diff -Nru igv-2.3.88+dfsg/debian/changelog igv-2.3.90+dfsg/debian/changelog
--- igv-2.3.88+dfsg/debian/changelog	2016-12-13 11:18:16.000000000 +0000
+++ igv-2.3.90+dfsg/debian/changelog	2017-01-14 08:41:54.000000000 +0000
@@ -1,3 +1,10 @@
+igv (2.3.90+dfsg-1) unstable; urgency=medium
+
+  * Team upload.
+  * New upstream version.
+
+ -- Sascha Steinbiss <satta@debian.org>  Sat, 14 Jan 2017 08:41:54 +0000
+
 igv (2.3.88+dfsg-1) unstable; urgency=medium
 
   * New upstream version
diff -Nru igv-2.3.88+dfsg/src/org/broad/igv/batch/CommandExecutor.java igv-2.3.90+dfsg/src/org/broad/igv/batch/CommandExecutor.java
--- igv-2.3.88+dfsg/src/org/broad/igv/batch/CommandExecutor.java	2016-11-07 10:42:41.000000000 +0000
+++ igv-2.3.90+dfsg/src/org/broad/igv/batch/CommandExecutor.java	2017-01-09 04:30:59.000000000 +0000
@@ -467,6 +467,7 @@
 
         log.debug("Run load files");
 
+
         List<String> files = StringUtils.breakQuotedString(fileString, ',');
         List<String> names = StringUtils.breakQuotedString(nameString, ',');
         List<String> indexFiles = StringUtils.breakQuotedString(indexString, ',');
diff -Nru igv-2.3.88+dfsg/src/org/broad/igv/batch/CommandListener.java igv-2.3.90+dfsg/src/org/broad/igv/batch/CommandListener.java
--- igv-2.3.88+dfsg/src/org/broad/igv/batch/CommandListener.java	2016-11-07 10:42:41.000000000 +0000
+++ igv-2.3.90+dfsg/src/org/broad/igv/batch/CommandListener.java	2017-01-09 04:30:59.000000000 +0000
@@ -360,7 +360,7 @@
                 String sortTag = params.get("sortTag");
                 result = cmdExe.loadFiles(file, index, coverage, name, format, locus, merge, params, sort, sortTag);
             } else {
-                return ("ERROR Parameter \"file\" is required");
+                result = "OK";  // No files, perhaps genome only
             }
         } else if (command.equals("/reload") || command.equals("/goto")) {
             String locus = params.get("locus");
diff -Nru igv-2.3.88+dfsg/src/org/broad/igv/data/expression/ProbeToLocusMap.java igv-2.3.90+dfsg/src/org/broad/igv/data/expression/ProbeToLocusMap.java
--- igv-2.3.88+dfsg/src/org/broad/igv/data/expression/ProbeToLocusMap.java	2016-11-07 10:42:41.000000000 +0000
+++ igv-2.3.90+dfsg/src/org/broad/igv/data/expression/ProbeToLocusMap.java	2017-01-09 04:30:59.000000000 +0000
@@ -54,7 +54,7 @@
 
     enum Platform {Affymetrix, Agilient, Illumina, Methylation, Mirna, unknown}
 
-    public static final String SERVER_URL = "http://data.broadinstitute.org";
+    public static final String SERVER_URL = "https://data.broadinstitute.org";
 
     private static Logger log = Logger.getLogger(ProbeToLocusMap.class);
     private static String affyGenesMappingURL =
diff -Nru igv-2.3.88+dfsg/src/org/broad/igv/feature/AminoAcidManager.java igv-2.3.90+dfsg/src/org/broad/igv/feature/AminoAcidManager.java
--- igv-2.3.88+dfsg/src/org/broad/igv/feature/AminoAcidManager.java	2016-11-07 10:42:41.000000000 +0000
+++ igv-2.3.90+dfsg/src/org/broad/igv/feature/AminoAcidManager.java	2017-01-09 04:30:59.000000000 +0000
@@ -174,6 +174,7 @@
      * @param sequence
      * @return
      */
+
     List<AminoAcid> getAminoAcids(Strand direction, String sequence) {
 
