 
     // generate keys into the scratch table
     parallel<system>::for_each(thrust::make_counting_iterator(0u),
-                     thrust::make_counting_iterator(0u) + context.cigar.cigar_event_read_coordinates.size(),
-                     covariate_gatherer<system, covariate_table>(context, batch.device));
+                               thrust::make_counting_iterator(0u) + context.cigar.cigar_event_read_coordinates.size(),
+                               covariate_gatherer<system, covariate_table>(context, batch.device));
 
     covariates_gather.stop();
 

    // compute the "high quality" windows (i.e., clip off low quality ends from each read)
    cv.high_quality_window.resize(batch.device.num_reads);
    parallel<system>::for_each(context.active_read_list.begin(),
                     context.active_read_list.end(),
                     compute_high_quality_windows<system>(context, batch.device));

    build_covariates_table<covariate_table_quality<system> >(cv.quality, context, batch);
    build_covariates_table<covariate_table_cycle_illumina<system> >(cv.cycle, context, batch);


    // set up a scratch table space with enough room for 3 keys per cigar event
    scratch_table.resize(context.cigar.cigar_events.size() * 3);
    flags.resize(context.cigar.cigar_events.size() * 3);

    // mark all keys as invalid
