/*************************************************************************************
                           The MIT License

   BWA-MEM2  (Sequence alignment using Burrows-Wheeler Transform),
   Copyright (C) 2019  Intel Corporation, Heng Li.

   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.

Authors: Vasimuddin Md <vasimuddin.md@intel.com>; Sanchit Misra <sanchit.misra@intel.com>.
*****************************************************************************************/

#include<stdio.h>
#include<stdlib.h>
#include<stdint.h>
#include <omp.h>
#include <string.h>
#include "bwa.h"
#include "FMI_search.h"

#ifdef VTUNE_ANALYSIS
#include <ittnotify.h>
#endif

#define QUERY_DB_SIZE 1280000000

int myrank, num_ranks;

int main(int argc, char **argv) {
#ifdef VTUNE_ANALYSIS
    __itt_pause();
#endif

    if(argc!=6)
    {
        printf("Need five arguments : ref_file query_set batch_size minSeedLen n_threads\n");
        return 1;
    }

    int32_t numReads = 0;
    int64_t total_size = 0;
    gzFile fp = gzopen(argv[2], "r");
	if (fp == 0)
	{
		fprintf(stderr, "[E::%s] fail to open file `%s'.\n", __func__, argv[2]);
        exit(EXIT_FAILURE);
	}
    
    printf("before reading sequences\n");
    bseq1_t *seqs = bseq_read_one_fasta_file(QUERY_DB_SIZE, &numReads, fp, &total_size);

    if(seqs == NULL)
    {
        printf("ERROR! seqs = NULL\n");
        exit(EXIT_FAILURE);
    }
    int32_t *query_cum_len_ar = (int32_t *)_mm_malloc(numReads * sizeof(int32_t), 64);

    FMI_search *fmiSearch = new FMI_search(argv[1]);
    fmiSearch->load_index();


    int max_readlength = seqs[0].l_seq;
    int min_readlength = seqs[0].l_seq;
    for(int i = 1; i < numReads; i++)
    {
        if(max_readlength < seqs[i].l_seq)
            max_readlength = seqs[i].l_seq;
        if(min_readlength > seqs[i].l_seq)
            min_readlength = seqs[i].l_seq;
    }
    assert(max_readlength > 0);
    assert(max_readlength < 10000);
    assert(numReads > 0);
    printf("numReads = %d, max_readlength = %d, min_readlength = %d\n", numReads, max_readlength, min_readlength);
    assert(numReads * max_readlength < QUERY_DB_SIZE);

    uint8_t *enc_qdb=(uint8_t *)malloc(numReads * max_readlength * sizeof(uint8_t));

    int64_t cind,st;
#if 0
    printf("Priting query\n");
    for(st = 0; st < max_readlength; st++)
    {
        printf("%c", seqs[0].seq[st]);
    }
    printf("\n");
#endif
    uint64_t r;
    for (st=0; st < numReads; st++) {
        query_cum_len_ar[st] = st * max_readlength;
        cind=st*max_readlength;
        for(r = 0; r < max_readlength; ++r) {
            switch(seqs[st].seq[r])
            {
                case 'A': enc_qdb[r+cind]=0;
                          break;
                case 'C': enc_qdb[r+cind]=1;
                          break;
                case 'G': enc_qdb[r+cind]=2;
                          break;
                case 'T': enc_qdb[r+cind]=3;
                          break;
                default: enc_qdb[r+cind]=4;
            }
            //printf("%c %d\n", seqs[st].seq[r], enc_qdb[r + cind]);
        }
    }

    int batch_size=0;
    batch_size=atoi(argv[3]);
    assert(batch_size > 0);
    assert(batch_size <= numReads);


    int32_t minSeedLen = atoi(argv[4]);
    int numthreads=atoi(argv[5]);
    assert(numthreads > 0);
    assert(numthreads <= omp_get_max_threads());
    SMEM *matchArray[numthreads];

    int64_t num_batches = (numReads + batch_size - 1 ) / batch_size;
    int64_t *numTotalSmem = (int64_t *)_mm_malloc(num_batches * sizeof(int64_t), 64);;
    // Per-batch (tid, offset) lookup. matchArray[tid] is grown on demand
    // with realloc() below, which can relocate the buffer — so we publish
    // a stable index pair instead of a raw SMEM* into the (mutable) buffer
    // and resolve to a pointer at print time once all growth is done.
    int32_t *batchTid    = (int32_t *)_mm_malloc(num_batches * sizeof(int32_t), 64);
    int64_t *batchOffset = (int64_t *)_mm_malloc(num_batches * sizeof(int64_t), 64);
#pragma omp parallel num_threads(numthreads)
    {
        int tid = omp_get_thread_num();

        if(tid == 0)
            printf("Running %d threads\n", omp_get_num_threads());
    }

    int32_t *min_intv_array = (int32_t *)_mm_malloc(numReads * sizeof(int32_t), 64);
    int64_t i;
    for(i = 0; i < numReads; i++)
    {
        min_intv_array[i] = 1;
    }

    int64_t startTick, endTick;
#ifdef VTUNE_ANALYSIS
    __itt_resume();
#endif
    startTick = __rdtsc();
    memset(numTotalSmem, 0, num_batches * sizeof(int64_t));
    memset(batchTid, 0, num_batches * sizeof(int32_t));
    memset(batchOffset, 0, num_batches * sizeof(int64_t));
    int64_t workTicks[numthreads];
    memset(workTicks, 0, numthreads * sizeof(int64_t));
    int64_t perThreadQuota = numReads / numthreads;

