gact.cpp

/*
Copyright 2018 Yatish Turakhia, Gill Bejerano and William Dally
Copyright 2018 Tong Dong Qiu

Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions:

The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software.

THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
*/

#include <iostream>
#include <fstream>
#include <string>
#include <stdio.h>
#include <cstdlib>
#include <queue>
#include <mutex>
#include "align.h"
#include "gact.h"

// only report overlaps with a score higher than SCORE_THRESHOLD
#define SCORE_THRESHOLD 0

#ifdef TIME
    #include <chrono>
#endif

int sub_mat[25] = {
    1, -1, -1, -1, 0,
    -1, 1, -1, -1, 0,
    -1, -1, 1, -1, 0,
    -1, -1, -1, 1, 0,
    0, 0, 0, 0, 0
};

// declared in reference_guided.cpp
extern bool same_file;
extern std::vector<std::string> reference_seqs;
extern std::vector<long long int> reference_lengths;
extern std::vector<std::string> reads_seqs;
extern std::vector<std::string> rev_reads_seqs;
extern std::vector<long long int> reads_lengths;
extern std::vector<std::vector<std::string> > reference_descrips;
extern std::vector<std::vector<std::string> > reads_descrips;

void GACT (char *ref_str, char *query_str, \
    int ref_length, int query_length, \
    int tile_size, int tile_overlap, \
    int ref_pos, int query_pos, int first_tile_score_threshold, \
    int ref_id, int query_id, bool complement, \
    int match_score, int mismatch_score, \
    int gap_open, int gap_extend, \
    std::ofstream &fout) {

    std::queue<int> BT_states;

    // result of one alignment, note that is used to calculate the total score
    std::string aligned_ref_str = "";
    std::string aligned_query_str = "";
    
    int ref_tile_length = tile_size;
    int query_tile_length = tile_size;
    
    int abpos, bbpos;

    static int callidx = 0;

    // beginning for the left or the right extension
    //original starting point for the whole query
    int rev_ref_pos = ref_pos;
    int rev_query_pos = query_pos;
    
    int i = 0;
    int j = 0;
    
    int first_tile_score = 0;
    bool first_tile = true;

    // not for the first tile
    while ((ref_pos > 0) && (query_pos > 0) && (((i > 0) && (j > 0)) || first_tile)) {
        //change the tile length if elements less than that of the tile size
        ref_tile_length = (ref_pos > tile_size) ? tile_size : ref_pos;
        query_tile_length = (query_pos > tile_size) ? tile_size : query_pos;

        BT_states = AlignWithBT(\
            ref_str + ref_pos - ref_tile_length, \
            ref_tile_length, \
            query_str + query_pos - query_tile_length, \
            query_tile_length, \
            match_score, mismatch_score, gap_open, gap_extend, \
            query_tile_length, ref_tile_length, false, \
            first_tile, (tile_size - tile_overlap));
        i = 0;
        j = 0;
        int tile_score = BT_states.front();
        BT_states.pop();
        if (first_tile) {
            ref_pos = ref_pos - ref_tile_length + BT_states.front();
            BT_states.pop();
            query_pos = query_pos - query_tile_length + BT_states.front();
            BT_states.pop();
            rev_ref_pos = ref_pos;
            rev_query_pos = query_pos;
            first_tile_score = tile_score;
            if (tile_score < first_tile_score_threshold) {
                break;
            }
        }
        while (!BT_states.empty()) {
            first_tile = false;
            int state = BT_states.front();
            BT_states.pop();
            if (state == M) {
                aligned_ref_str.insert(0, 1, ref_str[ref_pos - j - 1]);
                aligned_query_str.insert(0, 1, query_str[query_pos - i - 1]);
                i += 1;
                j += 1;
            }
            if (state == I) {
                aligned_ref_str.insert(0, 1, ref_str[ref_pos - j - 1]);
                aligned_query_str.insert(0, 1, '-');
                j += 1;
            }
            if (state == D) {
                aligned_ref_str.insert(0, 1, '-');
                aligned_query_str.insert(0, 1, query_str[query_pos - i - 1]);
                i += 1;
            }
        }
        ref_pos -= (j);
        query_pos -= (i);
    }

    abpos = ref_pos;
    bbpos = query_pos;
    ref_pos = rev_ref_pos;
    query_pos = rev_query_pos;
    i = tile_size;
    j = tile_size;
    
