package main

import (
	"fmt"
	"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/obimatrix"
)

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(
		"obimatrix",
		"",
		obimatrix.OptionSet,
	)

	_, args := optionParser(os.Args)

	fs, err := obiconvert.CLIReadBioSequences(args...)
	obiconvert.OpenSequenceDataErrorMessage(args, err)

	matrix := obimatrix.IMatrix(fs)

	if obimatrix.CLIOutFormat() == "matrix" {
		obimatrix.CLIWriteCSVToStdout(matrix)
	} else {
		obimatrix.CLIWriteThreeColumnsToStdout(matrix)
	}
	fmt.Printf("\n")
}