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pull in new libbdsg with ref overlay fix #4821

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pull in new libbdsg with ref overlay fix #4821

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5865bc9
pull in new libbdsg with ref overlay fix
glennhickey Feb 5, 2026
09fdbce
let overlay index all paths when not gbz
glennhickey Feb 5, 2026
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2 changes: 1 addition & 1 deletion deps/libbdsg
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Submodule libbdsg updated 2 files
+11 −5 bdsg/include/bdsg/overlays/reference_path_overlay.hpp
+25 −12 bdsg/src/reference_path_overlay.cpp
4 changes: 3 additions & 1 deletion src/subcommand/call_main.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -435,6 +435,8 @@ int main_call(int argc, char** argv) {
// Apply overlays as necessary
bool need_path_positions = vcf_filename.empty();
bool need_vectorizable = !pack_filename.empty();
// When not using GBWT/GBZ, embedded HAPLOTYPE paths are the sample alleles
bool all_paths = gbwt_filename.empty() && !gbz_graph;
bdsg::ReferencePathOverlayHelper pp_overlay_helper;
bdsg::ReferencePathVectorizableOverlayHelper ppv_overlay_helper;
bdsg::PathVectorizableOverlayHelper pv_overlay_helper;
Expand All @@ -444,7 +446,7 @@ int main_call(int argc, char** argv) {
if (need_path_positions && need_vectorizable) {
graph = dynamic_cast<PathHandleGraph*>(ppv_overlay_helper.apply(graph));
} else if (need_path_positions && !need_vectorizable) {
graph = dynamic_cast<PathHandleGraph*>(pp_overlay_helper.apply(graph));
graph = dynamic_cast<PathHandleGraph*>(pp_overlay_helper.apply(graph, all_paths));
} else if (!need_path_positions && need_vectorizable) {
graph = dynamic_cast<PathHandleGraph*>(pv_overlay_helper.apply(graph));
}
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4 changes: 3 additions & 1 deletion src/subcommand/deconstruct_main.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -258,7 +258,9 @@ int main_deconstruct(int argc, char** argv) {
std::chrono::time_point<std::chrono::system_clock> overlay_start_time = std::chrono::system_clock::now();

// Make the overlay
PathPositionHandleGraph* graph = overlay_helper.apply(path_handle_graph);
// When not using GBWT/GBZ, embedded HAPLOTYPE paths are the sample alleles
bool all_paths = gbwt_file_name.empty() && !gbz_graph;
PathPositionHandleGraph* graph = overlay_helper.apply(path_handle_graph, all_paths);

// See how long that took
clock_t overlay_stop_clock = clock();
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