bitmagic-sys 0.2.4+bitmagic.7.7.7

/*
Copyright(c) 2018 Anatoliy Kuznetsov(anatoliy_kuznetsov at yahoo.com)

Licensed under the Apache License, Version 2.0 (the "License");
you may not use this file except in compliance with the License.
You may obtain a copy of the License at

    http://www.apache.org/licenses/LICENSE-2.0

Unless required by applicable law or agreed to in writing, software
distributed under the License is distributed on an "AS IS" BASIS,
WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
See the License for the specific language governing permissions and
limitations under the License.

For more information please visit:  http://bitmagic.io
*/

/** \example xsample04.cpp

*/

/*! \file xsample04.cpp
    \brief Example: DNA substring search

*/

#include <iostream>
#include <sstream>
#include <chrono>
#include <regex>
#include <time.h>
#include <stdio.h>

#include <stdexcept>
#include <memory>
#include <vector>
#include <chrono>
#include <map>
#include <utility>
#include <algorithm>
#include <unordered_map>

#include "bm.h"
#include "bmalgo.h"
#include "bmserial.h"
#include "bmaggregator.h"

#include "bmdbg.h"
#include "bmtimer.h"
#include "bmundef.h" /* clear the pre-proc defines from BM */

using namespace std;

static
void show_help()
{
    std::cerr
        << "BitMagic DNA Search Sample (c) 2018" << std::endl
        << "-fa   file-name            -- input FASTA file" << std::endl
        << "-s hi|lo                   -- run substring search benchmark" << std::endl
        << "-diag                      -- run diagnostics"  << std::endl
        << "-timing                    -- collect timings"  << std::endl
      ;
}




// Arguments
//
std::string  ifa_name;
bool         is_diag = false;
bool         is_timing = false;
bool         is_bench = false;
bool         is_search = false;
bool         h_word_set = true;

static
int parse_args(int argc, char *argv[])
{
    for (int i = 1; i < argc; ++i)
    {
        std::string arg = argv[i];
        if ((arg == "-h") || (arg == "--help"))
        {
            show_help();
            return 0;
        }

        if (arg == "-fa" || arg == "--fa")
        {
            if (i + 1 < argc)
            {
                ifa_name = argv[++i];
            }
            else
            {
                std::cerr << "Error: -fa requires file name" << std::endl;
                return 1;
            }
            continue;
        }

        if (arg == "-diag" || arg == "--diag" || arg == "-d" || arg == "--d")
            is_diag = true;
        if (arg == "-timing" || arg == "--timing" || arg == "-t" || arg == "--t")
            is_timing = true;
        if (arg == "-bench" || arg == "--bench" || arg == "-b" || arg == "--b")
            is_bench = true;
        if (arg == "-search" || arg == "--search" || arg == "-s" || arg == "--s")
        {
            is_search = true;
            if (i + 1 < argc)
            {
                std::string a = argv[i+1];
                if (a != "-")
                {
                    if (a == "l" || a == "lo")
                    {
                        h_word_set = false;
                        ++i;
                    }
                    else
                    if (a == "h" || a == "hi")
                    {
                        h_word_set = true;
                        ++i;
                    }
                }
            }
        }

    } // for i
    return 0;
}


// Global types
//
typedef std::map<std::string, unsigned>                     freq_map;
typedef std::vector<std::pair<unsigned, std::string> >      dict_vect;

typedef bm::aggregator<bm::bvector<> >  aggregator_type;

// ----------------------------------------------------------------------------

bm::chrono_taker::duration_map_type  timing_map;

// FASTA format parser
static
int load_FASTA(const std::string& fname, std::vector<char>& seq_vect)
{
    bm::chrono_taker tt1("1. Parse FASTA", 1, &timing_map);

    seq_vect.resize(0);
    std::ifstream fin(fname.c_str(), std::ios::in);
    if (!fin.good())
        return -1;

    std::string line;
    for (unsigned i = 0; std::getline(fin, line); ++i)
    {
        if (line.empty() ||
            line.front() == '>')
            continue;

        for (std::string::iterator it = line.begin(); it != line.end(); ++it)
            seq_vect.push_back(*it);
    } // for
    return 0;
}



