From c8c8fc363bc1ace29701d99ee4dd4386002f4c2b Mon Sep 17 00:00:00 2001
From: hextraza <sebastiancbenjamin@gmail.com>
Date: Fri, 9 Aug 2024 11:45:20 -0700
Subject: [PATCH] Change mismatch threshold for lenient profile

---
 singlecell/src/org/labkey/singlecell/run/NimbleHelper.java | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/singlecell/src/org/labkey/singlecell/run/NimbleHelper.java b/singlecell/src/org/labkey/singlecell/run/NimbleHelper.java
index 9850e99ed..4d92330ca 100644
--- a/singlecell/src/org/labkey/singlecell/run/NimbleHelper.java
+++ b/singlecell/src/org/labkey/singlecell/run/NimbleHelper.java
@@ -339,7 +339,7 @@ private void updateNimbleConfigFile(File configFile, NimbleGenome genome) throws
             String alignTemplate = genome.getTemplate();
             if ("lenient".equals(alignTemplate))
             {
-                config.put("num_mismatches", 5);
+                config.put("num_mismatches", 2);
                 config.put("intersect_level", 0);
                 config.put("score_threshold", 45);
                 config.put("score_percent", 0.45);