void mem_pestat(const mem_opt_t *opt, int64_t l_pac, int n, const mem_alnreg_v *regs, mem_pestat_t pes[4]) {
int i, d, max;
uint64_v isize[4];
memset(pes, 0, 4 * sizeof(mem_pestat_t));
memset(isize, 0, sizeof(kvec_t(int)) * 4);
/* infer based on the first reg from the two reads */
for (i = 0; i < n>>1; ++i) {
int dir;
int64_t is;
mem_alnreg_v *r[2];
r[0] = (mem_alnreg_v*)®s[i<<1|0];
r[1] = (mem_alnreg_v*)®s[i<<1|1];
if (r[0]->n == 0 || r[1]->n == 0) continue;
if (cal_sub(opt, r[0]) > MIN_RATIO * r[0]->a[0].score) continue;
if (cal_sub(opt, r[1]) > MIN_RATIO * r[1]->a[0].score) continue;
if (r[0]->a[0].rid != r[1]->a[0].rid) continue; // not on the same chr
if (r[0]->a[0].bss != r[1]->a[0].bss) continue; /* not on the same bisulfite strand */
dir = mem_infer_dir(l_pac, r[0]->a[0].rb, r[1]->a[0].rb, &is);
if (is && is <= opt->max_ins) kv_push(uint64_t, isize[dir], is);
}
if (bwa_verbose >= 3) fprintf(stderr, "[M::%s] # candidate unique pairs for (FF, FR, RF, RR): (%ld, %ld, %ld, %ld)\n", __func__, isize[0].n, isize[1].n, isize[2].n, isize[3].n);
for (d = 0; d < 4; ++d) { // TODO: this block is nearly identical to the one in bwtsw2_pair.c. It would be better to merge these two.
mem_pestat_t *r = &pes[d];
uint64_v *q = &isize[d];
int p25, p50, p75, x;
if (q->n < MIN_DIR_CNT) {
fprintf(stderr, "[M::%s] skip orientation %c%c as there are not enough pairs\n", __func__, "FR"[d>>1&1], "FR"[d&1]);
r->failed = 1;
free(q->a);
continue;
} else fprintf(stderr, "[M::%s] analyzing insert size distribution for orientation %c%c...\n", __func__, "FR"[d>>1&1], "FR"[d&1]);
int main(int argc, char **argv)
{
double time_spent; /* To add time */
int time_spent_m, time_spent_s; /* To add time */
time_t begin, end; /* To add time */
int i, r, n1, n2;
int rounds, maxnum; /* rounds is how many iterations of the game there will be
maxnum is the biggest values used in the sums */
int score = 0;
/* initial settings for rounds & turns */
rounds = (argv[1] && isdigit(argv[1][0])) ? atoi(argv[1]) : ROUNDS;
maxnum = (argv[2] && isdigit(argv[2][0])) ? atoi(argv[2]) : MAXNUM;
/* start the timer */
begin = time(NULL);
/* return HOWTO instead of play */
if(argv[1] && (argv[1][0] == 'h')){
help();
return 0;
}
/* the main dispach switch */
srand ( (unsigned)time ( NULL ) );
for(i = 0; i < rounds; i++){
r = rand() % 4;
n1 = rand() % maxnum;
n2 = rand() % maxnum;
switch(r){
case 0: /* addition */
score += cal_add(n1, n2);
break;
case 1: /* subtraction - call function with biggest number first,
so we don't need to have negatives in the answer */
score += (n1 >= n2) ? cal_sub(n1, n2) : cal_sub(n2, n1);
break;
case 2: /* multiplication */
score += cal_mul(n1, n2);
break;
case 3: /* division - we avoid 0 in the division, just to simplify things
like subtraction, we also use the bigger val divided by the smaller */
while(n1 == 0 || n2 == 0){
n1 = rand() % MAXNUM;
n2 = rand() % MAXNUM;
}
score += (n1 >= n2) ? cal_div(n1, n2) : cal_sub(n2, n1);
break;
default: /* catch imposible */
printf("Something isn't working rights\n");
return 0;
}
}
/* end timer */
end = time(NULL);
time_spent = difftime(end, begin);
time_spent_m = (int)(time_spent)/60;
time_spent_s = (int)(time_spent)%60;
/* Report */
printf("\n");
printf("You got %d out of %d in %d ", score, rounds, time_spent_m);
printf("%s", (time_spent_m == 1)?"minute":"minutes");
printf(", %d ", time_spent_s);
printf("%s", (time_spent_s == 1)?"second":"seconds");
if((rounds - score) < 4){
printf("!");
}
else{
printf(".");
}
printf("\n\n");
return 0;
}