/**
    Utility for keeping all DNA finger print vectors and search
    using various techniques
*/
class DNA_FingerprintScanner
{
public:
    enum { eA = 0, eC, eG, eT, eN, eEnd };

    DNA_FingerprintScanner() {}

    /// Build fingerprint bit-vectors from the original sequence
    ///
    void Build(const vector<char>& sequence)
    {
        // use bulk insert iterator (faster way to construct a bit-index)
        //
        bm::bvector<>::bulk_insert_iterator iA(m_FPrintBV[eA], bm::BM_SORTED);
        bm::bvector<>::bulk_insert_iterator iC(m_FPrintBV[eC], bm::BM_SORTED);
        bm::bvector<>::bulk_insert_iterator iG(m_FPrintBV[eG], bm::BM_SORTED);
        bm::bvector<>::bulk_insert_iterator iT(m_FPrintBV[eT], bm::BM_SORTED);
        bm::bvector<>::bulk_insert_iterator iN(m_FPrintBV[eN], bm::BM_SORTED);

        for (size_t i = 0; i < sequence.size(); ++i)
        {
            unsigned pos = unsigned(i);
            switch (sequence[i])
            {
            case 'A':
                iA = pos;
                break;
            case 'C':
                iC = pos;
                break;
            case 'G':
                iG = pos;
                break;
            case 'T':
                iT = pos;
                break;
            case 'N':
                iN = pos;
                break;
            default:
                break;
            }
        }
    }

    /// Return fingerprint bit-vector
    const bm::bvector<>& GetVector(char letter) const
    {
        switch (letter)
        {
        case 'A':
            return m_FPrintBV[eA];
        case 'C':
            return m_FPrintBV[eC];
        case 'G':
            return m_FPrintBV[eG];
        case 'T':
            return m_FPrintBV[eT];
        case 'N':
            return m_FPrintBV[eN];
        default:
            break;
        }
        throw runtime_error("Error. Invalid letter!");
    }

    /// Find word strings
    ///    using shift + and on fingerprint vectors
    /// (horizontal, non-fused basic method)
    ///
    void Find(const string& word, vector<unsigned>& res)
    {
        if (word.empty())
            return;
        bm::bvector<> bv(GetVector(word[0])); // step 1: copy first vector

        // run series of shifts + logical ANDs
        for (size_t i = 1; i < word.size(); ++i)
        {
            bv.shift_right();  // SHIFT the accumulator bit-vector
            // get and AND the next fingerprint
            const bm::bvector<>& bv_mask = GetVector(word[i]);
            bv &= bv_mask;
            
            auto any = bv.any();
            if (!any)
                break;
        }

        // translate results from bvector of word ends to result
        unsigned ws = unsigned(word.size()) - 1;
        TranslateResults(bv, ws, res);
    };


    /// This method uses cache blocked aggregator with fused SHIFT+AND kernel
    ///
    void FindAggFused(const string& word, vector<unsigned>& res)
    {
        if (word.empty())
            return;
        // first we setup aggregator, add a group of vectors to be processed
        m_Agg.reset();
        for (size_t i = 0; i < word.size(); ++i)
        {
            const bm::bvector<>& bv_mask = GetVector(word[i]);
            m_Agg.add(&bv_mask);
        }

        // now run the whole algorithm to get benefits of cache blocking
        //
        bm::bvector<> bv;
        m_Agg.combine_shift_right_and(bv);

        // translate results from bvector of word ends to result
        unsigned ws = unsigned(word.size()) - 1;
        TranslateResults(bv, ws, res);
    };
    
    /// Find a set of words in one pass using pipeline
    /// of aggregators (this is very experimental)
    ///
    void FindCollection(const vector<tuple<string,int> >& words,
                        vector<vector<unsigned>>& hits)
    {
        vector<unique_ptr<aggregator_type> > agg_pipeline;
        unsigned ws = 0;

        for (const auto& w : words)
        {
            unique_ptr<aggregator_type> agg_ptr(new aggregator_type());
            agg_ptr->set_operation(aggregator_type::BM_SHIFT_R_AND);
            
            const string& word = get<0>(w);
            for (size_t i = 0; i < word.size(); ++i)
            {
                const bm::bvector<>& bv_mask = GetVector(word[i]);
                agg_ptr->add(&bv_mask);
            }
            
            agg_pipeline.emplace_back(agg_ptr.release());
            ws = unsigned(word.size()) - 1;
        }