         // Sequence must be divisible by 3. It is the responsibility of the
@@ -184,7 +185,7 @@
         for (int i = 0; i <= sequence.length() - 3; i += 3) {
             String codon = sequence.substring(i, i + 3).toUpperCase();
             if (direction == Strand.NEGATIVE) {
-                codon = getNucleotideComplement(codon);
+                codon = getReverseComplement(codon);
             }
             AminoAcid aa = currentCodonTable.getAminoAcid(codon);
             acids.add(aa);
@@ -210,9 +211,14 @@
         if (seqBytes == null) {
             return null;
         } else {
+
+            int l = seqBytes.length;
+            int rem = l % 3;
+            int aaStart = strand == Strand.POSITIVE ? 0 : rem;
+
             String nucSequence = new String(seqBytes);
             List<AminoAcid> acids = getAminoAcids(strand, nucSequence);
-            return new AminoAcidSequence(strand, startPosition, acids, currentCodonTable.getKey());
+            return new AminoAcidSequence(strand, startPosition + aaStart, acids, currentCodonTable.getKey());
         }
     }
 
@@ -255,7 +261,7 @@
         return aa;
     }
 
-    public static String getNucleotideComplement(String sequence) {
+    public static String getReverseComplement(String sequence) {
         char[] complement = new char[sequence.length()];
         int jj = complement.length;
         for (int ii = 0; ii < sequence.length(); ii++) {
@@ -263,21 +269,29 @@
             jj--;
             switch (c) {
                 case 'T':
-                case 't':
                     complement[jj] = 'A';
                     break;
                 case 'A':
-                case 'a':
                     complement[jj] = 'T';
                     break;
                 case 'C':
-                case 'c':
                     complement[jj] = 'G';
                     break;
                 case 'G':
-                case 'g':
                     complement[jj] = 'C';
                     break;
+                case 't':
+                    complement[jj] = 'a';
+                    break;
+                case 'a':
+                    complement[jj] = 't';
+                    break;
+                case 'c':
+                    complement[jj] = 'g';
+                    break;
+                case 'g':
+                    complement[jj] = 'c';
+                    break;
                 default:
                     complement[jj] = c;
             }
diff -Nru igv-2.3.88+dfsg/src/org/broad/igv/feature/basepair/BasePairFeature.java igv-2.3.90+dfsg/src/org/broad/igv/feature/basepair/BasePairFeature.java
--- igv-2.3.88+dfsg/src/org/broad/igv/feature/basepair/BasePairFeature.java	2016-11-07 10:42:41.000000000 +0000
+++ igv-2.3.90+dfsg/src/org/broad/igv/feature/basepair/BasePairFeature.java	2017-01-09 04:30:59.000000000 +0000
@@ -70,4 +70,23 @@
     public int getEnd() {
         return endRight;
     }
+
+    public int getStartLeft() { return startLeft; }
+
+    public int getStartRight() { return startRight; }
+
+    public int getEndLeft() { return endLeft; }
+
+    public int getEndRight() { return endRight; }
+
+    public Color getColor() { return color; }
+
+
+    public String toStringNoColor() {
+        return getChr() + "\t" + startLeft + "\t" + startRight + "\t" + endLeft + "\t" + endRight;
+    }
+
+    public String toString() {
+        return toStringNoColor() + "\t" + color;
+    }
 }
diff -Nru igv-2.3.88+dfsg/src/org/broad/igv/feature/basepair/BasePairFileParser.java igv-2.3.90+dfsg/src/org/broad/igv/feature/basepair/BasePairFileParser.java
--- igv-2.3.88+dfsg/src/org/broad/igv/feature/basepair/BasePairFileParser.java	2016-11-07 10:42:41.000000000 +0000
+++ igv-2.3.90+dfsg/src/org/broad/igv/feature/basepair/BasePairFileParser.java	2017-01-09 04:30:59.000000000 +0000
@@ -17,9 +17,7 @@
 
     static Logger log = Logger.getLogger(BasePairFileParser.class);
 
-    BasePairTrack track;
-
-    public BasePairTrack loadTrack(ResourceLocator locator, Genome genome) {
+    public static BasePairData loadData(ResourceLocator locator, Genome genome) {
         AsciiLineReader reader = null;
 
