A SAM sanitiser in go.

samsana

package main

import (
        "fmt"
        "github.com/biogo/hts/sam"
        "io"
        "os"
)

func main() {

        reader, err := sam.NewReader(os.Stdin)
        if err != nil {
                panic(err)
        }

        writer, err := sam.NewWriter(os.Stdout, reader.Header(), 0)

        for {
                record, err := reader.Read()
                if err == io.EOF {
                        break
                }
                if err != nil {
                        fmt.Fprintf(os.Stderr, "Parse error: %s\n", err)
                } else {
                        writer.Write(record)
                }
        }
}