int main(int argc, char **argv)
{
char **eglist ;
int numeg ;
int i, j, k, pos;
int *vv ;
SNP *cupt, *cupt2 ;
Indiv *indx ;
double y1, y2, y ;
int n0, n1, nkill ;
int nindiv = 0 ;
int nignore, numrisks = 1 ;
SNP **xsnplist ;
Indiv **xindlist ;
int *xindex ;
int nrows, ncols, m ;
double *XTX, *cc, *evecs, *ww ;
double *lambda ;
double *tvecs ;
int weightmode = NO ;
int t ;
double *xmean, *xfancy ;
double *ldmat = NULL, *ldmat2 = NULL;
double *ldvv = NULL, *ldvv2 = NULL, *vv2 = NULL ;
int chrom, numclear ;
double gdis ;
int outliter, numoutiter, *badlist, nbad ;
int a, b, n ;
FILE *outlfile ;
int xblock, blocksize=10000 ;
double *tblock ;
OUTLINFO *outpt ;
int *idperm, *vecind ; // for sort
readcommands(argc, argv) ;
printf("## smartrel version: %s\n", WVERSION) ;
packmode = YES ;
setomode(&outputmode, omode) ;
if (parname == NULL) return 0 ;
if (xchrom == (numchrom+1)) noxdata = NO ;
if (fstonly) {
printf("fstonly\n") ;
numeigs = 0 ;
numoutliter = 0 ;
numoutiter = 0 ;
outputname = NULL ;
snpeigname = NULL ;
}
if (fancynorm) printf("norm used\n\n") ;
else printf("no norm used\n\n") ;
nostatslim = MAX(nostatslim, 3) ;
outlfile = ofile = stdout;
if (outputname != NULL) openit(outputname, &ofile, "w") ;
if (outliername != NULL) openit(outliername, &outlfile, "w") ;
if (fstdetailsname != NULL) openit(fstdetailsname, &fstdetails, "w") ;
numsnps =
getsnps(snpname, &snpmarkers, 0.0, badsnpname, &nignore, numrisks) ;
numindivs = getindivs(indivname, &indivmarkers) ;
k = getgenos(genotypename, snpmarkers, indivmarkers,
numsnps, numindivs, nignore) ;
if (poplistname != NULL)
{
ZALLOC(eglist, numindivs, char *) ;
numeg = loadlist(eglist, poplistname) ;
seteglist(indivmarkers, numindivs, poplistname);
}
else
{
setstatus(indivmarkers, numindivs, NULL) ;
ZALLOC(eglist, MAXPOPS, char *) ;
numeg = makeeglist(eglist, MAXPOPS, indivmarkers, numindivs) ;
}
for (i=0; i<numeg; i++)
{
/* printf("%3d %s\n",i, eglist[i]) ; */
}
nindiv=0 ;
for (i=0; i<numindivs; i++)
{
indx = indivmarkers[i] ;
if(indx -> affstatus == YES) ++nindiv ;
}
for (i=0; i<numsnps; i++)
{
cupt = snpmarkers[i] ;
chrom = cupt -> chrom ;
if ((noxdata) && (chrom == (numchrom+1))) cupt-> ignore = YES ;
if (chrom == 0) cupt -> ignore = YES ;
if (chrom > (numchrom+1)) cupt -> ignore = YES ;
}
for (i=0; i<numsnps; i++)
{
cupt = snpmarkers[i] ;
pos = nnint(cupt -> physpos) ;
if ((xchrom>0) && (cupt -> chrom != xchrom)) cupt -> ignore = YES ;
if ((xchrom > 0) && (pos < lopos)) cupt -> ignore = YES ;
if ((xchrom > 0) && (pos > hipos)) cupt -> ignore = YES ;
if (cupt -> ignore) continue ;
if (numvalidgtx(indivmarkers, cupt, YES) <= 1)
{
printf("nodata: %20s\n", cupt -> ID) ;
cupt -> ignore = YES ;
}
}
if (killr2) {
nkill = killhir2(snpmarkers, numsnps, numindivs, r2physlim, r2genlim, r2thresh) ;
if (nkill>0) printf("killhir2. number of snps killed: %d\n", nkill) ;
}
ZALLOC(vv, numindivs, int) ;
numvalidgtallind(vv, snpmarkers, numsnps, numindivs) ;
for (i=0; i<numindivs; ++i) {
if (vv[i] == 0) {
indx = indivmarkers[i] ;
indx -> ignore = YES ;
}
}
free(vv) ;
numsnps = rmsnps(snpmarkers, numsnps, NULL) ; // rid ignorable snps
if (missingmode)
{
setmiss(snpmarkers, numsnps) ;
fancynorm = NO ;
}
if (weightname != NULL)
{
weightmode = YES ;
getweights(weightname, snpmarkers, numsnps) ;
}
if (ldregress>0)
{
ZALLOC(ldvv, ldregress*numindivs, double) ;
ZALLOC(ldvv2, ldregress*numindivs, double) ;
ZALLOC(vv2, numindivs, double) ;
ZALLOC(ldmat, ldregress*ldregress, double) ;
ZALLOC(ldmat2, ldregress*ldregress, double) ;
setidmat(ldmat, ldregress) ;
vst(ldmat, ldmat, 1.0e-6, ldregress*ldregress) ;
}
ZALLOC(xindex, numindivs, int) ;
ZALLOC(xindlist, numindivs, Indiv *) ;
