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Refactoring codes for removing buffer size options. An some other changes...

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Former-commit-id: 10b57cc1a27446ade3c444217341e9651e89cdce
This commit is contained in:
Eric Coissac
2023-03-07 11:12:13 +07:00
parent 9811e440b8
commit d88de15cdc
52 changed files with 1172 additions and 421 deletions
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pkg/obitools/obiconvert/options.go
+17 -14
View File
@@ -60,6 +60,21 @@ func InputOptionSet(options *getoptions.GetOpt) {
}
func OutputModeOptionSet(options *getoptions.GetOpt) {
options.BoolVar(&__no_progress_bar__, "no-progressbar", false,
options.Description("Disable the progress bar printing"))
options.BoolVar(&__compressed__, "compress", false,
options.Alias("Z"),
options.Description("Output is compressed"))
options.StringVar(&__output_file_name__, "out", __output_file_name__,
options.Alias("o"),
options.ArgName("FILENAME"),
options.Description("Filename used for saving the output"),
)
}
func OutputOptionSet(options *getoptions.GetOpt) {
options.BoolVar(&__output_in_fasta__, "fasta-output", false,
options.Description("Read data following the ecoPCR output format."))
@@ -73,19 +88,7 @@ func OutputOptionSet(options *getoptions.GetOpt) {
options.Alias("O"),
options.Description("output FASTA/FASTQ title line annotations follow OBI format."))
options.BoolVar(&__no_progress_bar__, "no-progressbar", false,
options.Description("Disable the progress bar printing"))
options.BoolVar(&__compressed__, "compress", false,
options.Alias("Z"),
options.Description("Output is compressed"))
options.StringVar(&__output_file_name__, "out", __output_file_name__,
options.Alias("o"),
options.ArgName("FILENAME"),
options.Description("Filename used for saving the output"),
)
OutputModeOptionSet(options)
}
func PairedFilesOptionSet(options *getoptions.GetOpt) {
@@ -197,4 +200,4 @@ func CLIHasPairedFile() bool {
}
func CLIPairedFileName() string {
return __paired_file_name__
}
}
pkg/obitools/obiconvert/sequence_reader.go
+5 -2
View File
@@ -48,6 +48,10 @@ func _ExpandListOfFiles(check_ext bool, filenames ...string) ([]string, error) {
strings.HasSuffix(path, "fasta.gz") ||
strings.HasSuffix(path, "fastq") ||
strings.HasSuffix(path, "fastq.gz") ||
strings.HasSuffix(path, "seq") ||
strings.HasSuffix(path, "seq.gz") ||
strings.HasSuffix(path, "gb") ||
strings.HasSuffix(path, "gb.gz") ||
strings.HasSuffix(path, "dat") ||
strings.HasSuffix(path, "dat.gz") ||
strings.HasSuffix(path, "ecopcr") ||
@@ -82,13 +86,12 @@ func CLIReadBioSequences(filenames ...string) (obiiter.IBioSequence, error) {
opts = append(opts, obiformats.OptionsFastSeqHeaderParser(obiformats.ParseGuessedFastSeqHeader))
}
nworkers := obioptions.CLIParallelWorkers() // / 4
nworkers := obioptions.CLIParallelWorkers()
if nworkers < 2 {
nworkers = 2
}
opts = append(opts, obiformats.OptionsParallelWorkers(nworkers))
opts = append(opts, obiformats.OptionsBufferSize(obioptions.CLIBufferSize()))
opts = append(opts, obiformats.OptionsBatchSize(obioptions.CLIBatchSize()))
opts = append(opts, obiformats.OptionsQualityShift(CLIInputQualityShift()))
pkg/obitools/obiconvert/sequence_writer.go
-1
View File
@@ -60,7 +60,6 @@ func CLIWriteBioSequences(iterator obiiter.IBioSequence,
}
opts = append(opts, obiformats.OptionsParallelWorkers(nworkers))
opts = append(opts, obiformats.OptionsBufferSize(obioptions.CLIBufferSize()))
opts = append(opts, obiformats.OptionsBatchSize(obioptions.CLIBatchSize()))
opts = append(opts, obiformats.OptionsQualityShift(CLIOutputQualityShift()))