         List<Color> colors = new ArrayList();
@@ -34,37 +32,35 @@
             // read lines specifying arc colors
             nextLine = reader.readLine();
             rowCounter++;
-            while (nextLine.substring(0,6).equals("color:")){
-                String[] tokens = Globals.tabPattern.split(nextLine, -1);
+            while (nextLine.substring(0, 6).equals("color:")) {
+                String[] tokens = Globals.whitespacePattern.split(nextLine, -1);
                 int r = Integer.parseInt(tokens[1]);
                 int g = Integer.parseInt(tokens[2]);
                 int b = Integer.parseInt(tokens[3]);
-                Color color = new Color(r,g,b,255);
+                Color color = new Color(r, g, b, 255);
                 colors.add(color);
                 nextLine = reader.readLine();
                 rowCounter++;
             }
 
-            for (Color color : colors){
+            for (Color color : colors) {
                 rowsByColor.put(color, new ArrayList());
             }
 
             while (nextLine != null) {
 
-                String[] tokens = Globals.tabPattern.split(nextLine, -1);
-
-                int nTokens = tokens.length;
+                String[] tokens = Globals.whitespacePattern.split(nextLine, -1);
 
                 String chr = (genome == null ? tokens[0] : genome.getCanonicalChrName(tokens[0]));   // TODO Future use
 
-                int startLeftNuc = Integer.parseInt(tokens[1])-1; // stick to IGV's 0-based coordinate convention
-                int startRightNuc = Integer.parseInt(tokens[2])-1;
-                int endLeftNuc = Integer.parseInt(tokens[3])-1;
-                int endRightNuc = Integer.parseInt(tokens[4])-1;
+                int startLeftNuc = Integer.parseInt(tokens[1]) - 1; // stick to IGV's 0-based coordinate convention
+                int startRightNuc = Integer.parseInt(tokens[2]) - 1;
+                int endLeftNuc = Integer.parseInt(tokens[3]) - 1;
+                int endRightNuc = Integer.parseInt(tokens[4]) - 1;
                 Color color = colors.get(Integer.parseInt(tokens[5]));
 
                 BasePairFeature feature;
-                if (startLeftNuc <= endRightNuc){
+                if (startLeftNuc <= endRightNuc) {
                     feature = new BasePairFeature(chr,
                             Math.min(startLeftNuc, startRightNuc),
                             Math.max(startLeftNuc, startRightNuc),
@@ -87,7 +83,7 @@
 
             }
 
-            basePairData.finish();   // Insure features are sorted by start position, important for rendering optimization
+            basePairData.finish();   // ensure features are sorted by start position, important for rendering optimization
 
         } catch (Exception e) {
             log.error("Error parsing base pair file", e);
@@ -106,8 +102,7 @@
         //    System.out.println(row);
         //}
 
-        track = new BasePairTrack(basePairData, locator.getTrackName());
-        return track;
+        return basePairData;
     }
 
-}
\ No newline at end of file
+}
diff -Nru igv-2.3.88+dfsg/src/org/broad/igv/feature/basepair/BasePairRenderer.java igv-2.3.90+dfsg/src/org/broad/igv/feature/basepair/BasePairRenderer.java
--- igv-2.3.88+dfsg/src/org/broad/igv/feature/basepair/BasePairRenderer.java	2016-11-07 10:42:41.000000000 +0000
+++ igv-2.3.90+dfsg/src/org/broad/igv/feature/basepair/BasePairRenderer.java	2017-01-09 04:30:59.000000000 +0000
@@ -12,6 +12,7 @@
 import java.awt.geom.GeneralPath;
 
 // TODO: add vertical scaling option so arcs fit on track, or clip arcs outside of track rect?
+// TODO: add visualization for very zoomed-out views
 
 public class BasePairRenderer {
 
@@ -44,7 +45,7 @@
         int end = (int) (origin + trackRectangle.width * nucsPerPixel) + 1;
         if (end <= start) return;
 
-        // TODO: should make this a function (ugh no multiple value return from java functions)
+        // TODO: make this a function
 
         java.util.List<BasePairFeature> featureList = data.getFeatures(context.getChr());
 
@@ -57,8 +58,6 @@
 
                 //System.out.println("Color: "+data.colors[i]);
                 int arcCount = 0;
-                // TODO: only render arcs whose interior overlaps the viewing area - i.e. if an arc starts left of the window and ends right of the window, should still render
-
 
