diff --git a/src/main/java/org/igv/batch/CommandExecutor.java b/src/main/java/org/igv/batch/CommandExecutor.java
old mode 100755
new mode 100644
index 631509e046..b368e633df
--- a/src/main/java/org/igv/batch/CommandExecutor.java
+++ b/src/main/java/org/igv/batch/CommandExecutor.java
@@ -1,7 +1,3 @@
-/*
- * To change this template, choose Tools | Templates
- * and open the template in the editor.
- */
 
 package org.igv.batch;
 
diff --git a/src/main/java/org/igv/bedpe/ContactMapView.java b/src/main/java/org/igv/bedpe/ContactMapView.java
new file mode 100644
index 0000000000..cf6497c201
--- /dev/null
+++ b/src/main/java/org/igv/bedpe/ContactMapView.java
@@ -0,0 +1,780 @@
+package org.igv.bedpe;
+
+import org.igv.Globals;
+import org.igv.event.IGVEvent;
+import org.igv.event.IGVEventBus;
+import org.igv.event.IGVEventObserver;
+import org.igv.event.ViewChange;
+import org.igv.hic.ContactRecord;
+import org.igv.hic.HicFile;
+import org.igv.hic.Region;
+import org.igv.renderer.ContinuousColorScale;
+import org.igv.ui.panel.ReferenceFrame;
+import org.igv.ui.panel.RulerPanel;
+
+import javax.swing.*;
+import java.awt.*;
+import java.awt.event.*;
+import java.awt.image.BufferedImage;
+import java.io.IOException;
+import java.util.HashMap;
+import java.util.List;
+import java.util.Map;
+import java.util.concurrent.ExecutorService;
+import java.util.concurrent.Executors;
+import java.util.concurrent.Future;
+import java.util.stream.Collectors;
+
+public class ContactMapView extends JPanel implements IGVEventObserver {
+
+    private InteractionTrack track;
+    private HicFile hicFile;
+    private String normalization;
+    private Color color;
+    private Map<String, ContinuousColorScale> colorScaleCache = new HashMap<>();  // Key: "normalization_binSize"
+    private Map<String, String> colorScaleDataKeys = new HashMap<>();  // Tracks which data cache key was used for each color scale
+    private ReferenceFrame frame;  // Current genomic region frame (dynamic)
+    private int binSize; // Bin size for the current genomic region (dynamic)
+    private int startBin; // Start bin for the current genomic region (dynamic)
+    private int nBins;  // Number of map bins for the current genomic region (dynamic)
+    private RulerPanel rulerPanel;  // Reference to ruler panel for synchronized updates
+    private JTextField maxField;
+    private JSlider maxSlider;
+    private double sliderMinValue = 0;
+    private double sliderMaxValue = 100;
+
+    // Cached data for rendering
+    private volatile List<ContactRecord> cachedRecords;
+    private volatile boolean isLoading = false;
+    private volatile String loadingError = null;
+
+    // Background executor for data fetching
+    private final ExecutorService dataFetchExecutor = Executors.newSingleThreadExecutor();
+    private Future<?> currentFetchTask;
+
+    // Cache key to detect when data needs to be refetched
+    private volatile String dataCacheKey = null;
+
+    public ContactMapView(InteractionTrack track, HicFile hicFile, String normalization, ReferenceFrame frame, Color color) {
+
+        this.track = track;
+        this.hicFile = hicFile;
+        this.normalization = normalization;
+        this.frame = frame;
+        this.color = color;
+        binSize = hicFile.getBinSize(frame.getChrName(), frame.getScale());
+        startBin = (int) (frame.getOrigin() / binSize);
+
+        // Adjust frame to align with bin boundaries
+        int endBin = (int) (frame.getEnd() / binSize);
+        int nBins = endBin - startBin;
+        this.nBins = nBins;  // Store the initial number of bins
+        frame.setOrigin(startBin * binSize);
+        frame.setScale(binSize);
+        frame.setWidthInPixels(nBins);
+
+        // Set initial preferred size but don't constrain min/max to allow resizing
+        setPreferredSize(new Dimension(nBins, nBins));
+
+        // Add component listener to handle resize events
+        this.addComponentListener(new ComponentAdapter() {
+            @Override
+            public void componentResized(ComponentEvent e) {
+                updateFrameForSize();
+                if (rulerPanel != null) {
+                    rulerPanel.repaint();
+                }
+                repaint();
+            }
+        });
+
+        this.addMouseMotionListener(new MouseMotionAdapter() {
+            @Override
+            public void mouseMoved(MouseEvent e) {
+                super.mouseMoved(e);
+                // Calculate coordinates based on current scale
+                double scaleFactor = (double) getWidth() / ContactMapView.this.nBins;
+                int binX = (int) (e.getX() / scaleFactor) + startBin;
+                int binY = (int) (e.getY() / scaleFactor) + startBin;
+                int coordX = binX * binSize + binSize / 2;
+                int coordY = binY * binSize + binSize / 2;
+                track.setMarkerBounds(new int[]{coordX, coordY});
+
+                //String tooltip = String.format("Bin1: %d (Coord: %d), Bin2: %d (Coord: %d)", binX, coordX, binY, coordY);
+                //setToolTipText(tooltip);
+            }
+        });
+
+        this.addMouseListener(new MouseAdapter() {
+            @Override
+            public void mouseExited(MouseEvent e) {
+                super.mouseExited(e);
+                track.setMarkerBounds(null);
+            }
+        });
+
+        track.setContactMapView(this);
+
+        // Initial data fetch
+        fetchDataAsync();
+
+        IGVEventBus.getInstance().subscribe(ViewChange.class, this);
+    }
+
+    /**
+     * Generate a cache key based on current view parameters.
+     * If this key changes, we need to refetch data.
+     */
+    private String generateCacheKey() {
+        return String.format("%s:%d:%d:%d:%s",
+                frame.getChrName(),
+                (int) frame.getOrigin(),
+                (int) frame.getEnd(),
+                binSize,
+                normalization);
+    }
+
+    /**
+     * Generate a compound key for the color scale cache.
+     * Combines normalization and binSize so each combination has its own cached color scale.
+     */
+    private String getColorScaleCacheKey() {
+        return normalization + "_" + binSize;
+    }
+
+    /**
+     * Fetch contact records asynchronously in a background thread.
+     * When complete, triggers a repaint on the EDT.
+     */
+    private void fetchDataAsync() {
+        String newCacheKey = generateCacheKey();
+
+        // Check if we already have valid cached data
+        if (newCacheKey.equals(dataCacheKey) && cachedRecords != null && !isLoading) {
+            return; // Data is already cached
+        }
+
+        // Cancel any pending fetch task
+        if (currentFetchTask != null && !currentFetchTask.isDone()) {
+            currentFetchTask.cancel(true);
+        }
+
+        isLoading = true;
+        loadingError = null;
+        // DON'T update dataCacheKey yet - only update it when data actually arrives
+        // This prevents the race condition where dataMatchesCurrentView returns true
+        // but we're still using stale cachedRecords
+
+        // Trigger repaint to show loading indicator
+        repaint();
+
+        // Capture current state for the background thread
+        final String chrName = frame.getChrName();
+        final int origin = (int) frame.getOrigin();
+        final int end = (int) frame.getEnd();
+        final int currentBinSize = binSize;
+        final String fetchCacheKey = newCacheKey;
+
+        currentFetchTask = dataFetchExecutor.submit(() -> {
+            try {
+                Region region = new Region(chrName, origin, end);
+                List<ContactRecord> records = hicFile.getContactRecords(
+                        region,
+                        region,
+                        "BP",
+                        currentBinSize,
+                        normalization,
+                        true
+                );
+
+                // Update cache on EDT to avoid race conditions
+                SwingUtilities.invokeLater(() -> {
+                    // Always update - we have fresh data for this fetch
+                    cachedRecords = records;
+                    dataCacheKey = fetchCacheKey;  // NOW update dataCacheKey with the fresh data
+                    isLoading = false;
+                    loadingError = null;
+                    repaint();
+                });
+
+            } catch (IOException e) {
+                SwingUtilities.invokeLater(() -> {
+                    dataCacheKey = fetchCacheKey;  // Update cache key even on error
+                    isLoading = false;
+                    loadingError = e.getMessage();
+                    repaint();
+                });
+            } catch (Exception e) {
+                SwingUtilities.invokeLater(() -> {
+                    dataCacheKey = fetchCacheKey;  // Update cache key even on error
+                    isLoading = false;
+                    loadingError = "Unexpected error: " + e.getMessage();
+                    repaint();
+                });
+            }
+        });
+    }
+
+    /**
+     * Shutdown the executor service. Should be called when the view is disposed.
+     */
+    public void dispose() {
+        // Cancel any pending fetch task
+        if (currentFetchTask != null) {
+            currentFetchTask.cancel(true);
+        }
+
+        // Gracefully shutdown the executor
+        dataFetchExecutor.shutdown();
+        try {
+            // Wait up to 2 seconds for current task to complete
+            if (!dataFetchExecutor.awaitTermination(2, java.util.concurrent.TimeUnit.SECONDS)) {
+                // Force shutdown if task doesn't complete in time
+                dataFetchExecutor.shutdownNow();
+            }
+        } catch (InterruptedException e) {
+            // If interrupted while waiting, force shutdown
+            dataFetchExecutor.shutdownNow();
+            Thread.currentThread().interrupt();
+        }
+    }
+
+    /**
+     * Change the genomic position by supplying a new ReferenceFrame.
+     * The frame will be adjusted to align with bin boundaries of the hicFile.
+     * If the bin size changes, the frame scale is adjusted to fit the specified
+     * genomic range within the existing component size (no resize).
+     *
+     * @param newFrame the new ReferenceFrame specifying the genomic region to display
+     */
+    public void setReferenceFrame(ReferenceFrame newFrame) {
+
+        String currentChr = frame.getChrName();
+
+        // Recalculate bin size for the new frame's scale
+        int newBinSize = hicFile.getBinSize(newFrame.getChrName(), newFrame.getScale());
+
+        if (newBinSize == binSize && newFrame.getChrName().equals(currentChr)) {
+            // No change in bin size or chromosome, just update frame's origin
+            // Update startBin to match the new origin
+            startBin = (int) (newFrame.getOrigin() / binSize);
+            frame.setOrigin(startBin * binSize);
+
+            // Update frame end based on initialNBins
+            int endBin = startBin + nBins;
+            int genomicEnd = endBin * binSize;
+
+            // Don't update frame.setEnd() as it's calculated, just ensure scale is correct
+            updateFrameForSize();
+
+            fetchDataAsync();
+            return;
+        }
+
+        // Update to the new frame
+        this.frame = new ReferenceFrame(newFrame);
+        binSize = newBinSize;
+
+        // Calculate how many bins are needed to span the requested genomic range
+        int genomicSpan = (int) (newFrame.getEnd() - newFrame.getOrigin());
+        int requestedNBins = (int) Math.ceil((double) genomicSpan / binSize);
+
+        // Use the requested number of bins (this represents the genomic span)
+        nBins = requestedNBins;
+
+        // Align to bin boundaries - startBin is the first bin we'll display
+        startBin = (int) (newFrame.getOrigin() / binSize);
+
+        // Set frame origin to align with bin boundaries
+        frame.setOrigin(startBin * binSize);
+
+        // The end is determined by the requested genomic span
+        int endBin = startBin + nBins;
+
+        // Set the frame scale and width based on the requested region
+        frame.setScale(binSize);
+        frame.setWidthInPixels(nBins);
+
+        // Update the frame scale to fit the requested genomic span in the current component width
+        // This will adjust the scale so the genomic region fits in the available pixels
+        updateFrameForSize();
+
+        // Trigger async data fetch
+        fetchDataAsync();
+
+        // Trigger repaint to show the new region
+        if (rulerPanel != null) {
+            rulerPanel.repaint();
+        }
+        repaint();
+    }
+
+    /**
+     * Update the ReferenceFrame scale and widthInPixels based on the current component size.
+     * This allows the view to be responsive to window resizing while maintaining the same genomic region.
+     */
+    private void updateFrameForSize() {
+        int currentWidth = getWidth();
+        if (currentWidth <= 0) return;
+
+        // Calculate the scale factor: how many pixels per bin
+        double pixelsPerBin = (double) currentWidth / nBins;
+
+        // Update the frame's scale to reflect the new pixels-per-base-pair ratio
+        // Scale is base pairs per pixel, so we need binSize / pixelsPerBin
+        double newScale = binSize / pixelsPerBin;
+        frame.setScale(newScale);
+
+        // Update width in pixels to match the current component width
+        frame.setWidthInPixels(currentWidth);
+    }
+
+    @Override
+    public Dimension getPreferredSize() {
+        // Maintain square aspect ratio
+        Dimension pref = super.getPreferredSize();
+        int size = Math.min(pref.width, pref.height);
+        return new Dimension(size, size);
+    }
+
+    @Override
+    public Dimension getMinimumSize() {
+        // Maintain square aspect ratio with a reasonable minimum
+        int minSize = Math.max(100, nBins / 10);
+        return new Dimension(minSize, minSize);
+    }
+
+    @Override
+    public Dimension getMaximumSize() {
+        // Maintain square aspect ratio
+        Dimension max = super.getMaximumSize();
+        int size = Math.min(max.width, max.height);
+        return new Dimension(size, size);
+    }
+
+    @Override
+    public void setBounds(int x, int y, int width, int height) {
+        // Force square dimensions by using the smaller of width/height
+        int size = Math.min(width, height);
+        super.setBounds(x, y, size, size);
+    }
+
+    @Override
+    protected void paintComponent(Graphics g) {
+        super.paintComponent(g);
+        Graphics2D g2D = (Graphics2D) g.create();
+        try {
+            if (isLoading) {
+                // Show loading indicator
+                drawLoadingIndicator(g2D);
+            } else if (loadingError != null) {
+                // Show error message
+                g2D.setColor(Color.RED);
+                g2D.drawString("Error: " + loadingError, 10, 20);
+            } else if (cachedRecords != null) {
+                // Render from cached data
+                Image img = renderMapFromCache();
+                if (img != null) {
+                    g2D.drawImage(img, 0, 0, null);
+                }
+            }
+        } finally {
+            g2D.dispose();
+        }
+    }
+
+    /**
+     * Draw a loading indicator while data is being fetched.
+     */
+    private void drawLoadingIndicator(Graphics2D g2D) {
+        int width = getWidth();
+        int height = getHeight();
+
+        // Draw semi-transparent overlay if we have cached data
+        if (cachedRecords != null) {
+            Image img = renderMapFromCache();
+            if (img != null) {
+                g2D.drawImage(img, 0, 0, null);
+            }
+            g2D.setColor(new Color(255, 255, 255, 128));
+            g2D.fillRect(0, 0, width, height);
+        }
+
+        // Draw loading text
+        g2D.setColor(Color.DARK_GRAY);
+        String message = "Loading...";
+        FontMetrics fm = g2D.getFontMetrics();
+        int textWidth = fm.stringWidth(message);
+        int textHeight = fm.getHeight();
+        g2D.drawString(message, (width - textWidth) / 2, (height + textHeight) / 2);
+    }
+
+    /**
+     * Render the contact map from cached data.
+     * This is called from paintComponent and only uses cached data.
+     */
+    private Image renderMapFromCache() {
+        if (cachedRecords == null) {
+            return null;
+        }
+
+        int width = getWidth();
+        int height = getHeight();
+
+        if (width <= 0 || height <= 0) {
+            return null;
+        }
+
+        BufferedImage img = new BufferedImage(width, height, BufferedImage.TYPE_INT_ARGB);
+
+        // Calculate scale factor for rendering
+        double scaleFactor = (double) width / nBins;
+
+        String colorScaleKey = getColorScaleCacheKey();
+        ContinuousColorScale colorScale = colorScaleCache.get(colorScaleKey);
+
+        // Check if the cached records match the current view parameters
+        // If they don't, we have stale data and shouldn't compute a new color scale yet
+        String currentCacheKey = generateCacheKey();
+        boolean dataMatchesCurrentView = currentCacheKey.equals(dataCacheKey);
+
+        // Check if this color scale was computed from the current data
+        String colorScaleDataKey = colorScaleDataKeys.get(colorScaleKey);
+        boolean colorScaleNeedsUpdate = colorScale == null || !currentCacheKey.equals(colorScaleDataKey);
+
+        // We need to compute/recompute the color scale if:
+        // 1. No color scale exists for this key, OR
+        // 2. The color scale exists but was computed from different data
+        if (dataMatchesCurrentView && colorScaleNeedsUpdate) {
+            // We have fresh data and need to compute/update color scale from it
+            // First, compute the percentile and update slider range
+            double upper = computePercentileOnly(cachedRecords, .5);
+
+            if (colorScale == null) {
+                // Create new color scale
+                Color lowerColor = Globals.isDarkMode() ? Color.BLACK : Color.WHITE;
+                colorScale = new ContinuousColorScale(0, upper, lowerColor, color);
+                colorScaleCache.put(colorScaleKey, colorScale);
+            } else {
+                // Update existing color scale with new max value
+                colorScale.setPosEnd(upper);
+            }
+
+            // Track that this color scale was computed from the current data
+            colorScaleDataKeys.put(colorScaleKey, currentCacheKey);
+
+            // Now update text field and slider position based on the new color scale
+            maxField.setText(String.format("%.2f", colorScale.getMaximum()));
+            updateSliderFromValue(colorScale.getMaximum());
+        } else if (colorScale == null) {
+            // We don't have fresh data and no color scale exists
+            // Just return null and wait for fresh data
+            return null;
+        }
+
+
+        // paint pixels directly with scaling
+        for (ContactRecord record : cachedRecords) {
+            int binX = record.bin1() - startBin;
+            int binY = record.bin2() - startBin;
+
+            // Scale the bin positions to pixel positions
+            int x = (int) (binX * scaleFactor);
+            int y = (int) (binY * scaleFactor);
+
+            if (x >= 0 && y >= 0) {
+                Color color = colorScale.getColor(record.counts());
+
+                // Calculate the size of each scaled bin
+                int pixelSize = Math.max(1, (int) Math.ceil(scaleFactor));
+
+                // Fill the scaled pixel area
+                for (int dx = 0; dx < pixelSize && (x + dx) < width; dx++) {
+                    for (int dy = 0; dy < pixelSize && (y + dy) < height; dy++) {
+                        if ((x + dx) < width && (y + dy) < height) {
+                            img.setRGB(x + dx, y + dy, color.getRGB());
+                        }
+                        // Mirror for symmetry
+                        if ((y + dx) < width && (x + dy) < height) {
+                            img.setRGB(y + dx, x + dy, color.getRGB());
+                        }
+                    }
+                }
+            }
+        }
+
+        return img;
+    }
+
+    /**
+     * Open the ContactMatrixView in a simple popup JFrame. The frame is created with DISPOSE_ON_CLOSE
+     * so closing it won't exit the application.
+     */
+    public static void showPopup(InteractionTrack track, HicFile hicFile, String normalization, ReferenceFrame frame, Color color) {
+
+        ReferenceFrame refFrame = new ReferenceFrame(frame);
+
+        SwingUtilities.invokeLater(() -> {
+            JFrame jf = new JFrame(track.getDisplayName());
+            jf.setDefaultCloseOperation(JFrame.DISPOSE_ON_CLOSE);
+
+            // Main panel with a border layout
+            JPanel mainPanel = new JPanel(new BorderLayout());
+
+            // ContactMatrixView
+            ContactMapView contactMapView = new ContactMapView(track, hicFile, normalization, refFrame, color);
+            mainPanel.add(contactMapView, BorderLayout.CENTER);
+
+            // Create a panel to hold both the control panel and ruler panel
+            JPanel topPanel = new JPanel(new BorderLayout());
+
+            // Control panel with color scale max adjustment
+            JPanel controlPanel = contactMapView.createControlPanel();
+            topPanel.add(controlPanel, BorderLayout.NORTH);
+
+            // RulerPanel
+            RulerPanel rulerPanel = new RulerPanel(refFrame);
+            Dimension rulerSize = new Dimension(contactMapView.getPreferredSize().width, 50);
+            rulerPanel.setPreferredSize(rulerSize);
+            topPanel.add(rulerPanel, BorderLayout.CENTER);
+
+            mainPanel.add(topPanel, BorderLayout.NORTH);
+
+            // Store ruler panel reference for synchronized updates
+            contactMapView.rulerPanel = rulerPanel;
+
+            // Add component listener to keep ruler panel width in sync with contact matrix view
+            contactMapView.addComponentListener(new ComponentAdapter() {
+                @Override
+                public void componentResized(ComponentEvent e) {
+                    int width = contactMapView.getWidth();
+                    rulerPanel.setPreferredSize(new Dimension(width, 50));
+                    rulerPanel.revalidate();
+                }
+            });
+
+            // Add window listener to unsubscribe from event bus when window closes
+            jf.addWindowListener(new WindowAdapter() {
+                @Override
+                public void windowClosing(WindowEvent e) {
+                    IGVEventBus.getInstance().unsubscribe(contactMapView);
+                    contactMapView.dispose();
+                    track.setContactMapView(null);
+                }
+            });
+
+            jf.getContentPane().add(mainPanel);
+            jf.pack();
+            jf.setLocationRelativeTo(null);
+            jf.setVisible(true);
+        });
+    }
+
+    /**
+     * Create a control panel with input controls for adjusting visualization parameters.
+     * Currently includes a max value control for the color scale with both slider and text field.
+     * This panel can be extended with additional controls in the future.
+     */
+    private JPanel createControlPanel() {
+        JPanel controlPanel = new JPanel(new FlowLayout(FlowLayout.LEFT));
+        controlPanel.setBorder(BorderFactory.createEmptyBorder(5, 5, 5, 5));
+
+        // Label for max value
+        JLabel maxLabel = new JLabel("Color Scale Max:");
+        controlPanel.add(maxLabel);
+
+        // Slider for max value - instance variable for this view
+        // Initial range 0-100, will be updated dynamically
+        this.maxSlider = new JSlider(0, 100, 50);
+        this.maxSlider.setPreferredSize(new Dimension(200, 25));
+        this.maxSlider.setToolTipText(String.format("Range: %.2f - %.2f", sliderMinValue, sliderMaxValue));
+        this.maxSlider.addChangeListener(e -> {
+            if (!this.maxSlider.getValueIsAdjusting()) {
+                // Map slider value (0-100) to actual range (sliderMinValue to sliderMaxValue)
+                double value = sliderMinValue + (sliderMaxValue - sliderMinValue) * this.maxSlider.getValue() / 100.0;
+                this.maxField.setText(String.format("%.2f", value));
+
+                // Update tooltip to show current value
+                this.maxSlider.setToolTipText(String.format("Value: %.2f (Range: %.2f - %.2f)",
+                        value, sliderMinValue, sliderMaxValue));
+
+                // Update the color scale
+                String colorScaleKey = getColorScaleCacheKey();
+                ContinuousColorScale colorScale = this.colorScaleCache.get(colorScaleKey);
+                if (colorScale != null) {
+                    colorScale.setPosEnd(value);
+                    this.repaint();
+                }
+            }
+        });
+        controlPanel.add(this.maxSlider);
+
+        // Text field for max value - instance variable for this view
+        this.maxField = new JTextField("10", 10);
+        this.maxField.addActionListener(e -> {
+            try {
+                double newMax = Double.parseDouble(this.maxField.getText().trim());
+                String colorScaleKey = getColorScaleCacheKey();
+                ContinuousColorScale colorScale = this.colorScaleCache.get(colorScaleKey);
+                if (colorScale != null) {
+                    colorScale.setPosEnd(newMax);
+                    this.maxField.setText(String.format("%.2f", newMax));
+
+                    // Update slider position based on text field value
+                    updateSliderFromValue(newMax);
+
+                    this.repaint();
+                }
+            } catch (NumberFormatException ex) {
+                JOptionPane.showMessageDialog(controlPanel,
+                        "Invalid number format. Please enter a valid number.",
+                        "Input Error",
+                        JOptionPane.ERROR_MESSAGE);
+            }
+        });
+        controlPanel.add(this.maxField);
+
+        // Apply button
+        JButton applyButton = new JButton("Apply");
+        applyButton.addActionListener(e -> {
+            try {
+                String colorScaleKey = getColorScaleCacheKey();
+                ContinuousColorScale colorScale = this.colorScaleCache.get(colorScaleKey);
+                double newMax = Double.parseDouble(this.maxField.getText().trim());
+                if (colorScale != null) {
+                    colorScale.setPosEnd(newMax);
+                    // Update the maxField value with the newMax
+                    this.maxField.setText(String.format("%.2f", newMax));
+
+                    // Update slider position based on text field value
+                    updateSliderFromValue(newMax);
+
+                    this.repaint();
+                }
+            } catch (NumberFormatException ex) {
+                JOptionPane.showMessageDialog(controlPanel,
+                        "Invalid number format. Please enter a valid number.",
+                        "Input Error",
+                        JOptionPane.ERROR_MESSAGE);
+            }
+        });
+        controlPanel.add(applyButton);
+
+        return controlPanel;
+    }
+
+    /**
+     * Update slider position based on a value within the current range.
+     * If value exceeds sliderMaxValue, expand the range.
+     */
+    private void updateSliderFromValue(double value) {
+        // Expand slider range if value exceeds current maximum
+        if (value > sliderMaxValue) {
+            sliderMaxValue = value;
+        }
+
+        if (sliderMaxValue > sliderMinValue) {
+            double normalized = (value - sliderMinValue) / (sliderMaxValue - sliderMinValue);
+            int sliderPos = (int) Math.round(normalized * 100);
+            sliderPos = Math.max(0, Math.min(100, sliderPos)); // Clamp to 0-100
+            this.maxSlider.setValue(sliderPos);
+
+            // Update tooltip to show current value and range
+            this.maxSlider.setToolTipText(String.format("Value: %.2f (Range: %.2f - %.2f)",
+                    value, sliderMinValue, sliderMaxValue));
+        }
+    }
+
+    /**
+     * Update the slider range based on min and max values from the filtered data.
+     */
+    private void updateSliderRange(double minValue, double maxValue) {
+        this.sliderMinValue = minValue;
+        this.sliderMaxValue = maxValue;
+
+        // Update slider position to maintain current value if possible
+        String colorScaleKey = getColorScaleCacheKey();
+        ContinuousColorScale colorScale = this.colorScaleCache.get(colorScaleKey);
+        if (colorScale != null) {
+            updateSliderFromValue(colorScale.getMaximum());
+        }
+    }
+
+    /**
+     * Format bin size for display (e.g., 1000 -> "1 kb", 1000000 -> "1 Mb")
+     */
+    private static String formatBinSize(int binSize) {
+        if (binSize >= 1000000) {
+            return String.format("%.1f Mb", binSize / 1000000.0);
+        } else if (binSize >= 1000) {
+            return String.format("%.1f kb", binSize / 1000.0);
+        } else {
+            return binSize + " bp";
+        }
+    }
+
+    @Override
+    public void receiveEvent(IGVEvent event) {
+        if (event instanceof ViewChange) {
+            ViewChange vc = (ViewChange) event;
+            if (!vc.panning) {
+                setReferenceFrame(vc.referenceFrame);
+            }
+        }
+    }
+
+    /**
+     * Compute a percentile of the "counts" value in contactRecords,
+     * filtering records where Math.abs(bin2 - bin1) < 5.
+     * Also updates the slider range based on the min/max of filtered counts.
+     * Does NOT update the slider position - caller should do that after updating the color scale.
+     *
+     * @return the percentile value, or -1 if contactRecords is empty
+     */
+    private double computePercentileOnly(List<ContactRecord> contactRecords, double percentile) {
+        if (contactRecords == null || contactRecords.isEmpty()) {
+            return -1; // Return -1 if there are no records
+        }
+
+        // Filter records where Math.abs(bin2 - bin1) < 5
+        List<Float> counts = contactRecords.stream()
+                .filter(record -> Math.abs(record.bin2() - record.bin1()) < 5)
+                .map(ContactRecord::counts)
+                .sorted()
+                .collect(Collectors.toList());
+
+        if (counts.isEmpty()) {
+            return -1; // Return -1 if no records pass the filter
+        }
+
+        int index = (int) Math.ceil(percentile * counts.size()) - 1;
+        float midCount = counts.get(index);
+
+        // Update slider range based on min and max of filtered counts
+        float minCount = counts.get(0);
+        float maxCount = 2 * midCount;
+        this.sliderMinValue = minCount;
+        this.sliderMaxValue = maxCount;
+
+
+        return midCount;
+    }
+
+    public void setNormalization(String type) {
+        if (this.normalization != null && this.normalization.equals(type)) {
+            return; // No change
+        }
+
+        this.normalization = type;
+
+        // Clear cached data since normalization affects the contact record values
+        this.cachedRecords = null;
+        this.dataCacheKey = null;
+
+        // No need to clear colorScaleCache since it uses compound keys (normalization_binSize)
+        // Each normalization + binSize combination maintains its own color scale
+
+        // Trigger async data fetch with new normalization
+        fetchDataAsync();
+    }
+}
diff --git a/src/main/java/org/igv/bedpe/HicSource.java b/src/main/java/org/igv/bedpe/HicSource.java
index 1aaab47ed8..1fff8bd8db 100644
--- a/src/main/java/org/igv/bedpe/HicSource.java
+++ b/src/main/java/org/igv/bedpe/HicSource.java
@@ -34,7 +34,7 @@ public HicSource(String path, Genome genome) throws IOException {
     @Override
     public List<BedPE> getFeatures(String chr, int start, int end, double bpPerPixel, String normalization, int maxFeatureCount) throws IOException {
 