    //starts with the first tile
    while ((ref_pos < ref_length) && (query_pos < query_length) && (((i > 0) && (j > 0)) || first_tile)) {
        
        ref_tile_length = (ref_pos + tile_size < ref_length) ? tile_size : ref_length - ref_pos;
        query_tile_length = (query_pos + tile_size < query_length) ? tile_size : query_length - query_pos;

        BT_states = AlignWithBT (\
            ref_str + ref_pos, \
            ref_tile_length, \
            query_str + query_pos, \
            query_tile_length, \
            match_score, mismatch_score, gap_open, gap_extend, \
            query_tile_length, ref_tile_length, true, \
            first_tile, (tile_size - tile_overlap));

        i = 0;
        j = 0;
        int tile_score = BT_states.front();
        BT_states.pop();
        if (first_tile) {
            ref_pos = ref_pos + ref_tile_length - BT_states.front();
            BT_states.pop();
            query_pos = query_pos + query_tile_length - BT_states.front();
            BT_states.pop();
            first_tile_score = tile_score;
            if (tile_score < first_tile_score_threshold) {
                break;
            }
        }
        while (!BT_states.empty()) {
            first_tile = false;
            int state = BT_states.front();
            BT_states.pop();
            if (state == M) {
                aligned_ref_str += ref_str[ref_pos + j];
                aligned_query_str += (query_str[query_pos + i]);
                i += 1;
                j += 1;
            }
            if (state == I) {
                aligned_ref_str += ref_str[ref_pos + j];
                aligned_query_str += '-';
                j += 1;
            }
            if (state == D) {
                aligned_ref_str += '-';
                aligned_query_str += query_str[query_pos + i];
                i += 1;
            }
        }
        ref_pos += (j);
        query_pos += (i);
    }

    int total_score = 0;
    bool open = true;
    for (uint32_t j = 0; j < aligned_ref_str.length(); j++) {
        char ref_nt = aligned_ref_str[j];
        char query_nt = aligned_query_str[j];
        if (ref_nt == '-' || query_nt == '-') {
            total_score += (open) ? gap_open : gap_extend;
            open = false;
        }
        else {
            total_score += (query_nt == ref_nt) ? match_score : mismatch_score;
            open = true;
        }
    }

    // either print whole name, or only id (integer)
    if(!(same_file && ref_id == query_id) && total_score > SCORE_THRESHOLD){
        fout
        << "ref_id: " << reference_descrips[ref_id][0]
        << ", query_id: " << reads_descrips[query_id][0]
        //<< "ref_id: " << ref_id
        //<< ", query_id: " << query_id
        << ", ab: " << abpos
        << ", ae: " << ref_pos
        << ", bb: " << bbpos
        << ", be: " << query_pos
        << ", score: " << total_score
        << ", comp: " << complement << std::endl;//*/
    }
    callidx++;

} // end GACT()

#ifdef GPU
void GACT_Batch(std::vector<GACT_call> calls, int num_calls, \
bool complement, int offset, GPU_storage *s, \
int match_score, int mismatch_score, \
int gap_open, int gap_extend, \
std::ofstream &fout)
{
    int early_terminate = tile_size - tile_overlap;

    std::vector<std::queue<int> > BT_statess(BATCH_SIZE);

    std::vector<std::string> *reads_seqs_p;

    if(complement == true){
        reads_seqs_p = &rev_reads_seqs;
    }else{
        reads_seqs_p = &reads_seqs;
    }

    printf("GACT_Batch, num_calls: %d, complement: %d\n", num_calls, complement);

