// OPT: don't create a new FacetComplex, use a non modifying alg on the old one
bool FacetComplex::AreConnected_new(const facet& g1,const facet& g2)const
{
if (g1.IamEmpty() || g2.IamEmpty()) return false;
if (g1==g2 || AreDirectlyConnected(g1,g2)) return true;
if (this->mySize()==2) return false;// they are 2, they are not directly connected, they are not connected
unsigned int g1_index=myGetIndex(g1);
unsigned int g2_index=myGetIndex(g2);
vector<unsigned int> P,P1;
for (unsigned int i=0;i!=mySize();++i)
P.push_back(i);
list<unsigned int> xj;
vector<unsigned int> g;
for (unsigned int j=0;j!=myNumIndets();++j)
{
myMakeXj(xj,j);
if (xj.size()>1)
{
myMakeG(g,P,xj);
P1.clear();
for (vector<unsigned int>::const_iterator it1=P.begin();it1!=P.end();++it1)
P1.push_back(g[P[*it1]]);
P1.swap(P);
}//if
}//for
return (P[g1_index]==P[g2_index]);
}// AreConnected_new
void MyBamWrap::testFetch(char* fileName, string chrName, uint32_t lpos, uint32_t rpos)
{
mySamOpen(fileName);
myGetIndex(fileName);
region_t region;
myPassRegion(region,chrName,lpos,rpos);
myFetchWrap(region, fetch_func_test);
}
