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worker1 -> mem_align1_core -> mem_chain

worker2 -> mem_reg2sam -> mem_aln2sam

typedef struct {
	int a, b;               // match score and mismatch penalty
	int o_del, e_del;       // ??
	int o_ins, e_ins;	// ??
	int pen_unpaired;       // ?? phred-scaled penalty for unpaired reads
	int pen_clip5,pen_clip3;// ?? clipping penalty. This score is not deducted from the DP score.
	int w;                  // ?? band width
	int zdrop;              // ? Z-dropoff

	uint64_t max_mem_intv;	// ??

	int T;                  // ?? output score threshold; only affecting output
	int flag;               // ?? see MEM_F_* macros
	int min_seed_len;       // ? minimum seed length
	int min_chain_weight;	// ??
	int max_chain_extend;	// ?
	float split_factor;     // ? split into a seed if MEM is longer than min_seed_len*split_factor
	int split_width;        // ? split into a seed if its occurence is smaller than this value
	int max_occ;            // ? skip a seed if its occurence is larger than this value
	int max_chain_gap;      // do not chain seed if it is max_chain_gap-bp away from the closest seed
	int n_threads;          // number of threads
	int chunk_size;         // ? process chunk_size-bp sequences in a batch
	float mask_level;       // ? regard a hit as redundant if the overlap with another better hit is over mask_level times the min length of the two hits
	float drop_ratio;       // ? drop a chain if its seed coverage is below drop_ratio times the seed coverage of a better chain overlapping with the small chain
	float XA_drop_ratio;    // ? when counting hits for the XA tag, ignore alignments with score < XA_drop_ratio * max_score; only effective for the XA tag
	float mask_level_redun;	// ??
	float mapQ_coef_len;	// ??
	int mapQ_coef_fac;	// ??
	int max_ins;            // when estimating insert size distribution, skip pairs with insert longer than this value
	int max_matesw;         // perform maximally max_matesw rounds of mate-SW for each end
	int max_XA_hits, max_XA_hits_alt; // if there are max_hits or fewer, output them all
	int8_t mat[25];         // ? scoring matrix; mat[0] == 0 if unset
} mem_opt_t;