From f60af88fd41a8aae3625d9b3ee77fe4a4eea43f7 Mon Sep 17 00:00:00 2001
From: Glenn Hickey <glenn.hickey@gmail.com>
Date: Mon, 9 Dec 2024 11:27:31 -0500
Subject: [PATCH] leave default opts empty; renorm

---
 src/cactus/cactus_progressive_config.xml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/src/cactus/cactus_progressive_config.xml b/src/cactus/cactus_progressive_config.xml
index 0154d8998..d070475f2 100644
--- a/src/cactus/cactus_progressive_config.xml
+++ b/src/cactus/cactus_progressive_config.xml
@@ -413,7 +413,7 @@
 	<!-- vcfwaveOptions: options to pass to vcfwave (from vcflib) -->
 	<!-- vcfwaveNorm: run bcftools norm -f (left shift) after vcfwave -->
 	<!-- bcftoolsNorm: Run bcftools norm -f (left shifting) on (non-raw, non-wave) VCF output (may result in overlapping variants) -->
-	<!-- mergeDuplicatesOptions: Run merge_duplicates script with these options after bcftools norm to prevent multiple entries at the same position.  If empty or 0, merge_duplicates will not be run.  This applies to normalization as toggled by vcfwaveNorm and/or bctoolsNorm (and is ever run after bcftools norm) -->
+	<!-- mergeDuplicatesOptions: Run merge_duplicates script with these options (empty string means default options) after bcftools norm to prevent multiple entries at the same position.  If "0", merge_duplicates will not be run.  This applies to normalization as toggled by vcfwaveNorm and/or bctoolsNorm (and is ever run after bcftools norm) -->
 	<graphmap_join
 		 maxNodeLength="1024"
 		 gfaffix="1"
@@ -430,7 +430,7 @@
 		 vcfwaveOptions="-I 1000"
 		 vcfwaveNorm="1"
 		 bcftoolsNorm="0"
-		 mergeDuplicatesOptions="--merge-mis-as-ref"
+		 mergeDuplicatesOptions=""
 		 />
 	<!-- hal2vg options -->
 	<!-- includeMinigraph: include minigraph node sequences as paths in output (note that cactus-graphmap-join will still remove them by default) -->