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) ;
}
int checkmatch(SNP *cupt1, SNP *cupt2)
{
char a1, a2, b1 , b2 ;
if (docheck == NO) return 1 ;
if (cupt1 -> alleles == NULL) return -1 ;
if (cupt2 -> alleles == NULL) return -1 ;
a1 = cupt1 -> alleles[0] ;
a2 = cupt1 -> alleles[1] ;
b1 = cupt2 -> alleles[0] ;
b2 = cupt2 -> alleles[1] ;
if ((a1 == 'X') && (a2 == 'X') && (strandcheck)) return -1 ; // flipcheck impossible
if (strandcheck) {
if ((a1 == 'A') && (a2 == 'T')) return -1 ;
if ((a1 == 'T') && (a2 == 'A')) return -1 ;
if ((a1 == 'C') && (a2 == 'G')) return -1 ;
if ((a1 == 'G') && (a2 == 'C')) return -1 ;
if ((b1 == 'A') && (b2 == 'T')) return -1 ;
if ((b1 == 'T') && (b2 == 'A')) return -1 ;
if ((b1 == 'C') && (b2 == 'G')) return -1 ;
if ((b1 == 'G') && (b2 == 'C')) return -1 ;
}
if ((a1 == b1) && (a2 == 'X')) {
cupt1 -> alleles[1] = b2 ;
return 1 ;
}
if ((a1 == b2) && (a2 == 'X')) {
cupt1 -> alleles[1] = b1 ;
return 2 ;
}
if ((a1 == b1) && (a2 == b2)) return 1 ;
if ((a1 == b2) && (a2 == b1)) return 2 ;
if ((a1 == b1) && (b2 =='X')) return 1 ;
if ((a2 == b1) && (b2 =='X')) return 2 ;
if (strandcheck == NO) return 0 ;
b1 = compbase(b1) ;
b2 = compbase(b2) ;
if ((a1 == b1) && (a2 == 'X')) {
cupt1 -> alleles[1] = b2 ;
return 1 ;
}
if ((a1 == b2) && (a2 == 'X')) {
cupt1 -> alleles[1] = b1 ;
return 2 ;
}
if ((a1 == b1) && (a2 == b2)) return 1 ;
if ((a1 == b2) && (a2 == b1)) return 2 ;
if ((a1 == b1) && (b2 =='X')) return 1 ;
if ((a2 == b1) && (b2 =='X')) return 2 ;
return 0 ;
}