ZALLOC(xsnplist, numsnps, SNP *) ;
if (popsizelimit > 0)
{
setplimit(indivmarkers, numindivs, eglist, numeg, popsizelimit) ;
}
nrows = loadindx(xindlist, xindex, indivmarkers, numindivs) ;
ncols = loadsnpx(xsnplist, snpmarkers, numsnps, indivmarkers) ;
printf("number of samples used: %d number of snps used: %d\n", nrows, ncols) ;
/**
cupt = xsnplist[0] ;
for (j=0; j<nrows; ++j) {
k = xindex[j] ;
g = getgtypes(cupt, k) ;
indx = indivmarkers[k] ;
t = indxindex(eglist, numeg, indx -> egroup) ;
printf("yy1 %20s %20s %20s %d %d %d\n", cupt ->ID, indx -> ID, indx -> egroup, j, k, g) ;
}
printf("yya: ") ; printimat(xindex, 1, nrows) ;
printf("zzindxa: %s\n", indivmarkers[230] -> egroup) ;
*/
/* printf("## nrows: %d ncols %d\n", nrows, ncols) ; */
ZALLOC(xmean, ncols, double) ;
ZALLOC(xfancy, ncols, double) ;
ZALLOC(XTX, nrows*nrows, double) ;
ZALLOC(evecs, nrows*nrows, double) ;
ZALLOC(tvecs, nrows*nrows, double) ;
ZALLOC(lambda, nrows, double) ;
ZALLOC(cc, nrows, double) ;
ZALLOC(ww, nrows, double) ;
ZALLOC(badlist, nrows, int) ;
blocksize = MIN(blocksize, ncols) ;
ZALLOC(tblock, nrows*blocksize, double) ;
// xfancy is multiplier for column xmean is mean to take off
// badlist is list of rows to delete (outlier removal)
numoutiter = 1 ;
if (numoutliter>=1)
{
numoutiter = numoutliter+1 ;
ZALLOC(outinfo, nrows, OUTLINFO *) ;
for (k=0; k<nrows; k++)
{
ZALLOC(outinfo[k], 1, OUTLINFO) ;
}
/* fprintf(outlfile, "##%18s %4s %6s %9s\n", "ID", "iter","eigvec", "score") ; */
}
for (outliter = 1; outliter <= numoutiter ; ++outliter) {
if (fstonly) {
setidmat(XTX, nrows) ;
vclear(lambda, 1.0, nrows) ;
break ;
}
if (outliter>1) {
ncols = loadsnpx(xsnplist, snpmarkers, numsnps, indivmarkers) ;
}
vzero(XTX, nrows*nrows) ;
vzero(tblock, nrows*blocksize) ;
xblock = 0 ;
vzero(xmean, ncols) ;
vclear(xfancy, 1.0, ncols) ;
for (i=0; i<ncols; i++)
{
cupt = xsnplist[i] ;
chrom = cupt -> chrom ;
getcolxz(cc, cupt, xindex, nrows, i, xmean, xfancy, &n0, &n1) ;
t = MIN(n0, n1) ;
if (t <= minallelecnt) {
cupt -> ignore = YES ;
vzero(cc, nrows) ;
}
if (weightmode)
{
vst(cc, cc, xsnplist[i] -> weight, nrows) ;
}
if (ldregress>0)
{
numclear = 0 ;
for (k=1; k<= ldregress; ++k)
{
j = i-k ;
if (j<0)
{
numclear = ldregress-k+1 ;
break ;
}
cupt2 = xsnplist[j] ;
if (cupt2 -> chrom != chrom) gdis = ldlimit + 1.0 ;
else gdis = cupt -> genpos - cupt2 -> genpos ;
if (gdis>=ldlimit)
{
numclear = ldregress-k+1 ;
break ;
}
}
if (numclear>0) clearld(ldmat, ldvv, ldregress, nrows, numclear) ;
ldreg(ldmat, ldmat2, cc, vv2, ldvv, ldvv2, ldregress, nrows) ;
copyarr(ldmat2, ldmat, ldregress*ldregress) ;
copyarr(vv2, cc, nrows) ;
copyarr(ldvv2, ldvv, ldregress*nrows) ;
}
copyarr(cc, tblock+xblock*nrows, nrows) ;
++xblock ;
/** this is the key code to parallelize */
if (xblock==blocksize)
{
domult(tvecs, tblock, xblock, nrows) ;
vvp(XTX, XTX, tvecs, nrows*nrows) ;
xblock = 0 ;
vzero(tblock, nrows*blocksize) ;
}
}
if (xblock>0)
{
domult(tvecs, tblock, xblock, nrows) ;
vvp(XTX, XTX, tvecs, nrows*nrows) ;
}
symit(XTX, nrows) ;
/**
a = 0; b=0 ;
printf("zz1 %12.6f ", XTX[a*nrows+b]) ;
a = nrows-1; b=nrows-1 ;
printf(" %12.6f %15.9g\n", XTX[a*nrows+b], asum(XTX, nrows*nrows)) ;
*/
if (verbose)
{
printdiag(XTX, nrows) ;
}
y = trace(XTX, nrows) / (double) (nrows-1) ;
if (isnan(y)) fatalx("bad XTX matrix\n") ;
/* printf("trace: %9.3f\n", y) ; */
if (y<=0.0) fatalx("XTX has zero trace (perhaps no data)\n") ;
vst(XTX, XTX, 1.0/y, nrows * nrows) ;
/// mean eigenvalue is 1
eigvecs(XTX, lambda, evecs, nrows) ;
// eigenvalues are in decreasing order
if (outliter > numoutliter) break ;
// last pass skips outliers
numoutleigs = MIN(numoutleigs, nrows-1) ;
