Debug autoFindBarcode

DeplanckeLab · Jan 9, 2018 · 91585eb · 91585eb
1 parent a4f613f
commit 91585eb
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Showing 2 changed files with 2 additions and 2 deletions.
diff --git a/releases/BRBseqTools.1.0.jar b/releases/BRBseqTools.1.0.jar
diff --git a/src/TrimmingManager.java b/src/TrimmingManager.java
@@ -155,7 +155,7 @@ private static String autoFindBarcode(BufferedReader br) throws Exception
 		}
 		System.out.println("The limit of 100 occurences was not reached.");
 		System.out.println("Most occuring barcode is " + reverseComplement(maxbc) + " ("+max+" times)");
-		return maxbc;
+		return null;
 	}
 
 	private static BufferedReader readFileFromBeginning(String fastQFile) throws Exception
@@ -225,7 +225,7 @@ public static Excel trimFastQ(String fastQFile) throws Exception
 		String barcode_RC = null;
 		if(Parameters.autoFindBarcode)
 		{
-			autoFindBarcode(br);
+			barcode_RC = autoFindBarcode(br);
 			br.close();
 			if(barcode_RC == null) System.err.println("No barcode was detected during the automatic search... Switching to standard trimming mode.");
 			br = readFileFromBeginning(fastQFile);