void
remapind(SNP **snpmarkers, int numsnps, Indiv **indivmarkers, Indiv **indm2, int numindivs, int numind2)
{
int *g1, *g2, *w1 ;
int *tind, t, i, j, k ;
Indiv *indx ;
SNP *cupt ;
if (numindivs != numind2) fatalx("different remapind sizes %d %d\n", numindivs, numind2) ;
ZALLOC(tind, numind2, int) ;
ZALLOC(g2, numind2, int) ;
ZALLOC(g1, numind2, int) ;
ZALLOC(w1, numind2, int) ;
for (k=0; k<numind2; ++k) {
indx = indm2[k] ;
t = tind[k] = indindex(indivmarkers, numindivs, indx -> ID) ;
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) {
g1[j] = getgtypes(cupt, j) ;
}
copyiarr(g1, w1, numind2) ;
for (k=0; k< numind2; ++k) {
g2[k] = g1[tind[k]] ;
}
ivclear(g1, -1, numind2) ;
copyiarr(g2, g1, numind2) ;
for (k=0; k<numind2; ++k) {
putgtypes(cupt, k, g1[k]) ;
}
/**
if (i<100) {
printf("zzz %s\n", cupt -> ID) ;
for (j=0; j<numind2; ++j) {
g1[j] = getgtypes(cupt, j) ;
}
printimat(w1, 1, numind2) ;
printimat(g1, 1, numind2) ;
}
*/
}
free(w1) ;
free(g1) ;
free(g2) ;
free(tind) ;
}
void ipsortitp(int **a, int *ind, int len, int rlen, int *order)
/**
sort integer array pointers
rows of array are sorted in lexicographical order
compiarr can be called outside the sort
*/
{
int i,k ;
int *inda ;
if (len==0) fatalx("(ipsortit) len = 0\n") ;
ZALLOC(pttt, len, int *) ;
ZALLOC(inda, len, int) ;
setorder(order, rlen) ; // order defines order as sorted in ascending order.
for (i=0; i<len; i++) {
if (a[i] == NULL) fatalx("(ipsortit) array pointer %d NULL\n",i) ;
inda[i] = i ;
}
copyiparr(a,pttt,len) ;
qsort((int *) inda, len,
sizeof(int), (int (*) (const void *, const void *)) ipcompit);
for (i=0; i<len; i++) {
k = inda[i] ;
a[i] = pttt[k] ;
}
if (ind != NULL) copyiarr(inda, ind, len) ;
free(inda) ;
free (pttt) ;
}
void mapit(int *a, int *b, int n, int inval, int outval)
{
int k ;
copyiarr(b, a, n) ;
for (k=0; k<n; ++k) {
if (a[k]==inval) a[k] = outval ;
}
}
void reviarr(int *b,int *a,int n)
{
int i ;
int *x ;
ZALLOC(x, n, int) ;
for (i=0; i<n; i++) {
x[n-i-1] = a[i] ;
}
copyiarr(x, b, n) ;
free(x) ;
}
void isortit(int *a, int *ind, int len)
{
int i,k ;
int *inda ;
if (len==0) fatalx("(isortit) len = 0\n") ;
ZALLOC(ittt, len, int) ;
ZALLOC(inda, len, int) ;
for (i=0; i<len; i++) {
inda[i] = i ;
}
copyiarr(a,ittt,len) ;
qsort((int *) inda, len, sizeof(int), (int (*) (const void *, const void *)) icompit);
for (i=0; i<len; i++) {
k = inda[i] ;
a[i] = ittt[k] ;
}
free (ittt) ;
if (ind != NULL) copyiarr(inda, ind, len) ;
free(inda) ;
}
void flipiarr(int *a, int *b, int n)
{
int *x, k ;
ZALLOC(x, n, int) ;
for (k=0; k<n; ++k) {
x[n-1-k] = b[k] ;
}
copyiarr(x, a, n) ;
free(x) ;
}
void ipermute(int *a, int *ind, int len)
{
int i , k ;
int *rrr ;
ZALLOC(rrr, len, int) ;
copyiarr(a, rrr, len) ;
for (i=0; i<len; i++) {
k = ind[i] ;
a[i] = rrr[k] ;
}
free (rrr) ;
}
void imulmat(int *a, int *b, int *c, int a1, int a2, int a3)
/* b is a1 x a2 , c a2 x a3 so a is a1 x a3 */
{
int *t ;
int i,j,k ;
ZALLOC(t, a1*a3, int) ;
for (i=0; i<a1; i++)
for (j=0; j<a3; j++)
for (k=0; k<a2; k++)
t[i*a3+j] += b[i*a2+k]*c[k*a3+j] ;
copyiarr(t, a, a1*a3) ;
free (t) ;
}
void invperm(int *a, int *b, int n) {
/**
a, b can be same
*/
int i, j ;
int *x ;
if (n==0) return ;
ZALLOC(x, n, int) ;
ivclear(x,-1,n) ;
for (i=0; i<n; i++) {
j=b[i] ;
x[j]=i ;
}
copyiarr(x, a, n) ;
free(x) ;
}
void setorder(int *pp, int rlen)
{
int *tt ;
if (plen > 0) {
if (porder != NULL) free(porder) ;
}
if (pp==NULL) {
porder = NULL ;
plen = rlen ;
return ;
}
ZALLOC(porder, rlen, int) ;
ZALLOC(tt, rlen, int) ;
copyiarr(pp, tt, rlen) ;
isortit(tt, porder, rlen) ;
free(tt) ;
plen = rlen ;
}
