case "calls-from-preds":
		cmd.RunCallsFromPreds(os.Args[2:])

	case "calls":
		cmd.RunCalls(os.Args[2:])

	fmt.Fprintf(os.Stderr, "  calls-from-preds  Extract clustered calls from ML predictions CSV\n")

	fmt.Fprintf(os.Stderr, "  calls             Extract/analyze bird calls (subcommands: from-preds)\n")

	fmt.Fprintf(os.Stderr, "  %s calls-from-preds --csv predictions.csv > calls.json\n", os.Args[0])

	fmt.Fprintf(os.Stderr, "  %s calls from-preds --csv predictions.csv > calls.json\n", os.Args[0])

package cmd
import (
	"encoding/json"
	"flag"
	"fmt"
	"os"
	"skraak/tools"
)
// RunCallsFromPreds handles the "calls-from-preds" command
func RunCallsFromPreds(args []string) {
	fs := flag.NewFlagSet("calls-from-preds", flag.ExitOnError)
	csvPath := fs.String("csv", "", "Path to predictions CSV file (required)")
	fs.Usage = func() {
		fmt.Fprintf(os.Stderr, "Usage: skraak calls-from-preds [options]\n\n")
		fmt.Fprintf(os.Stderr, "Extract clustered bird calls from ML predictions CSV.\n")
		fmt.Fprintf(os.Stderr, "Reads prediction CSV with columns: file, start_time, end_time, <ebird_codes...>\n")
		fmt.Fprintf(os.Stderr, "Each row is a clip with 1=present, 0=absent for each species.\n\n")
		fmt.Fprintf(os.Stderr, "Options:\n")
		fs.PrintDefaults()
		fmt.Fprintf(os.Stderr, "\nOutput:\n")
		fmt.Fprintf(os.Stderr, "  JSON with clustered calls (file, start_time, end_time, ebird_code, detections)\n")
		fmt.Fprintf(os.Stderr, "\nExamples:\n")
		fmt.Fprintf(os.Stderr, "  skraak calls-from-preds --csv predictions.csv > calls.json\n")
		fmt.Fprintf(os.Stderr, "  skraak calls-from-preds --csv preds.csv | jq '.calls[] | select(.ebird_code==\"kea1\")'\n")
	}
	if err := fs.Parse(args); err != nil {
		os.Exit(1)
	}
	// Validate required flags
	if *csvPath == "" {
		fmt.Fprintf(os.Stderr, "Error: --csv is required\n\n")
		fs.Usage()
		os.Exit(1)
	}
	input := tools.CallsFromPredsInput{
		CSVPath: *csvPath,
	}
	fmt.Fprintf(os.Stderr, "Extracting calls from predictions: %s\n", *csvPath)
	output, err := tools.CallsFromPreds(input)
	if err != nil {
		fmt.Fprintf(os.Stderr, "Error: %v\n", err)
		os.Exit(1)
	}
	fmt.Fprintf(os.Stderr, "Found %d clustered calls across %d species\n",
		output.TotalCalls, len(output.SpeciesCount))
	fmt.Fprintf(os.Stderr, "Clip duration: %.1fs, Gap threshold: %.1fs\n",
		output.ClipDuration, output.GapThreshold)
	// Output JSON to stdout
	enc := json.NewEncoder(os.Stdout)
	enc.SetIndent("", "  ")
	enc.Encode(output)
}

package cmd
import (
	"encoding/json"
	"flag"
	"fmt"
	"os"
	"skraak/tools"
)
// RunCalls handles the "calls" command
func RunCalls(args []string) {
	if len(args) < 1 {
		printCallsUsage()
		os.Exit(1)
	}
	switch args[0] {
	case "from-preds":
		runCallsFromPreds(args[1:])
	default:
		fmt.Fprintf(os.Stderr, "Unknown calls subcommand: %s\n\n", args[0])
		printCallsUsage()
		os.Exit(1)
	}
}
func printCallsUsage() {
	fmt.Fprintf(os.Stderr, "Usage: skraak calls <subcommand> [options]\n\n")
	fmt.Fprintf(os.Stderr, "Subcommands:\n")
	fmt.Fprintf(os.Stderr, "  from-preds  Extract clustered calls from ML predictions CSV\n")
	fmt.Fprintf(os.Stderr, "\nExamples:\n")
	fmt.Fprintf(os.Stderr, "  skraak calls from-preds --csv predictions.csv > calls.json\n")
	fmt.Fprintf(os.Stderr, "  skraak calls from-preds --csv preds.csv | jq '.calls[] | select(.ebird_code==\"kea1\")'\n")
}
// runCallsFromPreds handles the "calls from-preds" subcommand
func runCallsFromPreds(args []string) {
	fs := flag.NewFlagSet("calls from-preds", flag.ExitOnError)
	csvPath := fs.String("csv", "", "Path to predictions CSV file (required)")
	fs.Usage = func() {
		fmt.Fprintf(os.Stderr, "Usage: skraak calls from-preds [options]\n\n")
		fmt.Fprintf(os.Stderr, "Extract clustered bird calls from ML predictions CSV.\n")
		fmt.Fprintf(os.Stderr, "Reads prediction CSV with columns: file, start_time, end_time, <ebird_codes...>\n")
		fmt.Fprintf(os.Stderr, "Each row is a clip with 1=present, 0=absent for each species.\n\n")
		fmt.Fprintf(os.Stderr, "Options:\n")
		fs.PrintDefaults()
		fmt.Fprintf(os.Stderr, "\nOutput:\n")
		fmt.Fprintf(os.Stderr, "  JSON with clustered calls (file, start_time, end_time, ebird_code, detections)\n")
		fmt.Fprintf(os.Stderr, "\nExamples:\n")
		fmt.Fprintf(os.Stderr, "  skraak calls from-preds --csv predictions.csv > calls.json\n")
		fmt.Fprintf(os.Stderr, "  skraak calls from-preds --csv preds.csv | jq '.calls[] | select(.ebird_code==\"kea1\")'\n")
	}
	if err := fs.Parse(args); err != nil {
		os.Exit(1)
	}
	// Validate required flags
	if *csvPath == "" {
		fmt.Fprintf(os.Stderr, "Error: --csv is required\n\n")
		fs.Usage()
		os.Exit(1)
	}
	input := tools.CallsFromPredsInput{
		CSVPath: *csvPath,
	}
	fmt.Fprintf(os.Stderr, "Extracting calls from predictions: %s\n", *csvPath)
	output, err := tools.CallsFromPreds(input)
	if err != nil {
		fmt.Fprintf(os.Stderr, "Error: %v\n", err)
		os.Exit(1)
	}
	fmt.Fprintf(os.Stderr, "Found %d clustered calls across %d species\n",
		output.TotalCalls, len(output.SpeciesCount))
	fmt.Fprintf(os.Stderr, "Clip duration: %.1fs, Gap threshold: %.1fs\n",
		output.ClipDuration, output.GapThreshold)
	// Output JSON to stdout
	enc := json.NewEncoder(os.Stdout)
	enc.SetIndent("", "  ")
	enc.Encode(output)
}