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fix overlay gbz indexing for vg call #4822

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Merged
adamnovak merged 1 commit into from
Feb 10, 2026
+6 −6
Merged

fix overlay gbz indexing for vg call #4822

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2 changes: 1 addition & 1 deletion deps/libbdsg
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Submodule libbdsg updated 2 files
+14 −3 bdsg/include/bdsg/overlays/packed_reference_path_overlay.hpp
+19 −0 bdsg/src/packed_reference_path_overlay.cpp
6 changes: 3 additions & 3 deletions src/subcommand/call_main.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -436,17 +436,17 @@ int main_call(int argc, char** argv) {
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;
bool embedded_haplotype_paths = gbwt_filename.empty() && !gbz_graph;
bdsg::ReferencePathOverlayHelper pp_overlay_helper;
bdsg::ReferencePathVectorizableOverlayHelper ppv_overlay_helper;
bdsg::PathVectorizableOverlayHelper pv_overlay_helper;
if (show_progress) {
logger.info() << "Applying overlays if necessary (i.e. input not in XG format)" << endl;
}
if (need_path_positions && need_vectorizable) {
graph = dynamic_cast<PathHandleGraph*>(ppv_overlay_helper.apply(graph));
graph = dynamic_cast<PathHandleGraph*>(ppv_overlay_helper.apply(graph, embedded_haplotype_paths));
} else if (need_path_positions && !need_vectorizable) {
graph = dynamic_cast<PathHandleGraph*>(pp_overlay_helper.apply(graph, all_paths));
graph = dynamic_cast<PathHandleGraph*>(pp_overlay_helper.apply(graph, embedded_haplotype_paths));
} else if (!need_path_positions && need_vectorizable) {
graph = dynamic_cast<PathHandleGraph*>(pv_overlay_helper.apply(graph));
}
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4 changes: 2 additions & 2 deletions src/subcommand/deconstruct_main.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -259,8 +259,8 @@ int main_deconstruct(int argc, char** argv) {

// Make the overlay
// 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);
bool embedded_haplotype_paths = gbwt_file_name.empty() && !gbz_graph;
PathPositionHandleGraph* graph = overlay_helper.apply(path_handle_graph, embedded_haplotype_paths);

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