                 //System.out.println("In arcRenderer.draw(): ");
                 //System.out.println("    track.width = " + trackRectangle.width);
@@ -103,9 +102,10 @@
     /**
      * Draw a filled arc between two regions of equal length
      *
-     * @param startLeft  the starting position of the feature, whether on-screen or not
-     * @param endLeft    the ending position of the feature, whether on-screen or not
-     * @param pixelWidth  the width of the arc in pixels
+     * @param startLeft  the starting position of the feature, whether on-screen or not (outer left corner of arc)
+     * @param startRight (inner left corner of arc)
+     * @param endLeft    the ending position of the feature, whether on-screen or not (inner right corner of arc)
+     * @param endRight   (outer right corner of arc)
      * @param trackRectangle
      * @param context
      * @param featureColor       the color specified for this feature.  May be null.
@@ -239,4 +239,4 @@
         g2D.setRenderingHint(RenderingHints.KEY_ANTIALIASING, RenderingHints.VALUE_ANTIALIAS_DEFAULT);
         g2D.setRenderingHint(RenderingHints.KEY_TEXT_ANTIALIASING, RenderingHints.VALUE_TEXT_ANTIALIAS_DEFAULT);
     }
-}
\ No newline at end of file
+}
diff -Nru igv-2.3.88+dfsg/src/org/broad/igv/feature/basepair/BasePairTrack.java igv-2.3.90+dfsg/src/org/broad/igv/feature/basepair/BasePairTrack.java
--- igv-2.3.88+dfsg/src/org/broad/igv/feature/basepair/BasePairTrack.java	2016-11-07 10:42:41.000000000 +0000
+++ igv-2.3.90+dfsg/src/org/broad/igv/feature/basepair/BasePairTrack.java	2017-01-09 04:30:59.000000000 +0000
@@ -1,9 +1,11 @@
 package org.broad.igv.feature.basepair;
 
 import org.apache.log4j.Logger;
+import org.broad.igv.feature.genome.*;
 import org.broad.igv.renderer.*;
 import org.broad.igv.track.AbstractTrack;
 import org.broad.igv.track.RenderContext;
+import org.broad.igv.util.ResourceLocator;
 
 import java.awt.*;
 
@@ -19,9 +21,9 @@
     private BasePairRenderer basePairRenderer = new BasePairRenderer();
     private BasePairData basePairData;
 
-    public BasePairTrack(BasePairData data, String name) {
-        super(name);
-        basePairData = data;
+    public BasePairTrack(ResourceLocator locator, String id, String name, Genome genome) {
+        super(locator, id, name);
+        basePairData = BasePairFileParser.loadData(locator, genome);
     }
 