nbad = ridoutlier(evecs, nrows, numoutleigs, outlthresh, badlist, outinfo) ;
if (nbad == 0) break ;
for (i=0; i<nbad; i++)
{
j = badlist[i] ;
indx = xindlist[j] ;
outpt = outinfo[j] ;
fprintf(outlfile, "REMOVED outlier %s iter %d evec %d sigmage %.3f\n", indx -> ID, outliter, outpt -> vecno, outpt -> score) ;
indx -> ignore = YES ;
}
nrows = loadindx(xindlist, xindex, indivmarkers, numindivs) ;
printf("number of samples after outlier removal: %d\n", nrows) ;
}
if (outliername != NULL) fclose(outlfile) ;
m = numgtz(lambda, nrows) ;
/* printf("matrix rank: %d\n", m) ; */
if (m==0) fatalx("no data\n") ;
/** smartrel code */
for (i=0; i<numeigs; i++) {
y = sqrt(lambda[i]) ;
vst(ww, evecs+i*nrows, y, nrows) ;
subouter(XTX, ww, nrows) ;
}
free(tvecs) ;
n = 0 ;
ZALLOC(vecind, nrows*nrows/2, int) ;
for (i=0; i<nrows; i++) {
for (j=i+1; j<nrows; j++) {
k = i*nrows + j ;
y1 = XTX[i*nrows+i] ;
y2 = XTX[j*nrows+j] ;
y = XTX[k]/sqrt(y1*y2) ;
y += 1/(double)(nrows-1);
if (y<relthresh) continue ;
vecind[n] = k ;
evecs[n] = -y ;
++n ;
}
}
free(XTX) ;
if (n==0) {
printf("## nothing above relthresh!\n") ;
printf("##end of smartrel run\n") ;
return 0 ;
}
ZALLOC(idperm, n, int) ;
sortit(evecs, idperm, n) ;
for (i=0; i<n; i++) {
j = idperm[i] ;
k = vecind[j] ;
a = k/nrows ;
b = k%nrows ;
printf("rel: %20s ", xindlist[a] ->ID) ;
printf("%20s ", xindlist[b] ->ID) ;
printf(" %9.3f", -evecs[i]) ;
printnl() ;
}
printf("##end of smartrel run\n") ;
return 0 ;
}
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 ;
}
int main(int argc, char **argv)
{
char sss[MAXSTR] ;
int **snppos ;
int *snpindx ;
char **snpnamelist, **indnamelist ;
int lsnplist, lindlist ;
int i, j, k, k1, k2, k3, k4, kk ;
SNP *cupt, *cupt1, *cupt2, *cupt3 ;
Indiv *indx ;
double y1, y2, y, sig, tail, yy1, yy2 ;
char ss[11] ;
int *blstart, *blsize, nblocks ;
int xnblocks ; /* for xsnplist */
int *bcols ;
int **subsets ;
double maxgendis ;
char **eglist ;
int numeg ;
int ch1, ch2 ;
int fmnum , lmnum ;
int num, n1, n2 ;
int nindiv = 0, e, f, lag=1 ;
double xc[9], xd[4], xc2[9] ;
int nignore, numrisks = 1 ;
double *xrow, *xpt ;
SNP **xsnplist ;
int *tagnums ;
Indiv **xindlist ;
int *xindex, *xtypes ;
int nedge, m, nc ;
double zn, zvar ;
int weightmode = NO ;
double chisq, ynrows ;
int *numhits, t ;
double *xmean, *xfancy ;
double *divans, *divsd ;
double *hettop, *hetbot ;
int chrom, numclear ;
double gdis ;
int outliter, *badlist, nbad ;
int ***counts ;
char ***plists ;
int nplist, trun ;
int nrows, ncols ;
readcommands(argc, argv) ;
printf("## qpBound version: %s\n", WVERSION) ;
if (parname == NULL) return 0 ;
if (xchrom == 23) noxdata = NO ;
if (outpop == NULL) fatalx("no outpop\n") ;
setinbreed(inbreed) ;
numsnps =
getsnps(snpname, &snpmarkers, 0.0, badsnpname, &nignore, numrisks) ;
numindivs = getindivs(indivname, &indivmarkers) ;
setindm(indivmarkers) ;
k = getgenos(genotypename, snpmarkers, indivmarkers,
numsnps, numindivs, nignore) ;
for (i=0; i<numsnps; i++)
{
cupt = snpmarkers[i] ;
chrom = cupt -> chrom ;
if ((xchrom>0) && (chrom != xchrom)) cupt -> ignore = YES ;
if ((noxdata) && (chrom == 23)) cupt-> ignore = YES ;
if (chrom == 0) cupt -> ignore = YES ;
if (chrom > 23) cupt -> ignore = YES ;
if (chrom == zchrom) cupt -> ignore = YES ;
}
nplist = numlines(popfilename) ;
ZALLOC(plists, nplist, char **) ;
ZALLOC(lines, nplist, char *) ;
num = readpopx(popfilename, plists, 3) ;
nplist = num ;
printf("nplist: %d\n", nplist) ;
if (nplist == 0) return 0;
ZALLOC(eglist, nplist*3, char *) ;
numeg = 0 ;
for (trun=0; trun<nplist; ++trun) {
for (k=0; k<3; ++k) {
t = indxindex(eglist, numeg, plists[trun][k]) ;
if (t<0) {
