void flip1(SNP *cupt, int phasedmode, int flipreference)
{
if (phasedmode == NO) flipalleles(cupt) ;
if (phasedmode == YES) flipalleles_phased(cupt) ;
// just flips genotypes
if (flipreference) cswap(&cupt -> alleles[0], &cupt -> alleles[1]) ;
}
int
mergeit(SNP **snpm1, SNP **snpm2, Indiv ***pindm1, Indiv **indm2,
int nums1, int nums2, int numi1, int numi2)
{
SNP *cupt1, *cupt2 ;
int k, x, g, t ;
double y ;
long rlen, packlen ;
static unsigned char *packg ;
unsigned char *buff ;
Indiv **indm1 ;
static Indiv **indivmarkers ;
int numindivs, numsnps ;
indm1 = *pindm1 ;
numindivs = numi1 + numi2 ;
numsnps = nums1 ;
ZALLOC(indivmarkers, numindivs, Indiv *) ;
t = 0 ;
for (x=0; x<numi1; ++x) {
indivmarkers[t] = indm1[x] ;
++t ;
}
for (x=0; x<numi2; ++x) {
indivmarkers[t] = indm2[x] ;
++t ;
}
// we don't bother with a destructor here. Sloppy code
y = (double) (numindivs * 2) / (8 * (double) sizeof (char)) ;
rlen = nnint(ceil(y)) ;
rlen = MAX(rlen, 48) ;
packlen = numsnps*rlen ;
ZALLOC(packg, packlen, unsigned char) ;
cclear((unsigned char *) packg, 0XFF, packlen) ;
// wipe to invalid
buff = packg ;
for (k=0; k<nums1; k++) {
cupt1 = snpm1[k] ;
x = cupt1 -> tagnumber ;
if (x < 0 ) cupt1 -> ignore = YES ;
if (cupt1 -> ignore) continue ;
cupt2 = snpm2[x] ;
if (cupt2 -> isrfake) {
if (phasedmode == NO) flipalleles(cupt2) ;
if (phasedmode == YES) flipalleles_phased(cupt2) ;
}
for (t=0; t<numi1; ++t) {
g = getgtypes(cupt1, t) ;
if (g<0) continue ;
wbuff((unsigned char *)buff, t, g) ;
}
for (t=0; t<numi2; ++t) {
g = getgtypes(cupt2, t) ;
if (g<0) continue ;
wbuff((unsigned char *)buff, numi1+t, g) ;
}
cupt1 -> ngtypes = numindivs ;
cupt1 -> pbuff = (char *) buff ;
buff += rlen ;
}
*pindm1 = indivmarkers ;
return numindivs ;
}
