obitools4/cmd/obitools/obicount/main.go

package main

import (
	"fmt"
	"log"
	"os"

	"git.metabarcoding.org/lecasofts/go/obitools/pkg/obitools/obiconvert"
	"git.metabarcoding.org/lecasofts/go/obitools/pkg/obitools/obicount"

	"git.metabarcoding.org/lecasofts/go/obitools/pkg/obioptions"
)

func main() {

	// f, err := os.Create("cpu.pprof")
	// if err != nil {
	// 	log.Fatal(err)
	// }
	// pprof.StartCPUProfile(f)
	// defer pprof.StopCPUProfile()

	// ftrace, err := os.Create("cpu.trace")
	// if err != nil {
	// 	log.Fatal(err)
	// }
	// trace.Start(ftrace)
	// defer trace.Stop()

	optionParser := obioptions.GenerateOptionParser(
		obiconvert.InputOptionSet,
		obicount.OptionSet,
	)

	_, args, _ := optionParser(os.Args)

	fs, _ := obiconvert.ReadBioSequences(args...)
	nread := 0
	nvariant := 0
	nsymbol := 0
	for fs.Next() {
		s := fs.Get()
		if s==nil {
			log.Panicln("Read sequence is nil")
		}
		nread += s.Count()
		nvariant++
		nsymbol += s.Length()
		s.Recycle()
	}

	if obicount.CLIIsPrintingVariantCount() {
		fmt.Printf(" %d", nvariant)
	}

	if obicount.CLIIsPrintingReadCount() {
		fmt.Printf(" %d", nread)
	}

	if obicount.CLIIsPrintingSymbolCount() {
		fmt.Printf(" %d", nsymbol)
	}

	fmt.Printf("\n")
}