read_bam.go

package main

//Import the required libraries:
import (
	"fmt"
	"github.com/biogo/hts/bam"
	"github.com/biogo/hts/sam"
	"io"
	"os"
)

func main() {
	//Open the input file for reading:
	ifh, err := os.Open(os.Args[1])
	//Panic if something went wrong:
	if err != nil {
		panic(err)
	}

	//Create a new BAM reader with maximum
	//concurrency:
	bamReader, err := bam.NewReader(ifh, 0)
	if err != nil {
		panic(err)
	}

	for {
		//Read next record:
		record, err := bamReader.Read()
		//Break out of loop if we reached the end
		//of the file:
		if err == io.EOF {
			break
		}
		// Print out record name if read is mapped:
		if record.Flags&sam.Unmapped == 0 {
			fmt.Println(record.Name)
		}
	}
}