structure()
{
VERT v, *head;
if (progress)
fprintf(stderr," getreach:\n");
getreach();
if (routerr) return;
if (progress)
fprintf(stderr," getflow:\n");
getflow();
if (progress)
fprintf(stderr," getthen:\n");
getthen(START);
head = challoc(nodenum * sizeof(*head));
for (v = 0; v < nodenum; ++v)
head[v] = UNDEFINED;
for (v = START; DEFINED(v); v = RSIB(v))
fixhd(v,UNDEFINED,head);
/* fixhd must be called before getloop so that
it gets applied to IFVX which becomes NXT(w) for UNTVX w */
if (progress)
fprintf(stderr," getloop:\n");
getloop();
if (progress)
fprintf(stderr," getbranch:\n");
getbranch(head);
chfree(head,nodenum * sizeof(*head));
head = 0;
}
static int set_hyp(char *line, flow_list *hy, const char *s) // 2 hypothesis first.
{
int pos;
char ref[1000], targ[1000];
unsigned char f[100];
int fs[100];
//printf("PPP=%s", line);
chomp(line);
//fprintf(outp, "%s", line);
sscanf(line, "%*s %d %*s %s %s", &pos, ref, targ);
cur_pos = pos;
pos--; // to o-offset
int i = getflow(f, fs, s, pos-1, pos+strlen(ref), ref, CONTEXT);
hy->add_list(f, fs, i, 1.0);
i = getflow(f, fs, s, pos-1, pos+strlen(ref), targ, CONTEXT);
int rv = 0;
if (strlen(ref) == strlen(targ)) {
hy->add_list(f, fs, i, 0.005);
} else {
hy->set_is_indel();
hy->add_list(f, fs, i, 0.001);
/*
if (strlen(ref) == 2 && strlen(targ) ==1) { // for deletion, try alternative SNP cases.
int y = strlen(ref)-strlen(targ);
fs[CONTEXT-1]+=y;
hy->add_list(f, fs, i, 0.005);
fs[CONTEXT-1] -= y;
fs[i-CONTEXT] += y;
hy->add_list(f, fs, i, 0.005);
}
*/
}
//int b= count_of_flow(targ);
//rv = b-1;
rv = i-(CONTEXT*2+1);
return rv;
}