-        final int binSize = getBinSize(chr, bpPerPixel);
+        final int binSize = hicFile.getBinSize(chr, bpPerPixel);
 
         List<ContactRecord> records = getRecords(chr, start, end, binSize);
 
@@ -159,26 +159,6 @@ public List<BedPE> getFeatures(String chr, int start, int end, double bpPerPixel
         return features;
     }
 
-    private int getBinSize(String chr, double bpPerPixel) {
-
-        if("all".equalsIgnoreCase(chr)) {
-            // Special case, the whole-genome psuedo-chromosome all has a single resolution
-            return hicFile.getWGResolution();
-        }
-
-        // choose resolution
-        List<Integer> resolutions = hicFile.getBpResolutions();
-        int index = 0;
-        for (int i = resolutions.size() - 1; i >= 0; i--) {
-            if (resolutions.get(i) >= bpPerPixel) {
-                index = i;
-                break;
-            }
-        }
-        int binSize = resolutions.get(index);
-        return binSize;
-    }
-
     @Override
     public List<String> getNormalizationTypes() {
         return hicFile.getNormalizationTypes();
@@ -186,7 +166,7 @@ public List<String> getNormalizationTypes() {
 
     @Override
     public boolean hasNormalizationVector(String type, String chr, double bpPerPixel) {
-        return hicFile.hasNormalizationVector(type, chr, "BP", getBinSize(chr, bpPerPixel));
+        return hicFile.hasNormalizationVector(type, chr, "BP", hicFile.getBinSize(chr, bpPerPixel));
     }
 
     /**
@@ -209,17 +189,18 @@ private List<ContactRecord> getRecords(String chr, int start, int end, int binSi
                 region1,
                 "BP",
                 binSize,
+                "NONE",
                 false
         );
 
         if(start > 0) {
             Region adjacent = new Region(chr, Math.max(0, start - (end - start)), start);
-            List<ContactRecord> adjacentRecords = hicFile.getContactRecords(region1, adjacent, "BP", binSize, false);
+            List<ContactRecord> adjacentRecords = hicFile.getContactRecords(region1, adjacent, "BP", binSize, "NONE", false);
             records.addAll(adjacentRecords);
         }
 
         Region adjacent2 = new Region(chr, end, end + (end - start));
-        List<ContactRecord> adjacentRecords2 = hicFile.getContactRecords(region1, adjacent2, "BP", binSize, false);
+        List<ContactRecord> adjacentRecords2 = hicFile.getContactRecords(region1, adjacent2, "BP", binSize, "NONE", false);
         records.addAll(adjacentRecords2);
 
         return records;
@@ -244,4 +225,7 @@ public void setNVIString(String nviString) {
         hicFile.setNVIString(nviString);
     }
 
+    public HicFile getHicFile() {
+        return hicFile;
+    }
 }
\ No newline at end of file
diff --git a/src/main/java/org/igv/bedpe/InteractionTrack.java b/src/main/java/org/igv/bedpe/InteractionTrack.java
index b87eaf4213..c61a44be96 100644
--- a/src/main/java/org/igv/bedpe/InteractionTrack.java
+++ b/src/main/java/org/igv/bedpe/InteractionTrack.java
@@ -3,11 +3,13 @@
 import org.igv.Globals;
 import org.igv.event.IGVEvent;
 import org.igv.event.IGVEventObserver;
+import org.igv.hic.HicFile;
 import org.igv.jbrowse.CircularViewUtilities;
 import org.igv.logging.LogManager;
 import org.igv.logging.Logger;
 import org.igv.prefs.Constants;
 import org.igv.prefs.PreferencesManager;
+import org.igv.renderer.ContinuousColorScale;
 import org.igv.renderer.GraphicUtils;
 import org.igv.track.AbstractTrack;
 import org.igv.track.RenderContext;
@@ -76,10 +78,13 @@ enum ArcOption {ALL, ONE_END, BOTH_ENDS}
     private Map<GraphType, BedPERenderer> renderers;
 
     private boolean isHIC;
+    ContactMapView contactMapView;
     float transparency = 1.0f;
     String normalization = "NONE";
     private int maxFeatureCount = 5000;
 
+    int[] markerBounds = null;
+
     transient Map<ReferenceFrame, List<BedPE>> lastRenderedFeatures = new HashMap<>();
 
     transient Map<ReferenceFrame, LoadedInterval> loadedIntervalMap = new HashMap<>();
@@ -144,6 +149,10 @@ public InteractionTrack(ResourceLocator locator, InteractionSource src) {
         }
     }
 
+    void setContactMapView(ContactMapView contactMapView) {
+        this.contactMapView = contactMapView;
+    }
+
     protected boolean isShowFeatures(ReferenceFrame frame) {
 
         if (frame.getChrName().equals(Globals.CHR_ALL)) {
@@ -254,6 +263,8 @@ public void render(RenderContext context, Rectangle trackRectangle) {
             if (showBlocks) {
                 renderers.get(GraphType.BLOCK).render(filteredFeatures, context, trackRectangle, this.arcOption);
             }
+            if(contactMapView != null && !FrameManager.isGeneListMode()) {
+            }
 
         } finally {
             context.clearGraphicsCache();
@@ -499,13 +510,31 @@ public IGVPopupMenu getPopupMenu(TrackClickEvent te) {
                     normItem.setSelected(type.equals(normalization));
                     normItem.addActionListener(e -> {
                         this.normalization = type;
+                        if(contactMapView != null) {
+                            contactMapView.setNormalization(type);
+                        }
                         InteractionTrack.this.repaint();
+
                     });
                     normGroup.add(normItem);
                     menu.add(normItem);
                 }
             }
 
+            menu.addSeparator();
+            JMenuItem mapItem = new JMenuItem("Open Contact Map View");
+            mapItem.setEnabled(contactMapView == null && !FrameManager.isGeneListMode());
+            mapItem.addActionListener(e -> {
+                ReferenceFrame frame = te.getFrame() != null ? te.getFrame() : FrameManager.getDefaultFrame();
+                if (contactMapView == null) {
+                    ContinuousColorScale colorScale = this.getColorScale();
+
+                    HicFile hicFile = ((HicSource) featureSource).getHicFile();
+                    ContactMapView.showPopup(this, hicFile, normalization, frame, colorScale.getMaxColor());
+                }
+            });
+            menu.add(mapItem);
+
         } else {
             menu.addSeparator();
             menu.add(TrackMenuUtils.getChangeFeatureWindow(Collections.singletonList(this)));
@@ -666,6 +695,11 @@ public void receiveEvent(IGVEvent event) {
         }
     }
 
+    public void setMarkerBounds(int[] markerBounds) {
+        this.markerBounds = markerBounds;
+        this.repaint();
+    }
+
 
     public record LoadedInterval(String chr, int start, int end, int zoom, String normalization,
                                  List<BedPE> features) {
diff --git a/src/main/java/org/igv/bedpe/NestedArcRenderer.java b/src/main/java/org/igv/bedpe/NestedArcRenderer.java
index 2ff75510f1..1719ec6f02 100644
--- a/src/main/java/org/igv/bedpe/NestedArcRenderer.java
+++ b/src/main/java/org/igv/bedpe/NestedArcRenderer.java
@@ -133,6 +133,14 @@ public void render(List<BedPE> features,
 
                 }
             }
+
+            if(track.markerBounds != null) {
+                int l1 = (int) ((track.markerBounds[0] - origin) / locScale);
+                int l2 = (int) ((track.markerBounds[1] - origin) / locScale);
+                g.setColor(Color.black);
+                g.drawLine(l1, trackRectangle.y, l1, trackRectangle.y + trackRectangle.height - 1);
+                g.drawLine(l2, trackRectangle.y, l2, trackRectangle.y + trackRectangle.height - 1);
+            }
         } finally {
             if(g != null) g.dispose();
         }
diff --git a/src/main/java/org/igv/blast/BlastMapping.java b/src/main/java/org/igv/blast/BlastMapping.java
index e96859fe01..e9d8852c45 100644
--- a/src/main/java/org/igv/blast/BlastMapping.java
+++ b/src/main/java/org/igv/blast/BlastMapping.java
@@ -1,6 +1,5 @@
 package org.igv.blast;
 
-//~--- non-JDK imports --------------------------------------------------------
 
 import org.igv.feature.BasicFeature;
 import org.igv.feature.Strand;
diff --git a/src/main/java/org/igv/data/AbstractDataSource.java b/src/main/java/org/igv/data/AbstractDataSource.java
index 1edf9c06f3..4dd9498dde 100644
--- a/src/main/java/org/igv/data/AbstractDataSource.java
+++ b/src/main/java/org/igv/data/AbstractDataSource.java
@@ -1,6 +1,5 @@
 package org.igv.data;
 
-//~--- non-JDK imports --------------------------------------------------------
 
 import org.igv.logging.*;
 import org.igv.Globals;
diff --git a/src/main/java/org/igv/data/BasicScore.java b/src/main/java/org/igv/data/BasicScore.java
index dc4c21a1b3..c3e22c735a 100644
--- a/src/main/java/org/igv/data/BasicScore.java
+++ b/src/main/java/org/igv/data/BasicScore.java
@@ -1,7 +1,3 @@
-/*
- * To change this template, choose Tools | Templates
- * and open the template in the editor.
- */
 package org.igv.data;
 
 import org.igv.feature.LocusScore;
diff --git a/src/main/java/org/igv/data/Bin.java b/src/main/java/org/igv/data/Bin.java
index ad6af39391..c0eaa659eb 100644
--- a/src/main/java/org/igv/data/Bin.java
+++ b/src/main/java/org/igv/data/Bin.java
@@ -1,7 +1,3 @@
-/*
- * To change this template, choose Tools | Templates
- * and open the template in the editor.
- */
 
 package org.igv.data;
 
diff --git a/src/main/java/org/igv/data/CharArrayList.java b/src/main/java/org/igv/data/CharArrayList.java
index 37b7813103..72bd968de0 100644
--- a/src/main/java/org/igv/data/CharArrayList.java
+++ b/src/main/java/org/igv/data/CharArrayList.java
@@ -1,7 +1,3 @@
-/*
- * To change this template, choose Tools | Templates
- * and open the template in the editor.
- */
 
 package org.igv.data;
 
diff --git a/src/main/java/org/igv/data/ChromosomeSummary.java b/src/main/java/org/igv/data/ChromosomeSummary.java
index 7c3ddf12aa..5961f1ef5b 100644
--- a/src/main/java/org/igv/data/ChromosomeSummary.java
+++ b/src/main/java/org/igv/data/ChromosomeSummary.java
@@ -1,7 +1,3 @@
-/*
- * To change this template, choose Tools | Templates
- * and open the template in the editor.
- */
 package org.igv.data;
 
 /**
diff --git a/src/main/java/org/igv/data/CompositeScore.java b/src/main/java/org/igv/data/CompositeScore.java
index ce4585370d..f294e2d065 100644
--- a/src/main/java/org/igv/data/CompositeScore.java
+++ b/src/main/java/org/igv/data/CompositeScore.java
@@ -1,6 +1,5 @@
 package org.igv.data;
 
-//~--- non-JDK imports --------------------------------------------------------
 
 import org.igv.feature.LocusScore;
 import org.igv.track.WindowFunction;
diff --git a/src/main/java/org/igv/data/DataSource.java b/src/main/java/org/igv/data/DataSource.java
index 78713b9679..0964f6b8a6 100644
--- a/src/main/java/org/igv/data/DataSource.java
+++ b/src/main/java/org/igv/data/DataSource.java
@@ -1,7 +1,3 @@
-/*
- * To change this template, choose Tools | Templates
- * and open the template in the editor.
- */
 
 package org.igv.data;
 
diff --git a/src/main/java/org/igv/data/DataStatistics.java b/src/main/java/org/igv/data/DataStatistics.java
index 606464ca29..76cd79f90b 100644
--- a/src/main/java/org/igv/data/DataStatistics.java
+++ b/src/main/java/org/igv/data/DataStatistics.java
@@ -1,7 +1,3 @@
-/*
- * To change this template, choose Tools | Templates
- * and open the template in the editor.
- */
 package org.igv.data;
 
 import org.igv.track.WindowFunction;
diff --git a/src/main/java/org/igv/data/DataTile.java b/src/main/java/org/igv/data/DataTile.java
index c17199fd39..fe35a300a9 100644
--- a/src/main/java/org/igv/data/DataTile.java
+++ b/src/main/java/org/igv/data/DataTile.java
@@ -1,7 +1,3 @@
-/*
- * To change this template, choose Tools | Templates
- * and open the template in the editor.
- */
 package org.igv.data;
 
 /**
diff --git a/src/main/java/org/igv/data/Dataset.java b/src/main/java/org/igv/data/Dataset.java
index e1ebc7788d..aec2902782 100644
--- a/src/main/java/org/igv/data/Dataset.java
+++ b/src/main/java/org/igv/data/Dataset.java
@@ -1,7 +1,3 @@
-/*
- * To change this template, choose Tools | Templates
- * and open the template in the editor.
- */
 package org.igv.data;
 
 import org.igv.track.TrackProperties;
diff --git a/src/main/java/org/igv/data/DatasetDataSource.java b/src/main/java/org/igv/data/DatasetDataSource.java
index ee00d83993..f9713fc025 100644
--- a/src/main/java/org/igv/data/DatasetDataSource.java
+++ b/src/main/java/org/igv/data/DatasetDataSource.java
@@ -1,10 +1,5 @@
-/*
- * To change this template, choose Tools | Templates
- * and open the template in the editor.
- */
 package org.igv.data;
 
-//~--- non-JDK imports --------------------------------------------------------
 
 import org.igv.logging.*;
 import org.igv.Globals;
diff --git a/src/main/java/org/igv/data/GenomeSummaryData.java b/src/main/java/org/igv/data/GenomeSummaryData.java
index ecfc8c006d..a07377a842 100644
--- a/src/main/java/org/igv/data/GenomeSummaryData.java
+++ b/src/main/java/org/igv/data/GenomeSummaryData.java
@@ -1,7 +1,3 @@
-/*
- * To change this template, choose Tools | Templates
- * and open the template in the editor.
- */
 package org.igv.data;
 
 import org.igv.logging.*;
diff --git a/src/main/java/org/igv/data/IGVDataset.java b/src/main/java/org/igv/data/IGVDataset.java
index 8ce00813e3..cb6a50d4bf 100644
--- a/src/main/java/org/igv/data/IGVDataset.java
+++ b/src/main/java/org/igv/data/IGVDataset.java
@@ -1,7 +1,3 @@
-/*
- * To change this template, choose Tools | Templates
- * and open the template in the editor.
- */
 package org.igv.data;
 
 import org.igv.feature.genome.Genome;
diff --git a/src/main/java/org/igv/data/IGVDatasetParser.java b/src/main/java/org/igv/data/IGVDatasetParser.java
index 093d0699c6..2c86dee264 100644
--- a/src/main/java/org/igv/data/IGVDatasetParser.java
+++ b/src/main/java/org/igv/data/IGVDatasetParser.java
@@ -1,6 +1,5 @@
 package org.igv.data;
 
