fix PEStat GUI to execute on batch of BAM files

This update fixes the GUI PEStat bugs that cause the PEStat tool to quit execution after the first BAM file has its stats calculated. It also fixes the GUI so that BAM files without BAI do not interrupt execution of a set of BAMs.

window_interface/PEStatWindow
-fix default and base output directory information
window_interface/PEStatOutput
-fix default output filename
-rename output variables to be more specific (output directory vs output file basename)
-perform check so that close attempts are not made for null PrintStream objects
scripts/PEStats
-moved or stripped some unnecessary print statements
-display null charts when BAI does not exist (prevents thrown Exceptions that terminate execution of the whole set of BAM files prematurely)
-removed the redundant PrintStream close statements (remaining close statements in PEStatOutput class)

Author: owlang

src/scripts/BAM_Statistics/PEStats.java

@@ -27,7 +27,6 @@
 public class PEStats {
 
 	public static Vector<ChartPanel> getPEStats( File out_basename, File bamFile, boolean DUP_STATUS, int MIN_INSERT, int MAX_INSERT, PrintStream PS_INSERT, PrintStream PS_DUP, boolean SUM_STATUS ){
-		System.out.println("getPEStats called");
 		final SamReaderFactory factory = SamReaderFactory.makeDefault().enable(SamReaderFactory.Option.INCLUDE_SOURCE_IN_RECORDS, SamReaderFactory.Option.VALIDATE_CRC_CHECKSUMS).validationStringency(ValidationStringency.SILENT);
 
 		// Output Vecotr of Charts to be returned
@@ -40,6 +39,7 @@ public static Vector<ChartPanel> getPEStats( File out_basename, File bamFile, bo
 		PrintStream OUT_DUP = null;
 		File OUT_DUPPNG = null;
 
+		// Set output PrintStreams and PNG file objects
 		if( out_basename!=null ) {
 			try {
 				OUT_INSERT = new PrintStream(new File( out_basename.getCanonicalPath() + "_InsertHistogram.out"));
@@ -60,9 +60,7 @@ public static Vector<ChartPanel> getPEStats( File out_basename, File bamFile, bo
 		printBoth( null, OUT_INSERT_SUM, time );
 		printBoth( PS_INSERT, OUT_INSERT, time );
 		printBoth( PS_DUP, OUT_DUP, time );
-		
-		if(PS_DUP!=null){ PS_DUP.println("YO!"); }
-		
+
 		//Check if BAI index file exists
 		File f = new File(bamFile + ".bai");
 		if(f.exists() && !f.isDirectory()) {
@@ -77,6 +75,7 @@ public static Vector<ChartPanel> getPEStats( File out_basename, File bamFile, bo
 			//Code to get individual chromosome stats
 			SamReader reader = factory.open(bamFile);
 			AbstractBAMFileIndex bai = (AbstractBAMFileIndex) reader.indexing().getIndex();
+			System.out.println(bamFile);
 
 			//Variables to keep track of insert size histogram
 			double InsertAverage = 0;
@@ -197,13 +196,13 @@ public static Vector<ChartPanel> getPEStats( File out_basename, File bamFile, bo
 			try{
 				charts.add( 0, Histogram.createBarChart(HIST, DOMAIN, OUT_INSPNG) );
 			}catch( IOException e ){ e.printStackTrace(); }
-			
+
+			//Duplication statistics
 			if(DUP_STATUS) {
-				//Duplication statistics
 				double UNIQUE_MOLECULES = 0;
 				String[] BIN_NAME = initializeBIN_Names();
 				ArrayList<Double> BIN = new ArrayList<Double>();
-				initializeBINS(BIN);	
+				initializeBINS(BIN);
 
 				Iterator<Integer> keys = ALL_COMPLEXITY.keySet().iterator();
 				while(keys.hasNext()) {
@@ -223,14 +222,13 @@ public static Vector<ChartPanel> getPEStats( File out_basename, File bamFile, bo
 					charts.add( 1, LineChart.createLineChart(BIN, BIN_NAME, OUT_DUPPNG) );
 				}catch( IOException e ){ e.printStackTrace(); }
 			}
-			
 		} else {
+			charts.add(0, new ChartPanel(null));
+			charts.add(1, new ChartPanel(null));
 			printBoth( PS_INSERT, OUT_INSERT, "BAI Index File does not exist for: " + bamFile.getName() );
 			printBoth( System.err, OUT_INSERT_SUM, "BAI Index File does not exist for: " + bamFile.getName() );
 			printBoth( PS_DUP, OUT_DUP, "BAI Index File does not exist for: " + bamFile.getName() );
 		}
-		if(PS_INSERT != null){ PS_INSERT.close(); }
-		if(PS_DUP!=null){ PS_DUP.close(); }
 
