void flipstrand(char *fsname, SNP **snpm, int numsnps)
// move alleles to opposite strand
{
FILE *fff ;
char line[MAXSTR] ;
char *spt[MAXFF] ;
char *ss ;
int nsplit, n, k ;
SNP *cupt ;
if (fsname == NULL) return ;
openit (fsname, &fff, "r") ;
freesnpindex() ;
while (fgets(line, MAXSTR, fff) != NULL) {
nsplit = splitup(line, spt, MAXFF) ;
if (nsplit==0) continue ;
if (spt[0][0] == '#') {
freeup(spt, nsplit) ;
continue ;
}
k = snpindex(snpm, numsnps, spt[0]) ;
if (k>=0) {
cupt = snpm[k] ;
cupt -> alleles[0] = compbase(cupt -> alleles[0]) ;
cupt -> alleles[1] = compbase(cupt -> alleles[1]) ;
}
freeup(spt, nsplit) ;
}
fclose (fff) ;
}
void flipsnps(char *fsname, SNP **snpm, int numsnps, int phasedmode)
{
FILE *fff ;
char line[MAXSTR] ;
char *spt[MAXFF] ;
char *ss ;
int nsplit, n, k ;
SNP *cupt ;
if (fsname == NULL) return ;
openit (fsname, &fff, "r") ;
freesnpindex() ;
while (fgets(line, MAXSTR, fff) != NULL) {
nsplit = splitup(line, spt, MAXFF) ;
if (nsplit==0) continue ;
if (spt[0][0] == '#') {
freeup(spt, nsplit) ;
continue ;
}
k = snpindex(snpm, numsnps, spt[0]) ;
if (k>=0) {
flip1(snpm[k], phasedmode, flipreference) ;
}
freeup(spt, nsplit) ;
}
fclose (fff) ;
}
void remap(SNP **s1, int nums1, SNP **s2, int nums2)
{
SNP *cupt1, *cupt2 ;
SNP tcupt, *cupt ;
int i, k ;
for (i=0; i<nums2; ++i) {
cupt2 = s2[i] ;
k = snpindex(s1, nums1, cupt2 -> ID) ;
if (k<0) {
printf("%20s not found\n") ;
cupt2 -> ignore = YES ;
continue ;
}
cupt1 = s1[k] ;
fixaa(cupt1, cupt2) ;
if (cupt1 -> alleles[1] == 'X') {
cupt1 -> alleles[1] = cxx(cupt1 -> alleles, cupt2 -> alleles) ;
}
tcupt = *cupt2 ;
*cupt2 = *cupt1 ;
cupt = &tcupt ;
cupt2 -> chrom = cupt -> chrom ;
cupt2 -> genpos = cupt -> genpos ;
cupt2 -> physpos = cupt -> physpos ;
cupt2 -> alleles[0] = cupt -> alleles[0] ;
cupt2 -> alleles[1] = cupt -> alleles[1] ;
}
freesnpindex() ;
}
int main(int argc, char **argv)
{
SNP **snpmarkers ;
Indiv **indivmarkers ;
int numsnps, numindivs ;
unsigned char *packg1, *packg2 ;
int **snppos ;
int *snpindx ;
int lsnplist, lindlist, numeg ;
int i,j;
SNP *cupt, *cupt1, *cupt2, *cupt3 ;
Indiv *indx ;
int ch1, ch2 ;
int fmnum , lmnum ;
int num, n1, n2 ;
int nkill = 0 ;
int t, k, x ;
int nignore, numrisks = 1 ;
char **genolist ;
int numgenolist ;
int maxmiss ;
tersem = YES ; // no snp counts
readcommands(argc, argv) ;
setomode(&outputmode, omode) ;
packmode = YES ;
settersemode(tersem) ;
nums1 =
getsnps(snp1, &snpm1, 0.0, NULL, &nignore, numrisks) ;
putped(1) ;
freeped() ;
nums2 =
getsnps(snp2, &snpm2, 0.0, NULL, &nignore, numrisks) ;
putped(2) ;
freeped() ;
for (x=0; x<nums1; ++x) {
cupt1 = snpm1[x] ;
cupt1 -> tagnumber = -1 ;
}
for (x=0; x<nums2; ++x) {
cupt2 = snpm2[x] ;
t = x %1000 ;
// if (t==0) printf("zz %d %d\n", x, nums2) ;
k = snpindex(snpm1, nums1, cupt2 -> ID) ;
if (k<0) {
cupt2 -> ignore = YES ;
continue ;
}
cupt1 = snpm1[k] ;
cupt1 -> tagnumber = x ;
t = checkmatch(cupt1, cupt2) ;
if (t==1) continue ;
if (t==2) {
cupt2 -> isrfake = YES ;
continue ;
}
if (t<0) {
cupt1 -> ignore = cupt2 -> ignore = YES ;
continue ;
}
printf("allele funny: %s", cupt1 -> ID) ;
printalleles(cupt1, stdout) ;
printalleles(cupt2, stdout) ;
printnl() ;
cupt1 -> ignore = cupt2 -> ignore = YES ;
continue ;
}
freesnpindex() ;
numi1 = getindivs(ind1, &indm1) ;
numi2 = getindivs(ind2, &indm2) ;
for (x=0; x<numi2; ++x) {
k = indindex(indm1, numi1, indm2[x] -> ID) ;
// this code could be modified to allow duplicate individuals
if (k>=0) fatalx("dup ind: %s\n", indm2[x] -> ID) ; // fix later?
}
setgenotypename(&geno1, ind1) ;
getped(1) ;
getgenos(geno1, snpm1, indm1,
nums1, numi1, nignore) ;
packg1 = (unsigned char *) getpackgenos() ;
clearpackgenos() ;
setgenotypename(&geno2, ind2) ;
getped(2) ;
getgenos(geno2, snpm2, indm2,
nums2, numi2, nignore) ;
packg2 = (unsigned char *) getpackgenos() ;
numindivs = mergeit(snpm1, snpm2, &indm1, indm2, nums1, nums2, numi1, numi2) ;
snpmarkers = snpm1 ;
numsnps = nums1 ;
indivmarkers = indm1 ;
free(packg1) ;
free(packg2) ;
outfiles(snpoutfilename, indoutfilename, genooutfilename,
snpmarkers, indivmarkers, numsnps, numindivs, packout, ogmode) ;
printf("##end of mergeit run\n") ;
return 0 ;
}
