seq_align_multiple.h

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#ifndef SEQ_ALIGN_MULTIPLE_H
#define SEQ_ALIGN_MULTIPLE_H

#include "dp_hls_common.h"
#include "ap_int.h"
#include "ap_fixed.h"
#include <hls_stream.h>

#ifdef CMAKEDEBUG
#include "debug.h"
#endif

using namespace hls;

extern "C" {
    void seq_align_multiple_static(
        char_t (&querys)[MAX_QUERY_LENGTH][N_BLOCKS],
        char_t (&references)[MAX_REFERENCE_LENGTH][N_BLOCKS],
        idx_t (&query_lengths)[N_BLOCKS],
        idx_t (&reference_lengths)[N_BLOCKS],
        const Penalties (&penalties)[N_BLOCKS],
#ifdef LOCAL_TRANSITION_MATRIX
        const type_t (&transitions)[TRANSITION_MATRIX_SIZE][TRANSITION_MATRIX_SIZE],
#endif
        idx_t (&tb_is)[N_BLOCKS], idx_t (&tb_js)[N_BLOCKS]
#ifndef NO_TRACEBACK
        , tbr_t (&tb_streams)[MAX_REFERENCE_LENGTH + MAX_QUERY_LENGTH][N_BLOCKS]
#endif
#ifdef SCORED
        , type_t (&scores)[N_BLOCKS]
#endif
#ifdef CMAKEDEBUG
        , Container (&debugger)[N_BLOCKS]
#endif
        );

    // Have maximum input length of 2048 for 2 bit inputs. 
    // void seq_align_multiple_dynamic(
    //  stream<ArrayPack<char_t, MAX_QUERY_LENGTH>> &querys,
    //  stream<ArrayPack<char_t, MAX_REFERENCE_LENGTH>> &references,
    //  stream<idx_t> &query_lengths,
    //  stream<idx_t> &reference_lengths,
    //  stream<tbp_t> &tb_streams);
    
}

#endif