 		if(OUT_INSERT != null){ OUT_INSERT.close(); }
 		if(OUT_INSERT_SUM!=null){ OUT_INSERT_SUM.close(); }

src/window_interface/BAM_Statistics/PEStatOutput.java

@@ -23,7 +23,7 @@
 public class PEStatOutput extends JFrame {
 
 	Vector<File> bamFiles = null;
-	private File OUTPUT_PATH = null;
+	private File OUT_DIR = null;
 	private boolean OUTPUT_STATUS = false;
 	private boolean DUP_STATUS = false;
 	private static int MIN_INSERT = 0;
@@ -54,7 +54,7 @@ public PEStatOutput(Vector<File> input, File o, boolean out, boolean dup, int mi
 		layeredPane.add(tabbedPane);
 
 		bamFiles = input;
-		OUTPUT_PATH = o;
+		OUT_DIR = o;
 		OUTPUT_STATUS = out;
 		DUP_STATUS = dup;
 		MIN_INSERT = min;
@@ -76,17 +76,17 @@ public PEStatOutput(Vector<File> input, File o, boolean out, boolean dup, int mi
 	public void run() throws IOException {
 		//Iterate through all BAM files in Vector	
 		for(int x = 0; x < bamFiles.size(); x++) {
-			
 			// Construct Basename
-			File NAME = null;
+			File OUT_BASENAME = null;
 			if(OUTPUT_STATUS){
 				try{
-					NAME = new File( bamFiles.get(x).getName().split("\\.")[0] );
-					if(OUTPUT_PATH != null){ NAME = new File( OUTPUT_PATH.getCanonicalPath() + File.separator + NAME.getCanonicalPath() ); }
+					if(OUT_DIR == null) { OUT_BASENAME = new File(bamFiles.get(x).getName().split("\\.")[0]); }
+					else { OUT_BASENAME = new File( OUT_DIR.getCanonicalPath() + File.separator + bamFiles.get(x).getName().split("\\.")[0] ); }
 				}
 				catch (FileNotFoundException e) { e.printStackTrace(); }
 // 				catch (IOException e) {	e.printStackTrace(); }
 			}
+			
 			// Initialize PrintStream and TextArea for PE stats (insert sizes)
 			PrintStream ps_insert = null;
 			JTextArea PE_STATS = new JTextArea();
@@ -99,9 +99,9 @@ public void run() throws IOException {
 				DUP_STATS.setEditable(false);
 				ps_dup = new PrintStream(new CustomOutputStream( DUP_STATS ));
 			}
-			
+
 			//Call public static method from scripts
-			Vector<ChartPanel> charts = PEStats.getPEStats( NAME, bamFiles.get(x), DUP_STATUS, MIN_INSERT, MAX_INSERT, ps_insert, ps_dup, false );
+			Vector<ChartPanel> charts = PEStats.getPEStats( OUT_BASENAME, bamFiles.get(x), DUP_STATUS, MIN_INSERT, MAX_INSERT, ps_insert, ps_dup, false );
 
 			//Add pe stats to tabbed pane
 			PE_STATS.setCaretPosition(0);
@@ -117,7 +117,7 @@ public void run() throws IOException {
 				tabbedPane_Duplication.add(bamFiles.get(x).getName(), charts.get(1));
 			}
 
-			ps_dup.close();
+			if(ps_dup!=null) { ps_dup.close(); }
 			ps_insert.close();
 
 			firePropertyChange("bam",x, x + 1);	

src/window_interface/BAM_Statistics/PEStatWindow.java

@@ -52,7 +52,7 @@ public class PEStatWindow extends JFrame implements ActionListener, PropertyChan
 
 	final DefaultListModel<String> expList;
 	Vector<File> BAMFiles = new Vector<File>();
-	private File OUTPUT_PATH = null;
+	private File OUTPUT_PATH = new File(System.getProperty("user.dir"));
 
 	JProgressBar progressBar;
 	public Task task;
@@ -72,7 +72,7 @@ public void propertyChange(PropertyChangeEvent propertyChangeEvent) {
 			        	setProgress(percentComplete);
 				     }
 				 });
-				stat.setVisible(true);				
+				stat.setVisible(true);
 				stat.run();
 			} catch(NumberFormatException nfe){
 				JOptionPane.showMessageDialog(null, "Input Fields Must Contain Integers");