-//~--- non-JDK imports --------------------------------------------------------
 
 import htsjdk.samtools.seekablestream.SeekableStream;
 import org.igv.logging.*;
diff --git a/src/main/java/org/igv/data/SummaryTile.java b/src/main/java/org/igv/data/SummaryTile.java
index 618c62cbf5..96c2b775ba 100644
--- a/src/main/java/org/igv/data/SummaryTile.java
+++ b/src/main/java/org/igv/data/SummaryTile.java
@@ -1,6 +1,5 @@
 package org.igv.data;
 
-//~--- non-JDK imports --------------------------------------------------------
 
 import org.igv.feature.LocusScore;
 
diff --git a/src/main/java/org/igv/data/WiggleDataset.java b/src/main/java/org/igv/data/WiggleDataset.java
index dab40d67e0..3be4c086f5 100644
--- a/src/main/java/org/igv/data/WiggleDataset.java
+++ b/src/main/java/org/igv/data/WiggleDataset.java
@@ -1,10 +1,5 @@
-/*
- * To change this template, choose Tools | Templates
- * and open the template in the editor.
- */
 package org.igv.data;
 
-//~--- non-JDK imports --------------------------------------------------------
 
 import org.igv.feature.genome.Genome;
 import org.igv.track.TrackProperties;
diff --git a/src/main/java/org/igv/data/ZipUtils.java b/src/main/java/org/igv/data/ZipUtils.java
index 6b488e1ff2..3cd4ac5d77 100644
--- a/src/main/java/org/igv/data/ZipUtils.java
+++ b/src/main/java/org/igv/data/ZipUtils.java
@@ -1,7 +1,3 @@
-/*
- * To change this template, choose Tools | Templates
- * and open the template in the editor.
- */
 package org.igv.data;
 
 import org.igv.util.FileUtils;
diff --git a/src/main/java/org/igv/data/expression/ExpressionFileParser.java b/src/main/java/org/igv/data/expression/ExpressionFileParser.java
index e861e3feb6..87af3ba08d 100644
--- a/src/main/java/org/igv/data/expression/ExpressionFileParser.java
+++ b/src/main/java/org/igv/data/expression/ExpressionFileParser.java
@@ -10,7 +10,6 @@
  */
 package org.igv.data.expression;
 
-//~--- non-JDK imports --------------------------------------------------------
 
 import org.igv.logging.*;
 import org.igv.Globals;
diff --git a/src/main/java/org/igv/feature/AbstractFeature.java b/src/main/java/org/igv/feature/AbstractFeature.java
index b5388a5ff0..22f650bd67 100644
--- a/src/main/java/org/igv/feature/AbstractFeature.java
+++ b/src/main/java/org/igv/feature/AbstractFeature.java
@@ -1,6 +1,5 @@
 package org.igv.feature;
 
-//~--- non-JDK imports --------------------------------------------------------
 
 import org.igv.logging.*;
 import org.igv.ui.IGV;
diff --git a/src/main/java/org/igv/feature/AbstractFeatureParser.java b/src/main/java/org/igv/feature/AbstractFeatureParser.java
index b1d6d4e91b..39ea54e1f4 100644
--- a/src/main/java/org/igv/feature/AbstractFeatureParser.java
+++ b/src/main/java/org/igv/feature/AbstractFeatureParser.java
@@ -1,7 +1,3 @@
-/*
- * To change this template, choose Tools | Templates
- * and open the template in the editor.
- */
 package org.igv.feature;
 
 import org.igv.logging.*;
diff --git a/src/main/java/org/igv/feature/CytoBandFileParser.java b/src/main/java/org/igv/feature/CytoBandFileParser.java
index 935c53a079..84898fa4ac 100644
--- a/src/main/java/org/igv/feature/CytoBandFileParser.java
+++ b/src/main/java/org/igv/feature/CytoBandFileParser.java
@@ -1,6 +1,5 @@
 package org.igv.feature;
 
-//~--- non-JDK imports --------------------------------------------------------
 
 import org.igv.logging.*;
 import htsjdk.tribble.readers.AsciiLineReader;
diff --git a/src/main/java/org/igv/feature/EmblFeatureTableParser.java b/src/main/java/org/igv/feature/EmblFeatureTableParser.java
index 4d424b3a69..35a867a114 100644
--- a/src/main/java/org/igv/feature/EmblFeatureTableParser.java
+++ b/src/main/java/org/igv/feature/EmblFeatureTableParser.java
@@ -1,6 +1,5 @@
 package org.igv.feature;
 
-//~--- non-JDK imports --------------------------------------------------------
 
 import org.igv.logging.*;
 import org.igv.feature.genome.Genome;
diff --git a/src/main/java/org/igv/feature/FeatureDB.java b/src/main/java/org/igv/feature/FeatureDB.java
index 08d45fe514..363c7e685c 100644
--- a/src/main/java/org/igv/feature/FeatureDB.java
+++ b/src/main/java/org/igv/feature/FeatureDB.java
@@ -1,6 +1,5 @@
 package org.igv.feature;
 
-//~--- non-JDK imports --------------------------------------------------------
 
 import com.jidesoft.utils.SortedList;
 import htsjdk.tribble.Feature;
diff --git a/src/main/java/org/igv/feature/FeatureParser.java b/src/main/java/org/igv/feature/FeatureParser.java
index 16069593c8..1e47aac147 100644
--- a/src/main/java/org/igv/feature/FeatureParser.java
+++ b/src/main/java/org/igv/feature/FeatureParser.java
@@ -1,7 +1,3 @@
-/*
- * To change this template, choose Tools | Templates
- * and open the template in the editor.
- */
 
 package org.igv.feature;
 
diff --git a/src/main/java/org/igv/feature/GisticFileParser.java b/src/main/java/org/igv/feature/GisticFileParser.java
index e0c80fc122..4a6ecb06b5 100644
--- a/src/main/java/org/igv/feature/GisticFileParser.java
+++ b/src/main/java/org/igv/feature/GisticFileParser.java
@@ -8,7 +8,6 @@
  */
 package org.igv.feature;
 
-//~--- non-JDK imports --------------------------------------------------------
 
 import org.igv.logging.*;
 import org.igv.exceptions.ParserException;
diff --git a/src/main/java/org/igv/feature/GisticScore.java b/src/main/java/org/igv/feature/GisticScore.java
index 23d91d7da4..c245915f34 100644
--- a/src/main/java/org/igv/feature/GisticScore.java
+++ b/src/main/java/org/igv/feature/GisticScore.java
@@ -9,7 +9,6 @@
 
 package org.igv.feature;
 
-//~--- non-JDK imports --------------------------------------------------------
 
 import org.igv.track.WindowFunction;
 
diff --git a/src/main/java/org/igv/feature/Locus.java b/src/main/java/org/igv/feature/Locus.java
index b4af0ea8a7..db660e1d46 100644
--- a/src/main/java/org/igv/feature/Locus.java
+++ b/src/main/java/org/igv/feature/Locus.java
@@ -1,7 +1,3 @@
-/*
- * To change this template, choose Tools | Templates
- * and open the template in the editor.
- */
 package org.igv.feature;
 
 import java.text.NumberFormat;
diff --git a/src/main/java/org/igv/feature/LocusScore.java b/src/main/java/org/igv/feature/LocusScore.java
index 46b53e46c0..5a29483685 100644
--- a/src/main/java/org/igv/feature/LocusScore.java
+++ b/src/main/java/org/igv/feature/LocusScore.java
@@ -1,7 +1,3 @@
-/*
- * To change this template, choose Tools | Templates
- * and open the template in the editor.
- */
 package org.igv.feature;
 
 import org.igv.track.WindowFunction;
diff --git a/src/main/java/org/igv/feature/Mutation.java b/src/main/java/org/igv/feature/Mutation.java
index 93f77d913b..8e49fd5d9e 100644
--- a/src/main/java/org/igv/feature/Mutation.java
+++ b/src/main/java/org/igv/feature/Mutation.java
@@ -1,6 +1,5 @@
 package org.igv.feature;
 
-//~--- non-JDK imports --------------------------------------------------------
 
 import org.igv.feature.genome.GenomeManager;
 import org.igv.logging.*;
diff --git a/src/main/java/org/igv/feature/Strand.java b/src/main/java/org/igv/feature/Strand.java
index 41b559fe02..4f2b16e028 100644
--- a/src/main/java/org/igv/feature/Strand.java
+++ b/src/main/java/org/igv/feature/Strand.java
@@ -1,7 +1,3 @@
-/*
- * To change this template, choose Tools | Templates
- * and open the template in the editor.
- */
 
 package org.igv.feature;
 
diff --git a/src/main/java/org/igv/feature/aa/AminoAcid.java b/src/main/java/org/igv/feature/aa/AminoAcid.java
index 6d7e246a7f..5e6517ec74 100644
--- a/src/main/java/org/igv/feature/aa/AminoAcid.java
+++ b/src/main/java/org/igv/feature/aa/AminoAcid.java
@@ -1,7 +1,3 @@
-/*
- * To change this template, choose Tools | Templates
- * and open the template in the editor.
- */
 package org.igv.feature.aa;
 
 /**
diff --git a/src/main/java/org/igv/feature/aa/AminoAcidManager.java b/src/main/java/org/igv/feature/aa/AminoAcidManager.java
index 0af284b86c..fd8175ad62 100644
--- a/src/main/java/org/igv/feature/aa/AminoAcidManager.java
+++ b/src/main/java/org/igv/feature/aa/AminoAcidManager.java
@@ -1,7 +1,3 @@
-/*
- * To change this template, choose Tools | Templates
- * and open the template in the editor.
- */
 package org.igv.feature.aa;
 
 import org.igv.logging.*;
diff --git a/src/main/java/org/igv/feature/aa/AminoAcidSequence.java b/src/main/java/org/igv/feature/aa/AminoAcidSequence.java
index d481828fd9..51dfac7d6a 100644
--- a/src/main/java/org/igv/feature/aa/AminoAcidSequence.java
+++ b/src/main/java/org/igv/feature/aa/AminoAcidSequence.java
@@ -1,7 +1,3 @@
-/*
- * To change this template, choose Tools | Templates
- * and open the template in the editor.
- */
 package org.igv.feature.aa;
 
 import org.igv.feature.Strand;
diff --git a/src/main/java/org/igv/feature/aa/CodonTableManager.java b/src/main/java/org/igv/feature/aa/CodonTableManager.java
index b4ed808a02..26eab38708 100644
--- a/src/main/java/org/igv/feature/aa/CodonTableManager.java
+++ b/src/main/java/org/igv/feature/aa/CodonTableManager.java
@@ -1,7 +1,3 @@
-/*
- * To change this template, choose Tools | Templates
- * and open the template in the editor.
- */
 package org.igv.feature.aa;
 
 import org.igv.logging.*;
diff --git a/src/main/java/org/igv/feature/basepair/BasePairRenderer.java b/src/main/java/org/igv/feature/basepair/BasePairRenderer.java
index d1084825de..a30555a105 100644
--- a/src/main/java/org/igv/feature/basepair/BasePairRenderer.java
+++ b/src/main/java/org/igv/feature/basepair/BasePairRenderer.java
@@ -1,6 +1,5 @@
 package org.igv.feature.basepair;
 
-//~--- non-JDK imports --------------------------------------------------------
 
 import org.igv.logging.*;
 import org.igv.feature.basepair.BasePairTrack.*;
diff --git a/src/main/java/org/igv/feature/dranger/DRangerFeature.java b/src/main/java/org/igv/feature/dranger/DRangerFeature.java
index e3d3768734..efe808086b 100644
--- a/src/main/java/org/igv/feature/dranger/DRangerFeature.java
+++ b/src/main/java/org/igv/feature/dranger/DRangerFeature.java
@@ -1,7 +1,3 @@
-/*
- * To change this template, choose Tools | Templates
- * and open the template in the editor.
- */
 package org.igv.feature.dranger;
 
 import org.igv.feature.AbstractFeature;
diff --git a/src/main/java/org/igv/feature/dranger/DRangerParser.java b/src/main/java/org/igv/feature/dranger/DRangerParser.java
index 228f8a7001..d9aa765800 100644
--- a/src/main/java/org/igv/feature/dranger/DRangerParser.java
+++ b/src/main/java/org/igv/feature/dranger/DRangerParser.java
@@ -1,7 +1,3 @@
-/*
- * To change this template, choose Tools | Templates
- * and open the template in the editor.
- */
 package org.igv.feature.dranger;
 
 import org.igv.logging.*;
diff --git a/src/main/java/org/igv/feature/dranger/DRangerRenderer.java b/src/main/java/org/igv/feature/dranger/DRangerRenderer.java
index 387a322a2c..cbe2d2dff0 100644
--- a/src/main/java/org/igv/feature/dranger/DRangerRenderer.java
+++ b/src/main/java/org/igv/feature/dranger/DRangerRenderer.java
@@ -1,7 +1,3 @@
-/*
- * To change this template, choose Tools | Templates
- * and open the template in the editor.
- */
 package org.igv.feature.dranger;
 
 import org.igv.feature.IGVFeature;
diff --git a/src/main/java/org/igv/feature/genome/GenomeImporter.java b/src/main/java/org/igv/feature/genome/GenomeImporter.java
index 46e7e29ec6..1d9e01a200 100644
--- a/src/main/java/org/igv/feature/genome/GenomeImporter.java
+++ b/src/main/java/org/igv/feature/genome/GenomeImporter.java
@@ -1,7 +1,3 @@
-/*
- * To change this template, choose Tools | Templates
- * and open the template in the editor.
- */
 package org.igv.feature.genome;
 
 import org.igv.logging.*;
diff --git a/src/main/java/org/igv/feature/genome/SequenceWrapper.java b/src/main/java/org/igv/feature/genome/SequenceWrapper.java
index a59bb22345..2853458f6d 100644
--- a/src/main/java/org/igv/feature/genome/SequenceWrapper.java
+++ b/src/main/java/org/igv/feature/genome/SequenceWrapper.java
@@ -1,7 +1,3 @@
-/*
- * To change this template, choose Tools | Templates
- * and open the template in the editor.
- */
 package org.igv.feature.genome;
 
 import org.igv.feature.Chromosome;
diff --git a/src/main/java/org/igv/hic/DynamicBlockIndex.java b/src/main/java/org/igv/hic/DynamicBlockIndex.java
index 67d1c210fa..4667f82bbf 100644
--- a/src/main/java/org/igv/hic/DynamicBlockIndex.java
+++ b/src/main/java/org/igv/hic/DynamicBlockIndex.java
@@ -2,6 +2,7 @@
 
 import java.io.IOException;
 import java.nio.ByteBuffer;
+import java.nio.ByteOrder;
 import java.nio.channels.FileChannel;
 import java.util.HashMap;
 import java.util.Map;
@@ -60,6 +61,7 @@ private StaticBlockIndex.BlockIndexEntry searchForBlockIndexEntry(int blockNumbe
         if (boundsMax - boundsMin < chunkSize) {
             int len = (int) (boundsMax - boundsMin);
             ByteBuffer buf = ByteBuffer.allocate(len);
+            buf.order(ByteOrder.LITTLE_ENDIAN);
             fileChannel.read(buf, boundsMin);
             buf.flip();
 
@@ -84,6 +86,7 @@ private StaticBlockIndex.BlockIndexEntry searchForBlockIndexEntry(int blockNumbe
         long nEntries = (boundsMax - boundsMin) / ENTRY_SIZE;
         long pos1 = boundsMin + (nEntries / 2) * ENTRY_SIZE;
         ByteBuffer buf = ByteBuffer.allocate((int) ENTRY_SIZE);
+        buf.order(ByteOrder.LITTLE_ENDIAN);
         fileChannel.read(buf, pos1);
         buf.flip();
         int bn = buf.getInt();
diff --git a/src/main/java/org/igv/hic/HicFile.java b/src/main/java/org/igv/hic/HicFile.java
index 5f82bef931..6d5555a1ab 100644
--- a/src/main/java/org/igv/hic/HicFile.java
+++ b/src/main/java/org/igv/hic/HicFile.java
@@ -15,6 +15,9 @@
 import java.nio.ByteBuffer;
 import java.nio.ByteOrder;
 import java.util.*;
+import java.util.concurrent.CompletableFuture;
+import java.util.concurrent.ConcurrentHashMap;
+import java.util.concurrent.ExecutionException;
 
 /**
  * Representation of a .hic file, with methods to access contact recrods and normalization vectors.
@@ -69,6 +72,10 @@ public int getByteSize() {
     private List<String> normalizationTypes = new ArrayList<>(Collections.singletonList("NONE"));
     private Long normExpectedValueVectorsPosition;
 
+    // Map to track pending block read requests to prevent duplicate I/O operations
+    // Key is the block key, value is a CompletableFuture that will complete when the block is loaded
+    private final Map<String, CompletableFuture<Block>> pendingBlockRequests = new ConcurrentHashMap<>();
+
 
     public HicFile(String path, Genome genome) throws IOException {
         this.path = path;
@@ -253,6 +260,7 @@ public List<ContactRecord> getContactRecords(Region region1,
                                                  Region region2,
                                                  String units,
                                                  int binSize,
+                                                 String normalization,
                                                  boolean allRecords) throws IOException {
 
         int idx1 = chromosomeIndexMap.getOrDefault(getFileChrName(region1.chr()), -1);
@@ -274,12 +282,43 @@ public List<ContactRecord> getContactRecords(Region region1,
         double y1 = (double) region2.start() / binSize;
         double y2 = (double) region2.end() / binSize;
 
+
+        boolean useNormalization = normalization != null && !"NONE".equals(normalization);
+        NormalizationVector nv = useNormalization ? getNormalizationVector(normalization, region1.chr(), "BP", binSize) : null;
+        if (nv == null) {
+            useNormalization = false;
+        }
+
+
         for (Block block : blocks) {
             if (block == null) continue;
 
+            double[] normVector = null;
+
+            // Compute binMin and binMax from block.records
+            int binMin = Integer.MAX_VALUE;
+            int binMax = Integer.MIN_VALUE;
+            if (useNormalization) {
+                for (ContactRecord rec : block.records) {
+                    binMin = Math.min(binMin, Math.min(rec.bin1(), rec.bin2()));
+                    binMax = Math.max(binMax, Math.max(rec.bin1(), rec.bin2()));
+                }
+                normVector = nv.getValues(binMin, binMax);
+            }
+
             for (ContactRecord rec : block.records) {
                 if (allRecords || (rec.bin1() >= x1 && rec.bin1() < x2 && rec.bin2() >= y1 && rec.bin2() < y2) && rec.counts() > 1) {
-                    contactRecords.add(rec);
+                    if (normVector == null) {
+                        contactRecords.add(rec);
+                    } else {
+                        float value = rec.counts();
+                        double nvnv = normVector[rec.bin1() - binMin] * normVector[rec.bin2() - binMin];
+                        if (!Double.isNaN(nvnv)) {
+                            value /= nvnv;
+                            ContactRecord normRec = new ContactRecord(rec.bin1(), rec.bin2(), value);
+                            contactRecords.add(normRec);
+                        } 
+                    }
                 }
             }
         }
@@ -305,6 +344,27 @@ public int getWGResolution() {
         return wgResolution;
     }
 
+    public int getBinSize(String chr, double bpPerPixel) {
+
+        if ("all".equalsIgnoreCase(chr)) {
+            // Special case, the whole-genome psuedo-chromosome all has a single resolution
+            return this.getWGResolution();
+        }
+
+        // choose resolution
+        List<Integer> resolutions = this.getBpResolutions();
+        int index = 0;
+        for (int i = resolutions.size() - 1; i >= 0; i--) {
+            if (resolutions.get(i) >= bpPerPixel) {
+                index = i;
+                break;
+            }
+        }
+        int binSize = resolutions.get(index);
+        return binSize;
+
+    }
+
     private List<Block> getBlocks(Region region1, Region region2, String unit, int binSize) throws IOException {
         init();
         String chr1 = getFileChrName(region1.chr());
@@ -325,6 +385,7 @@ private List<Block> getBlocks(Region region1, Region region2, String unit, int b
         List<Integer> blockNumbers = zd.getBlockNumbers(region1, region2, this.version);
         List<Block> blocks = new ArrayList<>();
         List<Integer> toQuery = new ArrayList<>();
+
         for (Integer num : blockNumbers) {
             String key = zd.getKey() + "_" + num;
             if (blockCache.has(binSize, key)) {
@@ -334,17 +395,66 @@ private List<Block> getBlocks(Region region1, Region region2, String unit, int b
             }
         }
 
+        // Fetch blocks that aren't in cache, with deduplication for concurrent requests
         for (Integer bn : toQuery) {
-            Block b = readBlock(bn, zd);
-            if (b != null) {
-                blockCache.set(binSize, zd.getKey() + "_" + b.blockNumber, b);
-            }
-            blocks.add(b);
+            String key = zd.getKey() + "_" + bn;
+            Block block = getBlockWithDeduplication(key, bn, binSize, zd);
+            blocks.add(block);
         }
 
         return blocks;
     }
 
+    /**
+     * Get a block with request deduplication. If another thread is already fetching the same block,
+     * this method will wait for that operation to complete and return the same result instead of
+     * initiating a redundant read.
+     */
+    private Block getBlockWithDeduplication(String key, int blockNumber, int binSize, MatrixZoomData zd) throws IOException {
+        // Double-check cache (in case another thread just added it)
+        if (blockCache.has(binSize, key)) {
+            return blockCache.get(binSize, key);
+        }
+
+        // Create a new future for this request
+        CompletableFuture<Block> newFuture = new CompletableFuture<>();
+
+        // Try to be the first to register this request
+        CompletableFuture<Block> existingFuture = pendingBlockRequests.putIfAbsent(key, newFuture);
+
+        if (existingFuture != null) {
+            // Another thread is already fetching this block - wait for its result
+            try {
+                return existingFuture.get();
+            } catch (InterruptedException e) {
+                Thread.currentThread().interrupt();
+                throw new IOException("Interrupted while waiting for block data", e);
+            } catch (ExecutionException e) {
+                Throwable cause = e.getCause();
+                if (cause instanceof IOException) {
+                    throw (IOException) cause;
+                }
+                throw new IOException("Error reading block", cause);
+            }
+        }
+
+        // This thread won the race - perform the actual read
+        try {
+            Block block = readBlock(blockNumber, zd);
+            if (block != null) {
+                blockCache.set(binSize, key, block);
+            }
+            newFuture.complete(block);
+            return block;
+        } catch (IOException e) {
+            newFuture.completeExceptionally(e);
+            throw e;
+        } finally {
+            // Clean up the pending request
+            pendingBlockRequests.remove(key);
+        }
+    }
+
     private Block readBlock(int blockNumber, MatrixZoomData zd) throws IOException {
         StaticBlockIndex.BlockIndexEntry idx = zd.getBlockIndex().getBlockIndexEntry(blockNumber);
         if (idx == null) return null;
diff --git a/src/main/java/org/igv/hic/NormalizationVector.java b/src/main/java/org/igv/hic/NormalizationVector.java
index 6c01f9c36f..bf63d54f86 100644
--- a/src/main/java/org/igv/hic/NormalizationVector.java
+++ b/src/main/java/org/igv/hic/NormalizationVector.java
@@ -4,6 +4,7 @@
 
 import java.io.IOException;
 import java.nio.ByteBuffer;
+import java.nio.ByteOrder;
 import java.nio.channels.FileChannel;
 import java.util.Arrays;
 
