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https://github.com/metabarcoding/obitools4.git
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ac41dd8a22
Refactor k-mer matching to use a pipeline architecture with improved concurrency and memory management: - Replace sort.Slice with slices.SortFunc and cmp.Compare for better performance - Introduce PreparedQueries struct to encapsulate query buckets with metadata - Implement MergeQueries function to merge query buckets from multiple batches - Rewrite MatchBatch to use pre-allocated results and mutexes instead of map-based accumulation - Add seek optimization in matchPartition to reduce linear scanning - Refactor match command to use a multi-stage pipeline with proper batching and merging - Add index directory option for match command - Improve parallel processing of sequence batches This refactoring improves performance by reducing memory allocations, optimizing k-mer lookup, and implementing a more efficient pipeline for large-scale k-mer matching operations.
86 lines
3.1 KiB
Go
86 lines
3.1 KiB
Go
package obik
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import (
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"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obitools/obiconvert"
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"github.com/DavidGamba/go-getoptions"
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)
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// OptionSet registers all obik subcommands on the root GetOpt.
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func OptionSet(opt *getoptions.GetOpt) {
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// index: build or extend a kmer index from sequence files
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indexCmd := opt.NewCommand("index", "Build a disk-based kmer index from sequence files")
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obiconvert.InputOptionSet(indexCmd)
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obiconvert.OutputModeOptionSet(indexCmd, false)
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KmerIndexOptionSet(indexCmd)
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indexCmd.StringMapVar(&_setMetaTags, "tag", 1, 1,
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indexCmd.Alias("T"),
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indexCmd.ArgName("KEY=VALUE"),
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indexCmd.Description("Per-set metadata tag (repeatable)."))
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indexCmd.SetCommandFn(runIndex)
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// ls: list sets in a kmer index
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lsCmd := opt.NewCommand("ls", "List sets in a kmer index")
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OutputFormatOptionSet(lsCmd)
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SetSelectionOptionSet(lsCmd)
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lsCmd.SetCommandFn(runLs)
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// summary: detailed statistics
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summaryCmd := opt.NewCommand("summary", "Show detailed statistics of a kmer index")
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OutputFormatOptionSet(summaryCmd)
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summaryCmd.BoolVar(&_jaccard, "jaccard", false,
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summaryCmd.Description("Compute and display pairwise Jaccard distance matrix."))
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summaryCmd.SetCommandFn(runSummary)
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// cp: copy sets between indices
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cpCmd := opt.NewCommand("cp", "Copy sets between kmer indices")
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SetSelectionOptionSet(cpCmd)
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ForceOptionSet(cpCmd)
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cpCmd.SetCommandFn(runCp)
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// mv: move sets between indices
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mvCmd := opt.NewCommand("mv", "Move sets between kmer indices")
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SetSelectionOptionSet(mvCmd)
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ForceOptionSet(mvCmd)
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mvCmd.SetCommandFn(runMv)
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// rm: remove sets from an index
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rmCmd := opt.NewCommand("rm", "Remove sets from a kmer index")
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SetSelectionOptionSet(rmCmd)
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rmCmd.SetCommandFn(runRm)
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// spectrum: output k-mer frequency spectrum as CSV
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spectrumCmd := opt.NewCommand("spectrum", "Output k-mer frequency spectrum as CSV")
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SetSelectionOptionSet(spectrumCmd)
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obiconvert.OutputModeOptionSet(spectrumCmd, false)
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spectrumCmd.SetCommandFn(runSpectrum)
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// super: extract super k-mers from sequences
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superCmd := opt.NewCommand("super", "Extract super k-mers from sequence files")
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obiconvert.InputOptionSet(superCmd)
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obiconvert.OutputOptionSet(superCmd)
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SuperKmerOptionSet(superCmd)
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superCmd.SetCommandFn(runSuper)
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// lowmask: mask low-complexity regions
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lowmaskCmd := opt.NewCommand("lowmask", "Mask low-complexity regions in sequences using entropy")
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obiconvert.InputOptionSet(lowmaskCmd)
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obiconvert.OutputOptionSet(lowmaskCmd)
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LowMaskOptionSet(lowmaskCmd)
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lowmaskCmd.SetCommandFn(runLowmask)
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// match: annotate sequences with k-mer match positions from an index
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matchCmd := opt.NewCommand("match", "Annotate sequences with k-mer match positions from an index")
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IndexDirectoryOptionSet(matchCmd)
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obiconvert.InputOptionSet(matchCmd)
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obiconvert.OutputOptionSet(matchCmd)
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SetSelectionOptionSet(matchCmd)
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matchCmd.SetCommandFn(runMatch)
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// filter: filter an index to remove low-complexity k-mers
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filterCmd := opt.NewCommand("filter", "Filter a kmer index to remove low-complexity k-mers")
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obiconvert.OutputModeOptionSet(filterCmd, false)
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EntropyFilterOptionSet(filterCmd)
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SetSelectionOptionSet(filterCmd)
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filterCmd.SetCommandFn(runFilter)
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}
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