        // run the pipeline
        bm::aggregator_pipeline_execute<aggregator_type,
           vector<unique_ptr<aggregator_type> >::iterator>(agg_pipeline.begin(), agg_pipeline.end());

        // convert the results
        for (size_t i = 0; i < agg_pipeline.size(); ++i)
        {
            const aggregator_type* agg_ptr = agg_pipeline[i].get();
            auto bv = agg_ptr->get_target();
            vector<unsigned> res;
            res.reserve(12000);
            TranslateResults(*bv, ws, res);
            hits.emplace_back(res);
        }
    }

protected:

    /// Translate search results vector using (word size) left shift
    ///
    void TranslateResults(const bm::bvector<>& bv,
                          unsigned left_shift,
                          vector<unsigned>& res)
    {
        bm::bvector<>::enumerator en = bv.first();
        for (; en.valid(); ++en)
        {
            auto pos = *en;
            res.push_back(pos - left_shift);
        }
    }

private:
    bm::bvector<>   m_FPrintBV[eEnd];
    aggregator_type m_Agg;
};

static const size_t WORD_SIZE = 28;
using THitList = vector<unsigned>;

/// generate the most frequent words of specified length from the input sequence
///
static
void generate_kmers(vector<tuple<string,int>>& top_words,
                    vector<tuple<string,int>>& lo_words,
                    const vector<char>& data,
                    size_t N,
                    unsigned word_size)
{
    cout << "k-mer generation... " << endl;

    top_words.clear();
    lo_words.clear();

    if (data.size() < word_size)
        return;

    size_t end_pos = data.size() - word_size;
    size_t i = 0;
    map<string, int> words;
    while (i < end_pos)
    {
        string s(&data[i], word_size);
        if (s.find('N') == string::npos)
            words[s] += 1;
        i += word_size;
        if (i % 10000 == 0)
        {
            cout << "\r" << i << "/" << end_pos << flush;
        }
    }

    cout << endl << "Picking k-mer samples..." << flush;

    multimap<int,string, greater<int>> dst;
    for_each(words.begin(), words.end(), [&](const std::pair<string,int>& p)
    {
                 dst.emplace(p.second, p.first);
             });
    {
        auto it = dst.begin();
        for(size_t count = 0; count < N && it !=dst.end(); ++it,++count)
            top_words.emplace_back(it->second, it->first);
    }

    {
        auto it = dst.rbegin();
        for(size_t count = 0; count < N && it !=dst.rend(); ++it, ++count)
            lo_words.emplace_back(it->second, it->first);
    }

    cout << "OK" << endl;
}

/// 2-way string matching
///
static
void find_word_2way(vector<char>& data,
                       const char* word, unsigned word_size,
                       THitList& r)
{
    if (data.size() < word_size)
        return;

    size_t i = 0;
    size_t end_pos = data.size() - word_size;
    while (i < end_pos)
    {
        bool found = true;
        for (size_t j = i, k = 0, l = word_size - 1; l > k; ++j, ++k, --l)
        {
            if (data[j] != word[k] || data[i + l] != word[l])
            {
                found = false;
                break;
            }
        }
        if (found)
            r.push_back(unsigned(i));
        ++i;
    }
}

/// Find all words in one pass (cache coherent algorithm)
/// (variation of 2-way string matching for collection search)
///
static
void find_words(const vector<char>& data,
                vector<const char*> words,
                unsigned word_size,
                vector<vector<unsigned>>& hits)
{
    if (data.size() < word_size)
        return;

    size_t i = 0;
    size_t end_pos = data.size() - word_size;
    size_t words_size = words.size();
    while (i < end_pos)
    {
        for (size_t idx = 0; idx < words_size; ++idx)
        {
            auto& word = words[idx];
            bool found = true;
            for (size_t j = i, k = 0, l = word_size - 1; l > k; ++j, ++k, --l)
            {
                if (data[j] != word[k] || data[i + l] != word[l])
                {
                    found = false;
                    break;
                }
            } // for
            if (found)
            {
                hits[idx].push_back(unsigned(i));
                break;
            }
        } // for
        ++i;
    } // while
}


