From 04a4983e6cc31282214dc40065f232e45621f69f Mon Sep 17 00:00:00 2001
From: Mikhail Kolmogorov <fenderglass@gmail.com>
Date: Fri, 17 Jun 2022 11:00:22 -0700
Subject: [PATCH] don't do simple RR in haplotype mode

---
 flye/__build__.py                | 2 +-
 src/repeat_graph/main_repeat.cpp | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/flye/__build__.py b/flye/__build__.py
index e541e509d..465f7a7d4 100644
--- a/flye/__build__.py
+++ b/flye/__build__.py
@@ -1 +1 @@
-__build__ = 1778
+__build__ = 1779
diff --git a/src/repeat_graph/main_repeat.cpp b/src/repeat_graph/main_repeat.cpp
index 363b27fd9..ce3251271 100644
--- a/src/repeat_graph/main_repeat.cpp
+++ b/src/repeat_graph/main_repeat.cpp
@@ -251,7 +251,7 @@ int repeat_main(int argc, char** argv)
 		outGen.outputGfa(proc.getEdgesPaths(), outFolder + "/graph_before_rr.gfa");
 	}
 
-	if (isMeta) 
+	if (isMeta && !keepHaplotypes) 
 	{
 		repResolver.resolveSimpleRepeats();
 	}