     // 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));
+                               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);


    // 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));

    covariates_gather.stop();



    // flag valid keys
    parallel<system>::for_each(thrust::make_counting_iterator(0u),
                               thrust::make_counting_iterator(0u) + cv.scratch_table_space.keys.size(),
                               flag_valid_keys<system, covariate_table>(context, batch.device, flags));

    // count valid keys
    uint32 valid_keys = thrust::reduce(flags.begin(), flags.end(), uint32(0));