    //output of the function
    std::vector<std::string> aligned_ref_strs(num_calls);
    std::vector<std::string> aligned_query_strs(num_calls);

    // reserve space for aligned strings
    for(int i = 0; i < num_calls; ++i){
        aligned_ref_strs[i].reserve(200);
        aligned_query_strs[i].reserve(200);
    }

    int next_callidx = BATCH_SIZE;
    int calls_done = 0;

    std::vector<int> assignments(BATCH_SIZE);           // BATCH thread i will compute GACTcall assignments[i]
    std::vector<int> ref_tile_lengths(BATCH_SIZE);
    std::vector<int> query_tile_lengths(BATCH_SIZE);
    if(num_calls < BATCH_SIZE){
        printf("WARNING not enough callidxs for BATCH, I'll keep going anyway\n");
        int i = 0;
        for(; i < num_calls; ++i){
            assignments[i] = i;
        }
        for(; i < BATCH_SIZE; ++i){
            assignments[i] = -1;
        }
    }else{
        for(int i = 0; i < BATCH_SIZE; ++i){
            assignments[i] = i;
        }
    }

    // terminate :: 0: continue, 1: terminate
    std::vector<char> terminate(BATCH_SIZE);
    std::vector<std::string> ref_seqs(BATCH_SIZE);
    std::vector<std::string> query_seqs(BATCH_SIZE);
    std::vector<int> ref_lens(BATCH_SIZE);
    std::vector<int> query_lens(BATCH_SIZE);
    std::vector<char> reverses(BATCH_SIZE);
    std::vector<char> firsts_b(BATCH_SIZE);

#ifdef TIME
    std::chrono::high_resolution_clock::time_point t1, t2;
    auto time_gpu = 0, time_loop = 0;
    t1 = std::chrono::high_resolution_clock::now();
#endif

    while(calls_done < num_calls){
        for(int t = 0; t < BATCH_SIZE; ++t){
            char next_call = 0;
            int callidx = assignments[t];
            GACT_call *c = &(calls[callidx]);

            if(callidx == -1){
                ref_lens[t] = -1;
                continue;
            }

            int ref_pos = c->ref_pos;
            int query_pos = c->query_pos;
            int ref_length = reference_lengths[c->ref_id];
            int query_length = reads_lengths[c->query_id];

            // prepare assignments
            if(c->reverse == 1){
                if(ref_pos <= 0 || query_pos <= 0 || terminate[t]){
                    // store begin of alignment in ref_bpos and query_bpos
                    int t1 = c->ref_bpos;
                    int t2 = c->query_bpos;
                    c->ref_bpos = ref_pos;
                    c->query_bpos = query_pos;
                    ref_pos = t1;
                    query_pos = t2;
                    c->ref_pos = t1;
                    c->query_pos = t2;
                    c->reverse = 0;
                    terminate[t] = 0;
                }
            }else{
                if(ref_pos >= ref_length || query_pos >= query_length || terminate[t]){
                    int total_score = 0;
#ifndef NOSCORE
                    bool open = true;
                    for (uint32_t j = 0; j < aligned_ref_strs[callidx].length(); j++) {
                        char ref_nt = aligned_ref_strs[callidx][j];
                        char query_nt = aligned_query_strs[callidx][j];
                        if (ref_nt == '-' || query_nt == '-') {
                            total_score += (open) ? gap_open : gap_extend;
                            open = false;
                        }
                        else {
                            total_score += (query_nt == ref_nt) ? match_score : mismatch_score;
                            open = true;
                        }
                    }
#endif
#ifdef NOSCORE
                    if(!(same_file && c->ref_id == c->query_id))
#else
                    if(!(same_file && c->ref_id == c->query_id) && total_score > SCORE_THRESHOLD)
#endif
                    {
                        // either print whole name, or only id (integer)
                        fout
                        << "ref_id: " << reference_descrips[c->ref_id][0]
                        << ", query_id: " << reads_descrips[c->query_id][0]
                        //<< "ref_id: " << c->ref_id
                        //<< ", query_id: " << c->query_id
                        << ", ab: " << c->ref_bpos
                        << ", ae: " << ref_pos
                        << ", bb: " << c->query_bpos
                        << ", be: " << query_pos
                        << ", score: " << total_score
                        << ", comp: " << complement << std::endl;
                    }

