Go program to read and write a .gz file (fastq.gz)

main.go

package main

import (
	"fmt"
	// "compress/gzip"
	gzip "github.com/klauspost/pgzip"
	"bufio"
	"os"
	"log"
)

func GetReader(inputFilepath string) (*bufio.Reader, *os.File, *os.File) {
	// defer file.Close()
	// defer gzFile.Close()
	var reader *bufio.Reader
	var file *os.File
	var gzFile *os.File
	bufferSize := 1048576 // default 4096: 4KB ; 1048576 : 1MB ; 10485760 : 10MB

	file, err := os.Open(inputFilepath)
	if err != nil {
		log.Fatalf("Error opening file: %v\n", err)
	}

	gz, err := gzip.NewReader(file)
	if err != nil {
		log.Fatalf("Error opening file: %v\n", err)
	}

	reader = bufio.NewReaderSize(gz, bufferSize)

	return reader, file, gzFile
}

func GetWriter(outputFilepath string) (*os.File, *gzip.Writer) {
	// GzWriter.Flush()
	// GzWriter.Close()
	// File.Close()
	outputFile, err := os.Create(outputFilepath)
	if err != nil {
		log.Fatalf("Error creating output file: %v\n", err)
	}

	writer, err := gzip.NewWriterLevel(outputFile, gzip.BestCompression)
	if err != nil {
		log.Fatalf("Error creating output writer: %v\n", err)
	}
	return outputFile, writer
}

func main(){
	// input
	inputFilepath := "data/test1.fastq.gz"
	reader, file, gzFile := GetReader(inputFilepath)
	defer file.Close()
	defer gzFile.Close()

	// output
	outputFilepath := "data.gz"
	outputFile, writer := GetWriter(outputFilepath)
	defer outputFile.Close()

	var delim byte = '\n'

	for {
		line, err := reader.ReadBytes(delim) // includes the delim in the output line !!
		if err != nil {
			break // end of file io.EOF
		}
		writer.Write(line)
	}
	writer.Flush()
	writer.Close()

	fmt.Println("done")
}