public void installReferenceConfiguration(SequencesReader sr) throws IOException {
  final File sdfDir=sr.path();
  if (sdfDir == null) {
    throw new IOException("Could not find SDF directory");
  }
  final File refTxt=new File(sdfDir,ReferenceGenome.REFERENCE_FILE);
  if (refTxt.exists()) {
    throw new IOException(refTxt + " already exists");
  }
  try (OutputStream stream=FileUtils.createOutputStream(refTxt);InputStream refTxtStream=Resources.getResourceAsStream(mRefTxt)){
    FileUtils.streamToStream(refTxtStream,stream,4096);
  }
 }

public void installReferenceConfiguration ( SequencesReader sr ) throws IOException { final File sdfDir = sr . path ( ) ; if ( sdfDir == null ) { throw new IOException ( "Could not find SDF directory" ) ; } final File refTxt = new File ( sdfDir , ReferenceGenome . REFERENCE_FILE ) ; if ( refTxt . exists ( ) ) { throw new IOException ( refTxt + " already exists" ) ; } try ( OutputStream stream = FileUtils . createOutputStream ( refTxt ) ; InputStream refTxtStream = Resources . getResourceAsStream ( mRefTxt ) ) { FileUtils . streamToStream ( refTxtStream , stream , 4096 ) ; } }
installs linked reference configuration into sdf
