From 5865bc959c096873efe4b52726df71b49cbd86b6 Mon Sep 17 00:00:00 2001 From: Glenn Hickey Date: Thu, 5 Feb 2026 14:29:05 -0500 Subject: [PATCH 1/2] pull in new libbdsg with ref overlay fix --- deps/libbdsg | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/deps/libbdsg b/deps/libbdsg index 1c1df7b1b5..30c805e28f 160000 --- a/deps/libbdsg +++ b/deps/libbdsg @@ -1 +1 @@ -Subproject commit 1c1df7b1b541894f6413ed4a2cbefbd0565955af +Subproject commit 30c805e28f9095fa977c0da9ed4e3b9aa7ef65d1 From 09fdbcec8def9b6fd7deae3178e5114d0cd371b7 Mon Sep 17 00:00:00 2001 From: Glenn Hickey Date: Thu, 5 Feb 2026 17:35:24 -0500 Subject: [PATCH 2/2] let overlay index all paths when not gbz --- deps/libbdsg | 2 +- src/subcommand/call_main.cpp | 4 +++- src/subcommand/deconstruct_main.cpp | 4 +++- 3 files changed, 7 insertions(+), 3 deletions(-) diff --git a/deps/libbdsg b/deps/libbdsg index 30c805e28f..c075778651 160000 --- a/deps/libbdsg +++ b/deps/libbdsg @@ -1 +1 @@ -Subproject commit 30c805e28f9095fa977c0da9ed4e3b9aa7ef65d1 +Subproject commit c075778651956b27f212360bca8cff502b2abfc4 diff --git a/src/subcommand/call_main.cpp b/src/subcommand/call_main.cpp index 25cc1d6ea2..af8ee3cb89 100644 --- a/src/subcommand/call_main.cpp +++ b/src/subcommand/call_main.cpp @@ -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; @@ -444,7 +446,7 @@ int main_call(int argc, char** argv) { if (need_path_positions && need_vectorizable) { graph = dynamic_cast(ppv_overlay_helper.apply(graph)); } else if (need_path_positions && !need_vectorizable) { - graph = dynamic_cast(pp_overlay_helper.apply(graph)); + graph = dynamic_cast(pp_overlay_helper.apply(graph, all_paths)); } else if (!need_path_positions && need_vectorizable) { graph = dynamic_cast(pv_overlay_helper.apply(graph)); } diff --git a/src/subcommand/deconstruct_main.cpp b/src/subcommand/deconstruct_main.cpp index aa98720aaf..405fbfc70b 100644 --- a/src/subcommand/deconstruct_main.cpp +++ b/src/subcommand/deconstruct_main.cpp @@ -258,7 +258,9 @@ int main_deconstruct(int argc, char** argv) { std::chrono::time_point 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();