                    calls_done++;
                    assignments[t] = next_callidx;
                    if(next_callidx >= num_calls){
                        assignments[t] = -1;
                        ref_lens[t] = -1;
                        continue;
                    }
                    next_call = 1;
                }
            }

            if(next_call == 1){
                callidx = next_callidx++;
                c = &(calls[callidx]);
                ref_pos = c->ref_pos;
                query_pos = c->query_pos;
                ref_length = reference_lengths[c->ref_id];
                query_length = reads_lengths[c->query_id];
                terminate[t] = 0;
                if(ref_pos <= 0 || query_pos <= 0){
                    c->reverse = 0;
                    c->ref_bpos = ref_pos;
                    c->query_bpos = query_pos;
                }
            }

            // prepare batch
            // if first tile
            firsts_b[t] = c->first;

            // if reverse
            if(c->reverse == 1){
                ref_lens[t] = (ref_pos > tile_size) ? tile_size : ref_pos;
                query_lens[t] = (query_pos > tile_size) ? tile_size : query_pos;
                ref_seqs[t] = reference_seqs[c->ref_id].substr(ref_pos-ref_lens[t], ref_lens[t]);
                query_seqs[t] = reads_seqs_p->at(c->query_id).substr(query_pos-query_lens[t], query_lens[t]);
                reverses[t] = 1;
            }else{      // else forward
                ref_lens[t] = (ref_pos + tile_size < ref_length) ? tile_size : ref_length - ref_pos;
                query_lens[t] = (query_pos + tile_size < query_length) ? tile_size : query_length - query_pos;
                ref_seqs[t] = reference_seqs[c->ref_id].substr(ref_pos, ref_lens[t]);
                query_seqs[t] = reads_seqs_p->at(c->query_id).substr(query_pos, query_lens[t]);
                reverses[t] = 0;
            }
        }   // end prepare batch

#ifdef TIME
        t2 = std::chrono::high_resolution_clock::now();
        time_loop += std::chrono::duration_cast<std::chrono::milliseconds>(t2 - t1).count();
        t1 = std::chrono::high_resolution_clock::now();
#endif

        int *out = Align_Batch_GPU(ref_seqs, query_seqs, ref_lens, query_lens, sub_mat, gap_open, gap_extend, ref_lens, query_lens, reverses, firsts_b, early_terminate, tile_size, s, NUM_BLOCKS, THREADS_PER_BLOCK);

#ifdef TIME
        t2 = std::chrono::high_resolution_clock::now();
        time_gpu += std::chrono::duration_cast<std::chrono::milliseconds>(t2 - t1).count();
        t1 = std::chrono::high_resolution_clock::now();
#endif

        // postprocess
        for(int t = 0; t < BATCH_SIZE; ++t){
            int callidx = assignments[t];
            GACT_call *c = &(calls[callidx]);
            if(callidx == -1){continue;}

            int i = 0;
            int j = 0;
            int idx = 5;
#ifdef NOSCORE
            int *res = out + 5*t;
#else
            int *res = out + 2*tile_size*t;
#endif
            bool first_tile = c->first;
            int ref_pos = c->ref_pos;
            int query_pos = c->query_pos;
            int ref_tile_length = ref_lens[t];
            int query_tile_length = query_lens[t];
            int tile_score = res[0];
            int first_tile_score;