eglist[numeg] = strdup(plists[trun][k]) ;
++numeg ;
}
}
}
if (popsizelimit > 0) {
setplimit(indivmarkers, numindivs, eglist, numeg, popsizelimit) ;
}
if (outputname != NULL) openit (outputname, &ofile, "w") ;
outnum = 0 ;
ZALLOC(xindex, numindivs, int) ;
ZALLOC(xindlist, numindivs, Indiv *) ;
nrows = loadindx(xindlist, xindex, indivmarkers, numindivs) ;
ZALLOC(xtypes, nrows, int) ;
for (i=0; i<nrows; i++) {
indx = xindlist[i] ;
k = indxindex(eglist, numeg, indx -> egroup) ;
xtypes[i] = k+1 ; // dangerous bend
t = strcmp(indx -> egroup, outpop) ;
if (t==0) xtypes[i] = outnum ;
else fatalx("outpop bug\n") ;
}
ZALLOC(xsnplist, numsnps, SNP *) ;
ncols = loadsnpx(xsnplist, snpmarkers, numsnps, indivmarkers) ;
/**
ZALLOC(counts, ncols, int **) ;
for (k=0; k<ncols; ++k) {
counts[k] = initarray_2Dint( numeg, 2, 0) ;
}
countpops(counts, xsnplist, xindex, xtypes, nrows, ncols) ;
*/
for (trun=0; trun<nplist; ++trun) {
dopop3out(plists[trun], xsnplist, ncols, lines[trun], outpop) ;
}
if (outputname != NULL) fclose(ofile) ;
printf("##end of qpBound\n") ;
return 0 ;
}
int main(int argc, char **argv)
{
char sss[MAXSTR] ;
int **snppos ;
int *snpindx ;
char **snpnamelist, **indnamelist ;
char **eglist ;
int *nsamppops ;
int *ztypes ;
int lsnplist, lindlist, numeg ;
int i, j, k, k1, k2, k3, k4, kk;
SNP *cupt, *cupt1, *cupt2, *cupt3 ;
Indiv *indx ;
double y1, y2, y, sig, tail, yy1, yy2 ;
char ss[11] ;
int *blstart, *blsize, nblocks ;
int xnblocks ; /* for xsnplist */
int *bcols ;
double maxgendis ;
int xind[4] ;
int ch1, ch2 ;
int fmnum , lmnum ;
int num, n1, n2 ;
int nindiv = 0, e, f, lag=1 ;
double xc[9], xd[4], xc2[9] ;
int nignore, numrisks = 1 ;
double *xrow, *xpt ;
SNP **xsnplist ;
int *tagnums ;
Indiv **xindlist ;
int *xindex, *xtypes ;
int nrows, ncols, m, nc ;
double zn, zvar ;
int weightmode = NO ;
double chisq, ynrows ;
int *numhits, t ;
double *xmean, *xfancy ;
double *divans, *divsd ;
double *hettop, *hetbot ;
int chrom, numclear ;
double gdis ;
int outliter, *badlist, nbad ;
double **zdata, *z1, *z2 ;
int maxtag = -1 ;
double **zz ;
double *pmean, *pnum, rscore[3], dstat[3], hscore[3], rrr[3], ww[3], serr[3] ;
int ssize[3][3], *sz ;
int tpat[3][4] , rpat[3][4], *rrtmp, *rp ;
int *rawcol ; ;
int a, b, c, d, col ;
int aa, bb, cc, dd ;
double *qpscores ;
double *hest, *hsig ;
double mingenpos, maxgenpos ;
int *qhit ; /* number of times pair is clade in quartet */
int *qmiss ; /* number of times pair migration event implied */
int **qplist, numqp = 0, maxqp=10000 ;
double *qpscore ;
char ***qlist, *sx ;
int nqlist = 0 ;
int bbest[3] ;
double absscore[3] ;
double ascore[4], astat[4] ;
double **dsctop, **dscbot ;
double **abx, **bax, **f2 ;
int popx[4] ;
double tn[4*5], td[4*4] ;
double zzsig[5], zzest[5], zsc[5] ;
double ymin ;
double *f3, *f4, *f3sig, *f4sig ;
int t1, t2, tt ;
int ***counts, **ccc ;
double tlenz[5], tlen[5] ;
int lenz[5] ;
readcommands(argc, argv) ;
printf("## qpDstat version: %s\n", WVERSION) ;
if (parname == NULL) return 0 ;
if ((poplistname == NULL) && (popfilename == NULL)) fatalx("poplistname, popfilename both null\n") ;
if (!bankermode) forceclade = NO ;
//if (fancynorm) printf("fancynorm used\n") ;
//else printf("no fancynorm used\n") ;
setjquart(NO, jackweight, jackquart) ;
nostatslim = MAX(nostatslim, 3) ;
setinbreed(inbreed) ;
if (outputname != NULL) openit(outputname, &ofile, "w") ;
numsnps =
getsnps(snpname, &snpmarkers, 0.0, badsnpname, &nignore, numrisks) ;
numindivs = getindivs(indivname, &indivmarkers) ;
if (id2pops != NULL) {
setid2pops(id2pops, indivmarkers, numindivs) ;
}
setindm(indivmarkers) ;
k = getgenos(genotypename, snpmarkers, indivmarkers,
