 #include <nvbio/strings/infix.h>
 #include <nvbio/strings/seeds.h>
 #include <nvbio/fmindex/mem.h>
-#include <nvbio/io/reads/reads.h>
+#include <nvbio/io/sequence/sequence.h>
 #include <nvbio/io/fmi.h>
 
 using namespace nvbio;

        mem_filter.rank(
            f_index,
            r_index,
            d_read_data.const_read_string_set(),
            min_intv,
            max_intv,
            min_span );

    const uint32 mems_batch = 16*1024*1024;
    nvbio::vector<device_tag,mem_filter_type::mem_type> mems( mems_batch );

    io::SequenceDataHost<DNA_N> h_read_data;

    // load a batch of reads
    while (io::next( &h_read_data, read_data_file.get(), batch_reads, batch_bps ))
    {
        log_info(stderr, "  loading reads... started\n");

        // copy it to the device
        const io::SequenceDataDevice<DNA_N> d_read_data( h_read_data );

        const uint32 n_reads = d_read_data.size() / 2;

