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https://github.com/metabarcoding/obitools4.git
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64 lines
1.7 KiB
Go
64 lines
1.7 KiB
Go
package obipcr
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import (
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"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiapat"
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"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiiter"
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"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obioptions"
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log "github.com/sirupsen/logrus"
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)
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// CLIPCR iterates over sequences provided by a obiseq.IBioSequenceBatch
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// and returns an other obiseq.IBioSequenceBatch distributing
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// obiseq.BioSequenceBatch containing the selected amplicon sequences.
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func CLIPCR(iterator obiiter.IBioSequence) (obiiter.IBioSequence, error) {
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opts := make([]obiapat.WithOption, 0, 10)
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opts = append(opts,
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obiapat.OptionForwardPrimer(
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CLIForwardPrimer(),
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CLIAllowedMismatch(),
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),
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obiapat.OptionReversePrimer(
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CLIReversePrimer(),
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CLIAllowedMismatch(),
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),
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obiapat.OptionOnlyFullExtension(CLIOnlyFull()),
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)
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if CLIMinLength() > 0 {
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opts = append(opts, obiapat.OptionMinLength(CLIMinLength()))
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}
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if CLIWithExtension() {
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opts = append(opts, obiapat.OptionWithExtension(CLIExtension()))
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}
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opts = append(opts, obiapat.OptionMaxLength(CLIMaxLength()))
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if CLICircular() {
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opts = append(opts, obiapat.OptionCircular(CLICircular()))
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}
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worker := obiapat.PCRSliceWorker(opts...)
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if CLIFragmented() {
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frags := obiiter.IFragments(
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CLIMaxLength()*1000,
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CLIMaxLength()*100,
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CLIMaxLength()+max(len(CLIForwardPrimer()),
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len(CLIReversePrimer()))+min(len(CLIForwardPrimer()),
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len(CLIReversePrimer()))/2,
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100,
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obioptions.CLIParallelWorkers(),
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)
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log.Infof("Fragmenting sequence longer than %dbp into chuncks of %dbp",
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CLIMaxLength()*1000,
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CLIMaxLength()*100,
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)
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iterator = iterator.Pipe(frags)
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}
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return iterator.LimitMemory(0.5).MakeISliceWorker(worker, false, obioptions.CLIParallelWorkers()), nil
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}
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