            // if reverse
            if(c->reverse == 1){
                if (first_tile) {
                    int t1 = res[3];
                    int t2 = res[4];
                    ref_pos = ref_pos - ref_tile_length + t1;
                    query_pos = query_pos - query_tile_length + t2;
                    c->ref_bpos = ref_pos;
                    c->query_bpos = query_pos;
                    c->first_tile_score = tile_score;
                    if (tile_score < first_tile_score_threshold) {
                        terminate[t] = 1;
                        c->ref_pos = ref_pos;
                        c->query_pos = query_pos;
                        continue;
                    }
                }
#ifdef NOSCORE
                j = res[1];
                i = res[2];
                if(i + j > 0){
                    first_tile = false;
                }
#else
                int state;
                while ((state = res[idx++]) != -1)
                {
                    first_tile = false;
                    if (state == M) {
                        aligned_ref_strs[callidx].insert(0, 1, reference_seqs[c->ref_id][ref_pos - j - 1]);
                        aligned_query_strs[callidx].insert(0, 1, reads_seqs_p->at(c->query_id)[query_pos - i - 1]);
                        i += 1;
                        j += 1;
                    }
                    if (state == I) {
                        aligned_ref_strs[callidx].insert(0, 1, reference_seqs[c->ref_id][ref_pos - j - 1]);
                        aligned_query_strs[callidx].insert(0, 1, '-');
                        j += 1;
                    }
                    if (state == D) {
                        aligned_ref_strs[callidx].insert(0, 1, '-');
                        aligned_query_strs[callidx].insert(0, 1, reads_seqs_p->at(c->query_id)[query_pos - i - 1]);
                        i += 1;
                    }
                }
#endif // NOSCORE
                ref_pos -= (j);
                query_pos -= (i);
            }else{      // else forward
                if (first_tile) {
                    int t1 = res[3];
                    int t2 = res[4];
                    ref_pos = ref_pos + ref_tile_length - t1;
                    query_pos = query_pos + query_tile_length - t2;
                    c->first_tile_score = tile_score;
                    if (tile_score < first_tile_score_threshold) {
                        terminate[t] = 1;
                        c->ref_pos = ref_pos;
                        c->query_pos = query_pos;
                        continue;
                    }
                }
#ifdef NOSCORE
                j = res[1];
                i = res[2];
                if(i + j > 0){
                    first_tile = false;
                }
#else
                int state;
                while ((state = res[idx++]) != -1)
                {
                    first_tile = false;
                    if (state == M) {
                        aligned_ref_strs[callidx] += reference_seqs[c->ref_id][ref_pos + j];
                        aligned_query_strs[callidx] += (reads_seqs_p->at(c->query_id)[query_pos + i]);
                        i += 1;
                        j += 1;
                    }
                    if (state == I) {
                        aligned_ref_strs[callidx] += reference_seqs[c->ref_id][ref_pos + j];
                        aligned_query_strs[callidx] += '-';
                        j += 1;
                    }
                    if (state == D) {
                        aligned_ref_strs[callidx] += '-';
                        aligned_query_strs[callidx] += reads_seqs_p->at(c->query_id)[query_pos + i];
                        i += 1;
                    }
                }
#endif // NOSCORE
                ref_pos += (j);
                query_pos += (i);
            }   // end traceback

            c->first = first_tile;

            if(i == 0 || j == 0){
                terminate[t] = 1;
            }
            c->ref_pos = ref_pos;
            c->query_pos = query_pos;
        } // end postprocess

    } // end main loop

#ifdef TIME
        t2 = std::chrono::high_resolution_clock::now();
        time_loop += std::chrono::duration_cast<std::chrono::milliseconds>(t2 - t1).count();
        printf("time_loop: %d ms, time_gpu: %d ms\n", time_loop, time_gpu);
#endif

} // end GACT_Batch()
#endif // GPU