code: static String getSubjectId(final File fastaFile){
      	String fileAsString = fastaFile.toString();
      	List<String> alleleParts = Splitter.on("_").splitToList(fileAsString);
      	List<String> pathParts  = Splitter.on("/").splitToList(alleleParts.get(0));
      	return pathParts.get(pathParts.size()-1);
      }
docs: Extract consensus sequences from a file in HML format.
  
  @param inputHmlFile input HML file, if any