     uint32 input_set  = 0;
     uint32 n_reads    = 0;
 
+    io::SequenceDataHost local_read_data_host;
+
     // loop through the batches of reads
     for (uint32 read_begin = 0; true; read_begin += BATCH_SIZE)
     {

    uint32 input_set  = 0;
    uint32 n_reads    = 0;

    // loop through the batches of reads
    for (uint32 read_begin = 0; true; read_begin += BATCH_SIZE)
    {

        }

        // make a local copy of the host batch
        local_read_data_host = *read_data_host;

        // mark this set as ready to be reused
        input_thread.read_data[ input_set ] = NULL;
