Change mismatch threshold for lenient profile

BimberLab · Aug 9, 2024 · c8c8fc3 · c8c8fc3
1 parent ab24cc3
commit c8c8fc3
Showing 1 changed file with 1 addition and 1 deletion.
diff --git 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);