numsnps, numindivs, nignore) ;
for (i=0; i<numsnps; i++) {
cupt = snpmarkers[i] ;
if (cupt -> chrom >= 23) cupt -> ignore = YES ;
if (cupt -> chrom == zchrom) cupt -> ignore = YES ;
}
ZALLOC(eglist, numindivs, char *) ;
ZALLOC(ztypes, numindivs, int) ;
if (popfilename == NULL) {
if (bankermode == NO)
numeg = loadlist(eglist, poplistname) ;
else {
numeg = loadlist_type(eglist, poplistname, ztypes, 0) ;
numbanker = 0 ;
for (k=0; k<numeg; ++k) {
if (ztypes[k] == 2) ++numbanker ;
}
printf("bankermode: ") ;
printimat(ztypes, 1, numeg) ;
}
}
if (popfilename != NULL) {
bbestmode = NO ;
nqlist = numlines(popfilename) ;
ZALLOC(qlist, 4, char **) ;
for (k=0; k<4; ++k) {
ZALLOC(qlist[k], nqlist, char *) ;
}
nqlist = getnamesstripcolon(&qlist, nqlist, 4, popfilename, locount, hicount) ;
numeg = 0 ;
printf("number of quadruples %d\n", nqlist) ;
fflush(stdout) ;
for (k=0; k<4; ++k) {
for (j=0; j<nqlist; ++j) {
sx = qlist[k][j] ;
t1 = indxstring(eglist, numeg, sx) ;
if (t1 >=0) continue ;
eglist[numeg] = strdup(sx) ;
++numeg ;
setstatus(indivmarkers, numindivs, sx) ;
}
}
}
int main(int argc, char **argv)
{
double *V;
double *xx;
double *iscase;
double *iscasecorr;
int K;
int k,m,n;
int nignore;
double rowsum, rowsum1;
double chisq, Echisq, gamma, denom;
readcommands(argc, argv) ;
if (outputname != NULL)
openit(outputname, &fpout, "w") ;
else
fpout = stdout;
fprintf(fpout, "Chisq EIGENSTRAT\n");
setinmode(&inmode, imode);
packmode = YES;
numsnps =
getsnps(snpname, &snpmarkers, 0.0, NULL, &nignore, 1) ;
NSAMPLES = getindivs(indivname, &indivmarkers) ;
setstatus(indivmarkers, NSAMPLES, "Case") ;
setgenotypename(&genotypename, indivname) ;
if (genotypename != NULL) {
getgenos(genotypename, snpmarkers, indivmarkers,
numsnps, NSAMPLES, nignore) ;
}
/*******************************************************************/
/* Free memory: Usually this is done in outfiles: */
/* */
/* nind = rmindivs(&snpmarkers, numsnps, &indmarkers, NSAMPLES); */
/* */
/* But where is the snpmarkers array released? */
/*******************************************************************/
L = numpc;
readpcafile(&V, &outlier, &K, L, NSAMPLES);
getphenos(NSAMPLES, &iscase, outlier, &iscasecorr, L, V);
/* main eigenstrat loop here */
if ((xx = (double *)malloc(NSAMPLES*sizeof(*xx))) == NULL)
{ fprintf(stderr,"CM\n"); exit(1); }
for(m=0;m<numsnps;m++) {
SNP *cupt = snpmarkers[m];
for(n=0; n<NSAMPLES; n++)
{
int j = getgtypes(cupt,n);
if(j == 0) { xx[n] = 0.0; }
else if(j == 1) { xx[n] = 0.5; }
else if(j == 2 ) { xx[n] = 1.0; }
else if(j == -1) { xx[n] = -100.0; }
if(outlier[n] == 1) xx[n] = -100.0;
}
/* mean-adjust xx */
rowsum = 0.0; rowsum1 = 0.0;
for(n=0; n<NSAMPLES; n++)
{
if(qtmode == NO && ((outlier[n]) || (xx[n] < -99.0))) continue;
if(qtmode == YES && ((outlier[n]) || (xx[n] == -100.0))) continue;
rowsum += xx[n];
rowsum1 += 1.0;
}
for(n=0; n<NSAMPLES; n++)
{
if(outlier[n]) continue;
if(qtmode == NO) {
if (xx[n] < -99.0)
xx[n] = -100.0; /* still keep track */
else
xx[n] -= rowsum/rowsum1;
}
else {
if (xx[n] == -100.0)
xx[n] = -100.0; /* still keep track */
else
xx[n] -= rowsum/rowsum1;
}
}
/* Chisq */
chisq = compute_chisq(xx,iscase);
/* EIGENSTRAT */
for(k=0; k<L; k++)
{
gamma = 0.0;
denom = 0.0;
for(n=0; n<NSAMPLES; n++)
{
if(qtmode == NO && (outlier[n] || xx[n] < -99.0)) continue;
if(qtmode == YES && (outlier[n] || xx[n] == -100.0)) continue;
gamma += xx[n]*V[NSAMPLES*n+k];
denom += V[NSAMPLES*n+k]*V[NSAMPLES*n+k];
}
gamma /= denom;
for(n=0; n<NSAMPLES; n++)
{
if(qtmode == NO && (outlier[n] || xx[n] < -99.0)) continue;
if(qtmode == YES && (outlier[n] || xx[n] == -100.0)) continue;
xx[n] -= gamma*V[NSAMPLES*n+k];
}
}