/// Check search result match
///
static
bool hitlist_compare(const THitList& h1, const THitList& h2)
{
    if (h1.size() != h2.size())
    {
        cerr << "size1 = " << h1.size() << " size2 = " << h2.size() << endl;
        return false;
    }
    for (size_t i = 0; i < h1.size(); ++i)
    {
        if (h1[i] != h2[i])
            return false;
    }
    return true;
}




int main(int argc, char *argv[])
{
    if (argc < 3)
    {
        show_help();
        return 1;
    }

    std::vector<char> seq_vect;

    try
    {
        auto ret = parse_args(argc, argv);
        if (ret != 0)
            return ret;

        DNA_FingerprintScanner idx;

        if (!ifa_name.empty())
        {
            auto res = load_FASTA(ifa_name, seq_vect);
            if (res != 0)
                return res;
            std::cout << "FASTA sequence size=" << seq_vect.size() << std::endl;
            
            {
                bm::chrono_taker tt1("2. Build DNA index", 1, &timing_map);
                idx.Build(seq_vect);
            }
        }
        

        if (is_search)
        {
            vector<tuple<string,int> > h_words;
            vector<tuple<string,int> > l_words;

            vector<tuple<string,int>>& words = h_word_set ? h_words : l_words;

            // generate search sets for benchmarking
            //
            generate_kmers(h_words, l_words, seq_vect, 25, WORD_SIZE);

            
            vector<THitList> word_hits;
            vector<THitList> word_hits_agg;

            // search all words in one pass and
            // store results in list of hits according to the order of words
            // (this method uses memory proximity
            //  of searched words to maximize CPU cache hit rate)
            
            {
                vector<const char*> word_list;
                for (const auto& w : words)
                {
                    word_list.push_back(get<0>(w).c_str());
                }
                word_hits.resize(words.size());
                for_each(word_hits.begin(), word_hits.end(), [](THitList& ht) {
                        ht.reserve(12000);
                    });
                
                bm::chrono_taker tt1("6. String search 2-way single pass",
                                      unsigned(words.size()), &timing_map);
                find_words(seq_vect, word_list, unsigned(WORD_SIZE), word_hits);
            }
            
            // collection search, runs all hits at once
            //
            {
                bm::chrono_taker tt1("7. Aggregated search single pass",
                                      unsigned(words.size()), &timing_map);
                
                idx.FindCollection(words, word_hits_agg);
            }
            
            // a few variants of word-by-word searches
            //
            for (size_t word_idx = 0; word_idx < words.size(); ++ word_idx)
            {
                auto& word = get<0>(words[word_idx]);
                THitList hits1;
  
                {
                    bm::chrono_taker tt1("3. String search 2-way", 1, &timing_map);
                    find_word_2way(seq_vect,
                                      word.c_str(), unsigned(word.size()),
                                      hits1);
                }
                THitList hits2;
                {
                    bm::chrono_taker tt1("4. Search with bvector SHIFT+AND", 1, &timing_map);
                    idx.Find(word, hits2);
                }
                THitList hits4;
                {
                    bm::chrono_taker tt1("5. Search with aggregator fused SHIFT+AND", 1, &timing_map);
                    idx.FindAggFused(word, hits4);
                }

                // check correctness
                if (!hitlist_compare(hits1, hits2)
                    || !hitlist_compare(hits2, hits4))
                {
                    cout << "Mismatch ERROR for: " <<  word << endl;
                }
                else
                if (!hitlist_compare(word_hits[word_idx], hits1)
                    || !hitlist_compare(word_hits_agg[word_idx], hits1))
                {
                    cout << "Sigle pass mismatch ERROR for: " <<  word << endl;
                }
                else
                {
                    cout << word_idx << ": " <<  word << ": " << hits1.size() << " hits " << endl;
                }
            }
            
        }

        if (is_timing)  // print all collected timings
        {
            std::cout << std::endl << "Performance:" << std::endl;
            bm::chrono_taker::print_duration_map(timing_map, bm::chrono_taker::ct_all);
        }
    }
    catch (std::exception& ex)
    {
        std::cerr << "Error:" << ex.what() << std::endl;
        return 1;
    }

    return 0;
}