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Adds the command obimultiplex

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This commit is contained in:
Eric Coissac
2022-02-01 17:31:28 +01:00
parent 76d9309508
commit 8dbda68746
13 changed files with 688 additions and 79 deletions
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6
pkg/obitools/obiconvert/sequence_reader.go
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@ -81,14 +81,14 @@ func ReadBioSequencesBatch(filenames ...string) (obiseq.IBioSequenceBatch, error
opts = append(opts, obiformats.OptionsFastSeqHeaderParser(obiformats.ParseGuessedFastSeqHeader))
}
nworkers := obioptions.ParallelWorkers() / 4
nworkers := obioptions.CLIParallelWorkers() / 4
if nworkers < 2 {
nworkers = 2
}
opts = append(opts, obiformats.OptionsParallelWorkers(nworkers))
opts = append(opts, obiformats.OptionsBufferSize(obioptions.BufferSize()))
opts = append(opts, obiformats.OptionsBatchSize(obioptions.BatchSize()))
opts = append(opts, obiformats.OptionsBufferSize(obioptions.CLIBufferSize()))
opts = append(opts, obiformats.OptionsBatchSize(obioptions.CLIBatchSize()))
opts = append(opts, obiformats.OptionsQualityShift(InputQualityShift()))