@ var __output_fastobi_format__ = false var __no_progress_bar__ = false var __skip_empty__ = false +var __skip_on_error__ = false var __output_file_name__ = "-" var __paired_file_name__ = "" @@ -97,6 +98,9 @@ func OutputOptionSet(options *getoptions.GetOpt) { options.BoolVar(&__skip_empty__, "skip-empty", __skip_empty__, options.Description("Sequences of length equal to zero are suppressed from the output")) + // options.BoolVar(&__skip_on_error__, "skip-on-error", __skip_on_error__, + // options.Description("Skip sequence with parsing error")) + options.BoolVar(&__output_in_fasta__, "fasta-output", false, options.Description("Write sequence in fasta format (default if no quality data available).")) @@ -172,6 +176,10 @@ func CLISkipEmpty() bool { return __skip_empty__ } +func CLISkipOnError() bool { + return __skip_on_error__ +} + func CLIInputFastHeaderFormat() string { switch { case __input_fastjson_format__: