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h2d.c
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#include <stdio.h>
#include <string.h>
#include <unistd.h>
#include <math.h>
#include <nicklib.h>
#include <admutils.h>
extern int verbose;
extern long rlen, packlen ;
extern char *packgenos ;
static char *pack2 ;
static int pseudodip = YES ; // for hap to dip.
int
mkindh2d (Indiv ** indivmarkers, Indiv *** pindm2, int numindivs)
{
char ss[50];
Indiv *indx, **indm2, *indp;
int n, len, k;
int numind2;
numind2 = numindivs / 2;
ZALLOC (*pindm2, numind2, Indiv *);
indm2 = *pindm2;
n = 0;
for (k = 0; k < numindivs; k++) {
indx = indivmarkers[k];
strcpy (ss, indx->ID);
len = strlen (ss);
if (ss[len - 1] != 'A')
continue;
ss[len - 2] = CNULL;
ZALLOC (indm2[n], 1, Indiv);
indp = indm2[n];
*indp = *indx;
strcpy (indp->ID, ss);
++n;
}
if (n != numind2)
fatalx ("(mkindh2d) bug\n");
return n;
}
void
remaph2d (SNP ** snpmarkers, int numsnps, Indiv ** indivmarkers,
Indiv ** indm2, int numindivs, int numind2)
{
int *g1, *g2;
int *x1, *x2;
int *tind, tt, t, i, j, k, j1, j2;
Indiv *indx;
SNP *cupt;
char s1[50], s2[50];
ZALLOC (g2, numind2, int);
ZALLOC (g1, numindivs, int);
ZALLOC (x1, numindivs, int);
ZALLOC (x2, numindivs, int);
for (k = 0; k < numind2; ++k) {
indx = indm2[k];
sprintf (s1, "%s:A", indx->ID);
sprintf (s2, "%s:B", indx->ID);
t = x1[k] = indindex (indivmarkers, numindivs, s1);
if (t < 0) {
sprintf (s1, "%s_A", indx->ID);
sprintf (s2, "%s_B", indx->ID);
t = x1[k] = indindex (indivmarkers, numindivs, s1);
}
if (t < 0)
fatalx ("bad newindiv: %s\n", indx->ID);
t = x2[k] = indindex (indivmarkers, numindivs, s2);
if (t < 0)
fatalx ("bad newindiv: %s\n", indx->ID);
}
for (i = 0; i < numsnps; i++) {
cupt = snpmarkers[i];
for (j = 0; j < numind2; ++j) {
t = x1[j];
g1[j] = getgtypes (cupt, t);
t = x2[j];
g2[j] = getgtypes (cupt, t);
tt = -1;
if ((g1[j] >= 0) && (g2[j] >= 0)) {
tt = g1[j] + g2[j];
if (pseudodip) tt /= 2 ;
}
putgtypes (cupt, j, tt);
}
}
free (g1);
free (g2);
free (x1);
free (x2);
}
int mkindd2h (Indiv ** indivmarkers, Indiv *** pindm2, int numindivs)
{
char ss[50], s1[50], s2[50] ;
Indiv *indx, **indm2, *indp, *ind1, *ind2 ;
int n, len, k;
int numind2;
numind2 = numindivs * 2;
ZALLOC (*pindm2, numind2, Indiv *);
indm2 = *pindm2;
n = 0;
for (k = 0; k < numindivs; k++) {
indx = indivmarkers[k];
strcpy (s1, indx->ID);
strcat (s1, ":A") ;
strcpy (s2, indx->ID);
strcat (s2, ":B") ;
if (strlen(s1) >=IDSIZE) fatalx("d2h overflow: %s\n", indx -> ID) ;
ZALLOC (indm2[n], 1, Indiv);
indp = indm2[n];
*indp = *indx;
strcpy (indp->ID, s1);
++n;
ZALLOC (indm2[n], 1, Indiv);
indp = indm2[n];
*indp = *indx;
strcpy (indp->ID, s2);
++n;
}
if (n != numind2) fatalx ("(mkindh2d) bug\n");
return n;
}
void
remapd2h (SNP ** snpmarkers, int numsnps, Indiv ** indivmarkers,
Indiv ** indm2, int numindivs, int numind2)
{
int g1, g2, gg;
int *xx, *x2;
int *tind, tt, t, i, j, k, j1, j2, x;
Indiv *indx;
SNP *cupt;
char s1[50], s2[50];
long rlen2, packlen2 ;
char *pbuff ;
rlen2 = rlen * 2 ;
packlen2 = packlen * 2 ;
ZALLOC(pack2, packlen2, char) ;
pbuff = pack2 ;
ZALLOC (xx, numind2, int);
ZALLOC (x2, numindivs, int);
x = 0 ;
for (i=0 ; i < numsnps; ++i) {
cupt = snpmarkers[i] ;
ivclear(xx, -1, numind2) ;
for (k=0 ; k < numindivs; ++k) {
gg = getgtypes(cupt, k) ;
if (gg<0) gg = 3 ;
g1 = g2 = gg ;
if (gg == 1) {
x = ranmod(2) ;
g1 = 2*x ;
g2 = 2*(1-x) ;
}
xx[2*k] = g1 ;
xx[2*k+1] = g2 ;
}
for (k=0; k<numind2; ++k) {
gg = xx[k] ;
wbuff( (unsigned char *) pbuff, k, gg) ;
}
cupt -> pbuff = pbuff ;
pbuff += rlen2 ;
}
free (xx);
free (x2);
free (packgenos) ;
packgenos = pack2 ;
rlen = rlen2 ;
packlen = packlen2 ;
}