Change nimble default from 10 to 5 mismatches

bbimber · bbimber · commit 7f65a95720ee · 2023-10-19T10:50:48.000-07:00
diff --git a/singlecell/src/org/labkey/singlecell/run/NimbleHelper.java b/singlecell/src/org/labkey/singlecell/run/NimbleHelper.java
@@ -253,7 +253,7 @@ private void updateNimbleConfigFile(File configFile, NimbleGenome genome) throws
             String alignTemplate = genome.getTemplate();
             if ("lenient".equals(alignTemplate))
             {
-                config.put("num_mismatches", 10);
+                config.put("num_mismatches", 5);
                 config.put("intersect_level", 0);
                 config.put("score_threshold", 45);
                 config.put("score_percent", 0.75);

Original file line number	Diff line number	Diff line change
`@@ -253,7 +253,7 @@ private void updateNimbleConfigFile(File configFile, NimbleGenome genome) throws`
`253`	`253`	`String alignTemplate = genome.getTemplate();`
`254`	`254`	`if ("lenient".equals(alignTemplate))`
`255`	`255`	`{`
`256`		`- config.put("num_mismatches", 10);`
	`256`	`+ config.put("num_mismatches", 5);`
`257`	`257`	`config.put("intersect_level", 0);`
`258`	`258`	`config.put("score_threshold", 45);`
`259`	`259`	`config.put("score_percent", 0.75);`