graph.h

#pragma once
#define BOOST_LOCALE_NO_LIB
#define NOMINMAX
#include <atomic>
#include <string>
#include <tbb/flow_graph.h>
#include <vector>
#include "parameters.h"

#define DEFAULT_SEQ_BLOCK_SIZE 1000000000
#define DEFAULT_LASTZ_INTERVAL 10000000
#define DEFAULT_WGA_CHUNK 250000

using namespace tbb::flow;

struct Seed_config {
    std::string shape;
    int size;
    int kmer_size;
    bool transition;
};

struct segmentPair {
    uint32_t ref_start;
    uint32_t query_start;
    uint32_t len;
    int score;
};

struct Segment {
    uint32_t query_start;
    uint32_t len;
};

struct Configuration {
    //Input files/folder name
    std::string seq_filename;

    // Sequence parameters
    std::string strand;
    size_t seq_len;
    float prop_neigh_interval;
    uint32_t num_neigh_interval;

    // Scoring
    std::string scoring_file;
    std::string ambiguous;
    int sub_mat[NUC2];

    // Seed parameters
    Seed_config seed;
    std::string seed_shape;
    uint32_t step;
    
    // Filter parameters
    int xdrop; 
    int hspthresh;
    bool noentropy;

    // Output parameters
    uint32_t M;
    bool markend;

    // System parameters
    uint32_t wga_chunk_size;
    uint32_t lastz_interval_size;
    uint32_t seq_block_size;
    int num_gpu;
    int num_threads;
    bool debug;
};

extern Configuration cfg;

struct seq_block {
  int index;
  size_t start;
  uint32_t len;
};

struct seed_interval {
    uint32_t start;
    uint32_t end;
    uint32_t ref_start;
    uint32_t ref_end;
    uint32_t num_invoked;
    uint32_t num_intervals;
};

typedef std::vector<segmentPair> hsp_output; 
typedef std::vector<Segment> interval_output; 
typedef tbb::flow::tuple <seq_block, seed_interval> seeder_payload;
typedef tbb::flow::tuple <seq_block, int, interval_output> printer_payload;
typedef tbb::flow::tuple <seeder_payload, size_t> seeder_input;
typedef tbb::flow::tuple <printer_payload, size_t> printer_input;
typedef tbb::flow::multifunction_node<printer_input, tbb::flow::tuple<size_t>> printer_node;

struct seeder_body{
	static std::atomic<uint64_t> num_seed_hits;
	static std::atomic<uint64_t> num_seeds;
	static std::atomic<uint64_t> num_hsps;
    static std::atomic<uint32_t> total_xdrop;
    static std::atomic<uint32_t> num_seeded_regions;
	printer_input operator()(seeder_input input);
};

struct interval_printer_body{
	void operator()(printer_input input, printer_node::output_ports_type & op);
};