GAP 4.8.9 installation with standard packages -- copy to your CoCalc project to get it
gap> START_TEST("HAP library");
gap> Read(Concatenation(dir,"data249.txt"));
gap> G:=SymmetricMatrixToFilteredGraph(D,50,50);;
gap> K:=FilteredRegularCWComplex(CliqueComplex(G,2));
Filtered regular CW-complex of dimension 2
gap> BarCodeCompactDisplay(PersistentBettiNumbers(K,1));;
gap> Y:=FiltrationTerm(K,15);
Regular CW-complex of dimension 2
gap> M:=ContractedComplex(HomotopyGraph(Y));
Graph on 41 vertices.
gap> Display(M);
gap> STOP_TEST( "tst.tst", 1000 );