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Fix limit arg #4734

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Fix limit arg #4734

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38dc4ce
size limit fixes (PR #228)
faithokamoto Oct 31, 2025
c0479fb
add max snarl size hints
faithokamoto Oct 31, 2025
893563e
test oversized snarl behavior
faithokamoto Oct 31, 2025
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2 changes: 1 addition & 1 deletion deps/libbdsg
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Submodule libbdsg updated 7 files
+1 −1 CMakeLists.txt
+1 −1 bdsg/deps/hopscotch-map
+1 −1 bdsg/deps/pybind11
+1 −1 bdsg/deps/sdsl-lite
+12 −1 bdsg/include/bdsg/snarl_distance_index.hpp
+12 −4 bdsg/src/snarl_distance_index.cpp
+1 −1 make_and_run_binder.py
4 changes: 3 additions & 1 deletion src/snarl_distance_index.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -59,7 +59,8 @@ void fill_in_distance_index(SnarlDistanceIndex* distance_index, const HandleGrap
SnarlDistanceIndex::TemporaryDistanceIndex temp_index = make_temporary_distance_index(graph, snarl_finder, size_limit, only_top_level_chain_distances);

if (!silence_warnings && temp_index.use_oversized_snarls) {
cerr << "warning: distance index uses oversized snarls, which may make mapping slow" << endl;
cerr << "warning: distance index uses oversized snarls, (the biggest has "
<< temp_index.most_oversized_snarl_size << " nodes), which may make mapping slow" << endl;
cerr << "\ttry increasing --snarl-limit when building the distance index" << endl;
}

Expand Down Expand Up @@ -1110,6 +1111,7 @@ void populate_snarl_index(
}

if (size_limit != 0 && temp_snarl_record.node_count > size_limit) {
temp_index.most_oversized_snarl_size = std::max(temp_index.most_oversized_snarl_size, temp_snarl_record.node_count);
temp_index.use_oversized_snarls = true;
}

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21 changes: 21 additions & 0 deletions src/unittest/snarl_distance_index.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -6583,6 +6583,27 @@ namespace vg {
REQUIRE(distance_index.minimum_distance(n1->id(), false, 0, n8->id(), false, 0, false, &graph) == 8);
REQUIRE(distance_index.minimum_distance(n8->id(), false, 0, n2->id(), true, 0, false, &graph) == 1);
}
SECTION( "Is oversized" ) {
net_handle_t node_1 = distance_index.get_node_net_handle(n1->id());
net_handle_t snarl;
distance_index.follow_net_edges(node_1, &graph, false, [&](const net_handle_t& other) {
snarl=other;
return false;
});
REQUIRE(distance_index.is_oversized_snarl(snarl));
}
SECTION( "Is not oversized with size limit equal to snarl size " ) {
SnarlDistanceIndex distance_index2;
// Exactly equal to the snarl size
fill_in_distance_index(&distance_index2, &graph, &snarl_finder, 7);
net_handle_t node_1 = distance_index2.get_node_net_handle(n1->id());
net_handle_t snarl;
distance_index2.follow_net_edges(node_1, &graph, false, [&](const net_handle_t& other) {
snarl=other;
return false;
});
REQUIRE(!distance_index2.is_oversized_snarl(snarl));
}
}
TEST_CASE( "Nested oversized snarl","[snarl_distance]" ) {
VG graph;
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