Merge pull request #4513 from vgteam/skip-nonexistent-nodes

Don't extract nodes in ranges that didn't actually exist in the source graph
vgteam · Jan 31, 2025 · 511f840 · 511f840 · adamnovak · Jan 31, 2025
2 parents 5e13d76 + b64e48a
commit 511f840
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Showing 2 changed files with 4 additions and 1 deletion.
diff --git a/src/algorithms/subgraph.cpp b/src/algorithms/subgraph.cpp
@@ -265,7 +265,7 @@ void extract_context(const HandleGraph& source, MutableHandleGraph& subgraph, co
 
 void extract_id_range(const HandleGraph& source, const nid_t& id1, const nid_t& id2, MutableHandleGraph& subgraph) {
     for (nid_t i = id1; i <= id2; ++i) {
-        if (!subgraph.has_node(i)) {
+        if (!subgraph.has_node(i) && source.has_node(i)) {
             subgraph.create_handle(source.get_sequence(source.get_handle(i)), i);
         }
     }

diff --git a/src/chunker.hpp b/src/chunker.hpp
@@ -63,6 +63,9 @@ class PathChunker {
 
     /**
      * Like above, but use (inclusive) id range instead of region on path.
+     *
+     * Skips nodes in the ID range that do not actually exist in the source
+     * graph, or that already exist in the target graph.
      */
     void extract_id_range(vg::id_t start, vg::id_t end, int64_t context, int64_t length, bool forward_only,
                           MutablePathMutableHandleGraph& subgraph, Region& out_region);