Modified tag set to be equal to set align tag population depending on

Read 1, Read 2, All tags, or Midpoints. Ignore unmapped tags for
calculation

Author: William Lai

src/scripts/Tag_Analysis/TagPileup.java

@@ -96,7 +96,7 @@ 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)); }
+				if(PARAM.getStandard()) { PARAM.setRatio(BAMUtilities.calculateStandardizationRatio(BAM, PARAM.getRead())); }
 
 				for(int BED_Index = 0; BED_Index < BEDFiles.size(); BED_Index++) {
 					JTextArea STATS = new JTextArea(); //Generate statistics object

src/util/BAMUtilities.java

@@ -11,10 +11,10 @@
 import htsjdk.samtools.util.CloseableIterator;
 
 public class BAMUtilities {
-	public static double calculateStandardizationRatio(File BAM) throws IOException {
+	
+	public static double calculateStandardizationRatio(File BAM, int read) throws IOException {
 		SamReader inputSam = SamReaderFactory.makeDefault().open(BAM);
 		AbstractBAMFileIndex bai = (AbstractBAMFileIndex) inputSam.indexing().getIndex();
-		double counter = 0;
 		double totalAligned = 0;
 		double totalGenome = 0;
 
@@ -23,20 +23,34 @@ public static double calculateStandardizationRatio(File BAM) throws IOException
 			totalAligned += inputSam.indexing().getIndex().getMetaData(x).getAlignedRecordCount();
 			totalGenome += seq.getSequenceLength();
 		}
+		
+		double READ1 = 0;
+		double READ2 = 0;
+		double MID = 0;
 		CloseableIterator<SAMRecord> iter = inputSam.iterator();
 		while (iter.hasNext()) {
 			SAMRecord sr = iter.next();
-			if(sr.getReadPairedFlag()) {
-				if(sr.getSecondOfPairFlag()) { counter++; } //count read 2 to remove from aligned reads
+			if(!sr.getReadUnmappedFlag()) { //Test for mappability
+				if(sr.getReadPairedFlag()) { //Test for paired-end status
+					if(sr.getSecondOfPairFlag()) { READ2++; } //count read 2
+					else if(sr.getFirstOfPairFlag()) { READ1++; } // count read 1
+					if(sr.getProperPairFlag() && sr.getFirstOfPairFlag()) { MID++; } //count properly paired reads
+				} else { //If the read is mapped but not paired-end, default to read 1
+					READ1++;
+				}
 			}
 		}
+		iter.close();
 		inputSam.close();
 		bai.close();
-		iter.close();
 
-		totalAligned -= counter;
+		//System.out.println("Genome Size: " + totalGenome + "\nTotal tags: " + totalAligned + "\nDetected Read 1: " + READ1 + "\nDetected Read 2: " + READ2 + "\nDetected Midpoints: " + MID);
+		if(read == 0) { totalAligned = READ1; }
+		else if(read == 1) { totalAligned = READ2; }
+		else if(read == 2) { totalAligned = READ1 + READ2; }
+		else if(read == 3) { totalAligned = MID; }
+
 		if(totalAligned > 0) { return (totalAligned / totalGenome); }
 		else { return 1; }
 	}
-	
 }