CGraph* CreateRandomGraphWithToyQMRSpecific(int num_nodes,
int num_indep_nodes, int max_size_family)
{
PNL_CHECK_LEFT_BORDER( num_nodes, 10 );
PNL_CHECK_RANGES( num_indep_nodes, 1, num_nodes-1 );
PNL_CHECK_RANGES( max_size_family, 2, num_nodes );
int i, j, k;
CGraph *pGraph = CGraph::Create(0, NULL, NULL, NULL);
PNL_CHECK_IF_MEMORY_ALLOCATED( pGraph );
srand((unsigned int)time(NULL));
pGraph->AddNodes(num_nodes);
int num_parents;
int ind_parent;
intVector prev_nodes(0);
for ( i = num_indep_nodes; i < num_nodes; i++)
{
prev_nodes.resize(0);
for ( j = 0; j < num_indep_nodes; j++)
prev_nodes.push_back(j);
num_parents = rand() % (max_size_family - 1);
num_parents += 1;
num_parents = (num_parents > i) ? i : num_parents;
for ( j = 0; j < num_parents; j++)
{
ind_parent = rand() % prev_nodes.size();
pGraph->AddEdge(prev_nodes[ind_parent], i, 1);
prev_nodes.erase(prev_nodes.begin() + ind_parent);
}
}
return pGraph;
}
CGraph* CreateRandomAndSpecificForIDNetGraph(int num_nodes,
int num_indep_nodes, int max_size_family)
{
PNL_CHECK_LEFT_BORDER(num_nodes, 10);
PNL_CHECK_RANGES(num_indep_nodes, 1, num_nodes-1);
PNL_CHECK_RANGES(max_size_family, 2, num_nodes);
int i, j, k;
CGraph *pGraph = CGraph::Create(0, NULL, NULL, NULL);
PNL_CHECK_IF_MEMORY_ALLOCATED(pGraph);
srand((unsigned int)time(NULL));
pGraph->AddNodes(num_nodes);
int num_parents;
int ind_parent;
intVector prev_nodes(0);
for (i = num_indep_nodes; i < num_nodes; i++)
{
prev_nodes.resize(0);
for (j = 0; j < i; j++)
prev_nodes.push_back(j);
num_parents = rand() % (max_size_family - 1);
num_parents += 1;
num_parents = (num_parents > i) ? i : num_parents;
for (j = 0; j < num_parents; j++)
{
ind_parent = rand() % prev_nodes.size();
pGraph->AddEdge(prev_nodes[ind_parent], i, 1);
prev_nodes.erase(prev_nodes.begin() + ind_parent);
}
}
intVector parents(0);
intVector childs(0);
for (i = 0; i < num_nodes; i++)
{
if (pGraph->GetNumberOfChildren(i) == 0)
{
pGraph->GetParents(i, &parents);
for (j = 0; j < parents.size(); j++)
{
pGraph->GetChildren(parents[j], &childs);
for (k = 0; k < childs.size(); k++)
if ((childs[k] != i) &&
(pGraph->GetNumberOfChildren(childs[k]) == 0) &&
(pGraph->GetNumberOfParents(childs[k]) == 1))
{
if (i < childs[k])
{
pGraph->RemoveEdge(parents[j], childs[k]);
pGraph->AddEdge(i, childs[k], 1);
}
else
{
pGraph->AddEdge(childs[k], i, 1);
}
}
}
}
}
return pGraph;
}
void Caller::create_node_calls(const NodePileup& np) {
int n = _node->sequence().length();
const string& seq = _node->sequence();
int cur = 0;
int cat = call_cat(_node_calls[cur]);
NodePair prev_nodes(-1, -1);
// scan contiguous chunks of a node with same call
// (note: snps will always be 1-base -- never merged)
for (int next = 1; next <= n; ++next) {
int next_cat = next == n ? -1 : call_cat(_node_calls[next]);
if (cat == 2 || cat != next_cat) {
NodePair new_nodes(-1, -1);
bool secondary_snp = false;
// process first genotype if it's not missing
if (_node_calls[cur].first == '.') {
// add single node for stretch of reference node
string new_seq = seq.substr(cur, next - cur);
new_nodes.first = ++_max_id;
_call_graph.create_node(new_seq, new_nodes.first);
} else if (_node_calls[cur].first != '-') {
// add snp node
assert(next - cur == 1);
string new_seq(1, _node_calls[cur].first);
new_nodes.first = ++_max_id;
_call_graph.create_node(new_seq, new_nodes.first);
create_snp_path(new_nodes.first, secondary_snp);
secondary_snp = true;
}
// process second genotype if difference from first
if (_node_calls[cur].second != _node_calls[cur].first) {
if (_node_calls[cur].second == '.') {
// add single node for stretch of reference node
string new_seq = seq.substr(cur, next - cur);
new_nodes.second = ++_max_id;
_call_graph.create_node(new_seq, new_nodes.second);
} else if (_node_calls[cur].second != '-') {
// add snp node
assert(next - cur == 1);
string new_seq(1, _node_calls[cur].second);
new_nodes.second = ++_max_id;
_call_graph.create_node(new_seq, new_nodes.second);
create_snp_path(new_nodes.second, secondary_snp);
}
}
// update maps if new node abuts end of original node
// so that edges can be updated later on:
if (new_nodes.first != -1 || new_nodes.second != -1) {
if (cur == 0) {
_start_node_map[_node->id()] = new_nodes;
}
if (next == n) {
_end_node_map[_node->id()] = new_nodes;
}
}
// add edges
if (prev_nodes.first != -1 && new_nodes.first != -1) {
_call_graph.create_edge(prev_nodes.first, new_nodes.first);
}
if (prev_nodes.first != -1 && new_nodes.second != -1) {
_call_graph.create_edge(prev_nodes.first, new_nodes.second);
}
if (prev_nodes.second != -1 && new_nodes.first != -1) {
_call_graph.create_edge(prev_nodes.second, new_nodes.first);
}
if (prev_nodes.second != -1 && new_nodes.second != -1) {
_call_graph.create_edge(prev_nodes.second, new_nodes.second);
}
// shift right
cur = next;
cat = next_cat;
prev_nodes = new_nodes;
}
}
}
