Make java actually quiet when requested. Fixes #3

s-andrews · Aug 25, 2020 · 3ce725c · 3ce725c
1 parent 0d80d9b
commit 3ce725c
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Showing 2 changed files with 6 additions and 2 deletions.
diff --git a/sleuth.py b/sleuth.py
@@ -62,7 +62,11 @@ def run_snp_calling(options):
     if options.quiet:
         quiet_value = "true"
 
-    subprocess.run([options.java,"-cp",joined_classpath,f'-Dquiet="{quiet_value}',"uk/ac/babraham/CellLineSleuth/CellLineSleuthApplication",options.snpfile, options.bamfile,outfile], check=True)
+    command_options = [options.java,"-cp",joined_classpath,f'-Dquiet={quiet_value}',"uk/ac/babraham/CellLineSleuth/CellLineSleuthApplication",options.snpfile, options.bamfile,outfile]
+
+    #print(f"Command options are {command_options}")
+
+    subprocess.run(command_options, check=True)
 
     return outfile
 

diff --git a/uk/ac/babraham/CellLineSleuth/CellLineSleuthApplication.java b/uk/ac/babraham/CellLineSleuth/CellLineSleuthApplication.java
@@ -16,7 +16,7 @@ public class CellLineSleuthApplication {
 	private CellLineCollection cells;
 
 	public CellLineSleuthApplication (File snpFile, File bamFile, File outFile) {
-
+				
 		if (System.getProperty("quiet").equals("true")) {
 			CellLineSleuthApplication.QUIET = true;
 		}