@@ -55,6 +56,10 @@ public NormalizationVector(SeekableStream fileChannel, long filePosition, int nV
         this.cache = null;
     }
 
+    public int getnValues() {
+        return nValues;
+    }
+
     /**
      * Return values in range [start, end) as a double[].
      * Returns null if the underlying read fails.
@@ -87,6 +92,7 @@ public double[] getValues(int startBin, int endBin) throws IOException {
                 return null;
             }
             ByteBuffer buf = ByteBuffer.wrap(byteArray);
+            buf.order(ByteOrder.LITTLE_ENDIAN);
 
             double[] values = new double[n];
             for (int i = 0; i < n; i++) {
diff --git a/src/main/java/org/igv/maf/MAFReader.java b/src/main/java/org/igv/maf/MAFReader.java
index 8d45b6f675..4d33f9fac1 100644
--- a/src/main/java/org/igv/maf/MAFReader.java
+++ b/src/main/java/org/igv/maf/MAFReader.java
@@ -1,7 +1,3 @@
-/*
- * To change this template, choose Tools | Templates
- * and open the template in the editor.
- */
 
 package org.igv.maf;
 
diff --git a/src/main/java/org/igv/maf/MAFTile.java b/src/main/java/org/igv/maf/MAFTile.java
index dd00312f2d..6cfb57629a 100644
--- a/src/main/java/org/igv/maf/MAFTile.java
+++ b/src/main/java/org/igv/maf/MAFTile.java
@@ -1,6 +1,5 @@
 package org.igv.maf;
 
-//~--- non-JDK imports --------------------------------------------------------
 
 import java.util.ArrayList;
 import java.util.LinkedHashMap;
diff --git a/src/main/java/org/igv/maf/MAFTileCodec.java b/src/main/java/org/igv/maf/MAFTileCodec.java
index e89d467286..a211d4c989 100644
--- a/src/main/java/org/igv/maf/MAFTileCodec.java
+++ b/src/main/java/org/igv/maf/MAFTileCodec.java
@@ -1,7 +1,3 @@
-/*
- * To change this template, choose Tools | Templates
- * and open the template in the editor.
- */
 package org.igv.maf;
 
 import org.igv.maf.MAFTile.MASequence;
diff --git a/src/main/java/org/igv/maf/MAFUtils.java b/src/main/java/org/igv/maf/MAFUtils.java
index 2767f08406..a1d7c74c1b 100644
--- a/src/main/java/org/igv/maf/MAFUtils.java
+++ b/src/main/java/org/igv/maf/MAFUtils.java
@@ -1,7 +1,3 @@
-/*
- * To change this template, choose Tools | Templates
- * and open the template in the editor.
- */
 
 package org.igv.maf;
 
diff --git a/src/main/java/org/igv/maf/Multiz44ConfigurationDialog.java b/src/main/java/org/igv/maf/Multiz44ConfigurationDialog.java
index ceefe1c810..73046eadf6 100644
--- a/src/main/java/org/igv/maf/Multiz44ConfigurationDialog.java
+++ b/src/main/java/org/igv/maf/Multiz44ConfigurationDialog.java
@@ -1,7 +1,3 @@
-/*
- * To change this template, choose Tools | Templates
- * and open the template in the editor.
- */
 
 /*
  * MAFConfigurationDialog.java
diff --git a/src/main/java/org/igv/prefs/IGVPreferences.java b/src/main/java/org/igv/prefs/IGVPreferences.java
index babc6d93e8..583b5d6a6d 100644
--- a/src/main/java/org/igv/prefs/IGVPreferences.java
+++ b/src/main/java/org/igv/prefs/IGVPreferences.java
@@ -1,7 +1,3 @@
-/*
- * To change this template, choose Tools | Templates
- * and open the template in the editor.
- */
 package org.igv.prefs;
 
 
diff --git a/src/main/java/org/igv/renderer/AbstractColorScale.java b/src/main/java/org/igv/renderer/AbstractColorScale.java
index 2ccaab25f8..eb5d98ae4a 100644
--- a/src/main/java/org/igv/renderer/AbstractColorScale.java
+++ b/src/main/java/org/igv/renderer/AbstractColorScale.java
@@ -1,7 +1,3 @@
-/*
- * To change this template, choose Tools | Templates
- * and open the template in the editor.
- */
 
 package org.igv.renderer;
 
diff --git a/src/main/java/org/igv/renderer/ColorScale.java b/src/main/java/org/igv/renderer/ColorScale.java
index 0c970be6eb..0a3909635a 100644
--- a/src/main/java/org/igv/renderer/ColorScale.java
+++ b/src/main/java/org/igv/renderer/ColorScale.java
@@ -1,7 +1,3 @@
-/*
- * To change this template, choose Tools | Templates
- * and open the template in the editor.
- */
 package org.igv.renderer;
 
 import java.awt.*;
diff --git a/src/main/java/org/igv/renderer/ColorScaleFactory.java b/src/main/java/org/igv/renderer/ColorScaleFactory.java
index a1eac78fb4..48eb389b9d 100644
--- a/src/main/java/org/igv/renderer/ColorScaleFactory.java
+++ b/src/main/java/org/igv/renderer/ColorScaleFactory.java
@@ -1,7 +1,3 @@
-/*
- * To change this template, choose Tools | Templates
- * and open the template in the editor.
- */
 package org.igv.renderer;
 
 import java.util.HashMap;
diff --git a/src/main/java/org/igv/renderer/ContinuousColorScale.java b/src/main/java/org/igv/renderer/ContinuousColorScale.java
index 015452bf5d..309b92005a 100644
--- a/src/main/java/org/igv/renderer/ContinuousColorScale.java
+++ b/src/main/java/org/igv/renderer/ContinuousColorScale.java
@@ -1,10 +1,5 @@
-/*
-* To change this template, choose Tools | Templates
-* and open the template in the editor.
-*/
 package org.igv.renderer;
 
-//~--- non-JDK imports --------------------------------------------------------
 
 import org.igv.prefs.Constants;
 import org.igv.prefs.PreferencesManager;
@@ -377,6 +372,15 @@ public ColorGradient(double min, double max, Color negColor, Color posColor) {
             posImage = createGradientImage(negColor, posColor);
         }
 
+        public void setMax(double max) {
+            this.max = max;
+            posImage = createGradientImage(minColor, maxColor);
+        }
+
+        public double getMax() {
+            return max;
+        }
+
         /**
          * Creates a gradient image given specified <CODE>Color</CODE>(s)
          *
diff --git a/src/main/java/org/igv/renderer/DataRange.java b/src/main/java/org/igv/renderer/DataRange.java
index 55601bde94..7ae5c6361f 100644
--- a/src/main/java/org/igv/renderer/DataRange.java
+++ b/src/main/java/org/igv/renderer/DataRange.java
@@ -1,7 +1,3 @@
-/*
- * To change this template, choose Tools | Templates
- * and open the template in the editor.
- */
 package org.igv.renderer;
 
 import org.igv.session.Persistable;
diff --git a/src/main/java/org/igv/renderer/DataRenderer.java b/src/main/java/org/igv/renderer/DataRenderer.java
index e9d8bf7e2f..8f239e3f8e 100644
--- a/src/main/java/org/igv/renderer/DataRenderer.java
+++ b/src/main/java/org/igv/renderer/DataRenderer.java
@@ -10,7 +10,6 @@
 
 package org.igv.renderer;
 
-//~--- non-JDK imports --------------------------------------------------------
 
 import org.igv.logging.*;
 import org.igv.Globals;
diff --git a/src/main/java/org/igv/renderer/FeatureRenderer.java b/src/main/java/org/igv/renderer/FeatureRenderer.java
index 163d4c887f..04da18904b 100644
--- a/src/main/java/org/igv/renderer/FeatureRenderer.java
+++ b/src/main/java/org/igv/renderer/FeatureRenderer.java
@@ -1,7 +1,3 @@
-/*
- * To change this template, choose Tools | Templates
- * and open the template in the editor.
- */
 package org.igv.renderer;
 
 import org.igv.Globals;
diff --git a/src/main/java/org/igv/renderer/GeneTrackRenderer.java b/src/main/java/org/igv/renderer/GeneTrackRenderer.java
index 7c6ef41c11..b6a9d44051 100644
--- a/src/main/java/org/igv/renderer/GeneTrackRenderer.java
+++ b/src/main/java/org/igv/renderer/GeneTrackRenderer.java
@@ -1,10 +1,5 @@
-/*
-* To change this template, choose Tools | Templates
-* and open the template in the editor.
-*/
 package org.igv.renderer;
 
-//~--- non-JDK imports --------------------------------------------------------
 
 import org.igv.logging.*;
 
diff --git a/src/main/java/org/igv/renderer/GisticTrackRenderer.java b/src/main/java/org/igv/renderer/GisticTrackRenderer.java
index 8584dc7bbc..7f7c2e5221 100644
--- a/src/main/java/org/igv/renderer/GisticTrackRenderer.java
+++ b/src/main/java/org/igv/renderer/GisticTrackRenderer.java
@@ -1,7 +1,3 @@
-/*
- * To change this template, choose Tools | Templates
- * and open the template in the editor.
- */
 package org.igv.renderer;
 
 import org.igv.feature.GisticScore;
diff --git a/src/main/java/org/igv/renderer/GraphicUtils.java b/src/main/java/org/igv/renderer/GraphicUtils.java
index c953f4a3be..778c4b25b9 100644
--- a/src/main/java/org/igv/renderer/GraphicUtils.java
+++ b/src/main/java/org/igv/renderer/GraphicUtils.java
@@ -1,7 +1,3 @@
-/*
- * To change this template, choose Tools | Templates
- * and open the template in the editor.
- */
 package org.igv.renderer;
 
 import org.igv.Globals;
diff --git a/src/main/java/org/igv/renderer/MappedColorScale.java b/src/main/java/org/igv/renderer/MappedColorScale.java
index 6ec6626957..9d6fc0bf42 100644
--- a/src/main/java/org/igv/renderer/MappedColorScale.java
+++ b/src/main/java/org/igv/renderer/MappedColorScale.java
@@ -1,7 +1,3 @@
-/*
- * To change this template, choose Tools | Templates
- * and open the template in the editor.
- */
 
 package org.igv.renderer;
 
diff --git a/src/main/java/org/igv/renderer/Renderer.java b/src/main/java/org/igv/renderer/Renderer.java
index d702567bee..3161c9a900 100644
--- a/src/main/java/org/igv/renderer/Renderer.java
+++ b/src/main/java/org/igv/renderer/Renderer.java
@@ -1,7 +1,3 @@
-/*
- * To change this template, choose Tools | Templates
- * and open the template in the editor.
- */
 
 package org.igv.renderer;
 
diff --git a/src/main/java/org/igv/renderer/SequenceRenderer.java b/src/main/java/org/igv/renderer/SequenceRenderer.java
index 9ac39e556e..9fbb37e4b5 100644
--- a/src/main/java/org/igv/renderer/SequenceRenderer.java
+++ b/src/main/java/org/igv/renderer/SequenceRenderer.java
@@ -1,7 +1,3 @@
-/*
- * To change this template, choose Tools | Templates
- * and open the template in the editor.
- */
 package org.igv.renderer;
 
 import org.igv.Globals;
diff --git a/src/main/java/org/igv/renderer/SpliceJunctionRenderer.java b/src/main/java/org/igv/renderer/SpliceJunctionRenderer.java
index 5a89603df4..b01843fd2a 100644
--- a/src/main/java/org/igv/renderer/SpliceJunctionRenderer.java
+++ b/src/main/java/org/igv/renderer/SpliceJunctionRenderer.java
@@ -1,6 +1,5 @@
  package org.igv.renderer;
 
-//~--- non-JDK imports --------------------------------------------------------
 
  import htsjdk.tribble.Feature;
  import org.igv.Globals;
diff --git a/src/main/java/org/igv/renderer/XYPlotRenderer.java b/src/main/java/org/igv/renderer/XYPlotRenderer.java
index 166ecd518d..45f30b6264 100644
--- a/src/main/java/org/igv/renderer/XYPlotRenderer.java
+++ b/src/main/java/org/igv/renderer/XYPlotRenderer.java
@@ -1,10 +1,5 @@
-/*
- * To change this template, choose Tools | Templates
- * and open the template in the editor.
- */
 package org.igv.renderer;
 
-//~--- non-JDK imports --------------------------------------------------------
 
 import org.igv.feature.LocusScore;
 import org.igv.prefs.IGVPreferences;
diff --git a/src/main/java/org/igv/sam/Alignment.java b/src/main/java/org/igv/sam/Alignment.java
index c1559a55b0..c89b8d27b9 100644
--- a/src/main/java/org/igv/sam/Alignment.java
+++ b/src/main/java/org/igv/sam/Alignment.java
@@ -1,7 +1,3 @@
-/*
- * To change this template, choose Tools | Templates
- * and open the template in the editor.
- */
 package org.igv.sam;
 
 import htsjdk.samtools.Cigar;
diff --git a/src/main/java/org/igv/sam/AlignmentBlockImpl.java b/src/main/java/org/igv/sam/AlignmentBlockImpl.java
index 8345a56721..ee08041ef8 100644
--- a/src/main/java/org/igv/sam/AlignmentBlockImpl.java
+++ b/src/main/java/org/igv/sam/AlignmentBlockImpl.java
@@ -1,7 +1,3 @@
-/*
- * To change this template, choose Tools | Templates
- * and open the template in the editor.
- */
 package org.igv.sam;
 
 public class AlignmentBlockImpl implements AlignmentBlock {
diff --git a/src/main/java/org/igv/sam/AlignmentPacker.java b/src/main/java/org/igv/sam/AlignmentPacker.java
index 50c81afd20..ec02ced9d6 100644
--- a/src/main/java/org/igv/sam/AlignmentPacker.java
+++ b/src/main/java/org/igv/sam/AlignmentPacker.java
@@ -1,7 +1,3 @@
-/*
- * To change this template, choose Tools | Templates
- * and open the template in the editor.
- */
 package org.igv.sam;
 
 import htsjdk.samtools.SAMTag;
diff --git a/src/main/java/org/igv/sam/CoverageTrack.java b/src/main/java/org/igv/sam/CoverageTrack.java
index 3a8a5a559d..6c0448e1c6 100644
--- a/src/main/java/org/igv/sam/CoverageTrack.java
+++ b/src/main/java/org/igv/sam/CoverageTrack.java
@@ -1,7 +1,3 @@
-/*
- * To change this template, choose Tools | Templates
- * and open the template in the editor.
- */
 package org.igv.sam;
 
 import org.igv.Globals;
diff --git a/src/main/java/org/igv/sam/DotAlignedAlignment.java b/src/main/java/org/igv/sam/DotAlignedAlignment.java
index e1ff0029bf..6136f9ff3e 100644
--- a/src/main/java/org/igv/sam/DotAlignedAlignment.java
+++ b/src/main/java/org/igv/sam/DotAlignedAlignment.java
@@ -1,7 +1,3 @@
-/*
- * To change this template, choose Tools | Templates
- * and open the template in the editor.
- */
 package org.igv.sam;
 
 import org.igv.feature.LocusScore;
diff --git a/src/main/java/org/igv/sam/EWigTrack.java b/src/main/java/org/igv/sam/EWigTrack.java
index c51ea81f57..a8715fbdeb 100644
--- a/src/main/java/org/igv/sam/EWigTrack.java
+++ b/src/main/java/org/igv/sam/EWigTrack.java
@@ -1,7 +1,3 @@
-/*
- * To change this template, choose Tools | Templates
- * and open the template in the editor.
- */
 package org.igv.sam;
 
 import org.igv.feature.Locus;
diff --git a/src/main/java/org/igv/sam/EmptyAlignmentIterator.java b/src/main/java/org/igv/sam/EmptyAlignmentIterator.java
index abffe64428..45e1aa2496 100644
--- a/src/main/java/org/igv/sam/EmptyAlignmentIterator.java
+++ b/src/main/java/org/igv/sam/EmptyAlignmentIterator.java
@@ -1,7 +1,3 @@
-/*
- * To change this template, choose Tools | Templates
- * and open the template in the editor.
- */
 package org.igv.sam;
 
 import htsjdk.samtools.util.CloseableIterator;
diff --git a/src/main/java/org/igv/sam/ReadMate.java b/src/main/java/org/igv/sam/ReadMate.java
index 5629d0b2d5..293ceb6c8d 100644
--- a/src/main/java/org/igv/sam/ReadMate.java
+++ b/src/main/java/org/igv/sam/ReadMate.java
@@ -1,7 +1,3 @@
-/*
- * To change this template, choose Tools | Templates
- * and open the template in the editor.
- */
 package org.igv.sam;
 
 
diff --git a/src/main/java/org/igv/sam/ReducedMemoryAlignment.java b/src/main/java/org/igv/sam/ReducedMemoryAlignment.java
index fa1291d07b..e672b8284e 100644
--- a/src/main/java/org/igv/sam/ReducedMemoryAlignment.java
+++ b/src/main/java/org/igv/sam/ReducedMemoryAlignment.java
@@ -1,7 +1,3 @@
-/*
- * To change this template, choose Tools | Templates
- * and open the template in the editor.
- */
 package org.igv.sam;
 
 import org.igv.logging.*;
diff --git a/src/main/java/org/igv/sam/SAMAlignment.java b/src/main/java/org/igv/sam/SAMAlignment.java
index d422d6cd94..a849ba3755 100644
--- a/src/main/java/org/igv/sam/SAMAlignment.java
+++ b/src/main/java/org/igv/sam/SAMAlignment.java
@@ -1,7 +1,3 @@
-/*
- * To change this template, choose Tools | Templates
- * and open the template in the editor.
- */
 package org.igv.sam;
 
 import htsjdk.samtools.*;
diff --git a/src/main/java/org/igv/sam/reader/AlignmentParser.java b/src/main/java/org/igv/sam/reader/AlignmentParser.java
index fc4efde09d..a77f3d8c97 100644
--- a/src/main/java/org/igv/sam/reader/AlignmentParser.java
+++ b/src/main/java/org/igv/sam/reader/AlignmentParser.java
@@ -1,7 +1,3 @@
-/*
- * To change this template, choose Tools | Templates
- * and open the template in the editor.
- */
 
 package org.igv.sam.reader;
 
diff --git a/src/main/java/org/igv/sam/reader/AlignmentReader.java b/src/main/java/org/igv/sam/reader/AlignmentReader.java
old mode 100755
new mode 100644
index 891a2e480a..9629912825
--- a/src/main/java/org/igv/sam/reader/AlignmentReader.java
+++ b/src/main/java/org/igv/sam/reader/AlignmentReader.java
@@ -1,7 +1,3 @@
-/*
- * To change this template, choose Tools | Templates
- * and open the template in the editor.
- */
 
 package org.igv.sam.reader;
 
diff --git a/src/main/java/org/igv/sam/reader/DotAlignedCodec.java b/src/main/java/org/igv/sam/reader/DotAlignedCodec.java
index b2f80bd9ad..892a2077aa 100644
--- a/src/main/java/org/igv/sam/reader/DotAlignedCodec.java
+++ b/src/main/java/org/igv/sam/reader/DotAlignedCodec.java
@@ -1,7 +1,3 @@
-/*
- * To change this template, choose Tools | Templates
- * and open the template in the editor.
- */
 package org.igv.sam.reader;
 
 import org.igv.util.collections.SortingCollection;
diff --git a/src/main/java/org/igv/sam/reader/DotAlignedParser.java b/src/main/java/org/igv/sam/reader/DotAlignedParser.java
index 343760f8f9..7da86b4aa7 100644
--- a/src/main/java/org/igv/sam/reader/DotAlignedParser.java
+++ b/src/main/java/org/igv/sam/reader/DotAlignedParser.java
@@ -1,7 +1,3 @@
-/*
- * To change this template, choose Tools | Templates
- * and open the template in the editor.
- */
 package org.igv.sam.reader;
 
 import org.igv.logging.*;
diff --git a/src/main/java/org/igv/sam/reader/SAMReader.java b/src/main/java/org/igv/sam/reader/SAMReader.java
index 6352a70420..786a9da099 100644
--- a/src/main/java/org/igv/sam/reader/SAMReader.java
+++ b/src/main/java/org/igv/sam/reader/SAMReader.java
@@ -1,7 +1,3 @@
-/*
- * To change this template, choose Tools | Templates
- * and open the template in the editor.
- */
 package org.igv.sam.reader;
 
 import htsjdk.samtools.*;
diff --git a/src/main/java/org/igv/sam/reader/SamUtils.java b/src/main/java/org/igv/sam/reader/SamUtils.java
index 30a1357307..c360fa3126 100644
--- a/src/main/java/org/igv/sam/reader/SamUtils.java
+++ b/src/main/java/org/igv/sam/reader/SamUtils.java
@@ -1,6 +1,5 @@
 package org.igv.sam.reader;
 
-//~--- non-JDK imports --------------------------------------------------------
 
 //~--- JDK imports ------------------------------------------------------------
 
diff --git a/src/main/java/org/igv/sashimi/SashimiJunctionRenderer.java b/src/main/java/org/igv/sashimi/SashimiJunctionRenderer.java
index 541369dec8..0ea75cd2a7 100644
--- a/src/main/java/org/igv/sashimi/SashimiJunctionRenderer.java
+++ b/src/main/java/org/igv/sashimi/SashimiJunctionRenderer.java
@@ -1,6 +1,5 @@
 package org.igv.sashimi;
 
