#ifndef MMPRIV2_H
#define MMPRIV2_H

#include <assert.h>
#include "minimap.h"
#include "bseq.h"

#ifndef kroundup32
#define kroundup32(x) (--(x), (x)|=(x)>>1, (x)|=(x)>>2, (x)|=(x)>>4, (x)|=(x)>>8, (x)|=(x)>>16, ++(x))
#endif

#ifndef KSTRING_T
#define KSTRING_T kstring_t
typedef struct __kstring_t {
	unsigned l, m;
	char *s;
} kstring_t;
#endif

#ifdef __cplusplus
extern "C" {
#endif

double cputime(void);
double realtime(void);

void radix_sort_128x(mm128_t *beg, mm128_t *end);
void radix_sort_64(uint64_t *beg, uint64_t *end);
uint32_t ks_ksmall_uint32_t(size_t n, uint32_t arr[], size_t kk);

void mm_write_paf(kstring_t *s, const mm_idx_t *mi, bseq1_t *t, int which, mm_reg1_t *r);
void mm_write_sam(kstring_t *s, const mm_idx_t *mi, bseq1_t *t, int which, mm_reg1_t *r);
int mm_chain_dp(int max_dist, int bw, int max_skip, int min_cnt, int min_sc, int n, mm128_t *a, uint64_t **_u, void *km);
mm_reg1_t *mm_align_skeleton(void *km, const mm_mapopt_t *opt, const mm_idx_t *mi, int qlen, const char *qstr, int *n_regs_, mm_reg1_t *regs, mm128_t *a);

#ifdef __cplusplus
}
#endif

static inline void mm_reg_set_coor(mm_reg1_t *r, int32_t qlen, const mm128_t *a)
{
	int32_t k = r->as;
	r->rev = a[k].x>>63;
	r->rid = a[k].x<<1>>33;
	assert(r->rid != 0x7fffffff);
	r->rs = (int32_t)a[k].x + 1 > (int32_t)(a[k].y>>32)? (int32_t)a[k].x + 1 - (int32_t)(a[k].y>>32) : 0;
	r->re = (int32_t)a[k + r->cnt - 1].x + 1;
	if (!r->rev) {
		r->qs = (int32_t)a[k].y + 1 - (int32_t)(a[k].y>>32);
		r->qe = (int32_t)a[k + r->cnt - 1].y + 1;
	} else {
		r->qs = qlen - ((int32_t)a[k + r->cnt - 1].y + 1);
		r->qe = qlen - ((int32_t)a[k].y + 1 - (int32_t)(a[k].y>>32));
	}
}

#endif