From 89af9b6c89ad058234544cf8ec6468a94407d688 Mon Sep 17 00:00:00 2001
From: Glenn Hickey <glenn.hickey@gmail.com>
Date: Fri, 5 Apr 2024 09:57:04 -0400
Subject: [PATCH] auto-add rgfa prefix during rgfa conversion

---
 src/subcommand/convert_main.cpp | 8 ++++++++
 1 file changed, 8 insertions(+)

diff --git a/src/subcommand/convert_main.cpp b/src/subcommand/convert_main.cpp
index 7474f5a521e..d8981e1f02d 100644
--- a/src/subcommand/convert_main.cpp
+++ b/src/subcommand/convert_main.cpp
@@ -6,6 +6,7 @@
 #include "../algorithms/find_gbwtgraph.hpp"
 #include "../io/save_handle_graph.hpp"
 #include "../gfa.hpp"
+#include "../rgfa.hpp"
 #include "../gbwt_helper.hpp"
 #include "../gbwtgraph_helper.hpp"
 #include <vg/io/stream.hpp>
@@ -236,6 +237,13 @@ int main_convert(int argc, char** argv) {
           cerr << "[vg convert] warning: vg-protobuf output (-v / --vg-out) is deprecated. please use -p instead." << endl;
     }
 
+    // we interpret the user path selections as reference path selections (consistent with vg paths)
+    // so we need to add the rgfa keyword to pick up the nonref paths
+    if ((!rgfa_paths.empty() || !rgfa_prefixes.empty()) &&
+        std::find(rgfa_prefixes.begin(), rgfa_prefixes.end(), RGFACover::rgfa_sample_name) == rgfa_prefixes.end()) {
+        rgfa_prefixes.push_back(RGFACover::rgfa_sample_name);
+    }
+
     
     // with -F or -G we convert an alignment and not a graph
     if (input == input_gam || input == input_gaf) {