From 8dd5b41b3545a7f5593fd243776dade391a41fa6 Mon Sep 17 00:00:00 2001
From: faithokamoto <faith.purpleflower@gmail.com>
Date: Fri, 12 Jun 2026 15:10:19 -0700
Subject: [PATCH] rip out vg join

---
 src/subcommand/join_main.cpp | 93 ------------------------------------
 src/vg.cpp                   | 45 -----------------
 src/vg.hpp                   |  6 ---
 3 files changed, 144 deletions(-)
 delete mode 100644 src/subcommand/join_main.cpp

diff --git a/src/subcommand/join_main.cpp b/src/subcommand/join_main.cpp
deleted file mode 100644
index 8e7f2d845e6..00000000000
--- a/src/subcommand/join_main.cpp
+++ /dev/null
@@ -1,93 +0,0 @@
-/** \file join_main.cpp
- *
- * Defines the "vg join" subcommand, which attaches graphs together.
- */
-
-
-#include <omp.h>
-#include <unistd.h>
-#include <getopt.h>
-
-#include <iostream>
-
-#include "subcommand.hpp"
-
-#include "../vg.hpp"
-
-using namespace std;
-using namespace vg;
-using namespace vg::subcommand;
-
-void help_join(char** argv) {
-    cerr << "usage: " << argv[0] << " join [options] <graph1.vg> [graph2.vg ...] >joined.vg" << endl
-         << "Joins graphs and sub-graphs into a single variant graph by connecting their" << endl
-         << "heads to a single root node with sequence 'N'." << endl
-         << "Assumes a single id namespace for all graphs to join." << endl
-         << "  -h, --help                print this help message to stderr and exit" << endl;
-}
-
-int main_join(int argc, char** argv) {
-
-    if (argc == 2) {
-        help_join(argv);
-        return 1;
-    }
-
-    int c;
-    optind = 2; // force optind past command positional argument
-    while (true) {
-        static struct option long_options[] =
-        {
-            {"help", no_argument, 0, 'h'},
-            {0, 0, 0, 0}
-        };
-
-        int option_index = 0;
-        c = getopt_long (argc, argv, "h?",
-                         long_options, &option_index);
-
-        // Detect the end of the options.
-        if (c == -1)
-            break;
-
-        switch (c)
-        {
-            case 'h':
-            case '?':
-                help_join(argv);
-                exit(1);
-                break;
-
-            default:
-                abort ();
-        }
-    }
-
-    list<VG*> graphs;
-
-    while (optind < argc) {
-        VG* graph;
-        get_input_file(optind, argc, argv, [&](istream& in) {
-            graph = new VG(in);
-        });
-        graphs.push_back(graph);
-    }
-
-    VG joined;
-    for (list<VG*>::iterator g = graphs.begin(); g != graphs.end(); ++g) {
-        // Stick all the graphs together, complaining if they use the same node IDs (since they probably shouldn't).
-        joined.extend(**g, true);
-    }
-
-    // combine all subgraphs
-    joined.join_heads();
-
-    // output
-    joined.serialize_to_ostream(std::cout);
-
-    return 0;
-}
-
-// Register subcommand
-static Subcommand vg_join("join", "combine graphs via a new head", DEPRECATED, main_join);
-
diff --git a/src/vg.cpp b/src/vg.cpp
index f0206908dfd..2faaf84fb26 100644
--- a/src/vg.cpp
+++ b/src/vg.cpp
@@ -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,
diff --git a/src/vg.hpp b/src/vg.hpp
index 9c20f2023e8..7a732136bf4 100644
--- a/src/vg.hpp
+++ b/src/vg.hpp
@@ -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