obitools/obitools4
2
0
Fork 0
mirror of https://github.com/metabarcoding/obitools4.git synced 2026-04-30 03:50:39 +00:00
Code Issues Packages Projects Releases Wiki Activity

introduce obidefault

Browse Source
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
Download Patch File Download Diff File Expand all files Collapse all files
pkg/obitools/obiconvert/sequence_reader.go
+3 -4
View File
@@ -12,7 +12,6 @@ import (
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obidefault"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiformats"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiiter"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obioptions"
)
func ExpandListOfFiles(check_ext bool, filenames ...string) ([]string, error) {
@@ -102,13 +101,13 @@ func CLIReadBioSequences(filenames ...string) (obiiter.IBioSequence, error) {
opts = append(opts, obiformats.OptionsReadQualities(obidefault.ReadQualities()))
nworkers := obioptions.CLIReadParallelWorkers()
nworkers := obidefault.ReadParallelWorkers()
if nworkers < 2 {
nworkers = 2
}
opts = append(opts, obiformats.OptionsParallelWorkers(nworkers))
opts = append(opts, obiformats.OptionsBatchSize(obioptions.CLIBatchSize()))
opts = append(opts, obiformats.OptionsBatchSize(obidefault.BatchSize()))
opts = append(opts, obiformats.OptionsFullFileBatch(FullFileBatch()))
@@ -159,7 +158,7 @@ func CLIReadBioSequences(filenames ...string) (obiiter.IBioSequence, error) {
nreader := 1
if CLINoInputOrder() {
nreader = obioptions.ParallelFilesRead()
nreader = obidefault.ParallelFilesRead()
}
iterator = obiformats.ReadSequencesBatchFromFiles(
pkg/obitools/obiconvert/sequence_writer.go
+3 -3
View File
@@ -8,9 +8,9 @@ import (
log "github.com/sirupsen/logrus"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obidefault"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiformats"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiiter"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obioptions"
)
func BuildPairedFileNames(filename string) (string, string) {
@@ -53,10 +53,10 @@ func CLIWriteBioSequences(iterator obiiter.IBioSequence,
opts = append(opts, obiformats.OptionsFastSeqHeaderFormat(obiformats.FormatFastSeqJsonHeader))
}
nworkers := obioptions.CLIWriteParallelWorkers()
nworkers := obidefault.WriteParallelWorkers()
opts = append(opts, obiformats.OptionsParallelWorkers(nworkers))
opts = append(opts, obiformats.OptionsBatchSize(obioptions.CLIBatchSize()))
opts = append(opts, obiformats.OptionsBatchSize(obidefault.BatchSize()))
opts = append(opts, obiformats.OptionsCompressed(CLICompressed()))