code: public static void writeGeneSequence(File file, Collection<GeneSequence> geneSequences,boolean showExonUppercase) throws Exception {
  		FileOutputStream outputStream = new FileOutputStream(file);
  		BufferedOutputStream bo = new BufferedOutputStream(outputStream);
  		writeGeneSequence(bo, geneSequences,showExonUppercase);
  		bo.close();
  		outputStream.close();
  	}
docs: Write a collection of GeneSequences to a file where if the gene is negative strand it will flip and complement the sequence
  @param file
  @param geneSequences
  @throws Exception