-//~--- non-JDK imports --------------------------------------------------------
 
 import htsjdk.tribble.Feature;
 import org.igv.Globals;
diff --git a/src/main/java/org/igv/seg/SegmentFileParser.java b/src/main/java/org/igv/seg/SegmentFileParser.java
index fd783db79d..487545b575 100644
--- a/src/main/java/org/igv/seg/SegmentFileParser.java
+++ b/src/main/java/org/igv/seg/SegmentFileParser.java
@@ -1,6 +1,5 @@
 package org.igv.seg;
 
-//~--- non-JDK imports --------------------------------------------------------
 
 import htsjdk.tribble.readers.AsciiLineReader;
 import org.igv.Globals;
diff --git a/src/main/java/org/igv/seg/SegmentedDataSet.java b/src/main/java/org/igv/seg/SegmentedDataSet.java
index 4c8158f30c..0ce8c6aadc 100644
--- a/src/main/java/org/igv/seg/SegmentedDataSet.java
+++ b/src/main/java/org/igv/seg/SegmentedDataSet.java
@@ -5,7 +5,6 @@
  */
 package org.igv.seg;
 
-//~--- non-JDK imports --------------------------------------------------------
 
 import org.igv.Globals;
 import org.igv.feature.FeatureUtils;
diff --git a/src/main/java/org/igv/session/RendererFactory.java b/src/main/java/org/igv/session/RendererFactory.java
index a778acc2fc..f46bef265e 100644
--- a/src/main/java/org/igv/session/RendererFactory.java
+++ b/src/main/java/org/igv/session/RendererFactory.java
@@ -1,7 +1,3 @@
-/*
- * To change this template, choose Tools | Templates
- * and open the template in the editor.
- */
 package org.igv.session;
 
 import org.igv.renderer.*;
diff --git a/src/main/java/org/igv/tdf/Accumulator.java b/src/main/java/org/igv/tdf/Accumulator.java
index 8b7898e8ec..03a71bc7de 100644
--- a/src/main/java/org/igv/tdf/Accumulator.java
+++ b/src/main/java/org/igv/tdf/Accumulator.java
@@ -1,7 +1,3 @@
-/*
- * To change this template, choose Tools | Templates
- * and open the template in the editor.
- */
 package org.igv.tdf;
 
 import org.apache.commons.math3.stat.StatUtils;
diff --git a/src/main/java/org/igv/tdf/BufferedByteWriter.java b/src/main/java/org/igv/tdf/BufferedByteWriter.java
index 0ec7a5c589..07f9e92aed 100644
--- a/src/main/java/org/igv/tdf/BufferedByteWriter.java
+++ b/src/main/java/org/igv/tdf/BufferedByteWriter.java
@@ -1,7 +1,3 @@
-/*
- * To change this template, choose Tools | Templates
- * and open the template in the editor.
- */
 package org.igv.tdf;
 
 import java.io.ByteArrayOutputStream;
diff --git a/src/main/java/org/igv/tdf/IBFAttributes.java b/src/main/java/org/igv/tdf/IBFAttributes.java
index cebd376dec..376661da4a 100644
--- a/src/main/java/org/igv/tdf/IBFAttributes.java
+++ b/src/main/java/org/igv/tdf/IBFAttributes.java
@@ -1,7 +1,3 @@
-/*
- * To change this template, choose Tools | Templates
- * and open the template in the editor.
- */
 
 package org.igv.tdf;
 
diff --git a/src/main/java/org/igv/tdf/IBFBin.java b/src/main/java/org/igv/tdf/IBFBin.java
index c8bd8bb716..b529110c0a 100644
--- a/src/main/java/org/igv/tdf/IBFBin.java
+++ b/src/main/java/org/igv/tdf/IBFBin.java
@@ -1,7 +1,3 @@
-/*
- * To change this template, choose Tools | Templates
- * and open the template in the editor.
- */
 
 package org.igv.tdf;
 
diff --git a/src/main/java/org/igv/tdf/IBFIndex.java b/src/main/java/org/igv/tdf/IBFIndex.java
index c88beb92ba..cd29bf5cca 100644
--- a/src/main/java/org/igv/tdf/IBFIndex.java
+++ b/src/main/java/org/igv/tdf/IBFIndex.java
@@ -1,7 +1,3 @@
-/*
- * To change this template, choose Tools | Templates
- * and open the template in the editor.
- */
 
 package org.igv.tdf;
 
diff --git a/src/main/java/org/igv/tdf/LinearIndex.java b/src/main/java/org/igv/tdf/LinearIndex.java
index 7cb21bdb55..8fc709e323 100644
--- a/src/main/java/org/igv/tdf/LinearIndex.java
+++ b/src/main/java/org/igv/tdf/LinearIndex.java
@@ -1,7 +1,3 @@
-/*
- * To change this template, choose Tools | Templates
- * and open the template in the editor.
- */
 
 package org.igv.tdf;
 
diff --git a/src/main/java/org/igv/tdf/TDFBedTile.java b/src/main/java/org/igv/tdf/TDFBedTile.java
index 0042e87a90..6932fbee84 100644
--- a/src/main/java/org/igv/tdf/TDFBedTile.java
+++ b/src/main/java/org/igv/tdf/TDFBedTile.java
@@ -1,7 +1,3 @@
-/*
- * To change this template, choose Tools | Templates
- * and open the template in the editor.
- */
 package org.igv.tdf;
 
 import org.igv.util.StringUtils;
diff --git a/src/main/java/org/igv/tdf/TDFDataSource.java b/src/main/java/org/igv/tdf/TDFDataSource.java
index 57ee55502b..c90a20f2c0 100644
--- a/src/main/java/org/igv/tdf/TDFDataSource.java
+++ b/src/main/java/org/igv/tdf/TDFDataSource.java
@@ -1,7 +1,3 @@
-/*
- * To change this template, choose Tools | Templates
- * and open the template in the editor.
- */
 package org.igv.tdf;
 
 import org.igv.feature.genome.ChromAliasManager;
diff --git a/src/main/java/org/igv/tdf/TDFDataset.java b/src/main/java/org/igv/tdf/TDFDataset.java
index 5674f39910..581cee07c2 100644
--- a/src/main/java/org/igv/tdf/TDFDataset.java
+++ b/src/main/java/org/igv/tdf/TDFDataset.java
@@ -1,7 +1,3 @@
-/*
- * To change this template, choose Tools | Templates
- * and open the template in the editor.
- */
 package org.igv.tdf;
 
 import org.igv.util.StringUtils;
diff --git a/src/main/java/org/igv/tdf/TDFEntity.java b/src/main/java/org/igv/tdf/TDFEntity.java
index d9187689a0..22ce657e8d 100644
--- a/src/main/java/org/igv/tdf/TDFEntity.java
+++ b/src/main/java/org/igv/tdf/TDFEntity.java
@@ -1,7 +1,3 @@
-/*
- * To change this template, choose Tools | Templates
- * and open the template in the editor.
- */
 package org.igv.tdf;
 
 import org.igv.util.StringUtils;
diff --git a/src/main/java/org/igv/tdf/TDFFixedTile.java b/src/main/java/org/igv/tdf/TDFFixedTile.java
index aa90f32fc7..fef34b3cef 100644
--- a/src/main/java/org/igv/tdf/TDFFixedTile.java
+++ b/src/main/java/org/igv/tdf/TDFFixedTile.java
@@ -1,7 +1,3 @@
-/*
- * To change this template, choose Tools | Templates
- * and open the template in the editor.
- */
 package org.igv.tdf;
 
 import java.io.IOException;
diff --git a/src/main/java/org/igv/tdf/TDFGroup.java b/src/main/java/org/igv/tdf/TDFGroup.java
index 12ad6f7941..a476583db6 100644
--- a/src/main/java/org/igv/tdf/TDFGroup.java
+++ b/src/main/java/org/igv/tdf/TDFGroup.java
@@ -1,7 +1,3 @@
-/*
- * To change this template, choose Tools | Templates
- * and open the template in the editor.
- */
 package org.igv.tdf;
 
 import java.io.IOException;
diff --git a/src/main/java/org/igv/tdf/TDFReader.java b/src/main/java/org/igv/tdf/TDFReader.java
old mode 100755
new mode 100644
index 0e4979ef12..2d18a697aa
--- a/src/main/java/org/igv/tdf/TDFReader.java
+++ b/src/main/java/org/igv/tdf/TDFReader.java
@@ -1,7 +1,3 @@
-/*
- * To change this template, choose Tools | Templates
- * and open the template in the editor.
- */
 package org.igv.tdf;
 
 import htsjdk.samtools.seekablestream.SeekableStream;
diff --git a/src/main/java/org/igv/tdf/TDFTile.java b/src/main/java/org/igv/tdf/TDFTile.java
index fd03569224..f12e68f696 100644
--- a/src/main/java/org/igv/tdf/TDFTile.java
+++ b/src/main/java/org/igv/tdf/TDFTile.java
@@ -1,7 +1,3 @@
-/*
- * To change this template, choose Tools | Templates
- * and open the template in the editor.
- */
 
 package org.igv.tdf;
 
diff --git a/src/main/java/org/igv/tdf/TDFUtils.java b/src/main/java/org/igv/tdf/TDFUtils.java
index 46ab308381..22a2588627 100644
--- a/src/main/java/org/igv/tdf/TDFUtils.java
+++ b/src/main/java/org/igv/tdf/TDFUtils.java
@@ -1,7 +1,3 @@
-/*
- * To change this template, choose Tools | Templates
- * and open the template in the editor.
- */
 package org.igv.tdf;
 
 import org.igv.Globals;
diff --git a/src/main/java/org/igv/tdf/TDFVaryTile.java b/src/main/java/org/igv/tdf/TDFVaryTile.java
index 45ebc0dcbb..6fb5ecffb5 100644
--- a/src/main/java/org/igv/tdf/TDFVaryTile.java
+++ b/src/main/java/org/igv/tdf/TDFVaryTile.java
@@ -1,7 +1,3 @@
-/*
- * To change this template, choose Tools | Templates
- * and open the template in the editor.
- */
 package org.igv.tdf;
 
 import java.io.IOException;
diff --git a/src/main/java/org/igv/tdf/TDFWriter.java b/src/main/java/org/igv/tdf/TDFWriter.java
index 6d56d76f03..6bb7e99477 100644
--- a/src/main/java/org/igv/tdf/TDFWriter.java
+++ b/src/main/java/org/igv/tdf/TDFWriter.java
@@ -1,7 +1,3 @@
-/*
- * To change this template, choose Tools | Templates
- * and open the template in the editor.
- */
 package org.igv.tdf;
 
 import org.igv.logging.*;
diff --git a/src/main/java/org/igv/tdf/TileFactory.java b/src/main/java/org/igv/tdf/TileFactory.java
index 29ed8e72d1..702af96c91 100644
--- a/src/main/java/org/igv/tdf/TileFactory.java
+++ b/src/main/java/org/igv/tdf/TileFactory.java
@@ -1,7 +1,3 @@
-/*
- * To change this template, choose Tools | Templates
- * and open the template in the editor.
- */
 package org.igv.tdf;
 
 
diff --git a/src/main/java/org/igv/tools/CommandLineStatusMonitor.java b/src/main/java/org/igv/tools/CommandLineStatusMonitor.java
index adb4527ae8..632e3ca246 100644
--- a/src/main/java/org/igv/tools/CommandLineStatusMonitor.java
+++ b/src/main/java/org/igv/tools/CommandLineStatusMonitor.java
@@ -1,7 +1,3 @@
-/*
- * To change this template, choose Tools | Templates
- * and open the template in the editor.
- */
 package org.igv.tools;
 
 import java.io.PrintStream;
diff --git a/src/main/java/org/igv/tools/GenomeDesc.java b/src/main/java/org/igv/tools/GenomeDesc.java
index 20c613c54d..3add40ce1e 100644
--- a/src/main/java/org/igv/tools/GenomeDesc.java
+++ b/src/main/java/org/igv/tools/GenomeDesc.java
@@ -1,7 +1,3 @@
-/*
- * To change this template, choose Tools | Templates
- * and open the template in the editor.
- */
 package org.igv.tools;
 
 import java.util.List;
diff --git a/src/main/java/org/igv/tools/IgvTools.java b/src/main/java/org/igv/tools/IgvTools.java
index d956b7158f..425595b90e 100644
--- a/src/main/java/org/igv/tools/IgvTools.java
+++ b/src/main/java/org/igv/tools/IgvTools.java
@@ -1,7 +1,3 @@
-/*
- * To change this template, choose Tools | Templates
- * and open the template in the editor.
- */
 package org.igv.tools;
 
 
diff --git a/src/main/java/org/igv/tools/ListAccumulator.java b/src/main/java/org/igv/tools/ListAccumulator.java
index b4f7c915c1..6ab703643d 100644
--- a/src/main/java/org/igv/tools/ListAccumulator.java
+++ b/src/main/java/org/igv/tools/ListAccumulator.java
@@ -1,7 +1,3 @@
-/*
- * To change this template, choose Tools | Templates
- * and open the template in the editor.
- */
 package org.igv.tools;
 
 import org.igv.util.collections.DoubleArrayList;
diff --git a/src/main/java/org/igv/tools/PreprocessingException.java b/src/main/java/org/igv/tools/PreprocessingException.java
index 3db05eb215..93ec315645 100644
--- a/src/main/java/org/igv/tools/PreprocessingException.java
+++ b/src/main/java/org/igv/tools/PreprocessingException.java
@@ -1,7 +1,3 @@
-/*
- * To change this template, choose Tools | Templates
- * and open the template in the editor.
- */
 
 package org.igv.tools;
 
diff --git a/src/main/java/org/igv/tools/StatusMonitor.java b/src/main/java/org/igv/tools/StatusMonitor.java
index d62de67e3a..81fb9665e9 100644
--- a/src/main/java/org/igv/tools/StatusMonitor.java
+++ b/src/main/java/org/igv/tools/StatusMonitor.java
@@ -1,7 +1,3 @@
-/*
- * To change this template, choose Tools | Templates
- * and open the template in the editor.
- */
 
 package org.igv.tools;
 
diff --git a/src/main/java/org/igv/tools/TestFileGenerator.java b/src/main/java/org/igv/tools/TestFileGenerator.java
index cafe3f8560..66f7fac796 100644
--- a/src/main/java/org/igv/tools/TestFileGenerator.java
+++ b/src/main/java/org/igv/tools/TestFileGenerator.java
@@ -1,7 +1,3 @@
-/*
- * To change this template, choose Tools | Templates
- * and open the template in the editor.
- */
 package org.igv.tools;
 
 import org.igv.logging.*;
diff --git a/src/main/java/org/igv/tools/UCSCUtils.java b/src/main/java/org/igv/tools/UCSCUtils.java
index 78476bdc99..af3f41389f 100644
--- a/src/main/java/org/igv/tools/UCSCUtils.java
+++ b/src/main/java/org/igv/tools/UCSCUtils.java
@@ -1,7 +1,3 @@
-/*
- * To change this template, choose Tools | Templates
- * and open the template in the editor.
- */
 package org.igv.tools;
 
 import org.igv.logging.*;
diff --git a/src/main/java/org/igv/tools/parsers/AbstractParser.java b/src/main/java/org/igv/tools/parsers/AbstractParser.java
index c35a9824e3..970cc23fee 100644
--- a/src/main/java/org/igv/tools/parsers/AbstractParser.java
+++ b/src/main/java/org/igv/tools/parsers/AbstractParser.java
@@ -1,7 +1,3 @@
-/*
- * To change this template, choose Tools | Templates
- * and open the template in the editor.
- */
 
 package org.igv.tools.parsers;
 
diff --git a/src/main/java/org/igv/tools/parsers/CNParser.java b/src/main/java/org/igv/tools/parsers/CNParser.java
index c2fe52137b..6a607b4a91 100644
--- a/src/main/java/org/igv/tools/parsers/CNParser.java
+++ b/src/main/java/org/igv/tools/parsers/CNParser.java
@@ -1,7 +1,3 @@
-/*
- * To change this template, choose Tools | Templates
- * and open the template in the editor.
- */
 package org.igv.tools.parsers;
 
 import org.igv.logging.*;
diff --git a/src/main/java/org/igv/tools/parsers/DataConsumer.java b/src/main/java/org/igv/tools/parsers/DataConsumer.java
index 23add440bf..b1fac6be9b 100644
--- a/src/main/java/org/igv/tools/parsers/DataConsumer.java
+++ b/src/main/java/org/igv/tools/parsers/DataConsumer.java
@@ -1,7 +1,3 @@
-/*
- * To change this template, choose Tools | Templates
- * and open the template in the editor.
- */
 package org.igv.tools.parsers;
 
 import org.igv.track.TrackType;
diff --git a/src/main/java/org/igv/tools/parsers/ToolsWiggleParser.java b/src/main/java/org/igv/tools/parsers/ToolsWiggleParser.java
index fa27268ead..a9a5af4a06 100644
--- a/src/main/java/org/igv/tools/parsers/ToolsWiggleParser.java
+++ b/src/main/java/org/igv/tools/parsers/ToolsWiggleParser.java
@@ -1,6 +1,5 @@
 package org.igv.tools.parsers;
 
-//~--- non-JDK imports --------------------------------------------------------
 
 import org.igv.logging.*;
 import org.igv.Globals;
diff --git a/src/main/java/org/igv/tools/parsers/UnsortedException.java b/src/main/java/org/igv/tools/parsers/UnsortedException.java
index 9d7250689b..d463eca598 100644
--- a/src/main/java/org/igv/tools/parsers/UnsortedException.java
+++ b/src/main/java/org/igv/tools/parsers/UnsortedException.java
@@ -1,7 +1,3 @@
-/*
- * To change this template, choose Tools | Templates
- * and open the template in the editor.
- */
 
 package org.igv.tools.parsers;
 
diff --git a/src/main/java/org/igv/tools/sort/BedSorter.java b/src/main/java/org/igv/tools/sort/BedSorter.java
index f685a0dcf6..98633a98a5 100644
--- a/src/main/java/org/igv/tools/sort/BedSorter.java
+++ b/src/main/java/org/igv/tools/sort/BedSorter.java
@@ -1,7 +1,3 @@
-/*
- * To change this template, choose Tools | Templates
- * and open the template in the editor.
- */
 package org.igv.tools.sort;
 
 import htsjdk.tribble.readers.AsciiLineReader;
diff --git a/src/main/java/org/igv/tools/sort/CNSorter.java b/src/main/java/org/igv/tools/sort/CNSorter.java
index 0d6828656d..05459bc8e7 100644
--- a/src/main/java/org/igv/tools/sort/CNSorter.java
+++ b/src/main/java/org/igv/tools/sort/CNSorter.java
@@ -1,7 +1,3 @@
-/*
- * To change this template, choose Tools | Templates
- * and open the template in the editor.
- */
 package org.igv.tools.sort;
 
 import org.igv.logging.*;
diff --git a/src/main/java/org/igv/tools/sort/GenericSorter.java b/src/main/java/org/igv/tools/sort/GenericSorter.java
index a839a58748..24bd931873 100644
--- a/src/main/java/org/igv/tools/sort/GenericSorter.java
+++ b/src/main/java/org/igv/tools/sort/GenericSorter.java
@@ -1,7 +1,3 @@
-/*
- * To change this template, choose Tools | Templates
- * and open the template in the editor.
- */
 package org.igv.tools.sort;
 
 import htsjdk.tribble.readers.AsciiLineReader;
diff --git a/src/main/java/org/igv/tools/sort/InteractionSorter.java b/src/main/java/org/igv/tools/sort/InteractionSorter.java
index 514dbe1f9b..85bb87c4ae 100644
--- a/src/main/java/org/igv/tools/sort/InteractionSorter.java
+++ b/src/main/java/org/igv/tools/sort/InteractionSorter.java
@@ -1,7 +1,3 @@
-/*
- * To change this template, choose Tools | Templates
- * and open the template in the editor.
- */
 package org.igv.tools.sort;
 
 import htsjdk.tribble.readers.AsciiLineReader;
diff --git a/src/main/java/org/igv/tools/sort/RefgeneSorter.java b/src/main/java/org/igv/tools/sort/RefgeneSorter.java
index f9257c9523..252c953853 100644
--- a/src/main/java/org/igv/tools/sort/RefgeneSorter.java
+++ b/src/main/java/org/igv/tools/sort/RefgeneSorter.java
@@ -1,7 +1,3 @@
-/*
- * To change this template, choose Tools | Templates
- * and open the template in the editor.
- */
 package org.igv.tools.sort;
 
 import htsjdk.tribble.readers.AsciiLineReader;
diff --git a/src/main/java/org/igv/tools/sort/SAMSorter.java b/src/main/java/org/igv/tools/sort/SAMSorter.java
index d72966266f..be066c25b0 100644
--- a/src/main/java/org/igv/tools/sort/SAMSorter.java
+++ b/src/main/java/org/igv/tools/sort/SAMSorter.java
@@ -1,7 +1,3 @@
-/*
- * To change this template, choose Tools | Templates
- * and open the template in the editor.
- */
 package org.igv.tools.sort;
 
 import htsjdk.tribble.readers.AsciiLineReader;
diff --git a/src/main/java/org/igv/track/AbstractTrack.java b/src/main/java/org/igv/track/AbstractTrack.java
index da7b8b77a1..6b69a8f5de 100644
--- a/src/main/java/org/igv/track/AbstractTrack.java
+++ b/src/main/java/org/igv/track/AbstractTrack.java
@@ -1,6 +1,5 @@
 package org.igv.track;
 
-//~--- non-JDK imports --------------------------------------------------------
 
 import htsjdk.tribble.Feature;
 import org.igv.Globals;
diff --git a/src/main/java/org/igv/track/GisticTrack.java b/src/main/java/org/igv/track/GisticTrack.java
index 51330f74f8..06c92d3b84 100644
--- a/src/main/java/org/igv/track/GisticTrack.java
+++ b/src/main/java/org/igv/track/GisticTrack.java
@@ -8,7 +8,6 @@
 */
 package org.igv.track;
 
