/*-----------------*
* Function getsam |
*-----------------*
| Generates a gene genealogy for a locus.
*/
int gensam(struct params *pparam, char **list, int **pnbvariant, int *pS)
{
int nsegs=0, k=0, seg=0, ns=0, start=0, end=0, len=0, segsit=0, nsites=0, nsam=0;
/* The function returns ns, the number of sgregating sites.
* nsegs is the gametes were broken into in tracing back the history of the gametes.
* The histories of these segments are passed back to the calling function in the array of structures seglst[]
*/
struct segl *seglst=NULL;
double nsinv=0.0, tseg=0.0, tt=0.0, theta=0.0;
void make_gametes(int, struct node*, double, int, int, char**, int, int*, int**, int*, int*);
void inititable(int, int, int*);
void initimatrix(int, int, int, int**);
void biggerimatrix(int, int**);
void biggerlist(int, char**);
void locate(int, double, double, double*);
//// From make_gametes ////
void prtree(struct node*, int);
double ttime(struct node*, int);
int poisso(double);
//// From streec.c ////
struct segl*segtre_mig(struct c_params*, int*);
nsites=pparam->cp.nsites; // Locus lenght available for recombination
nsinv=1./nsites;
seglst=segtre_mig(&(pparam->cp), &nsegs); // Generate Xove and ARGr, record # segments
nsam=pparam->cp.nsam; // # chromo in the sample
theta=pparam->mp.theta; // mutation rate given by user
ns=0; // # seg sites
if(pparam->mp.treeflag) // Case output tree.
{
theta=pparam->mp.theta;
ns=0;
for(seg=0, k=0;k<nsegs;seg=seglst[seg].next, k++)
{
if((pparam->cp.r>0.0)||(pparam->cp.f>0.0))
{
end=(k<nsegs-1 ? seglst[seglst[seg].next].beg-1:nsites-1);
start=seglst[seg].beg;
len=end-start+1;
fprintf(stdout, "[%d]", len);
}
prtree(seglst[seg].ptree, nsam);
if((theta==0.0))
free(seglst[seg].ptree);
}
}
//--- Loop along all segments ---//
for(seg=0, k=0;k<nsegs; seg=seglst[seg].next, k++)
{
end=(k<nsegs-1 ? seglst[seglst[seg].next].beg-1:nsites-1); // End of segment
start=seglst[seg].beg; // beginning of segment
len=end-start+1; // Lengh of segment
tseg=len*(theta/nsites); // Mutation rate along the segment
tt=ttime(seglst[seg].ptree, nsam); // Total time in the tree for this segment
segsit=poisso(tseg*tt); // get # segsites along genealogy for the segment
//--- Realloc memory if # segsite bigger than max previously define ---//
if((segsit+ns)>=maxsites)
{
maxsites=segsit+ns+SITESINC; // Bigger Max sites
biggerlist(nsam, list); // Increase list of haplotype
typeseg=(int*)realloc(typeseg, maxsites*sizeof(int)); // Increase # seg sites in typeseg
biggerimatrix(pparam->cp.npop+1, pnbvariant); // Increase matrix of variant
}
//--- Initialize table of variant and segType ---//
initimatrix(ns, ns+segsit, pparam->cp.npop+1, pnbvariant);
inititable(ns, segsit+ns, typeseg);
make_gametes(nsam, seglst[seg].ptree, tt, segsit, ns, list, pparam->cp.npop, pparam->cp.config, pnbvariant, typeseg, pS); // Make gametes (Put segsites on gene genealogy)
free(seglst[seg].ptree); // Free memory
ns+=segsit; // Total # seg sites
}
for(k=0;k<nsam;k++) list[k][ns]='\0'; // End of haplotype strings
return(ns); // Total # segsites
}// End Gensam
int
gensam( char **list, double *pprobss, double *ptmrca, double *pttot )
{
int nsegs, h, i, k, j, seg, ns, start, end, len, segsit ;
struct segl *seglst, *segtre_mig(struct c_params *p, int *nsegs ) ; /* used to be: [MAXSEG]; */
double nsinv, tseg, tt, ttime(struct node *, int nsam), ttimemf(struct node *, int nsam, int mfreq) ;
double *pk;
int *ss;
int segsitesin,nsites;
double theta, es ;