Echisq = compute_chisqE(xx,iscasecorr);
if(rowsum1 == 0.0)
{
chisq = -1.0; Echisq = -1.0;
}
if(chisq >= 0.0) fprintf(fpout,"%.04f",chisq);
else fprintf(fpout,"NA");
if(Echisq >= 0.0) fprintf(fpout," %.04f\n",Echisq);
else fprintf(fpout," NA\n");
if(NSAMPLES*m > MAXSIZE)
{
fprintf(stderr,"OOPS genotype file has > %d genotypes\n",MAXSIZE);
fprintf(fpout,"OOPS genotype file has > %d genotypes\n",MAXSIZE);
exit(1);
}
}
}
int main(int argc, char* argv[])
{
program_name = argv[0];
if (argc < 3) {
print_help();
exit(EXIT_FAILURE);
}
char binfile[50];
base = argv[1];
strapp(binfile, ".nc");
int total_ids = atoi(argv[2]);
FILE *fp;
if (argc > 2) {
infile = argv[3];
fp = fopen(infile, "r");
if (!fp)
error(1, errno, "%s", infile);
} else {
infile = "stdin";
fp = stdin;
}
/* Get the first line with the SNP names */
char *line = NULL;
size_t n = 0;
int read = getlin(&line, &n, fp);
if (read == -1)
error(1, errno, "%s", infile);
int nsnps = getsnps(line);
free(line);
line = NULL;
printf("%d markers\n", nsnps);
printf("Converting intensity values to binary\n");
int ncid, stat, sampid, varid;
size_t nids = 0, perkey;
size_t count[3] = { 1, 0, 0 };
size_t start[3] = { 0, 0, 0 };
char *id;
float *vals;
while (getlin(&line, &n, fp) != -1) {
if (nids == 0) {
/* Count number of vals in first line to alloc indv_dat */
read = getstrings(line, NULL, DELIM) - 1;
if (read < 1)
error(2, 0, "No values found");
if (read % nsnps != 0)
error(2, 0, "Not same number of values for each marker");
perkey = read / nsnps;
printf("%zu values per marker\n", perkey);
vals = malloc(sizeof(float) * read);
if (vals == NULL)
error(1, errno, "dat.vals");
/* Create netcdf file and write snp names */
ncid = create_nc(binfile, total_ids, nsnps, perkey);
stat = nc_inq_varid(ncid, "sample", &sampid);
check_err(stat,__LINE__,__FILE__);
stat = nc_inq_varid(ncid, "intensity", &varid);
check_err(stat,__LINE__,__FILE__);
writesnps(ncid, nsnps);
count[1] = nsnps;
count[2] = perkey;
}
/* Read valuess from line */
id = linevals(line, vals);
/* Write sample id */
stat = nc_put_var1_string(ncid, sampid, &nids, (const char **) &id);
check_err(stat,__LINE__,__FILE__);
/* Write intensity values */
start[0] = nids;
stat = nc_put_vara_float(ncid, varid, start, count, vals);
check_err(stat,__LINE__,__FILE__);
free(line);
line = NULL;
nids++;
printf("Read %zu\r", nids);
fflush(stdout);
}
fclose(fp);
stat = nc_close(ncid);
check_err(stat,__LINE__,__FILE__);
free(vals);
free(line);
printf("Wrote %zu samples to [ %s ]\n", nids, binfile);
exit(EXIT_SUCCESS);
}
int main(int argc, char **argv)
{
int **snppos ;
int *snpindx ;
char **snpnamelist, **indnamelist ;
char **eglist ;
int lsnplist, lindlist, numeg ;
int i,j;
SNP *cupt, *cupt1, *cupt2, *cupt3 ;
Indiv *indx ;
double gpos1,gpos2,cpos1,cpos2,gd, cd, gd100 ;
double rthresh, zt ;
int mpflag, ret, numvalidind, nvalid, numvalidsnps ;
int ch1, ch2 ;
int fmnum , lmnum ;
int num, n1, n2 ;
int nkill = 0 ;
int t, k, g ;
int nindiv = 0, e, f, lag=1 ;
double xc[9], xd[4], xc2[9] ;
double ychi, zscore, zthresh = 20.0 ;
double y1, y2 ;
int nignore, numrisks = 1 ;
char **genolist ;
int numgenolist ;
char c1, c2 ;
int t1, t2 ;
malexhet = YES ; // convertf default is don't change the data
tersem = YES ; // no snp counts
readcommands(argc, argv) ;
setomode(&outputmode, omode) ;
packmode = YES ;
settersemode(tersem) ;
if (r2thresh > 0.0) killr2 = YES ;
if (badpedignore) setbadpedignore() ;
numsnps =
getsnps(snpname, &snpmarkers, 0.0, badsnpname, &nignore, numrisks) ;
for (i=0; i<numsnps; i++) {
if (xchrom == -1) break ;
cupt = snpmarkers[i] ;
if (cupt -> chrom != xchrom) cupt -> ignore = YES ;
if (cupt -> ignore) continue ;