-//~--- non-JDK imports --------------------------------------------------------
 
 import org.igv.logging.*;
 import org.igv.feature.IGVFeature;
diff --git a/src/main/java/org/igv/track/RegionScoreType.java b/src/main/java/org/igv/track/RegionScoreType.java
index 02974352be..b3fddb932f 100644
--- a/src/main/java/org/igv/track/RegionScoreType.java
+++ b/src/main/java/org/igv/track/RegionScoreType.java
@@ -1,7 +1,3 @@
-/*
- * To change this template, choose Tools | Templates
- * and open the template in the editor.
- */
 
 package org.igv.track;
 
diff --git a/src/main/java/org/igv/track/RenderContext.java b/src/main/java/org/igv/track/RenderContext.java
index b4d7c5048e..bbc7d8d7e6 100644
--- a/src/main/java/org/igv/track/RenderContext.java
+++ b/src/main/java/org/igv/track/RenderContext.java
@@ -1,7 +1,3 @@
-/*
- * To change this template, choose Tools | Templates
- * and open the template in the editor.
- */
 package org.igv.track;
 
 import org.igv.prefs.PreferencesManager;
diff --git a/src/main/java/org/igv/track/SequenceTrack.java b/src/main/java/org/igv/track/SequenceTrack.java
index cd2891b372..1a6ad0ac95 100644
--- a/src/main/java/org/igv/track/SequenceTrack.java
+++ b/src/main/java/org/igv/track/SequenceTrack.java
@@ -1,6 +1,5 @@
 package org.igv.track;
 
-//~--- non-JDK imports --------------------------------------------------------
 
 import org.igv.event.IGVEvent;
 import org.igv.logging.*;
diff --git a/src/main/java/org/igv/track/TestUtils.java b/src/main/java/org/igv/track/TestUtils.java
index 1f34d92fca..807c4599af 100644
--- a/src/main/java/org/igv/track/TestUtils.java
+++ b/src/main/java/org/igv/track/TestUtils.java
@@ -1,7 +1,3 @@
-/*
- * To change this template, choose Tools | Templates
- * and open the template in the editor.
- */
 
 package org.igv.track;
 
diff --git a/src/main/java/org/igv/track/Track.java b/src/main/java/org/igv/track/Track.java
index f8c39b84fb..d2490a85ba 100644
--- a/src/main/java/org/igv/track/Track.java
+++ b/src/main/java/org/igv/track/Track.java
@@ -1,7 +1,3 @@
-/*
- * To change this template, choose Tools | Templates
- * and open the template in the editor.
- */
 package org.igv.track;
 
 
diff --git a/src/main/java/org/igv/track/TrackGroup.java b/src/main/java/org/igv/track/TrackGroup.java
index 565fdf3159..9d70ceca86 100644
--- a/src/main/java/org/igv/track/TrackGroup.java
+++ b/src/main/java/org/igv/track/TrackGroup.java
@@ -1,7 +1,3 @@
-/*
-* To change this template, choose Tools | Templates
-* and open the template in the editor.
- */
 package org.igv.track;
 
 //~--- JDK imports ------------------------------------------------------------
diff --git a/src/main/java/org/igv/track/TrackReader.java b/src/main/java/org/igv/track/TrackReader.java
index 9eca9bb4c2..26a655f4de 100644
--- a/src/main/java/org/igv/track/TrackReader.java
+++ b/src/main/java/org/igv/track/TrackReader.java
@@ -1,7 +1,3 @@
-/*
- * To change this template, choose Tools | Templates
- * and open the template in the editor.
- */
 
 package org.igv.track;
 
diff --git a/src/main/java/org/igv/track/TrackType.java b/src/main/java/org/igv/track/TrackType.java
index 809195cdca..be21c180d5 100644
--- a/src/main/java/org/igv/track/TrackType.java
+++ b/src/main/java/org/igv/track/TrackType.java
@@ -1,7 +1,3 @@
-/*
- * To change this template, choose Tools | Templates
- * and open the template in the editor.
- */
 
 package org.igv.track;
 
diff --git a/src/main/java/org/igv/track/WindowFunction.java b/src/main/java/org/igv/track/WindowFunction.java
index 6be7f66ddf..47508b1cbf 100644
--- a/src/main/java/org/igv/track/WindowFunction.java
+++ b/src/main/java/org/igv/track/WindowFunction.java
@@ -1,7 +1,3 @@
-/*
- * To change this template, choose Tools | Templates
- * and open the template in the editor.
- */
 
 package org.igv.track;
 
diff --git a/src/main/java/org/igv/ui/AbstractDataPanelTool.java b/src/main/java/org/igv/ui/AbstractDataPanelTool.java
index 0b8accad5f..a28f9fd083 100644
--- a/src/main/java/org/igv/ui/AbstractDataPanelTool.java
+++ b/src/main/java/org/igv/ui/AbstractDataPanelTool.java
@@ -1,7 +1,3 @@
-/*
- * To change this template, choose Tools | Templates
- * and open the template in the editor.
- */
 
 package org.igv.ui;
 
diff --git a/src/main/java/org/igv/ui/AttributeCheckList.java b/src/main/java/org/igv/ui/AttributeCheckList.java
index 21f6abfd8d..c3ed6de28c 100644
--- a/src/main/java/org/igv/ui/AttributeCheckList.java
+++ b/src/main/java/org/igv/ui/AttributeCheckList.java
@@ -1,7 +1,3 @@
-/*
- * To change this template, choose Tools | Templates
- * and open the template in the editor.
- */
 
 package org.igv.ui;
 
diff --git a/src/main/java/org/igv/ui/DefaultExceptionHandler.java b/src/main/java/org/igv/ui/DefaultExceptionHandler.java
index cdd540e7fa..9e5b43636d 100644
--- a/src/main/java/org/igv/ui/DefaultExceptionHandler.java
+++ b/src/main/java/org/igv/ui/DefaultExceptionHandler.java
@@ -1,7 +1,3 @@
-/*
- * To change this template, choose Tools | Templates
- * and open the template in the editor.
- */
 package org.igv.ui;
 
 import org.igv.logging.*;
diff --git a/src/main/java/org/igv/ui/FontManager.java b/src/main/java/org/igv/ui/FontManager.java
index 64dc496176..df90ae4b14 100644
--- a/src/main/java/org/igv/ui/FontManager.java
+++ b/src/main/java/org/igv/ui/FontManager.java
@@ -1,7 +1,3 @@
-/*
- * To change this template, choose Tools | Templates
- * and open the template in the editor.
- */
 
 package org.igv.ui;
 
diff --git a/src/main/java/org/igv/ui/GlobalKeyDispatcher.java b/src/main/java/org/igv/ui/GlobalKeyDispatcher.java
index 443c93ce21..0624ea31cc 100644
--- a/src/main/java/org/igv/ui/GlobalKeyDispatcher.java
+++ b/src/main/java/org/igv/ui/GlobalKeyDispatcher.java
@@ -1,7 +1,3 @@
-/*
- * To change this template, choose Tools | Templates
- * and open the template in the editor.
- */
 package org.igv.ui;
 
 import htsjdk.tribble.Feature;
diff --git a/src/main/java/org/igv/ui/HeatmapScaleDialog.java b/src/main/java/org/igv/ui/HeatmapScaleDialog.java
index 5e5356e77d..dcfd59322f 100644
--- a/src/main/java/org/igv/ui/HeatmapScaleDialog.java
+++ b/src/main/java/org/igv/ui/HeatmapScaleDialog.java
@@ -1,7 +1,3 @@
-/*
- * To change this template, choose Tools | Templates
- * and open the template in the editor.
- */
 
 /*
  * HeatmapScaleDialog.java
diff --git a/src/main/java/org/igv/ui/ResourceFileBuilder.java b/src/main/java/org/igv/ui/ResourceFileBuilder.java
index ba278bc029..93bb9ab857 100644
--- a/src/main/java/org/igv/ui/ResourceFileBuilder.java
+++ b/src/main/java/org/igv/ui/ResourceFileBuilder.java
@@ -1,6 +1,5 @@
 package org.igv.ui;
 
-//~--- non-JDK imports --------------------------------------------------------
 
 
 import org.igv.ui.color.ColorUtilities;
diff --git a/src/main/java/org/igv/ui/ResourceFileBuilderDialog.java b/src/main/java/org/igv/ui/ResourceFileBuilderDialog.java
index 928130ea51..8168d49391 100644
--- a/src/main/java/org/igv/ui/ResourceFileBuilderDialog.java
+++ b/src/main/java/org/igv/ui/ResourceFileBuilderDialog.java
@@ -1,7 +1,3 @@
-/*
- * To change this template, choose Tools | Templates
- * and open the template in the editor.
- */
 package org.igv.ui;
 
 import com.jidesoft.plaf.LookAndFeelFactory;
diff --git a/src/main/java/org/igv/ui/UserDefinedGenomeCheckList.java b/src/main/java/org/igv/ui/UserDefinedGenomeCheckList.java
index 19b0f13ddc..008419ee83 100644
--- a/src/main/java/org/igv/ui/UserDefinedGenomeCheckList.java
+++ b/src/main/java/org/igv/ui/UserDefinedGenomeCheckList.java
@@ -1,7 +1,3 @@
-/*
- * To change this template, choose Tools | Templates
- * and open the template in the editor.
- */
 
 package org.igv.ui;
 
diff --git a/src/main/java/org/igv/ui/action/ClearRegionsMenuAction.java b/src/main/java/org/igv/ui/action/ClearRegionsMenuAction.java
index 66dca678e1..7b0990ebc6 100644
--- a/src/main/java/org/igv/ui/action/ClearRegionsMenuAction.java
+++ b/src/main/java/org/igv/ui/action/ClearRegionsMenuAction.java
@@ -1,7 +1,3 @@
-/*
- * To change this template, choose Tools | Templates
- * and open the template in the editor.
- */
 package org.igv.ui.action;
 
 import org.igv.logging.*;
diff --git a/src/main/java/org/igv/ui/action/ExportRegionsMenuAction.java b/src/main/java/org/igv/ui/action/ExportRegionsMenuAction.java
index 8439838c56..08dc272540 100644
--- a/src/main/java/org/igv/ui/action/ExportRegionsMenuAction.java
+++ b/src/main/java/org/igv/ui/action/ExportRegionsMenuAction.java
@@ -1,7 +1,3 @@
-/*
- * To change this template, choose Tools | Templates
- * and open the template in the editor.
- */
 package org.igv.ui.action;
 
 import org.igv.logging.*;
diff --git a/src/main/java/org/igv/ui/action/FilterTracksMenuAction.java b/src/main/java/org/igv/ui/action/FilterTracksMenuAction.java
index bfcdacca07..4514e57e9f 100644
--- a/src/main/java/org/igv/ui/action/FilterTracksMenuAction.java
+++ b/src/main/java/org/igv/ui/action/FilterTracksMenuAction.java
@@ -1,7 +1,3 @@
-/*
- * To change this template, choose Tools | Templates
- * and open the template in the editor.
- */
 package org.igv.ui.action;
 
 import org.igv.event.IGVEventBus;
diff --git a/src/main/java/org/igv/ui/action/FitDataToWindowMenuAction.java b/src/main/java/org/igv/ui/action/FitDataToWindowMenuAction.java
index 73c9357362..cb540479c9 100644
--- a/src/main/java/org/igv/ui/action/FitDataToWindowMenuAction.java
+++ b/src/main/java/org/igv/ui/action/FitDataToWindowMenuAction.java
@@ -1,7 +1,3 @@
-/*
- * To change this template, choose Tools | Templates
- * and open the template in the editor.
- */
 package org.igv.ui.action;
 
 import org.igv.logging.*;
diff --git a/src/main/java/org/igv/ui/action/GroupTracksMenuAction.java b/src/main/java/org/igv/ui/action/GroupTracksMenuAction.java
index 2e5fb33b9d..66fcca0aa4 100644
--- a/src/main/java/org/igv/ui/action/GroupTracksMenuAction.java
+++ b/src/main/java/org/igv/ui/action/GroupTracksMenuAction.java
@@ -1,7 +1,3 @@
-/*
- * To change this template, choose Tools | Templates
- * and open the template in the editor.
- */
 package org.igv.ui.action;
 
 import org.igv.ui.AttributeSelectionDialog;
diff --git a/src/main/java/org/igv/ui/action/ImportRegionsMenuAction.java b/src/main/java/org/igv/ui/action/ImportRegionsMenuAction.java
index 3d08722ad9..2c5b2c07bc 100644
--- a/src/main/java/org/igv/ui/action/ImportRegionsMenuAction.java
+++ b/src/main/java/org/igv/ui/action/ImportRegionsMenuAction.java
@@ -1,7 +1,3 @@
-/*
- * To change this template, choose Tools | Templates
- * and open the template in the editor.
- */
 package org.igv.ui.action;
 
 import org.igv.logging.*;
diff --git a/src/main/java/org/igv/ui/action/LoadFilesMenuAction.java b/src/main/java/org/igv/ui/action/LoadFilesMenuAction.java
index 7715c6ed1d..28322cd2d4 100644
--- a/src/main/java/org/igv/ui/action/LoadFilesMenuAction.java
+++ b/src/main/java/org/igv/ui/action/LoadFilesMenuAction.java
@@ -1,7 +1,3 @@
-/*
- * To change this template, choose Tools | Templates
- * and open the template in the editor.
- */
 package org.igv.ui.action;
 
 import org.igv.logging.LogManager;
diff --git a/src/main/java/org/igv/ui/action/LoadFromDatabaseAction.java b/src/main/java/org/igv/ui/action/LoadFromDatabaseAction.java
index 218025816c..7e296d64d2 100644
--- a/src/main/java/org/igv/ui/action/LoadFromDatabaseAction.java
+++ b/src/main/java/org/igv/ui/action/LoadFromDatabaseAction.java
@@ -1,10 +1,5 @@
-/*
- * To change this template, choose Tools | Templates
- * and open the template in the editor.
- */
 package org.igv.ui.action;
 
-//~--- non-JDK imports --------------------------------------------------------
 
 import org.igv.logging.*;
 import org.igv.prefs.IGVPreferences;
diff --git a/src/main/java/org/igv/ui/action/LoadFromServerAction.java b/src/main/java/org/igv/ui/action/LoadFromServerAction.java
index 3db2aed463..f85d05c9ba 100644
--- a/src/main/java/org/igv/ui/action/LoadFromServerAction.java
+++ b/src/main/java/org/igv/ui/action/LoadFromServerAction.java
@@ -1,10 +1,5 @@
-/*
- * To change this template, choose Tools | Templates
- * and open the template in the editor.
- */
 package org.igv.ui.action;
 
-//~--- non-JDK imports --------------------------------------------------------
 
 import org.igv.logging.*;
 import org.igv.feature.genome.GenomeManager;
diff --git a/src/main/java/org/igv/ui/action/LoadFromURLMenuAction.java b/src/main/java/org/igv/ui/action/LoadFromURLMenuAction.java
index 219173df7e..06876da92d 100644
--- a/src/main/java/org/igv/ui/action/LoadFromURLMenuAction.java
+++ b/src/main/java/org/igv/ui/action/LoadFromURLMenuAction.java
@@ -1,7 +1,3 @@
-/*
- * To change this template, choose Tools | Templates
- * and open the template in the editor.
- */
 package org.igv.ui.action;
 
 import org.igv.feature.genome.Genome;
diff --git a/src/main/java/org/igv/ui/action/NavigateRegionsMenuAction.java b/src/main/java/org/igv/ui/action/NavigateRegionsMenuAction.java
index 27d359cc82..2d564435b4 100644
--- a/src/main/java/org/igv/ui/action/NavigateRegionsMenuAction.java
+++ b/src/main/java/org/igv/ui/action/NavigateRegionsMenuAction.java
@@ -1,7 +1,3 @@
-/*
- * To change this template, choose Tools | Templates
- * and open the template in the editor.
- */
 package org.igv.ui.action;
 
 import org.igv.logging.*;
diff --git a/src/main/java/org/igv/ui/action/NewSessionMenuAction.java b/src/main/java/org/igv/ui/action/NewSessionMenuAction.java
index 90b3cd39a3..a7aa6172e7 100644
--- a/src/main/java/org/igv/ui/action/NewSessionMenuAction.java
+++ b/src/main/java/org/igv/ui/action/NewSessionMenuAction.java
@@ -1,7 +1,3 @@
-/*
- * To change this template, choose Tools | Templates
- * and open the template in the editor.
- */
 package org.igv.ui.action;
 
 import org.igv.ui.IGV;
diff --git a/src/main/java/org/igv/ui/action/OpenSessionMenuAction.java b/src/main/java/org/igv/ui/action/OpenSessionMenuAction.java
index d09e796719..4a0b5f6fa7 100644
--- a/src/main/java/org/igv/ui/action/OpenSessionMenuAction.java
+++ b/src/main/java/org/igv/ui/action/OpenSessionMenuAction.java
@@ -1,7 +1,3 @@
-/*
- * To change this template, choose Tools | Templates
- * and open the template in the editor.
- */
 package org.igv.ui.action;
 
 import org.igv.logging.LogManager;
diff --git a/src/main/java/org/igv/ui/action/OverlayTracksMenuAction.java b/src/main/java/org/igv/ui/action/OverlayTracksMenuAction.java
index 1803992d83..c317eefd91 100644
--- a/src/main/java/org/igv/ui/action/OverlayTracksMenuAction.java
+++ b/src/main/java/org/igv/ui/action/OverlayTracksMenuAction.java
@@ -1,7 +1,3 @@
-/*
- * To change this template, choose Tools | Templates
- * and open the template in the editor.
- */
 package org.igv.ui.action;
 
 import org.igv.track.DataTrack;
diff --git a/src/main/java/org/igv/ui/action/ReloadSessionMenuAction.java b/src/main/java/org/igv/ui/action/ReloadSessionMenuAction.java
index 17d9469e71..e475a8f562 100644
--- a/src/main/java/org/igv/ui/action/ReloadSessionMenuAction.java
+++ b/src/main/java/org/igv/ui/action/ReloadSessionMenuAction.java
@@ -1,10 +1,5 @@
-/*
- * To change this template, choose Tools | Templates
- * and open the template in the editor.
- */
 package org.igv.ui.action;
 
-//~--- non-JDK imports --------------------------------------------------------
 
 import org.igv.logging.*;
 import org.igv.ui.IGV;
diff --git a/src/main/java/org/igv/ui/action/ReloadTracksMenuAction.java b/src/main/java/org/igv/ui/action/ReloadTracksMenuAction.java
index f45db1980b..6ef9381684 100644
--- a/src/main/java/org/igv/ui/action/ReloadTracksMenuAction.java
+++ b/src/main/java/org/igv/ui/action/ReloadTracksMenuAction.java
@@ -1,10 +1,5 @@
-/*
- * To change this template, choose Tools | Templates
- * and open the template in the editor.
- */
 package org.igv.ui.action;
 
-//~--- non-JDK imports --------------------------------------------------------
 
 import org.igv.logging.*;
 import org.igv.session.Session;
diff --git a/src/main/java/org/igv/ui/action/RenameTracksMenuAction.java b/src/main/java/org/igv/ui/action/RenameTracksMenuAction.java
index a030f55ef4..973f1c35ba 100644
--- a/src/main/java/org/igv/ui/action/RenameTracksMenuAction.java
+++ b/src/main/java/org/igv/ui/action/RenameTracksMenuAction.java
@@ -1,7 +1,3 @@
-/*
- * To change this template, choose Tools | Templates
- * and open the template in the editor.
- */
 package org.igv.ui.action;
 
 import org.igv.prefs.Constants;
diff --git a/src/main/java/org/igv/ui/action/ResetPreferencesAction.java b/src/main/java/org/igv/ui/action/ResetPreferencesAction.java
index 7e859599f8..ea8009d3dd 100644
--- a/src/main/java/org/igv/ui/action/ResetPreferencesAction.java
+++ b/src/main/java/org/igv/ui/action/ResetPreferencesAction.java
@@ -1,7 +1,3 @@
-/*
- * To change this template, choose Tools | Templates
- * and open the template in the editor.
- */
 package org.igv.ui.action;
 
 import org.igv.ui.IGV;
diff --git a/src/main/java/org/igv/ui/action/SaveSessionMenuAction.java b/src/main/java/org/igv/ui/action/SaveSessionMenuAction.java
index 8267e73d0b..9c139b193b 100644
--- a/src/main/java/org/igv/ui/action/SaveSessionMenuAction.java
+++ b/src/main/java/org/igv/ui/action/SaveSessionMenuAction.java
@@ -1,10 +1,5 @@
-/*
- * To change this template, choose Tools | Templates
- * and open the template in the editor.
- */
 package org.igv.ui.action;
 
-//~--- non-JDK imports --------------------------------------------------------
 
 import org.igv.DirectoryManager;
 import org.igv.logging.*;
diff --git a/src/main/java/org/igv/ui/action/SearchCommand.java b/src/main/java/org/igv/ui/action/SearchCommand.java
index 7f565c8c6a..27e844485a 100644
--- a/src/main/java/org/igv/ui/action/SearchCommand.java
+++ b/src/main/java/org/igv/ui/action/SearchCommand.java
@@ -1,6 +1,5 @@
 package org.igv.ui.action;
 
-//~--- non-JDK imports --------------------------------------------------------
 
 import htsjdk.tribble.Feature;
 import htsjdk.tribble.NamedFeature;
diff --git a/src/main/java/org/igv/ui/action/SelectHubTracksAction.java b/src/main/java/org/igv/ui/action/SelectHubTracksAction.java
index 512af33d7f..91b33efe0b 100644
--- a/src/main/java/org/igv/ui/action/SelectHubTracksAction.java
+++ b/src/main/java/org/igv/ui/action/SelectHubTracksAction.java
@@ -1,7 +1,3 @@
-/*
- * To change this template, choose Tools | Templates
- * and open the template in the editor.
- */
 package org.igv.ui.action;
 
 import org.igv.feature.genome.load.TrackConfig;
diff --git a/src/main/java/org/igv/ui/action/SetTrackHeightMenuAction.java b/src/main/java/org/igv/ui/action/SetTrackHeightMenuAction.java
index 030fa07b39..98b84e6869 100644
--- a/src/main/java/org/igv/ui/action/SetTrackHeightMenuAction.java
+++ b/src/main/java/org/igv/ui/action/SetTrackHeightMenuAction.java
@@ -1,10 +1,5 @@
-/*
-* To change this template, choose Tools | Templates
-* and open the template in the editor.
-*/
 package org.igv.ui.action;
 
