docs: private Input processRegularFileInput(String input) throws IOException {
      File inputFile = new File(input);
      if (!inputFile.exists()) {
        throw new IOException("Input does not exist: " + input);
      }
      if (pipeFiles) {
        SamReader samReader = SamReaderFactory.makeDefault().open(inputFile);
        return new Input(input, STDIN_FILE_NAME, 
            new SamReaderToSAMFilePump(samReader)); 
      } else {
        return new Input(input, input, null);
      }
    }