From 165ed97479629ced90beb01a00d35d3f43b33e1a Mon Sep 17 00:00:00 2001
From: Adam Novak <anovak@soe.ucsc.edu>
Date: Thu, 16 May 2024 13:21:31 -0700
Subject: [PATCH 1/3] Update to current libvgio

---
 deps/libvgio | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/deps/libvgio b/deps/libvgio
index 9b0d0e11df6..def4827b903 160000
--- a/deps/libvgio
+++ b/deps/libvgio
@@ -1 +1 @@
-Subproject commit 9b0d0e11df6f9bd389ba4dba08d107953eabff8f
+Subproject commit def4827b9034d9624179c442c8568978ca33e5b8

From bea8e9ca5748bfea1b1bd9e540b909ce3d801ec5 Mon Sep 17 00:00:00 2001
From: Adam Novak <anovak@soe.ucsc.edu>
Date: Fri, 15 Mar 2024 15:31:47 -0400
Subject: [PATCH 2/3] Define PARAMS_JSON tag with the registry

---
 src/io/register_libvg_io.cpp           |  2 ++
 src/io/register_loader_params_json.cpp | 27 ++++++++++++++++++++++++++
 src/io/register_loader_params_json.hpp | 21 ++++++++++++++++++++
 3 files changed, 50 insertions(+)
 create mode 100644 src/io/register_loader_params_json.cpp
 create mode 100644 src/io/register_loader_params_json.hpp

diff --git a/src/io/register_libvg_io.cpp b/src/io/register_libvg_io.cpp
index 94c0a643a8c..4d8fb51f603 100644
--- a/src/io/register_libvg_io.cpp
+++ b/src/io/register_libvg_io.cpp
@@ -20,6 +20,7 @@
 #include "register_loader_saver_packed_graph.hpp"
 #include "register_loader_saver_hash_graph.hpp"
 #include "register_loader_saver_gfa.hpp"
+#include "register_loader_params_json.hpp"
 
 #include "register_libvg_io.hpp"
 
@@ -46,6 +47,7 @@ bool register_libvg_io() {
     register_loader_saver_xg();
     register_loader_saver_packed_graph();
     register_loader_saver_hash_graph();
+    register_loader_params_json();
     return true;
 }
     
diff --git a/src/io/register_loader_params_json.cpp b/src/io/register_loader_params_json.cpp
new file mode 100644
index 00000000000..e06f8f12855
--- /dev/null
+++ b/src/io/register_loader_params_json.cpp
@@ -0,0 +1,27 @@
+/**
+ * \file register_loader_params_json.cpp
+ * Defines IO for a VG graph from stream files of Graph objects.
+ */
+
+#include <vg/io/registry.hpp>
+#include "register_loader_params_json.hpp"
+
+
+namespace vg {
+
+namespace io {
+
+using namespace std;
+using namespace vg::io;
+
+void register_loader_params_json() {
+    Registry::register_loader<std::string>("PARAMS_JSON", wrap_bare_loader([](const std::istream& stream) -> void* {
+        // Read the whole stream with an iterator. See <https://stackoverflow.com/a/3203502>.
+        return new std::string(std::istreambuf_iterator<char>(stream), {});
+    });
+}
+
+}
+
+}
+
diff --git a/src/io/register_loader_params_json.hpp b/src/io/register_loader_params_json.hpp
new file mode 100644
index 00000000000..9455c73b36e
--- /dev/null
+++ b/src/io/register_loader_params_json.hpp
@@ -0,0 +1,21 @@
+#ifndef VG_IO_REGISTER_LOADER_PARAMS_JSON_HPP_INCLUDED
+#define VG_IO_REGISTER_LOADER_PARAMS_JSON_HPP_INCLUDED
+
+/**
+ * \file register_loader_params_json.hpp
+ * Defines IO for embedded parameters.
+ */
+
+namespace vg {
+
+namespace io {
+
+using namespace std;
+
+void register_loader_params_json();
+
+}
+
+}
+
+#endif

From 0c64463a9d321b5d7715f1b851dcc8d3e7833e63 Mon Sep 17 00:00:00 2001
From: Adam Novak <anovak@soe.ucsc.edu>
Date: Fri, 15 Mar 2024 15:32:21 -0400
Subject: [PATCH 3/3] Finish implementing PARAMS_JSON loader

---
 src/io/register_loader_params_json.cpp | 6 ++++--
 1 file changed, 4 insertions(+), 2 deletions(-)

diff --git a/src/io/register_loader_params_json.cpp b/src/io/register_loader_params_json.cpp
index e06f8f12855..bc82deb0235 100644
--- a/src/io/register_loader_params_json.cpp
+++ b/src/io/register_loader_params_json.cpp
@@ -6,6 +6,8 @@
 #include <vg/io/registry.hpp>
 #include "register_loader_params_json.hpp"
 
+#include <iterator>
+
 
 namespace vg {
 
@@ -15,10 +17,10 @@ using namespace std;
 using namespace vg::io;
 
 void register_loader_params_json() {
-    Registry::register_loader<std::string>("PARAMS_JSON", wrap_bare_loader([](const std::istream& stream) -> void* {
+    Registry::register_loader<std::string>("PARAMS_JSON", wrap_bare_loader([](std::istream& stream) -> void* {
         // Read the whole stream with an iterator. See <https://stackoverflow.com/a/3203502>.
         return new std::string(std::istreambuf_iterator<char>(stream), {});
-    });
+    }));
 }
 
 }