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Remove vg join (been deprecated since 2020) #4932

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Remove vg join (been deprecated since 2020) #4932

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93 changes: 0 additions & 93 deletions src/subcommand/join_main.cpp
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45 changes: 0 additions & 45 deletions src/vg.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -4880,51 +4880,6 @@ void VG::connect_nodes_to_node(vector<NodeTraversal>& nodes, NodeTraversal node)
}
}

// join all subgraphs together to a "null" head node
Node* VG::join_heads(void) {
// Find the head nodes
vector<Node*> heads;
head_nodes(heads);

// Then create the new node (so it isn't picked up as a head)
current_id = max_node_id()+1;
Node* root = create_node("N");

// Wire it to all the heads and return
connect_node_to_nodes(root, heads);
return root;
}

void VG::join_heads(Node* node, bool from_start) {
vector<Node*> heads;
head_nodes(heads);

// If the node we have been given shows up as a head, remove it.
for(auto i = heads.begin(); i != heads.end(); ++i) {
if(*i == node) {
heads.erase(i);
break;
}
}

connect_node_to_nodes(node, heads, from_start);
}

void VG::join_tails(Node* node, bool to_end) {
vector<Node*> tails;
tail_nodes(tails);

// If the node we have been given shows up as a tail, remove it.
for(auto i = tails.begin(); i != tails.end(); ++i) {
if(*i == node) {
tails.erase(i);
break;
}
}

connect_nodes_to_node(tails, node, to_end);
}

void VG::add_start_end_markers(int length,
char start_char, char end_char,
Node*& start_node, Node*& end_node,
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6 changes: 0 additions & 6 deletions src/vg.hpp
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Original file line number Diff line number Diff line change
Expand Up @@ -1256,12 +1256,6 @@ class VG : public Progressive, public MutablePathDeletableHandleGraph {
/// Collect the subgraph of a Node. TODO: what does that mean?
void collect_subgraph(Node* node, set<Node*>& subgraph);

/// Join head nodes of graph to common null node, creating a new single head.
Node* join_heads(void);
/// Join head nodes of graph to specified node. Optionally from the start/to the end of the new node.
void join_heads(Node* node, bool from_start = false);
/// Join tail nodes of graph to specified node. Optionally from the start/to the end of the new node.
void join_tails(Node* node, bool to_end = false);
/// Add singular head and tail null nodes to graph.
void wrap_with_null_nodes(void);
/// Add a start node and an end node, where all existing heads in the graph
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