From 6cc0138507efa363329bcd7a9ab147bc89980658 Mon Sep 17 00:00:00 2001 From: Jordan Eizenga Date: Tue, 18 Jun 2024 14:36:44 -0700 Subject: [PATCH 1/4] update to bdsg with new ref path overlay --- deps/libbdsg | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/deps/libbdsg b/deps/libbdsg index 97e42e0fb0f..aab874ee3c6 160000 --- a/deps/libbdsg +++ b/deps/libbdsg @@ -1 +1 @@ -Subproject commit 97e42e0fb0fe52c0953f52ba971317f83612726b +Subproject commit aab874ee3c6235b9cbeff57dd7e316a7f53c4613 From 9a7b605df4ce5a95f7658bd56087c778fae32062 Mon Sep 17 00:00:00 2001 From: Jordan Eizenga Date: Tue, 18 Jun 2024 14:37:57 -0700 Subject: [PATCH 2/4] fix include guard --- src/subpath_overlay.hpp | 12 ++++++------ 1 file changed, 6 insertions(+), 6 deletions(-) diff --git a/src/subpath_overlay.hpp b/src/subpath_overlay.hpp index 91444e14a43..81ab090c67e 100644 --- a/src/subpath_overlay.hpp +++ b/src/subpath_overlay.hpp @@ -1,11 +1,11 @@ -#ifndef VG_SUBGRAPH_OVERLAY_HPP_INCLUDED -#define VG_SUBGRAPH_OVERLAY_HPP_INCLUDED +#ifndef VG_SUBPATH_OVERLAY_HPP_INCLUDED +#define VG_SUBPATH_OVERLAY_HPP_INCLUDED /** - * \file subgraph_overlay.hpp + * \file subpath_overlay.hpp * - * Provides SourceSinkOverlay, a HandleGraph implementation that joins all the - * heads and tails of a backing graph to single source and sink nodes. + * Provides SubpathOverlay, a PathHandleGraph overlay that presents an subinterval + * of a path as a linearized graph. * */ @@ -104,4 +104,4 @@ class SubpathOverlay : public ExpandingOverlayGraph { } -#endif +#endif // VG_SUBPATH_OVERLAY_HPP_INCLUDED From c0e986c9c6667997cd5001e3159891126b84037d Mon Sep 17 00:00:00 2001 From: Jordan Eizenga Date: Tue, 18 Jun 2024 19:56:29 -0700 Subject: [PATCH 3/4] update to master-merged libbdsg --- deps/libbdsg | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/deps/libbdsg b/deps/libbdsg index aab874ee3c6..c8f6a1284f5 160000 --- a/deps/libbdsg +++ b/deps/libbdsg @@ -1 +1 @@ -Subproject commit aab874ee3c6235b9cbeff57dd7e316a7f53c4613 +Subproject commit c8f6a1284f5761fd905276b376a4e57044134c03 From 1664bdf6e9c2834f69646323ccdea4a43be1225f Mon Sep 17 00:00:00 2001 From: Jordan Eizenga Date: Mon, 8 Jul 2024 12:38:03 -0700 Subject: [PATCH 4/4] switch to libbdsg with faster ref overlay --- deps/libbdsg | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/deps/libbdsg b/deps/libbdsg index c8f6a1284f5..6b871a5a2e8 160000 --- a/deps/libbdsg +++ b/deps/libbdsg @@ -1 +1 @@ -Subproject commit c8f6a1284f5761fd905276b376a4e57044134c03 +Subproject commit 6b871a5a2e8367b97f09f81d59d7d192cff0caa1