Refactor k-mer index management with subcommands and enhanced metadata support

This commit refactors the k-mer index management tools to use a unified subcommand structure with obik, adds support for per-set metadata and ID management, enhances the k-mer set group builder to support appending to existing groups, and improves command-line option handling with a new global options registration system.

Key changes:
- Introduce obik command with subcommands (index, ls, summary, cp, mv, rm, super, lowmask)
- Add support for per-set metadata and ID management in kmer set groups
- Implement ability to append to existing kmer index groups
- Refactor option parsing to use a global options registration system
- Add new commands for listing, copying, moving, and removing sets
- Enhance low-complexity masking with new options and output formats
- Improve kmer index summary with Jaccard distance matrix support
- Remove deprecated obikindex and obisuperkmer commands
- Update build process to use the new subcommand structure

cmd/obitools/obik/main.go

@@ -0,0 +1,34 @@
+package main
+
+import (
+	"context"
+	"errors"
+	"os"
+
+	log "github.com/sirupsen/logrus"
+
+	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obioptions"
+	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiseq"
+	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obitools/obik"
+	"github.com/DavidGamba/go-getoptions"
+)
+
+func main() {
+	defer obiseq.LogBioSeqStatus()
+
+	opt, parser := obioptions.GenerateSubcommandParser(
+		"obik",
+		"Manage disk-based kmer indices",
+		obik.OptionSet,
+	)
+
+	_, remaining := parser(os.Args)
+
+	err := opt.Dispatch(context.Background(), remaining)
+	if err != nil {
+		if errors.Is(err, getoptions.ErrorHelpCalled) {
+			os.Exit(0)
+		}
+		log.Fatalf("Error: %v", err)
+	}
+}

cmd/obitools/obikindex/main.go

@@ -1,23 +0,0 @@
-package main
-
-import (
-	"os"
-
-	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obioptions"
-	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obitools/obiconvert"
-	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obitools/obikindex"
-)
-
-func main() {
-	optionParser := obioptions.GenerateOptionParser(
-		"obikindex",
-		"builds a disk-based kmer index from sequence files",
-		obikindex.OptionSet)
-
-	_, args := optionParser(os.Args)
-
-	sequences, err := obiconvert.CLIReadBioSequences(args...)
-	obiconvert.OpenSequenceDataErrorMessage(args, err)
-
-	obikindex.CLIBuildKmerIndex(sequences)
-}

cmd/obitools/obilowmask/main.go

@@ -1,47 +0,0 @@
-package main
-
-import (
-	"os"
-
-	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obioptions"
-	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiseq"
-	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obitools/obiconvert"
-	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obitools/obilowmask"
-	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiutils"
-)
-
-func main() {
-
-	defer obiseq.LogBioSeqStatus()
-
-	// go tool pprof -http=":8000" ./obipairing ./cpu.pprof
-	// f, err := os.Create("cpu.pprof")
-	// if err != nil {
-	// 	log.Fatal(err)
-	// }
-	// pprof.StartCPUProfile(f)
-	// defer pprof.StopCPUProfile()
-
-	// go tool trace cpu.trace
-	// ftrace, err := os.Create("cpu.trace")
-	// if err != nil {
-	// 	log.Fatal(err)
-	// }
-	// trace.Start(ftrace)
-	// defer trace.Stop()
-
-	optionParser := obioptions.GenerateOptionParser(
-		"obimicrosat",
-		"looks for microsatellites sequences in a sequence file",
-		obilowmask.OptionSet)
-
-	_, args := optionParser(os.Args)
-
-	sequences, err := obiconvert.CLIReadBioSequences(args...)
-	obiconvert.OpenSequenceDataErrorMessage(args, err)
-
-	selected := obilowmask.CLISequenceEntropyMasker(sequences)
-	obiconvert.CLIWriteBioSequences(selected, true)
-	obiutils.WaitForLastPipe()
-
-}

cmd/obitools/obisuperkmer/main.go

@@ -1,34 +0,0 @@
-package main
-
-import (
-	"os"
-
-	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obioptions"
-	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obitools/obiconvert"
-	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obitools/obisuperkmer"
-	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiutils"
-)
-
-func main() {
-	// Generate option parser
-	optionParser := obioptions.GenerateOptionParser(
-		"obisuperkmer",
-		"extract super k-mers from sequence files",
-		obisuperkmer.OptionSet)
-
-	// Parse command-line arguments
-	_, args := optionParser(os.Args)
-
-	// Read input sequences
-	sequences, err := obiconvert.CLIReadBioSequences(args...)
-	obiconvert.OpenSequenceDataErrorMessage(args, err)
-
-	// Extract super k-mers
-	superkmers := obisuperkmer.CLIExtractSuperKmers(sequences)
-
-	// Write output sequences
-	obiconvert.CLIWriteBioSequences(superkmers, true)
-
-	// Wait for pipeline completion
-	obiutils.WaitForLastPipe()
-}