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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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7
pkg/obitools/obiconvert/sequence_reader.go
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@ -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()))