-//~--- non-JDK imports --------------------------------------------------------
 
 import org.apache.commons.math3.stat.StatUtils;
 import org.igv.logging.*;
diff --git a/src/main/java/org/igv/ui/action/SortTracksMenuAction.java b/src/main/java/org/igv/ui/action/SortTracksMenuAction.java
index c4b5f6f96a..ff6d3dd644 100644
--- a/src/main/java/org/igv/ui/action/SortTracksMenuAction.java
+++ b/src/main/java/org/igv/ui/action/SortTracksMenuAction.java
@@ -1,7 +1,3 @@
-/*
- * To change this template, choose Tools | Templates
- * and open the template in the editor.
- */
 package org.igv.ui.action;
 
 import org.igv.track.AttributeManager;
diff --git a/src/main/java/org/igv/ui/panel/AttributeHeaderPanel.java b/src/main/java/org/igv/ui/panel/AttributeHeaderPanel.java
index 3ea297364a..5b217d7f8f 100644
--- a/src/main/java/org/igv/ui/panel/AttributeHeaderPanel.java
+++ b/src/main/java/org/igv/ui/panel/AttributeHeaderPanel.java
@@ -9,7 +9,6 @@
 
 package org.igv.ui.panel;
 
-//~--- non-JDK imports --------------------------------------------------------
 
 import org.igv.Globals;
 import org.igv.prefs.Constants;
diff --git a/src/main/java/org/igv/ui/panel/AttributePanel.java b/src/main/java/org/igv/ui/panel/AttributePanel.java
index 3ed04ffe7f..4bdf2b867b 100644
--- a/src/main/java/org/igv/ui/panel/AttributePanel.java
+++ b/src/main/java/org/igv/ui/panel/AttributePanel.java
@@ -8,7 +8,6 @@
  */
 package org.igv.ui.panel;
 
-//~--- non-JDK imports --------------------------------------------------------
 
 import org.igv.logging.LogManager;
 import org.igv.logging.Logger;
diff --git a/src/main/java/org/igv/ui/panel/CytobandPanel.java b/src/main/java/org/igv/ui/panel/CytobandPanel.java
index 5a96653d49..23d251f440 100644
--- a/src/main/java/org/igv/ui/panel/CytobandPanel.java
+++ b/src/main/java/org/igv/ui/panel/CytobandPanel.java
@@ -8,7 +8,6 @@
  */
 package org.igv.ui.panel;
 
-//~--- non-JDK imports --------------------------------------------------------
 
 import org.igv.Globals;
 import org.igv.event.IGVEventBus;
diff --git a/src/main/java/org/igv/ui/panel/DataPanel.java b/src/main/java/org/igv/ui/panel/DataPanel.java
index 57ffed9c6b..dfce739103 100644
--- a/src/main/java/org/igv/ui/panel/DataPanel.java
+++ b/src/main/java/org/igv/ui/panel/DataPanel.java
@@ -144,10 +144,6 @@ public void paintComponent(final Graphics g) {
 
             drawAllRegions(g);
 
-
-            long dt = System.currentTimeMillis() - lastPaintTime;
-            PanTool.repaintTime(dt);
-
         } catch (Exception e) {
             MessageUtils.showMessage("Unexpected error repainting view.  See igv.log for details.");
             log.error("Error painting DataPanel", e);
diff --git a/src/main/java/org/igv/ui/panel/DataPanelPainter.java b/src/main/java/org/igv/ui/panel/DataPanelPainter.java
index 1928fe3e89..1cb118c652 100644
--- a/src/main/java/org/igv/ui/panel/DataPanelPainter.java
+++ b/src/main/java/org/igv/ui/panel/DataPanelPainter.java
@@ -1,12 +1,7 @@
-/*
- * To change this template, choose Tools | Templates
- * and open the template in the editor.
- */
 
 
 package org.igv.ui.panel;
 
-//~--- non-JDK imports --------------------------------------------------------
 
 import org.igv.logging.*;
 import org.igv.sam.AlignmentTrack;
diff --git a/src/main/java/org/igv/ui/panel/IGVPanel.java b/src/main/java/org/igv/ui/panel/IGVPanel.java
index b687d348ae..9c65b3b7b2 100644
--- a/src/main/java/org/igv/ui/panel/IGVPanel.java
+++ b/src/main/java/org/igv/ui/panel/IGVPanel.java
@@ -1,7 +1,3 @@
-/*
- * To change this template, choose Tools | Templates
- * and open the template in the editor.
- */
 package org.igv.ui.panel;
 
 import org.igv.logging.*;
diff --git a/src/main/java/org/igv/ui/panel/MouseableRegion.java b/src/main/java/org/igv/ui/panel/MouseableRegion.java
index 9400250159..a70fee064d 100644
--- a/src/main/java/org/igv/ui/panel/MouseableRegion.java
+++ b/src/main/java/org/igv/ui/panel/MouseableRegion.java
@@ -1,7 +1,3 @@
-/*
- * To change this template, choose Tools | Templates
- * and open the template in the editor.
- */
 package org.igv.ui.panel;
 
 import org.igv.track.Track;
diff --git a/src/main/java/org/igv/ui/panel/NameHeaderPanel.java b/src/main/java/org/igv/ui/panel/NameHeaderPanel.java
index be2288bc91..760161a468 100644
--- a/src/main/java/org/igv/ui/panel/NameHeaderPanel.java
+++ b/src/main/java/org/igv/ui/panel/NameHeaderPanel.java
@@ -1,7 +1,3 @@
-/*
- * To change this template, choose Tools | Templates
- * and open the template in the editor.
- */
 package org.igv.ui.panel;
 
 import org.igv.Globals;
diff --git a/src/main/java/org/igv/ui/panel/PanTool.java b/src/main/java/org/igv/ui/panel/PanTool.java
index e00433b842..c0302d7177 100644
--- a/src/main/java/org/igv/ui/panel/PanTool.java
+++ b/src/main/java/org/igv/ui/panel/PanTool.java
@@ -1,10 +1,5 @@
-/*
- * To change this template, choose Tools | Templates
- * and open the template in the editor.
- */
 package org.igv.ui.panel;
 
-//~--- non-JDK imports --------------------------------------------------------
 
 import org.apache.commons.math3.stat.StatUtils;
 import org.igv.ui.AbstractDataPanelTool;
@@ -24,15 +19,10 @@ public class PanTool extends AbstractDataPanelTool {
 
     private static int throttleTimeMS = 50;
 
-    private static double [] repaintTimes = new double[100];
-    private static int repaintTimeCount = 0;
-
     private int previousYDirection = 0;    // Drag Directions: 1=up, 0=none 0r -1=down
-    //private int lastMousePressedY;
     private int cumulativeDeltaX;
     private int cumulativeDeltaY;
     private Point lastMousePoint;
-    //private JViewport viewport;
     private JScrollBar verticalScrollBar;
     private boolean isDragging = false;
     private long lastDragEventTime = 0;
@@ -44,25 +34,14 @@ public PanTool(DataPanel owner) {
         setName("Pan");
         if (owner != null) {
             verticalScrollBar = owner.getVerticalScrollbar();
-            Container parentContainer = owner.getParent();
-            if (parentContainer != null) {
-                Container parentOfParent = parentContainer.getParent();
-                if ((parentOfParent != null) && (parentOfParent instanceof JViewport)) {
-                    //viewport = (JViewport) parentOfParent;
-                }
-            }
         }
     }
 
-
     @Override
     public Cursor getCursor() {
         return Cursor.getDefaultCursor();
     }
 
-    public Point getLastMousePoint() {
-        return lastMousePoint;
-    }
 
     @Override
     public void mousePressed(final MouseEvent e) {
@@ -74,7 +53,6 @@ public void mousePressed(final MouseEvent e) {
         lastMousePoint = e.getPoint();
         cumulativeDeltaX = 0;
         cumulativeDeltaY = 0;
-
     }
 
     public void setReferenceFrame(ReferenceFrame frame) {
@@ -111,11 +89,9 @@ final public void mouseDragged(final MouseEvent e) {
             return;
         }
 
-        //System.out.println("T=" + ctr);
         lastDragEventTime = currentTime;
 
         try {
-            Component panel = (Component) e.getSource();
             if (lastMousePoint == null) {
                 lastMousePoint = e.getPoint();
                 return;
@@ -180,20 +156,4 @@ final public void mouseDragged(final MouseEvent e) {
             lastMousePoint = e.getPoint();    // Always save the last Point
         }
     }
-
-    /**
-     * Adaptively throttle the drag time based on repaint times.  Its pointless to drag faster than we can repaint.
-     *
-     * @param t
-     */
-    public static void repaintTime(double t) {
-            repaintTimes[repaintTimeCount++] = t;
-            if (repaintTimeCount == repaintTimes.length) {
-                double p = StatUtils.percentile(repaintTimes, 95);
-                throttleTimeMS = Math.max(5, Math.min(200, (int) p));
-                repaintTimeCount = 0;
-            }
-
-    }
-
 }
diff --git a/src/main/java/org/igv/ui/panel/ReferenceFrame.java b/src/main/java/org/igv/ui/panel/ReferenceFrame.java
index 2111d57a0c..e744561102 100644
--- a/src/main/java/org/igv/ui/panel/ReferenceFrame.java
+++ b/src/main/java/org/igv/ui/panel/ReferenceFrame.java
@@ -1,7 +1,3 @@
-/*
- * To change this template, choose Tools | Templates
- * and open the template in the editor.
- */
 package org.igv.ui.panel;
 
 import org.igv.Globals;
@@ -191,7 +187,10 @@ public void setBounds(int pixelX, int widthInPixels) {
             computeLocationScale();
             computeZoom();
         }
+    }
 
+    public void setWidthInPixels(int widthInPixels) {
+        this.widthInPixels = widthInPixels;
     }
 
     /**
@@ -682,6 +681,10 @@ private synchronized void computeLocationScale() {
         }
     }
 
+    public void setScale(double scale) {
+        this.scale = scale;
+    }
+
     /**
      * Recalculate the zoom value based on current start/end
      * locationScale is not altered
diff --git a/src/main/java/org/igv/ui/panel/RegionOfInterestPanel.java b/src/main/java/org/igv/ui/panel/RegionOfInterestPanel.java
index 7c336b3bca..23cc7aa956 100644
--- a/src/main/java/org/igv/ui/panel/RegionOfInterestPanel.java
+++ b/src/main/java/org/igv/ui/panel/RegionOfInterestPanel.java
@@ -1,7 +1,3 @@
-/*
- * To change this template, choose Tools | Templates
- * and open the template in the editor.
- */
 package org.igv.ui.panel;
 
 import org.igv.Globals;
diff --git a/src/main/java/org/igv/ui/panel/RegionOfInterestTool.java b/src/main/java/org/igv/ui/panel/RegionOfInterestTool.java
index a84020efb8..740f421760 100644
--- a/src/main/java/org/igv/ui/panel/RegionOfInterestTool.java
+++ b/src/main/java/org/igv/ui/panel/RegionOfInterestTool.java
@@ -1,7 +1,3 @@
-/*
- * To change this template, choose Tools | Templates
- * and open the template in the editor.
- */
 package org.igv.ui.panel;
 
 import org.igv.feature.RegionOfInterest;
diff --git a/src/main/java/org/igv/ui/panel/TrackPanelComponent.java b/src/main/java/org/igv/ui/panel/TrackPanelComponent.java
index 9c916b7769..88162cdcec 100644
--- a/src/main/java/org/igv/ui/panel/TrackPanelComponent.java
+++ b/src/main/java/org/igv/ui/panel/TrackPanelComponent.java
@@ -1,10 +1,5 @@
-/*
- * To change this template, choose Tools | Templates
- * and open the template in the editor.
- */
 package org.igv.ui.panel;
 
-//~--- non-JDK imports --------------------------------------------------------
 
 import org.igv.logging.*;
 import org.igv.Globals;
diff --git a/src/main/java/org/igv/ui/panel/TrackPanelScrollPane.java b/src/main/java/org/igv/ui/panel/TrackPanelScrollPane.java
index d9ebe59e52..b2e27a23a6 100644
--- a/src/main/java/org/igv/ui/panel/TrackPanelScrollPane.java
+++ b/src/main/java/org/igv/ui/panel/TrackPanelScrollPane.java
@@ -1,7 +1,3 @@
-/*
- * To change this template, choose Tools | Templates
- * and open the template in the editor.
- */
 package org.igv.ui.panel;
 
 import com.jidesoft.swing.JideScrollPane;
diff --git a/src/main/java/org/igv/ui/util/CheckList.java b/src/main/java/org/igv/ui/util/CheckList.java
index 6db58bea10..4908b0f2ce 100644
--- a/src/main/java/org/igv/ui/util/CheckList.java
+++ b/src/main/java/org/igv/ui/util/CheckList.java
@@ -1,7 +1,3 @@
-/*
- * To change this template, choose Tools | Templates
- * and open the template in the editor.
- */
 
 package org.igv.ui.util;
 
diff --git a/src/main/java/org/igv/ui/util/DataPanelTool.java b/src/main/java/org/igv/ui/util/DataPanelTool.java
index ea9cc3f6ad..b1e505277d 100644
--- a/src/main/java/org/igv/ui/util/DataPanelTool.java
+++ b/src/main/java/org/igv/ui/util/DataPanelTool.java
@@ -1,7 +1,3 @@
-/*
- * To change this template, choose Tools | Templates
- * and open the template in the editor.
- */
 
 package org.igv.ui.util;
 
diff --git a/src/main/java/org/igv/ui/util/MessageUtils.java b/src/main/java/org/igv/ui/util/MessageUtils.java
index 9cee1c717b..30075d2b8d 100644
--- a/src/main/java/org/igv/ui/util/MessageUtils.java
+++ b/src/main/java/org/igv/ui/util/MessageUtils.java
@@ -1,7 +1,3 @@
-/*
- * To change this template, choose Tools | Templates
- * and open the template in the editor.
- */
 package org.igv.ui.util;
 
 import org.igv.Globals;
diff --git a/src/main/java/org/igv/ui/util/Packable.java b/src/main/java/org/igv/ui/util/Packable.java
index 1169805659..ce146c3772 100644
--- a/src/main/java/org/igv/ui/util/Packable.java
+++ b/src/main/java/org/igv/ui/util/Packable.java
@@ -1,7 +1,3 @@
-/*
- * To change this template, choose Tools | Templates
- * and open the template in the editor.
- */
 
 package org.igv.ui.util;
 
diff --git a/src/main/java/org/igv/ui/util/TracingRepaintManager.java b/src/main/java/org/igv/ui/util/TracingRepaintManager.java
index d29909ac66..352fae166c 100644
--- a/src/main/java/org/igv/ui/util/TracingRepaintManager.java
+++ b/src/main/java/org/igv/ui/util/TracingRepaintManager.java
@@ -1,7 +1,3 @@
-/*
- * To change this template, choose Tools | Templates
- * and open the template in the editor.
- */
 
 package org.igv.ui.util;
 
diff --git a/src/main/java/org/igv/ui/util/UIUtilities.java b/src/main/java/org/igv/ui/util/UIUtilities.java
index 83e3f39b81..818d6d5138 100644
--- a/src/main/java/org/igv/ui/util/UIUtilities.java
+++ b/src/main/java/org/igv/ui/util/UIUtilities.java
@@ -1,10 +1,5 @@
-/*
- * To change this template, choose Tools | Templates
- * and open the template in the editor.
- */
 package org.igv.ui.util;
 
-//~--- non-JDK imports --------------------------------------------------------
 
 import org.igv.Globals;
 import org.igv.logging.*;
diff --git a/src/main/java/org/igv/util/ArrayHeapIntSorter.java b/src/main/java/org/igv/util/ArrayHeapIntSorter.java
old mode 100755
new mode 100644
index 155eb67cff..030fc517c9
--- a/src/main/java/org/igv/util/ArrayHeapIntSorter.java
+++ b/src/main/java/org/igv/util/ArrayHeapIntSorter.java
@@ -1,7 +1,3 @@
-/*
- * To change this template, choose Tools | Templates
- * and open the template in the editor.
- */
 package org.igv.util;
 
 public class ArrayHeapIntSorter {
diff --git a/src/main/java/org/igv/util/ArrayHeapObjectSorter.java b/src/main/java/org/igv/util/ArrayHeapObjectSorter.java
index 9d03b15cf0..c49be5ab75 100644
--- a/src/main/java/org/igv/util/ArrayHeapObjectSorter.java
+++ b/src/main/java/org/igv/util/ArrayHeapObjectSorter.java
@@ -1,7 +1,3 @@
-/*
- * To change this template, choose Tools | Templates
- * and open the template in the editor.
- */
 package org.igv.util;
 
 import java.util.Comparator;
diff --git a/src/main/java/org/igv/util/AsciiEcho.java b/src/main/java/org/igv/util/AsciiEcho.java
index 6a355fe08b..0f7b64c66f 100644
--- a/src/main/java/org/igv/util/AsciiEcho.java
+++ b/src/main/java/org/igv/util/AsciiEcho.java
@@ -1,7 +1,3 @@
-/*
- * To change this template, choose Tools | Templates
- * and open the template in the editor.
- */
 
 package org.igv.util;
 
diff --git a/src/main/java/org/igv/util/FilterElement.java b/src/main/java/org/igv/util/FilterElement.java
index 31f8dbbf9c..c6c725c2f5 100644
--- a/src/main/java/org/igv/util/FilterElement.java
+++ b/src/main/java/org/igv/util/FilterElement.java
@@ -1,7 +1,3 @@
-/*
- * To change this template, choose Tools | Templates
- * and open the template in the editor.
- */
 package org.igv.util;
 
 import org.igv.track.AttributeManager;
diff --git a/src/main/java/org/igv/util/IlluminaUtils.java b/src/main/java/org/igv/util/IlluminaUtils.java
index 6725d346fc..013e90696f 100644
--- a/src/main/java/org/igv/util/IlluminaUtils.java
+++ b/src/main/java/org/igv/util/IlluminaUtils.java
@@ -1,7 +1,3 @@
-/*
- * To change this template, choose Tools | Templates
- * and open the template in the editor.
- */
 package org.igv.util;
 
 import java.io.*;
diff --git a/src/main/java/org/igv/util/IntComparator.java b/src/main/java/org/igv/util/IntComparator.java
index d734c3537d..7d0c06b677 100644
--- a/src/main/java/org/igv/util/IntComparator.java
+++ b/src/main/java/org/igv/util/IntComparator.java
@@ -1,7 +1,3 @@
-/*
- * To change this template, choose Tools | Templates
- * and open the template in the editor.
- */
 
 package org.igv.util;
 
diff --git a/src/main/java/org/igv/util/RuntimeUtils.java b/src/main/java/org/igv/util/RuntimeUtils.java
index 02bd545eb3..4f64938657 100644
--- a/src/main/java/org/igv/util/RuntimeUtils.java
+++ b/src/main/java/org/igv/util/RuntimeUtils.java
@@ -1,7 +1,3 @@
-/*
- * To change this template, choose Tools | Templates
- * and open the template in the editor.
- */
 package org.igv.util;
 
 import org.igv.logging.*;
diff --git a/src/main/java/org/igv/util/SequenceGC.java b/src/main/java/org/igv/util/SequenceGC.java
index 9c80c51a4f..0b31023a0e 100644
--- a/src/main/java/org/igv/util/SequenceGC.java
+++ b/src/main/java/org/igv/util/SequenceGC.java
@@ -1,7 +1,3 @@
-/*
- * To change this template, choose Tools | Templates
- * and open the template in the editor.
- */
 
 package org.igv.util;
 
diff --git a/src/main/java/org/igv/util/TrackFilter.java b/src/main/java/org/igv/util/TrackFilter.java
index 9c1c9af10e..1dc3559387 100644
--- a/src/main/java/org/igv/util/TrackFilter.java
+++ b/src/main/java/org/igv/util/TrackFilter.java
@@ -1,7 +1,3 @@
-/*
- * To change this template, choose Tools | Templates
- * and open the template in the editor.
- */
 
 package org.igv.util;
 
diff --git a/src/main/java/org/igv/util/Utilities.java b/src/main/java/org/igv/util/Utilities.java
index 302e0090b6..e39d14063e 100644
--- a/src/main/java/org/igv/util/Utilities.java
+++ b/src/main/java/org/igv/util/Utilities.java
@@ -1,6 +1,5 @@
 package org.igv.util;
 