int nsam, mfreq ;
void prtree( struct node *ptree, int nsam);
void make_gametes(int nsam, int mfreq, struct node *ptree, double tt, int newsites, int ns, char **list );
void ndes_setup( struct node *, int nsam );
nsites = pars.cp.nsites ;
nsinv = 1./nsites;
seglst = segtre_mig(&(pars.cp), &nsegs ) ;
nsam = pars.cp.nsam;
segsitesin = pars.mp.segsitesin ;
theta = pars.mp.theta ;
mfreq = pars.mp.mfreq ;
if( pars.mp.treeflag ) {
ns = 0 ;
for( seg=0, k=0; k<nsegs; seg=seglst[seg].next, k++) {
if( (pars.cp.r > 0.0 ) || (pars.cp.f > 0.0) ) {
end = ( k<nsegs-1 ? seglst[seglst[seg].next].beg -1 : nsites-1 );
start = seglst[seg].beg ;
len = end - start + 1 ;
fprintf(stdout,"[%d]", len);
}
prtree( seglst[seg].ptree, nsam ) ;
if( (segsitesin == 0) && ( theta == 0.0 ) && ( pars.mp.timeflag == 0 ) )
free(seglst[seg].ptree) ;
}
}
if( pars.mp.timeflag ) {
tt = 0.0 ;
for( seg=0, k=0; k<nsegs; seg=seglst[seg].next, k++) {
if( mfreq > 1 ) ndes_setup( seglst[seg].ptree, nsam );
end = ( k<nsegs-1 ? seglst[seglst[seg].next].beg -1 : nsites-1 );
start = seglst[seg].beg ;
if( (nsegs==1) || ( ( start <= nsites/2) && ( end >= nsites/2 ) ) )
*ptmrca = (seglst[seg].ptree + 2*nsam-2) -> time ;
len = end - start + 1 ;
tseg = len/(double)nsites ;
if( mfreq == 1 ) tt += ttime(seglst[seg].ptree,nsam)*tseg ;
else tt += ttimemf(seglst[seg].ptree,nsam, mfreq)*tseg ;
if( (segsitesin == 0) && ( theta == 0.0 ) )
free(seglst[seg].ptree) ;
}
*pttot = tt ;
}
if( (segsitesin == 0) && ( theta > 0.0) ) {
ns = 0 ;
for( seg=0, k=0; k<nsegs; seg=seglst[seg].next, k++) {
if( mfreq > 1 ) ndes_setup( seglst[seg].ptree, nsam );
end = ( k<nsegs-1 ? seglst[seglst[seg].next].beg -1 : nsites-1 );
start = seglst[seg].beg ;
len = end - start + 1 ;
tseg = len*(theta/nsites) ;
if( mfreq == 1) tt = ttime(seglst[seg].ptree, nsam);
else tt = ttimemf(seglst[seg].ptree, nsam, mfreq );
segsit = poisso( tseg*tt );
if( (segsit + ns) >= maxsites ) {
maxsites = segsit + ns + SITESINC ;
posit = (double *)realloc(posit, maxsites*sizeof(double) ) ;
biggerlist(nsam, list) ;
}
make_gametes(nsam,mfreq,seglst[seg].ptree,tt, segsit, ns, list );
free(seglst[seg].ptree) ;
locate(segsit,start*nsinv, len*nsinv,posit+ns);
ns += segsit;
}
}
else if( segsitesin > 0 ) {
pk = (double *)malloc((unsigned)(nsegs*sizeof(double)));
ss = (int *)malloc((unsigned)(nsegs*sizeof(int)));
if( (pk==NULL) || (ss==NULL) ) perror("malloc error. gensam.2");
tt = 0.0 ;
for( seg=0, k=0; k<nsegs; seg=seglst[seg].next, k++) {
if( mfreq > 1 ) ndes_setup( seglst[seg].ptree, nsam );
end = ( k<nsegs-1 ? seglst[seglst[seg].next].beg -1 : nsites-1 );
start = seglst[seg].beg ;
len = end - start + 1 ;
tseg = len/(double)nsites ;
if( mfreq == 1 ) pk[k] = ttime(seglst[seg].ptree,nsam)*tseg ;
else pk[k] = ttimemf(seglst[seg].ptree,nsam, mfreq)*tseg ;
tt += pk[k] ;
}
if( theta > 0.0 ) {
es = theta * tt ;
*pprobss = exp( -es )*pow( es, (double) segsitesin) / segfac ;
}
if( tt > 0.0 ) {
for (k=0; k<nsegs; k++) pk[k] /= tt ;
mnmial(segsitesin,nsegs,pk,ss);
}
else
for( k=0; k<nsegs; k++) ss[k] = 0 ;
ns = 0 ;
for( seg=0, k=0; k<nsegs; seg=seglst[seg].next, k++) {
end = ( k<nsegs-1 ? seglst[seglst[seg].next].beg -1 : nsites-1 );
start = seglst[seg].beg ;
len = end - start + 1 ;
tseg = len/(double)nsites;
make_gametes(nsam,mfreq,seglst[seg].ptree,tt*pk[k]/tseg, ss[k], ns, list);
free(seglst[seg].ptree) ;
locate(ss[k],start*nsinv, len*nsinv,posit+ns);
ns += ss[k] ;
}
free(pk);
free(ss);
}
for(i=0; i<nsam; i++) list[i][ns] = '\0' ;
return( ns ) ;
}