t = nnint(cupt -> physpos) ;
if ( (t< lopos) || (t >hipos)) cupt -> ignore = YES ;
}
nignore = 0 ;
for (i=0; i<numsnps; i++) {
cupt = snpmarkers[i] ;
if (cupt -> chrom > maxchrom) cupt -> ignore = YES ;
if (cupt -> chrom < minchrom) cupt -> ignore = YES ;
if (cupt -> ignore) ++nignore ;
}
if (numsnps == nignore) fatalx("no valid snps\n") ;
numindivs = getindivs(indivname, &indivmarkers) ;
if (polarid != NULL) {
polarindex = indindex(indivmarkers, numindivs, polarid) ;
if (polarindex<0) fatalx("polarid %s not found\n") ;
}
if (genotypelist!= NULL) {
getgenos_list(genotypelist, snpmarkers, indivmarkers,
numsnps, numindivs, nignore) ;
}
else {
setgenotypename(&genotypename, indivname) ;
getgenos(genotypename, snpmarkers, indivmarkers,
numsnps, numindivs, nignore) ;
}
if (newsnpname != NULL) {
nums2 =
getsnps(newsnpname, &snpm2, 0.0, NULL, &nignore, numrisks) ;
remap(snpmarkers, numsnps, snpm2, nums2) ;
snpmarkers = snpm2 ;
numsnps = nums2 ;
}
if (newindivname != NULL) {
numind2 = getindivs(newindivname, &indm2) ;
remapind(snpmarkers, numsnps, indivmarkers, indm2, numindivs, numind2) ;
indivmarkers = indm2 ;
numindivs = numind2 ;
if (polarid != NULL) {
polarindex = indindex(indivmarkers, numindivs, polarid) ;
}
}
if (mkdiploid) {
numindivs = rmindivs(snpmarkers, numsnps, indivmarkers, numindivs) ;
numind2 = mkindh2d(indivmarkers, &indm2, numindivs) ;
remaph2d(snpmarkers, numsnps, indivmarkers, indm2, numindivs, numind2) ;
indivmarkers = indm2 ;
numindivs = numind2 ;
}
if (deletedup) dedupit(snpmarkers, numsnps) ; // only one marker per position
for (i=0; i<numsnps; i++) {
cupt = snpmarkers[i] ;
if (zerodistance) cupt -> genpos = 0.0 ;
c1 = cupt -> alleles[0] ;
c2 = cupt -> alleles[1] ;
t1 = pedval(&c1) % 5 ;
t2 = pedval(&c2) % 5 ; // 0 and 5 are no good
if ((t1==0) && (t2 >0)) flip1(cupt, phasedmode, YES) ;
}
flipstrand(flipstrandname, snpmarkers, numsnps) ;
flipsnps(flipsnpname, snpmarkers, numsnps, phasedmode) ;
if (polarindex>=0) {
for (i=0; i<numsnps; i++) {
cupt = snpmarkers[i] ;
g = getgtypes(cupt, polarindex) ;
if (g==0) {
printf("polarizing %s\n", cupt -> ID) ;
flip1(cupt, NO, YES) ;
g = getgtypes(cupt, polarindex) ;
if (g!=2) fatalx("badbug\n") ;
}
if (g != 2) cupt -> ignore = YES ;
}
}
if (outputall) {
outfiles(snpoutfilename, indoutfilename, genooutfilename,
snpmarkers, indivmarkers, numsnps, numindivs, packout, ogmode) ;
printf("##end of convertf run (outputall mode)\n") ;
return 0 ;
}
if (poplistname != NULL)
{
ZALLOC(eglist, numindivs, char *) ;
numeg = loadlist(eglist, poplistname) ;
seteglist(indivmarkers, numindivs, poplistname);
for (i=0; i<numindivs; ++i) {
indx = indivmarkers[i] ;
if (indx -> affstatus == NO) indx -> ignore = YES ;
}
}
else
setstatus(indivmarkers, numindivs, "Case") ;
numsnps = rmsnps(snpmarkers, numsnps, deletesnpoutname) ;
numindivs = rmindivs(snpmarkers, numsnps, indivmarkers, numindivs) ;
if (killr2) {
nkill = killhir2(snpmarkers, numsnps, numindivs, r2physlim, r2genlim, r2thresh) ;
if (nkill>0) printf("killhir2. number of snps killed: %d\n", nkill) ;
}
if ( nhwfilter > 0 ) {
hwfilter(snpmarkers, numsnps, numindivs, nhwfilter, deletesnpoutname);
}
if ( xregionname ) {
excluderegions(xregionname, snpmarkers, numsnps, deletesnpoutname);
}
numvalidind = 0 ;
for (i=0; i<numindivs; ++i) {
indx = indivmarkers[i] ;
if (indx -> ignore) continue ;
if (numvalidgtind(snpmarkers, numsnps, i) ==0) {
indx -> ignore = YES ;
printf("no data for individual: %s\n", indx -> ID) ;
}
if (indx -> ignore == NO) ++numvalidind ;
}
if (maxmiss<0) maxmiss = (int) (maxmissfrac * (double) numvalidind+1) ;
printf("numvalidind: %5d maxmiss: %5d\n", numvalidind, maxmiss) ;
