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Update PEStatOutput.java
Relating to issue #83, user interface does not notify user when stats can not be generated due to a missing BAI index. This commit pastes the BAI check code and if-statement from TagPileupOutput.
1 parent 07a3655 commit a84bf55

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Lines changed: 58 additions & 43 deletions

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‎src/window_interface/BAM_Statistics/PEStatOutput.java‎

Lines changed: 58 additions & 43 deletions
Original file line numberDiff line numberDiff line change
@@ -9,6 +9,7 @@
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import javax.swing.JFrame;
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import javax.swing.JLayeredPane;
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import javax.swing.JOptionPane;
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import javax.swing.JScrollPane;
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import javax.swing.JTabbedPane;
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import javax.swing.JTextArea;
@@ -74,53 +75,67 @@ public PEStatOutput(Vector<File> input, File o, boolean out, boolean dup, int mi
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}
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public void run() throws IOException {
77-
//Iterate through all BAM files in Vector
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// Check if BAI index file exists for all BAM files
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boolean[] BAMvalid = new boolean[bamFiles.size()];
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for (int z = 0; z < bamFiles.size(); z++) {
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File BAM = bamFiles.get(z); // Pull current BAM file
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File f = new File(BAM + ".bai"); // Generate file name for BAI index file
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if (!f.exists() || f.isDirectory()) {
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BAMvalid[z] = false;
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JOptionPane.showMessageDialog(null, "BAI Index File does not exist for: " + BAM.getName());
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System.err.println("BAI Index File does not exist for: " + BAM.getName());
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} else {
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BAMvalid[z] = true;
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}
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}
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//Iterate through all BAM files in Vector
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for(int x = 0; x < bamFiles.size(); x++) {
79-
// Construct Basename
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File OUT_BASENAME = null;
81-
if(OUTPUT_STATUS){
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try{
83-
if(OUT_DIR == null) { OUT_BASENAME = new File(bamFiles.get(x).getName().split("\\.")[0]); }
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else { OUT_BASENAME = new File( OUT_DIR.getCanonicalPath() + File.separator + bamFiles.get(x).getName().split("\\.")[0] ); }
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if (BAMvalid[x]) {
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// Construct Basename
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File OUT_BASENAME = null;
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if(OUTPUT_STATUS){
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try{
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if(OUT_DIR == null) { OUT_BASENAME = new File(bamFiles.get(x).getName().split("\\.")[0]); }
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else { OUT_BASENAME = new File( OUT_DIR.getCanonicalPath() + File.separator + bamFiles.get(x).getName().split("\\.")[0] ); }
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}
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catch (FileNotFoundException e) { e.printStackTrace(); }
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}
86-
catch (FileNotFoundException e) { e.printStackTrace(); }
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// catch (IOException e) { e.printStackTrace(); }
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}
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// Initialize PrintStream and TextArea for PE stats (insert sizes)
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PrintStream ps_insert = null;
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JTextArea PE_STATS = new JTextArea();
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PE_STATS.setEditable(false);
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ps_insert = new PrintStream(new CustomOutputStream( PE_STATS ));
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// Initialize PrintStream and TextArea for DUP stats
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PrintStream ps_dup = null;
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JTextArea DUP_STATS = new JTextArea();
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if(DUP_STATUS) {
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DUP_STATS.setEditable(false);
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ps_dup = new PrintStream(new CustomOutputStream( DUP_STATS ));
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}
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//Call public static method from scripts
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Vector<ChartPanel> charts = PEStats.getPEStats( OUT_BASENAME, bamFiles.get(x), DUP_STATUS, MIN_INSERT, MAX_INSERT, ps_insert, ps_dup, false );
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//Add pe stats to tabbed pane
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PE_STATS.setCaretPosition(0);
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JScrollPane pe_pane = new JScrollPane(PE_STATS, JScrollPane.VERTICAL_SCROLLBAR_ALWAYS, JScrollPane.HORIZONTAL_SCROLLBAR_AS_NEEDED);
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tabbedPane_InsertStats.add(bamFiles.get(x).getName(), pe_pane);
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tabbedPane_Histogram.add(bamFiles.get(x).getName(), charts.get(0));
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if(DUP_STATUS) {
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//Add duplication stats to tabbed pane
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DUP_STATS.setCaretPosition(0);
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JScrollPane dup_pane = new JScrollPane(DUP_STATS, JScrollPane.VERTICAL_SCROLLBAR_ALWAYS, JScrollPane.HORIZONTAL_SCROLLBAR_AS_NEEDED);
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tabbedPane_DupStats.add(bamFiles.get(x).getName(), dup_pane);
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tabbedPane_Duplication.add(bamFiles.get(x).getName(), charts.get(1));
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// Initialize PrintStream and TextArea for PE stats (insert sizes)
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PrintStream ps_insert = null;
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JTextArea PE_STATS = new JTextArea();
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PE_STATS.setEditable(false);
108+
ps_insert = new PrintStream(new CustomOutputStream( PE_STATS ));
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// Initialize PrintStream and TextArea for DUP stats
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PrintStream ps_dup = null;
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JTextArea DUP_STATS = new JTextArea();
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if(DUP_STATUS) {
113+
DUP_STATS.setEditable(false);
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ps_dup = new PrintStream(new CustomOutputStream( DUP_STATS ));
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}
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117+
//Call public static method from scripts
118+
Vector<ChartPanel> charts = PEStats.getPEStats( OUT_BASENAME, bamFiles.get(x), DUP_STATUS, MIN_INSERT, MAX_INSERT, ps_insert, ps_dup, false );
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120+
//Add pe stats to tabbed pane
121+
PE_STATS.setCaretPosition(0);
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JScrollPane pe_pane = new JScrollPane(PE_STATS, JScrollPane.VERTICAL_SCROLLBAR_ALWAYS, JScrollPane.HORIZONTAL_SCROLLBAR_AS_NEEDED);
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tabbedPane_InsertStats.add(bamFiles.get(x).getName(), pe_pane);
124+
tabbedPane_Histogram.add(bamFiles.get(x).getName(), charts.get(0));
125+
126+
if(DUP_STATUS) {
127+
//Add duplication stats to tabbed pane
128+
DUP_STATS.setCaretPosition(0);
129+
JScrollPane dup_pane = new JScrollPane(DUP_STATS, JScrollPane.VERTICAL_SCROLLBAR_ALWAYS, JScrollPane.HORIZONTAL_SCROLLBAR_AS_NEEDED);
130+
tabbedPane_DupStats.add(bamFiles.get(x).getName(), dup_pane);
131+
tabbedPane_Duplication.add(bamFiles.get(x).getName(), charts.get(1));
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}
133+
134+
if(ps_dup!=null) { ps_dup.close(); }
135+
ps_insert.close();
136+
137+
firePropertyChange("bam",x, x + 1);
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}
119-
120-
if(ps_dup!=null) { ps_dup.close(); }
121-
ps_insert.close();
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123-
firePropertyChange("bam",x, x + 1);
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}
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}
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}

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