public static boolean isPairedEndDirectory(final File dir){
  if (dir == null || !dir.exists() || !dir.isDirectory()) {
    return false;
  }
  final File lDir=new File(dir,"left");
  final File rDir=new File(dir,"right");
  return lDir.exists() && rDir.exists() && lDir.isDirectory()&& rDir.isDirectory();
}

public static boolean isPairedEndDirectory ( final File dir ) { if ( dir == null || ! dir . exists ( ) || ! dir . isDirectory ( ) ) { return false ; } final File lDir = new File ( dir , "left" ) ; final File rDir = new File ( dir , "right" ) ; return lDir . exists ( ) && rDir . exists ( ) && lDir . isDirectory ( ) && rDir . isDirectory ( ) ; }
tells you if the directory passed in contains a paired end sdf left / right folder
