From 78bff5934c1dcf9c27a866b90c906ae4991e4320 Mon Sep 17 00:00:00 2001
From: Erik Garrison <erik.garrison@gmail.com>
Date: Sat, 20 Jul 2024 17:45:32 +0200
Subject: [PATCH] tweak output format for multipatch

---
 src/common/wflign/src/wflign_patch.cpp | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/src/common/wflign/src/wflign_patch.cpp b/src/common/wflign/src/wflign_patch.cpp
index e6cb0b29..65859d18 100644
--- a/src/common/wflign/src/wflign_patch.cpp
+++ b/src/common/wflign/src/wflign_patch.cpp
@@ -2132,8 +2132,9 @@ query_start : query_end)
             mashmap_estimated_identity,
             false,  // Don't add an endline after each alignment
             true);  // This is a reverse complement alignment
-        // write tag indicating that this is a reverse complement alignment
-        out << "\t" << "rc:Z:true" << "\t"
+        // write tag indicating that this is a multipatch alignment
+        out << "\t" << "patch:Z:true" << "\t"
+            // and if the patch is inverted as well
             << "\t" << "inv:Z:" << (patch_aln.is_rev ? "true" : "false") << "\n";
     }
     out << std::flush;