Merge pull request #4296 from vgteam/read-lr-giraffe

Allow reading GAMs with embedded JSON metadata
vgteam · May 23, 2024 · db574a5 · db574a5 · adamnovak · May 23, 2024
2 parents 4a86fc5 + c70da62
commit db574a5
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Showing 4 changed files with 53 additions and 1 deletion.
diff --git a/deps/libvgio b/deps/libvgio
diff --git 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
@@ -0,0 +1,29 @@
+/**
+ * \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"
+
+#include <iterator>
+
+
+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([](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
@@ -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
+5 −1		include/vg/io/alignment_emitter.hpp
+4 −0		include/vg/io/blocked_gzip_input_stream.hpp
+1 −1		include/vg/io/message_iterator.hpp
+3 −5		include/vg/io/protobuf_iterator.hpp
+19 −3		include/vg/io/stream.hpp
+36 −0		src/alignment_emitter.cpp
+4 −0		src/blocked_gzip_input_stream.cpp
+7 −2		src/message_iterator.cpp