#pragma omp parallel num_threads(numthreads)
    {
        int32_t *rid_array = (int32_t *)_mm_malloc(batch_size * sizeof(int32_t), 64);
        int32_t tid = omp_get_thread_num();
        // Initial capacity must hold at least one batch's worst case so the
        // first grow check below has a real budget to compare against. When
        // numthreads > numReads, perThreadQuota is 0 and the legacy
        // `perThreadQuota * 20` would malloc(0).
        int64_t matchArrayAlloc = perThreadQuota * 20;
        const int64_t min_alloc = (int64_t)batch_size * max_readlength;
        if (matchArrayAlloc < min_alloc) matchArrayAlloc = min_alloc;
        matchArray[tid] = (SMEM *)malloc(matchArrayAlloc * sizeof(SMEM));
        int64_t myTotalSmems = 0;
        int64_t startTick = __rdtsc();

        // The lockstep variant of getSMEMsOnePosOneThread now owns its
        // per-slot prev/match buffers internally (sized by
        // MAX_READ_LEN_FOR_LOCKSTEP), so the harness no longer pre-allocates
        // them. matchArrayAlloc is grown on demand to keep the per-thread
        // output buffer ahead of the per-batch SMEM count.

#pragma omp for schedule(dynamic)
        for(i = 0; i < numReads; i += batch_size)
        {
            int64_t st1 = __rdtsc();
            int32_t batch_count = batch_size;
            if((i + batch_count) > numReads) batch_count = numReads - i;
            int32_t j;
            for(j = 0; j < batch_count; j++)
            {
                rid_array[j] = j;
            }
            int32_t batch_id = i/batch_size;
            //printf("%d] i = %d, batch_count = %d, batch_size = %d\n", tid, i, batch_count, batch_size);
            //fflush(stdout);
            if((matchArrayAlloc - myTotalSmems) < (batch_size * max_readlength))
            {
                matchArrayAlloc *= 2;
                matchArray[tid] = (SMEM *)realloc(matchArray[tid], matchArrayAlloc * sizeof(SMEM));
            }
            fmiSearch->getSMEMsAllPosOneThread(enc_qdb + i * max_readlength,
                    min_intv_array + i,
                    rid_array,
                    batch_count,
                    batch_size,
                    seqs + i,
                    query_cum_len_ar,
                    max_readlength,
                    minSeedLen,
                    matchArray[tid] + myTotalSmems,
                    numTotalSmem + batch_id);
            batchTid[batch_id]    = tid;
            batchOffset[batch_id] = myTotalSmems;
            fmiSearch->sortSMEMs(matchArray[tid] + myTotalSmems,
                    numTotalSmem + batch_id,
                    batch_count,
                    max_readlength,
                    1);
            for(j = 0; j < numTotalSmem[batch_id]; j++)
            {
                matchArray[tid][myTotalSmems + j].rid += i;
            }
            myTotalSmems += numTotalSmem[batch_id];
            int64_t et1 = __rdtsc();
            workTicks[tid] += (et1 - st1);
        }

        int64_t endTick = __rdtsc();
        printf("%d] %ld ticks, workTicks = %ld\n", tid, endTick - startTick, workTicks[tid]);
        _mm_free(rid_array);
    }

    endTick = __rdtsc();
#ifdef VTUNE_ANALYSIS
    __itt_pause();
#endif
    int64_t sumTicks = 0;
    int64_t maxTicks = 0;
    for(i = 0; i < numthreads; i++)
    {
        sumTicks += workTicks[i];
        if(workTicks[i] > maxTicks) maxTicks = workTicks[i];
    }
    double avgTicks = (sumTicks * 1.0) / numthreads;
    printf("avgTicks = %lf, maxTicks = %ld, load imbalance = %lf\n", avgTicks, maxTicks, maxTicks/avgTicks);

    printf("Consumed: %ld cycles\n", endTick - startTick);

    int64_t totalSmem = 0;
    int32_t batch_id = 0;
    for(batch_id = 0; batch_id < num_batches; batch_id++)
    {
        totalSmem += numTotalSmem[batch_id];
    }
    printf("totalSmems = %ld\n", totalSmem);

    /* SMEM output is emitted by default so this binary is diff-able for
       regression testing. The enclosing `#ifdef PRINT_OUTPUT` guard has
       been removed. */
    int32_t prevRid = -1;
    for(batch_id = 0; batch_id < num_batches; batch_id++)
    {
        // Resolve (tid, offset) to a stable pointer now — every batch's
        // owning thread has finished growing matchArray[tid].
        SMEM *myMatchArray = matchArray[batchTid[batch_id]] + batchOffset[batch_id];
        int64_t i;
        for(i = 0; i < numTotalSmem[batch_id]; i++)
        {
            SMEM smem = myMatchArray[i];
            if(smem.rid != prevRid)
            {
                int32_t j;
                for(j = prevRid + 1; j <= smem.rid; j++)
                    printf("%u:\n", j);
            }
            prevRid = smem.rid;
            printf("[%u,%u]", smem.m, smem.n + 1);
            // printf("%u, %u]", smem.k, smem.s);
#if 1
            printf(" ["); 
            int64_t u1, u2, u3;
            u1 = smem.k;
            u2 = smem.k + smem.s;
            for(u3 = u1; u3 < u2; u3++)
            {
                //printf("%ld,", fmiSearch->get_sa_entry(u3));
            }
            printf("]"); 
#endif
            printf("\n");
        }
    }
    _mm_free(query_cum_len_ar);
    free(enc_qdb);
    for(int tid = 0; tid < numthreads; tid++)
    {
        free(matchArray[tid]);
    }
    _mm_free(min_intv_array);
    _mm_free(numTotalSmem);
    _mm_free(batchTid);
    _mm_free(batchOffset);
    delete fmiSearch;
    return 0;
}

