void
ebl_wstrtabfinalize (struct Ebl_WStrtab *st, Elf_Data *data)
{
size_t copylen;
wchar_t *endp;
size_t nulllen = st->nullstr ? 1 : 0;
/* Fill in the information. */
data->d_buf = malloc ((st->total + nulllen) * sizeof (wchar_t));
if (data->d_buf == NULL)
abort ();
/* The first byte must always be zero if we created the table with a
null string. */
if (st->nullstr)
*((wchar_t *) data->d_buf) = L'\0';
data->d_type = ELF_T_BYTE;
data->d_size = st->total + nulllen;
data->d_off = 0;
data->d_align = 1;
data->d_version = EV_CURRENT;
/* Now run through the tree and add all the string while also updating
the offset members of the elfstrent records. */
endp = (wchar_t *) data->d_buf + nulllen;
copylen = sizeof (wchar_t) * nulllen;
copystrings (st->root, &endp, ©len);
assert (copylen == (st->total + nulllen) * sizeof (wchar_t));
}
static void
copystrings (struct Ebl_Strent *nodep, char **freep, size_t *offsetp)
{
if (nodep->left != NULL)
copystrings (nodep->left, freep, offsetp);
/* Process the current node. */
nodep->offset = *offsetp;
*freep = (char *) mempcpy (*freep, nodep->string, nodep->len);
*offsetp += nodep->len;
for (struct Ebl_Strent *subs = nodep->next; subs != NULL; subs = subs->next)
{
assert (subs->len < nodep->len);
subs->offset = nodep->offset + nodep->len - subs->len;
assert (subs->offset != 0 || subs->string[0] == '\0');
}
if (nodep->right != NULL)
copystrings (nodep->right, freep, offsetp);
}
void *
strtabfinalize (struct Strtab *st, size_t *size)
{
size_t copylen;
char *endp;
char *retval;
/* Fill in the information. */
endp = retval = (char *) xmalloc (st->total + 1);
/* Always put an empty string at the beginning so that a zero offset
can mean error. */
*endp++ = '\0';
/* Now run through the tree and add all the string while also updating
the offset members of the elfstrent records. */
copylen = 1;
copystrings (st->root, &endp, ©len);
assert (copylen == st->total + 1);
assert (endp = retval + st->total + 1);
*size = copylen;
return retval;
}
void dopop3out(char **fglist, SNP **xsnplist, int ncols, char *line, char *outpop)
{
Indiv **xindlist ;
Indiv *indx ;
int *xindex, *xtypes ;
int nrows ;
int t, k, i, trun ;
double f3score, f3scoresig ;
double f2score, f2scoresig, y, y1, y2, p, q ;
char *eglist[4] ;
int numeg = 4 ;
double ytop, ybot, yxbot ;
double ztop, zbot ;
int col ;
SNP *cupt ;
double zztop[6], yytop[6] ;
double u, s1, s2, atop, btop, alphabot, betabot, alphatop ;
double ya, yb, za, zb, yt ;
char obuff[1024], *sx ;
int nsnp = 0 ;
copystrings(fglist, eglist, 3) ;
eglist[3] = strdup(outpop) ;
ZALLOC(xindex, numindivs, int) ;
ZALLOC(xindlist, numindivs, Indiv *) ;
setstatusv(indivmarkers, numindivs, NULL, NO) ;
setstatuslist(indivmarkers, numindivs, eglist, numeg) ;
nrows = loadindx(xindlist, xindex, indivmarkers, numindivs) ;
if (nrows == 0) {
for (i=0; i<numeg; ++i) {
printf("zz %s\n", eglist[i]) ;
}
fatalx("fatal error (probably missing pop)\n") ;
}
ZALLOC(xtypes, nrows, int) ;
for (i=0; i<nrows; i++) {
indx = xindlist[i] ;
k = indxindex(eglist, numeg, indx -> egroup) ;
xtypes[i] = k ;
}
ztop = zbot = 0.0 ;
vzero(zztop, 6) ;
for (col=0; col<ncols; ++col) {
cupt = xsnplist[col] ;
if (cupt -> ignore) continue ;
loadaa(cupt, xindex, xtypes, nrows, numeg) ;
f3scz(&ytop, &ybot, cupt, indivmarkers, xindex, xtypes, nrows, 2, 0, 1) ;
if (isnan(ytop)) fatalx("zznan\n") ;
if (ybot < -0.5) continue ;
f3scz(&yytop[0], &yxbot, cupt, indivmarkers, xindex, xtypes, nrows, 3, 0, 1) ; if (yxbot < -0.5) continue ;
f3scz(&yytop[1], &yxbot, cupt, indivmarkers, xindex, xtypes, nrows, 3, 0, 2) ; if (yxbot < -0.5) continue ;
f3scz(&yytop[2], &yxbot, cupt, indivmarkers, xindex, xtypes, nrows, 3, 1, 2) ; if (yxbot < -0.5) continue ;
f2scz(&yytop[3], &yxbot, cupt, indivmarkers, xindex, xtypes, nrows, 3, 0, 3) ; if (yxbot < -0.5) continue ;
f2scz(&yytop[4], &yxbot, cupt, indivmarkers, xindex, xtypes, nrows, 3, 1, 3) ; if (yxbot < -0.5) continue ;
f2scz(&yytop[5], &yxbot, cupt, indivmarkers, xindex, xtypes, nrows, 3, 2, 3) ; if (yxbot < -0.5) continue ;
ztop += ytop ;
zbot += ybot ;
if ((ytop>0) || (ybot > 0)) ++nsnp ; // monomorphic snps not counted
vvp(zztop, zztop, yytop, 6) ;
}
//verbose = YES ;
ztop /= zbot ;
vst(zztop, zztop, 1.0/zbot, 6) ;
u = zztop[0] ;
vsp(yytop, zztop, -u, 6) ;
s1 = yytop[1] ; /* alpha a */
s2 = yytop[2] ;
atop = yytop[3] ;
btop = yytop[4] ;
alphabot = s1/atop ;
betabot = s2/btop ;
alphatop = 1.0-betabot ;
y1 = -ztop -s1 ;
if (s2>s1) {
alphabot = MAX(alphabot, y1/(s2-s1)) ;
}
if (s2<s1) {
alphatop = MIN(alphatop, y1/(s2-s1)) ;
}
sx = obuff ;
sx += sprintf(sx, "%s", line) ;
//printf(" %12.6f", ztop) ;
sx += sprintf(sx, " %9.3f", alphabot) ;
sx += sprintf(sx, " %9.3f", alphatop) ;
/**
// next code is computing bounds on h (drift -> C)
za = alphatop; zb = 1.0-za ;
ya = s1/za; yb = s2/zb; yt = -za*zb*(ya+yb) ; y1 = ztop - yt ;
za = alphabot; zb = 1.0-za ;
ya = s1/za; yb = s2/zb; yt = -za*zb*(ya+yb) ; y2 = ztop - yt ;
sx += sprintf(sx, " %9.3f %9.3f", y1, y2) ;
sx += sprintf(sx, " %7d", nsnp) ;
*/
printf("%s", obuff) ;
printnl() ;
if (verbose) printmatwl(yytop, 1, 6, 6) ;
if (outputname != NULL) {
fprintf(ofile, "%s\n", obuff) ;
fflush(ofile) ;
}
free(xtypes) ;
free(xindex) ;
free(xindlist) ;
freeup(eglist, 4) ;
destroyaa() ;
return ;
}
