From 3f6afa7ea131e6cd2a6c5360103211642528a111 Mon Sep 17 00:00:00 2001 From: Glenn Hickey Date: Fri, 6 Feb 2026 13:51:05 -0500 Subject: [PATCH] fix overlay gbz indexing for vg call --- deps/libbdsg | 2 +- src/subcommand/call_main.cpp | 6 +++--- src/subcommand/deconstruct_main.cpp | 4 ++-- 3 files changed, 6 insertions(+), 6 deletions(-) diff --git a/deps/libbdsg b/deps/libbdsg index c075778651..fc7321597d 160000 --- a/deps/libbdsg +++ b/deps/libbdsg @@ -1 +1 @@ -Subproject commit c075778651956b27f212360bca8cff502b2abfc4 +Subproject commit fc7321597d2732ff3986e3b5dc97ef3fba0cd9c8 diff --git a/src/subcommand/call_main.cpp b/src/subcommand/call_main.cpp index af8ee3cb89..b2034c2624 100644 --- a/src/subcommand/call_main.cpp +++ b/src/subcommand/call_main.cpp @@ -436,7 +436,7 @@ 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; @@ -444,9 +444,9 @@ int main_call(int argc, char** argv) { logger.info() << "Applying overlays if necessary (i.e. input not in XG format)" << endl; } if (need_path_positions && need_vectorizable) { - graph = dynamic_cast(ppv_overlay_helper.apply(graph)); + graph = dynamic_cast(ppv_overlay_helper.apply(graph, embedded_haplotype_paths)); } else if (need_path_positions && !need_vectorizable) { - graph = dynamic_cast(pp_overlay_helper.apply(graph, all_paths)); + graph = dynamic_cast(pp_overlay_helper.apply(graph, embedded_haplotype_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 405fbfc70b..fef15ea05e 100644 --- a/src/subcommand/deconstruct_main.cpp +++ b/src/subcommand/deconstruct_main.cpp @@ -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();