sufsort.h

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/*
 * nvbio
 * Copyright (c) 2011-2014, NVIDIA CORPORATION. All rights reserved.
 * 
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 * modification, are permitted provided that the following conditions are met:
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 *      notice, this list of conditions and the following disclaimer.
 *    * Redistributions in binary form must reproduce the above copyright
 *      notice, this list of conditions and the following disclaimer in the
 *      documentation and/or other materials provided with the distribution.
 *    * Neither the name of the NVIDIA CORPORATION nor the
 *      names of its contributors may be used to endorse or promote products
 *      derived from this software without specific prior written permission.
 * 
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#pragma once

#include <nvbio/strings/string_set.h>
#include <nvbio/basic/thrust_view.h>
#include <nvbio/basic/cuda/sort.h>
#include <thrust/device_vector.h>
#include <thrust/transform_scan.h>
#include <thrust/sort.h>



namespace nvbio {


struct BWTParams
{
    BWTParams() :
        host_memory(8u*1024u*1024u*1024llu),
        device_memory(2u*1024u*1024u*1024llu),
        bucketing_bits(16u),
        radix_slice(4u),
        cpu_bucketing(0u) {}

    uint64 host_memory;
    uint64 device_memory;
    uint32 bucketing_bits;
    uint32 radix_slice;
    uint32 cpu_bucketing;
};


namespace cuda {


template <typename string_type>
typename string_type::index_type find_primary(
    const typename string_type::index_type  string_len,
    const string_type                       string);

template <typename string_type, typename output_iterator>
void suffix_sort(
    const typename stream_traits<string_type>::index_type   string_len,
    const string_type                                       string,
    output_iterator                                         output,
    BWTParams*                                              params);

template <typename string_type, typename output_handler>
void blockwise_suffix_sort(
    const typename string_type::index_type  string_len,
    string_type                             string,
    output_handler&                         output,
    BWTParams*                              params);

template <typename string_type, typename output_iterator>
typename string_type::index_type bwt(
    const typename string_type::index_type  string_len,
    string_type                             string,
    output_iterator                         output,
    BWTParams*                              params);

template <typename string_set_type, typename output_handler>
void suffix_sort(
    const string_set_type&   string_set,
          output_handler&    output,
    BWTParams*               params = NULL);

template <uint32 SYMBOL_SIZE, bool BIG_ENDIAN, typename storage_type, typename output_handler>
void bwt(
    const ConcatenatedStringSet<
        PackedStream<storage_type,uint8,SYMBOL_SIZE,BIG_ENDIAN,uint64>,
        uint64*>                    string_set,
        output_handler&             output,
        BWTParams*                  params = NULL);


} // namespace cuda


template <uint32 SYMBOL_SIZE, bool BIG_ENDIAN, typename storage_type, typename output_handler>
void large_bwt(
    const ConcatenatedStringSet<
        PackedStream<storage_type,uint8,SYMBOL_SIZE,BIG_ENDIAN,uint64>,
        uint64*>                    string_set,
        output_handler&             output,
        BWTParams*                  params = NULL);


} // namespace nvbio

#include <nvbio/sufsort/sufsort_inl.h>