Tag Pileup Total Tag normalization with Blacklist filtering

Now allows user to add blacklist file (BED format) and use that to
modify how the total tag normalization is calculated. This parameter is
optional.

Author: WilliamKMLai

src/scripts/Read_Analysis/TagPileup.java

@@ -96,7 +96,9 @@ public void run() throws IOException {
 			else {
 
 				//Code to standardize tags sequenced to genome size (1 tag / 1 bp)
-				if(PARAM.getStandard()) { PARAM.setRatio(BAMUtilities.calculateStandardizationRatio(BAM, PARAM.getRead())); }
+				if(PARAM.getStandard() && PARAM.getBlacklist() != null) { PARAM.setRatio(BAMUtilities.calculateStandardizationRatio(BAM, PARAM.getBlacklist(), PARAM.getRead())); }
+				else if(PARAM.getStandard()) { PARAM.setRatio(BAMUtilities.calculateStandardizationRatio(BAM, PARAM.getRead())); }
+				//System.out.println(PARAM.getRatio());
 
 				for(int BED_Index = 0; BED_Index < BEDFiles.size(); BED_Index++) {
 					JTextArea STATS = new JTextArea(); //Generate statistics object
@@ -124,13 +126,14 @@ public void run() throws IOException {
 					int currentindex = 0;
 					for(int x = 0; x < CPU; x++) {
 						currentindex += subset;
-						if(CPU == 1) subset = INPUT.size();
-						else if(INPUT.size() % CPU == 0) subset = INPUT.size() / CPU;
+						if(CPU == 1) { subset = INPUT.size(); }
+						else if(INPUT.size() % CPU == 0) { subset = INPUT.size() / CPU; }
 						else {
 							int remainder = INPUT.size() % CPU;
 							if(x < remainder ) subset = (int)(((double)INPUT.size() / (double)CPU) + 1);
 							else subset = (int)(((double)INPUT.size() / (double)CPU));
 						}
+						//System.out.println("CPU: " + x + "\tInterval: " + currentindex + "\t" + subset);
 						PileupExtract extract = new PileupExtract(PARAM, BAM, INPUT, currentindex, subset);
 						parseMaster.execute(extract);
 					}