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https://github.com/metabarcoding/obitools4.git
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9babcc0fae
Refactor lowmask options to use shared kmer options and CLI getters This commit refactors the lowmask subcommand to use shared kmer options and CLI getters instead of local variables. It also moves the kmer size and minimizer size options to a shared location and adds new CLI getters for the lowmask options. - Move kmer size and minimizer size options to shared location - Add CLI getters for lowmask options - Refactor lowmask to use CLI getters - Remove unused strings import - Add MaskingMode type and related functions
50 lines
1.3 KiB
Go
50 lines
1.3 KiB
Go
package obik
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import (
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"context"
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"fmt"
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log "github.com/sirupsen/logrus"
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"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obidefault"
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"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obikmer"
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"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obitools/obiconvert"
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"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiutils"
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"github.com/DavidGamba/go-getoptions"
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)
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// runSuper implements the "obik super" subcommand.
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// It extracts super k-mers from DNA sequences.
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func runSuper(ctx context.Context, opt *getoptions.GetOpt, args []string) error {
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k := CLIKmerSize()
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m := CLIMinimizerSize()
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if k < 2 || k > 31 {
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return fmt.Errorf("invalid k-mer size: %d (must be between 2 and 31)", k)
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}
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if m < 1 || m >= k {
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return fmt.Errorf("invalid parameters: minimizer size (%d) must be between 1 and k-1 (%d)", m, k-1)
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}
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log.Printf("Extracting super k-mers with k=%d, m=%d", k, m)
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sequences, err := obiconvert.CLIReadBioSequences(args...)
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if err != nil {
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return fmt.Errorf("failed to open sequence files: %w", err)
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}
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worker := obikmer.SuperKmerWorker(k, m)
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superkmers := sequences.MakeIWorker(
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worker,
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false,
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obidefault.ParallelWorkers(),
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)
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obiconvert.CLIWriteBioSequences(superkmers, true)
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obiutils.WaitForLastPipe()
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return nil
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}
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