if (numvalidind == 0) fatalx("no valid samples!\n") ;
for (k=0; k<numsnps; ++k) {
if (maxmiss>numvalidind) break ;
cupt = snpmarkers[k] ;
t = numvalidind - numvalidgtypes(cupt) ;
// printf("zz %20s %4d %4d\n", cupt -> ID, t, numvalidind-t) ;
if (maxmiss < t) {
cupt -> ignore = YES ;
}
/**
if (numvalidind == t) {
printf("no data for snp: %s\n", cupt -> ID) ;
cupt -> ignore = YES ;
}
*/
}
if (fastdup) {
printf("fastdup set %d\n", fastdupnum) ;
if (fastdupnum > 0) {
setfastdupnum(fastdupnum) ;
setfastdupthresh(fastdupthresh, fastdupkill) ;
fastdupcheck(snpmarkers, indivmarkers, numsnps, numindivs) ;
}
}
if (decim>0) {
snpdecimate(snpmarkers, numsnps, decim, dmindis, dmaxdis) ;
}
outfiles(snpoutfilename, indoutfilename, genooutfilename,
snpmarkers, indivmarkers, numsnps, numindivs, packout, ogmode) ;
printf("##end of convertf run\n") ;
return 0 ;
}
int main(int argc, char **argv)
{
int **snppos ;
int *snpindx ;
char **snpnamelist, **indnamelist ;
char **eglist ;
int lsnplist, lindlist, numeg ;
int i,j;
SNP *cupt, *cupt1, *cupt2, *cupt3 ;
Indiv *indx ;
double gpos1,gpos2,cpos1,cpos2,gd, cd, gd100 ;
double rthresh, zt ;
int mpflag, ret, nvalid;
int ch1, ch2 ;
int fmnum , lmnum ;
int num, n1, n2 ;
int nkill = 0 ;
int t, k ;
int nindiv = 0, e, f, lag=1 ;
double xc[9], xd[4], xc2[9] ;
double ychi, zscore, zthresh = 20.0 ;
double y1, y2 ;
int nignore, numrisks = 1 ;
char **genolist ;
int numgenolist ;
int maxmiss ;
malexhet = YES ; // convertf default is don't change the data
tersem = YES ; // no snp counts
readcommands(argc, argv) ;
setomode(&outputmode, omode) ;
packmode = YES ;
settersemode(tersem) ;
numsnps =
getsnps(snpname, &snpmarkers, 0.0, badsnpname, &nignore, numrisks) ;
for (i=0; i<numsnps; i++) {
if (xchrom == -1) break ;
cupt = snpmarkers[i] ;
if (cupt -> chrom != xchrom) cupt -> ignore = YES ;
if (cupt -> ignore) continue ;
t = nnint(cupt -> physpos) ;
if ( (t< lopos) || (t >hipos)) cupt -> ignore = YES ;
}
nignore = 0 ;
for (i=0; i<numsnps; i++) {
cupt = snpmarkers[i] ;
if (cupt -> chrom > maxchrom) cupt -> ignore = YES ;
if (cupt -> chrom < minchrom) cupt -> ignore = YES ;
if (cupt -> ignore) ++nignore ;
}
if (numsnps == nignore) fatalx("no valid snps\n") ;
/**
cupt = snpmarkers[0] ;
printf("zz2: %d %d %d %20s: %d\n", numsnps, nignore, cupt -> chrom, cupt -> ID, cupt -> ignore) ;
*/
numindivs = getindivs(indivname, &indivmarkers) ;
if (genotypelist!= NULL) {
getgenos_list(genotypelist, snpmarkers, indivmarkers,
numsnps, numindivs, nignore) ;
}
else {
setgenotypename(&genotypename, indivname) ;
getgenos(genotypename, snpmarkers, indivmarkers,
numsnps, numindivs, nignore) ;
}
if (outputall) {
outfiles(snpoutfilename, indoutfilename, genooutfilename,
snpmarkers, indivmarkers, numsnps, numindivs, packout, ogmode) ;
printf("##end of convertf run (outputall mode)\n") ;
return 0 ;
}
if (killr2) {
nkill = killhir2(snpmarkers, numsnps, numindivs, r2physlim, r2genlim, r2thresh) ;
if (nkill>0) printf("killhir2. number of snps killed: %d\n", nkill) ;
}
setstatus(indivmarkers, numindivs, "Case") ;
/******************************************************************/
/* removesubthreshold(indivmarkers, snpmarkers, numindiv, numsnps,
maxmissfracind, maxmissfracsnp); */
/******************************************************************/
if (fastdup) {
if (fastdupnum > 0) setfastdupnum(fastdupnum) ;
fastdupcheck(snpmarkers, indivmarkers, numsnps, numindivs) ;
}
if (decim>0) {
snpdecimate(snpmarkers, numsnps, decim, dmindis, dmaxdis) ;
}
outfiles(snpoutfilename, indoutfilename, genooutfilename,
snpmarkers, indivmarkers, numsnps, numindivs, packout, ogmode) ;
printf("##end of convertf run\n") ;
return 0 ;
}