def subsample_input

      if @options[:skip_subsample]
        logger.info "Skipping subsample step (--skip-subsample is on)"
        @options[:left_subset] = @options[:left]
        @options[:right_subset] = @options[:right]
        return
      end

      logger.info "Subsampling reads"

      seed = @options[:seed]
      seed = Time.now.to_i if seed == -1
      logger.info "Using random seed #{seed}"
      l = @options[:left]
      r = @options[:right]
      size = @options[:subsample_size]

      sampler = Sampler.new
      if @options[:sampler] == "stream"
        ls, rs = sampler.sample_stream(l, r, size, seed)
      elsif @options[:sampler] == "graph"
        ls, rs = sampler.sample_graph(l, r, size, seed)
      else
        logger.error "sampler #{@options[:sampler]} was not a valid choice"
        logger.error "please user --help to see the options"
        exit 1
      end

      @options[:left_subset] = ls
      @options[:right_subset] = rs

    end
def subsample_input

      if @options[:skip_subsample]
        logger.info "Skipping subsample step (--skip-subsample is on)"
        @options[:left_subset] = @options[:left]
        @options[:right_subset] = @options[:right]
        return
      end

      logger.info "Subsampling reads"

      seed = @options[:seed]
      seed = Time.now.to_i if seed == -1
      logger.info "Using random seed #{seed}"
      l = @options[:left]
      r = @options[:right]
      size = @options[:subsample_size]

      sampler = Sampler.new
      if @options[:sampler] == "stream"
        ls, rs = sampler.sample_stream(l, r, size, seed)
      elsif @options[:sampler] == "graph"
        ls, rs = sampler.sample_graph(l, r, size, seed)
      else
        logger.error "sampler #{@options[:sampler]} was not a valid choice"
        logger.error "please user --help to see the options"
        exit 1
      end

      @options[:left_subset] = ls
      @options[:right_subset] = rs

    end
Run the subsampler on the input reads, storing
 the paths to the samples in the assembler_options
 hash.