-//~--- non-JDK imports --------------------------------------------------------
 
 import biz.source_code.base64Coder.Base64Coder;
 import org.igv.logging.*;
diff --git a/src/main/java/org/igv/util/collections/StringArrayList.java b/src/main/java/org/igv/util/collections/StringArrayList.java
index 8010d0d61c..23a93896df 100644
--- a/src/main/java/org/igv/util/collections/StringArrayList.java
+++ b/src/main/java/org/igv/util/collections/StringArrayList.java
@@ -1,7 +1,3 @@
-/*
- * To change this template, choose Tools | Templates
- * and open the template in the editor.
- */
 
 package org.igv.util.collections;
 
diff --git a/src/test/java/org/igv/data/IGVDatasetTest.java b/src/test/java/org/igv/data/IGVDatasetTest.java
index 5d728e5249..59b07e2388 100644
--- a/src/test/java/org/igv/data/IGVDatasetTest.java
+++ b/src/test/java/org/igv/data/IGVDatasetTest.java
@@ -1,7 +1,3 @@
-/*
- * To change this template, choose Tools | Templates
- * and open the template in the editor.
- */
 package org.igv.data;
 
 import org.igv.AbstractHeadlessTest;
diff --git a/src/test/java/org/igv/feature/FeatureUtilsTest.java b/src/test/java/org/igv/feature/FeatureUtilsTest.java
index bb8a3bc0d8..9be53022b4 100644
--- a/src/test/java/org/igv/feature/FeatureUtilsTest.java
+++ b/src/test/java/org/igv/feature/FeatureUtilsTest.java
@@ -1,7 +1,3 @@
-/*
- * To change this template, choose Tools | Templates
- * and open the template in the editor.
- */
 package org.igv.feature;
 
 import org.igv.feature.genome.Genome;
diff --git a/src/test/java/org/igv/feature/GeneTest.java b/src/test/java/org/igv/feature/GeneTest.java
index 6ab3316334..c3a9bbb707 100644
--- a/src/test/java/org/igv/feature/GeneTest.java
+++ b/src/test/java/org/igv/feature/GeneTest.java
@@ -1,7 +1,3 @@
-/*
- * To change this template, choose Tools | Templates
- * and open the template in the editor.
- */
 package org.igv.feature;
 
 import org.igv.AbstractHeadlessTest;
diff --git a/src/test/java/org/igv/feature/LocusTest.java b/src/test/java/org/igv/feature/LocusTest.java
index 6676a18701..e0dbd2f9d3 100644
--- a/src/test/java/org/igv/feature/LocusTest.java
+++ b/src/test/java/org/igv/feature/LocusTest.java
@@ -1,7 +1,3 @@
-/*
- * To change this template, choose Tools | Templates
- * and open the template in the editor.
- */
 
 package org.igv.feature;
 
diff --git a/src/test/java/org/igv/feature/ProbeToGeneMapTest.java b/src/test/java/org/igv/feature/ProbeToGeneMapTest.java
index da6fb0fd6b..bc1eceebe0 100644
--- a/src/test/java/org/igv/feature/ProbeToGeneMapTest.java
+++ b/src/test/java/org/igv/feature/ProbeToGeneMapTest.java
@@ -1,7 +1,3 @@
-/*
- * To change this template, choose Tools | Templates
- * and open the template in the editor.
- */
 package org.igv.feature;
 
 import org.igv.util.TestUtils;
diff --git a/src/test/java/org/igv/feature/TestLoadGeneManager.java b/src/test/java/org/igv/feature/TestLoadGeneManager.java
index 930c96ef79..b1f79a3980 100644
--- a/src/test/java/org/igv/feature/TestLoadGeneManager.java
+++ b/src/test/java/org/igv/feature/TestLoadGeneManager.java
@@ -1,7 +1,3 @@
-/*
- * To change this template, choose Tools | Templates
- * and open the template in the editor.
- */
 
 package org.igv.feature;
 
diff --git a/src/test/java/org/igv/feature/aa/AminoAcidManagerTest.java b/src/test/java/org/igv/feature/aa/AminoAcidManagerTest.java
index 699bf7a583..da14a2e03e 100644
--- a/src/test/java/org/igv/feature/aa/AminoAcidManagerTest.java
+++ b/src/test/java/org/igv/feature/aa/AminoAcidManagerTest.java
@@ -1,7 +1,3 @@
-/*
- * To change this template, choose Tools | Templates
- * and open the template in the editor.
- */
 package org.igv.feature.aa;
 
 import org.igv.AbstractHeadlessTest;
diff --git a/src/test/java/org/igv/feature/genome/GenomeManagerTest.java b/src/test/java/org/igv/feature/genome/GenomeManagerTest.java
index de6fb76e17..27d295e51d 100644
--- a/src/test/java/org/igv/feature/genome/GenomeManagerTest.java
+++ b/src/test/java/org/igv/feature/genome/GenomeManagerTest.java
@@ -1,7 +1,3 @@
-/*
- * To change this template, choose Tools | Templates
- * and open the template in the editor.
- */
 
 package org.igv.feature.genome;
 
diff --git a/src/test/java/org/igv/hic/HicFileLocalTest.java b/src/test/java/org/igv/hic/HicFileLocalTest.java
new file mode 100644
index 0000000000..3be2f7574c
--- /dev/null
+++ b/src/test/java/org/igv/hic/HicFileLocalTest.java
@@ -0,0 +1,49 @@
+package org.igv.hic;
+
+import org.igv.feature.genome.Genome;
+import org.igv.util.TestUtils;
+import org.junit.BeforeClass;
+import org.junit.Test;
+
+import java.io.IOException;
+import java.util.List;
+
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertTrue;
+
+public class HicFileLocalTest {
+
+    static String dataFile = TestUtils.DATA_DIR + "hic/test_chr22.hic";
+    static HicFile hicFile;
+
+    @BeforeClass
+    public static void setUp() throws Exception {
+        Genome genome = TestUtils.mockUCSCGenome();
+        hicFile = new HicFile(dataFile, genome);
+    }
+
+
+    @Test
+    public void getVersion() {
+        int version = hicFile.getVersion();
+        assertEquals(8, version);
+    }
+
+    @Test
+    public void getNormalizationVector() throws IOException {
+
+        String type = "KR";
+        String chr = "22";
+        String unit = "BP";
+        int binSize = 100000;
+        NormalizationVector normVector = hicFile.getNormalizationVector(type, chr, unit, binSize);
+        assertEquals(515, normVector.getnValues());
+
+        double[] values =  normVector.getValues(200, 300);
+        assertEquals(0.9477306190631148, values[0], 0.00001);
+
+        values = normVector.getValues(0, 100);
+        assertTrue(Double.isNaN(values[0]));
+    }
+
+}
diff --git a/src/test/java/org/igv/hic/HicFileTest.java b/src/test/java/org/igv/hic/HicFileTest.java
index 98638afd98..94bcd5ce32 100644
--- a/src/test/java/org/igv/hic/HicFileTest.java
+++ b/src/test/java/org/igv/hic/HicFileTest.java
@@ -33,7 +33,7 @@ public void getContactRecords() throws IOException {
         Region region1 = new Region("chr1", 0, 249000000);
         Region region2 = new Region("chr1", 0, 249000000);
         int binSize = 250000;
-        List<ContactRecord> records = hicFile.getContactRecords(region1, region2, "BP", binSize, true);
+        List<ContactRecord> records = hicFile.getContactRecords(region1, region2, "BP", binSize, "NONE", true);
         assertEquals(396963, records.size());
     }
 
@@ -52,4 +52,5 @@ public void getNVI() {
         String nvi = NVI.getNVI("https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/e351f7cc-7a2c-4515-ae0b-3bb2f91c986a/4DNFIMIMLMD3.hic");
         assertEquals("240094740,25900", nvi);
     }
+
 }
diff --git a/src/test/java/org/igv/preprocess/FeatureDatasetTest.java b/src/test/java/org/igv/preprocess/FeatureDatasetTest.java
index 1e7761a5d2..972e6f6ec7 100644
--- a/src/test/java/org/igv/preprocess/FeatureDatasetTest.java
+++ b/src/test/java/org/igv/preprocess/FeatureDatasetTest.java
@@ -1,7 +1,3 @@
-/*
- * To change this template, choose Tools | Templates
- * and open the template in the editor.
- */
 package org.igv.preprocess;
 
 import org.igv.AbstractHeadlessTest;
diff --git a/src/test/java/org/igv/renderer/MappedColorScaleTest.java b/src/test/java/org/igv/renderer/MappedColorScaleTest.java
index ba6e6c3456..f36ab772aa 100644
--- a/src/test/java/org/igv/renderer/MappedColorScaleTest.java
+++ b/src/test/java/org/igv/renderer/MappedColorScaleTest.java
@@ -1,7 +1,3 @@
-/*
- * To change this template, choose Tools | Templates
- * and open the template in the editor.
- */
 
 package org.igv.renderer;
 
diff --git a/src/test/java/org/igv/sam/AlignmentPackerTest.java b/src/test/java/org/igv/sam/AlignmentPackerTest.java
index c0b131548d..e3fcce6abf 100644
--- a/src/test/java/org/igv/sam/AlignmentPackerTest.java
+++ b/src/test/java/org/igv/sam/AlignmentPackerTest.java
@@ -1,7 +1,3 @@
-/*
- * To change this template, choose Tools | Templates
- * and open the template in the editor.
- */
 
 package org.igv.sam;
 
diff --git a/src/test/java/org/igv/sam/AlignmentTileLoaderTest.java b/src/test/java/org/igv/sam/AlignmentTileLoaderTest.java
index 5073bb17b5..0e08ca42be 100644
--- a/src/test/java/org/igv/sam/AlignmentTileLoaderTest.java
+++ b/src/test/java/org/igv/sam/AlignmentTileLoaderTest.java
@@ -1,7 +1,3 @@
-/*
- * To change this template, choose Tools | Templates
- * and open the template in the editor.
- */
 package org.igv.sam;
 
 import org.igv.AbstractHeadlessTest;
diff --git a/src/test/java/org/igv/sam/AsciiLineReaderTest.java b/src/test/java/org/igv/sam/AsciiLineReaderTest.java
index 83aed69eeb..62ff5087f8 100644
--- a/src/test/java/org/igv/sam/AsciiLineReaderTest.java
+++ b/src/test/java/org/igv/sam/AsciiLineReaderTest.java
@@ -1,7 +1,3 @@
-/*
- * To change this template, choose Tools | Templates
- * and open the template in the editor.
- */
 package org.igv.sam;
 
 import org.igv.util.TestUtils;
diff --git a/src/test/java/org/igv/sam/BAMFileReaderTest.java b/src/test/java/org/igv/sam/BAMFileReaderTest.java
index 78c032ef21..ed50520351 100644
--- a/src/test/java/org/igv/sam/BAMFileReaderTest.java
+++ b/src/test/java/org/igv/sam/BAMFileReaderTest.java
@@ -1,7 +1,3 @@
-/*
- * To change this template, choose Tools | Templates
- * and open the template in the editor.
- */
 
 package org.igv.sam;
 
diff --git a/src/test/java/org/igv/sam/SamIndexTest.java b/src/test/java/org/igv/sam/SamIndexTest.java
index a6082f243a..fc136fe844 100644
--- a/src/test/java/org/igv/sam/SamIndexTest.java
+++ b/src/test/java/org/igv/sam/SamIndexTest.java
@@ -1,7 +1,3 @@
-/*
- * To change this template, choose Tools | Templates
- * and open the template in the editor.
- */
 
 package org.igv.sam;
 
diff --git a/src/test/java/org/igv/sam/SamIndexerTest.java b/src/test/java/org/igv/sam/SamIndexerTest.java
index 672a0d82a2..932438d2a7 100644
--- a/src/test/java/org/igv/sam/SamIndexerTest.java
+++ b/src/test/java/org/igv/sam/SamIndexerTest.java
@@ -1,7 +1,3 @@
-/*
- * To change this template, choose Tools | Templates
- * and open the template in the editor.
- */
 
 package org.igv.sam;
 
diff --git a/src/test/java/org/igv/sam/SamQueryTextReaderTest.java b/src/test/java/org/igv/sam/SamQueryTextReaderTest.java
index 8ae7a8d568..4054a6e826 100644
--- a/src/test/java/org/igv/sam/SamQueryTextReaderTest.java
+++ b/src/test/java/org/igv/sam/SamQueryTextReaderTest.java
@@ -1,7 +1,3 @@
-/*
- * To change this template, choose Tools | Templates
- * and open the template in the editor.
- */
 package org.igv.sam;
 
 import htsjdk.samtools.util.CloseableIterator;
diff --git a/src/test/java/org/igv/sam/cram/CRAMReaderTest.java b/src/test/java/org/igv/sam/cram/CRAMReaderTest.java
index 7b518da0e6..d077eafd82 100644
--- a/src/test/java/org/igv/sam/cram/CRAMReaderTest.java
+++ b/src/test/java/org/igv/sam/cram/CRAMReaderTest.java
@@ -1,7 +1,3 @@
-/*
- * To change this template, choose Tools | Templates
- * and open the template in the editor.
- */
 
 package org.igv.sam.cram;
 
diff --git a/src/test/java/org/igv/sam/reader/BAMHttpReaderTest.java b/src/test/java/org/igv/sam/reader/BAMHttpReaderTest.java
index b023b9afce..b0a8d8a547 100644
--- a/src/test/java/org/igv/sam/reader/BAMHttpReaderTest.java
+++ b/src/test/java/org/igv/sam/reader/BAMHttpReaderTest.java
@@ -1,7 +1,3 @@
-/*
- * To change this template, choose Tools | Templates
- * and open the template in the editor.
- */
 
 package org.igv.sam.reader;
 
diff --git a/src/test/java/org/igv/tdf/TDFReadWriteTest.java b/src/test/java/org/igv/tdf/TDFReadWriteTest.java
index f5501f7489..e8f5c6727b 100644
--- a/src/test/java/org/igv/tdf/TDFReadWriteTest.java
+++ b/src/test/java/org/igv/tdf/TDFReadWriteTest.java
@@ -1,7 +1,3 @@
-/*
- * To change this template, choose Tools | Templates
- * and open the template in the editor.
- */
 package org.igv.tdf;
 
 import org.igv.track.TrackType;
diff --git a/src/test/java/org/igv/tools/AccumulatorTest.java b/src/test/java/org/igv/tools/AccumulatorTest.java
index fd52ec4834..df36b27dfa 100644
--- a/src/test/java/org/igv/tools/AccumulatorTest.java
+++ b/src/test/java/org/igv/tools/AccumulatorTest.java
@@ -1,7 +1,3 @@
-/*
- * To change this template, choose Tools | Templates
- * and open the template in the editor.
- */
 package org.igv.tools;
 
 import org.igv.track.WindowFunction;
diff --git a/src/test/java/org/igv/util/HeapSortTest.java b/src/test/java/org/igv/util/HeapSortTest.java
index bc5ee83752..dd807cc92c 100644
--- a/src/test/java/org/igv/util/HeapSortTest.java
+++ b/src/test/java/org/igv/util/HeapSortTest.java
@@ -1,7 +1,3 @@
-/*
- * To change this template, choose Tools | Templates
- * and open the template in the editor.
- */
 package org.igv.util;
 
 import org.junit.AfterClass;
diff --git a/src/test/java/org/igv/util/SequenceGCTest.java b/src/test/java/org/igv/util/SequenceGCTest.java
index 8eaebe9211..41753938e9 100644
--- a/src/test/java/org/igv/util/SequenceGCTest.java
+++ b/src/test/java/org/igv/util/SequenceGCTest.java
@@ -1,7 +1,3 @@
-/*
- * To change this template, choose Tools | Templates
- * and open the template in the editor.
- */
 
 package org.igv.util;
 
diff --git a/src/test/java/org/igv/util/collections/DoubleArrayListTest.java b/src/test/java/org/igv/util/collections/DoubleArrayListTest.java
index 411cd4ba1d..2c6e08189d 100644
--- a/src/test/java/org/igv/util/collections/DoubleArrayListTest.java
+++ b/src/test/java/org/igv/util/collections/DoubleArrayListTest.java
@@ -1,7 +1,3 @@
-/*
- * To change this template, choose Tools | Templates
- * and open the template in the editor.
- */
 
 package org.igv.util.collections;
 
diff --git a/src/test/java/org/igv/util/collections/IntArrayListTest.java b/src/test/java/org/igv/util/collections/IntArrayListTest.java
index 8c40ba83c2..a270ce2105 100644
--- a/src/test/java/org/igv/util/collections/IntArrayListTest.java
+++ b/src/test/java/org/igv/util/collections/IntArrayListTest.java
@@ -1,7 +1,3 @@
-/*
- * To change this template, choose Tools | Templates
- * and open the template in the editor.
- */
 
 package org.igv.util.collections;
 
diff --git a/test/data/hic/test_chr22.hic b/test/data/hic/test_chr22.hic
new file mode 100644
index 0000000000..30efc5b8c3
Binary files /dev/null and b/test/data/hic/test_chr22.hic differ
diff --git a/test/sessions/4dn_hic.xml b/test/sessions/4dn_hic.xml
new file mode 100644
index 0000000000..d733b94150
--- /dev/null
+++ b/test/sessions/4dn_hic.xml
@@ -0,0 +1,15 @@
+<?xml version="1.0" encoding="UTF-8" standalone="no"?>
+<Session genome="hg38" locus="chr1:83897302-85745024" nextAutoscaleGroup="2" version="8">
+    <Resources>
+        <Resource name="Hi-C on WTC-11 differentiated to cardiac muscle cell" path="https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/a844f39f-3aa7-4e21-ba09-7683e1d91ab2/4DNFIH1NZ1M8.hic" trackLine="color=&quot;rgb(0, 150, 0)&quot; altColor=&quot;rgb(0, 150, 0)&quot;" type="hic"/>
+    </Resources>
+    <Panel height="512" name="DataPanel" width="1200">
+        <Track altColor="0,150,0" arcOption="ALL" attributeKey="Hi-C on WTC-11 differentiated to cardiac muscle cell" autoscale="true" clazz="org.igv.bedpe.InteractionTrack" color="0,150,0" colorScale="ContinuousColorScale;0.0;10.0;255,255,255;0,150,0" direction="UP" fontSize="10" graphType="NESTED_ARC" height="250" id="https://4dn-open-data-public.s3.amazonaws.com/fourfront-webprod/wfoutput/a844f39f-3aa7-4e21-ba09-7683e1d91ab2/4DNFIH1NZ1M8.hic" name="Hi-C on WTC-11 differentiated to cardiac muscle cell" nvi="5303565251,25900" showBlocks="false" thickness="1" transparency="0.1" visible="true"/>
+    </Panel>
+    <Panel height="160" name="FeaturePanel" width="1200">
+        <Track attributeKey="Reference sequence" clazz="org.igv.track.SequenceTrack" fontSize="10" id="Reference sequence" name="Reference sequence" sequenceTranslationStrandValue="+" shouldShowTranslation="false" visible="true"/>
+        <Track attributeKey="MANE v1.0 - Ensembl" clazz="org.igv.track.FeatureTrack" featureNameProperty="nucAcc" featureVisibilityWindow="1615203887" fontSize="10" groupByStrand="false" id="https://ftp.ncbi.nlm.nih.gov/refseq/MANE/trackhub/data/release_1.0/MANE.GRCh38.v1.0.ensembl.bb" name="MANE v1.0 - Ensembl" visible="true"/>
+        <Track attributeKey="Refseq All" clazz="org.igv.track.FeatureTrack" fontSize="10" groupByStrand="false" id="https://hgdownload.soe.ucsc.edu/goldenPath/hg38/database/ncbiRefSeq.txt.gz" name="Refseq All" visible="true"/>
+    </Panel>
+    <PanelLayout dividerFractions="0.7569955817378498"/>
+</Session>
diff --git a/test/sessions/igv_session.xml b/test/sessions/igv_session.xml
deleted file mode 100644
index 0fe2d24803..0000000000
--- a/test/sessions/igv_session.xml
+++ /dev/null
@@ -1,35 +0,0 @@
-<?xml version="1.0" encoding="UTF-8" standalone="no"?>
-<Session genome="hg19" locus="chr8:128746987-128747034" version="8">
-    <Resources>
-        <Resource description="NA12889" index="gs://genomics-public-data/platinum-genomes/bam/NA12889_S1.bam.bai" name="NA12889" path="gs://genomics-public-data/platinum-genomes/bam/NA12889_S1.bam" type="bam"/>
-        <Resource description="NA12890" index="gs://genomics-public-data/platinum-genomes/bam/NA12890_S1.bam.bai" name="NA12890" path="gs://genomics-public-data/platinum-genomes/bam/NA12890_S1.bam" type="bam"/>
-    </Resources>
-    <Panel height="658" name="Panel1766440830967" width="1136">
-        <Track attributeKey="NA12889 Coverage" autoScale="false" clazz="org.igv.sam.CoverageTrack" colorScale="ContinuousColorScale;0.0;60.0;255,255,255;176,176,176" fontSize="10" id="gs://genomics-public-data/platinum-genomes/bam/NA12889_S1.bam_coverage" name="NA12889 Coverage" snpThreshold="0.2" visible="true">
-            <DataRange baseline="0.0" drawBaseline="true" flipAxis="false" maximum="60.0" minimum="0.0" type="LINEAR"/>
-        </Track>
-        <Track attributeKey="NA12889 Junctions" autoScale="true" clazz="org.igv.sam.SpliceJunctionTrack" fontSize="10" groupByStrand="false" height="60" id="gs://genomics-public-data/platinum-genomes/bam/NA12889_S1.bam_junctions" maxdepth="50" name="NA12889 Junctions" visible="false"/>
-        <Track attributeKey="NA12889" clazz="org.igv.sam.AlignmentTrack" color="185,185,185" displayMode="EXPANDED" experimentType="OTHER" fontSize="10" id="gs://genomics-public-data/platinum-genomes/bam/NA12889_S1.bam" name="NA12889" visible="true">
-            <RenderOptions duplicatesOption="FILTER" invertSorting="false" sortOption="BASE"/>
-        </Track>
-    </Panel>
-    <Panel height="826" name="Panel1766440833815" width="1136">
-        <Track attributeKey="NA12890 Coverage" autoScale="false" clazz="org.igv.sam.CoverageTrack" colorScale="ContinuousColorScale;0.0;60.0;255,255,255;176,176,176" fontSize="10" id="gs://genomics-public-data/platinum-genomes/bam/NA12890_S1.bam_coverage" name="NA12890 Coverage" snpThreshold="0.2" visible="true">
-            <DataRange baseline="0.0" drawBaseline="true" flipAxis="false" maximum="60.0" minimum="0.0" type="LINEAR"/>
-        </Track>
-        <Track attributeKey="NA12890 Junctions" autoScale="true" clazz="org.igv.sam.SpliceJunctionTrack" fontSize="10" groupByStrand="false" height="60" id="gs://genomics-public-data/platinum-genomes/bam/NA12890_S1.bam_junctions" maxdepth="50" name="NA12890 Junctions" visible="false"/>
-        <Track attributeKey="NA12890" clazz="org.igv.sam.AlignmentTrack" color="185,185,185" displayMode="EXPANDED" experimentType="OTHER" fontSize="10" id="gs://genomics-public-data/platinum-genomes/bam/NA12890_S1.bam" name="NA12890" visible="true">
-            <RenderOptions duplicatesOption="FILTER" invertSorting="false" sortOption="BASE"/>
-        </Track>
-    </Panel>
-    <Panel height="97" name="FeaturePanel" width="1136">
-        <Track attributeKey="Reference sequence" clazz="org.igv.track.SequenceTrack" fontSize="10" id="Reference sequence" name="Reference sequence" sequenceTranslationStrandValue="+" shouldShowTranslation="false" visible="true"/>
-        <Track attributeKey="Refseq All" clazz="org.igv.track.FeatureTrack" colorScale="ContinuousColorScale;0.0;696.0;255,255,255;0,0,178" fontSize="10" groupByStrand="false" id="https://hgdownload.soe.ucsc.edu/goldenPath/hg19/database/ncbiRefSeq.txt.gz" name="Refseq All" visible="true"/>
-    </Panel>
-    <PanelLayout dividerFractions="0.010771992818671455,0.40754039497307004,0.8168761220825853"/>
-    <HiddenAttributes>
-        <Attribute name="DATA FILE"/>
-        <Attribute name="DATA TYPE"/>
-        <Attribute name="NAME"/>
-    </HiddenAttributes>
-</Session>