     public void render(RenderContext context, Rectangle rect) {
diff -Nru igv-2.3.88+dfsg/src/org/broad/igv/feature/BasePairFileUtils.java igv-2.3.90+dfsg/src/org/broad/igv/feature/BasePairFileUtils.java
--- igv-2.3.88+dfsg/src/org/broad/igv/feature/BasePairFileUtils.java	1970-01-01 00:00:00.000000000 +0000
+++ igv-2.3.90+dfsg/src/org/broad/igv/feature/BasePairFileUtils.java	2017-01-09 04:30:59.000000000 +0000
@@ -0,0 +1,444 @@
+/*
+ * The MIT License (MIT)
+ *
+ * Copyright (c) 2007-2015 Broad Institute
+ *
+ * Permission is hereby granted, free of charge, to any person obtaining a copy
+ * of this software and associated documentation files (the "Software"), to deal
+ * in the Software without restriction, including without limitation the rights
+ * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+ * copies of the Software, and to permit persons to whom the Software is
+ * furnished to do so, subject to the following conditions:
+ *
+ * The above copyright notice and this permission notice shall be included in
+ * all copies or substantial portions of the Software.
+ *
+ *
+ * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+ * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+ * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+ * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+ * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+ * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
+ * THE SOFTWARE.
+ */
+
+package org.broad.igv.feature;
+
+
+import org.broad.igv.feature.basepair.BasePairFeature;
+import org.broad.igv.Globals;
+import org.broad.igv.util.Utilities;
+
+
+import java.awt.Color;
+import java.awt.Point;
+import java.io.*;
+import java.util.*;
+
+
+// multiple return from loadDotBracket() and loadConnectTable()
+class SeqLenAndPairs {
+    public int seqLen;
+    public ArrayList<Point> pairs;
+
+    public SeqLenAndPairs(int seqLen, ArrayList<Point> pairs) {
+        this.seqLen = seqLen;
+        this.pairs = pairs;
+    }
+}
+
+// multiple return from loadPairingProb()
+class SeqLenAndBinnedPairs {
+    public int seqLen;
+    public ArrayList<ArrayList<Point>> binnedPairs;
+
+    public SeqLenAndBinnedPairs(int seqLen, ArrayList<ArrayList<Point>> binnedPairs) {
+        this.seqLen = seqLen;
+        this.binnedPairs = binnedPairs;
+    }
+}
+
+
+/**
+ * @author sbusan
+ */
+public class BasePairFileUtils {
+
+    // TODO: support bpseq, stockholm, other formats?
+    // TODO: warning dialog on file overwrite
+
+    /**
+     * Convert RNA-based transcript coordinates to stranded chromosome coords for
+     * base-pairing arcs.
+     *
+     * @param arcs
+     * @param seqLen
+     * @param newLeft 1-based genomic coordinate for left-most
+     *                position for input pairs sequence after transformation.
+     *                If strand is "-", this will end up being the 3-prime end
+     *                of the transcript (but the left end in genomic coords).
+     * @param strand  "+" or "-"
+     * @return
+     */
+    static LinkedList<BasePairFeature> transformArcs(LinkedList<BasePairFeature> arcs,
+                                                     int seqLen,
+                                                     int newLeft,
+                                                     String strand) {
+        LinkedList<BasePairFeature> transArcs = new LinkedList<BasePairFeature>();
+        for (BasePairFeature arc : arcs) {
+            String chr = arc.getChr();
+            Color color = arc.getColor();
+            int startLeft, startRight, endLeft, endRight;
+            if (strand == "+") {
+                startLeft = arc.getStartLeft() + newLeft - 1;
+                startRight = arc.getStartRight() + newLeft - 1;
+                endLeft = arc.getEndLeft() + newLeft - 1;
+                endRight = arc.getEndRight() + newLeft - 1;
+            } else if (strand == "-") {
+                startLeft = seqLen - arc.getEndRight() + newLeft;
+                startRight = seqLen - arc.getEndLeft() + newLeft;
+                endLeft = seqLen - arc.getStartRight() + newLeft;
+                endRight = seqLen - arc.getStartLeft() + newLeft;
+            } else {
+                throw new RuntimeException("Unrecognized strand (options: \"+\",\"-\")");
+            }
+            BasePairFeature transArc = new BasePairFeature(chr,
+                    startLeft,
+                    startRight,
+                    endLeft,
+                    endRight,
+                    color);
+            transArcs.add(transArc);
+        }
+        return transArcs;
+    }
+
+    static SeqLenAndPairs loadDotBracket(String inFile) throws
+            FileNotFoundException, IOException {
+        // TODO: add error messages for misformatted file
+        ArrayList<Point> pairs = new ArrayList<Point>();
+        int seqLen = 0;
+
+        BufferedReader br = null;
+
+        try {
+            br = new BufferedReader(new FileReader(inFile));
+            String struct = "";
+
+            String nextLine;
+            while ((nextLine = br.readLine()) != null) {
+
+                // skip leading header lines if present
+                if (nextLine.startsWith(">") || nextLine.startsWith("#")) {
+                    continue;
+                }
+
+                String s = nextLine.trim();
+                if (Utilities.isAllLetters(s)) {
+                    // sequence line
+                    continue;
+                } else {
+                    // assumed structure line
+                    struct += s;
+                }
+            }
+
+            String leftBrackets = "([{<";
+            String rightBrackets = ")]}>";
+
+            ArrayList<LinkedList<Integer>> openIndices = new ArrayList<LinkedList<Integer>>();
+            for (int i = 0; i < leftBrackets.length(); ++i) {
+                openIndices.add(new LinkedList<Integer>());
+            }
+
+            for (int i = 0; i < struct.length(); ++i) {
+                int n = leftBrackets.indexOf(struct.charAt(i));
+                int k = rightBrackets.indexOf(struct.charAt(i));
+                if (n >= 0) {
+                    openIndices.get(n).add(i);
+                } else if (k >= 0) {
+                    int left = i + 1;
+                    int right = openIndices.get(k).pollLast() + 1;
+                    pairs.add(new Point(left, right));
+                }
+            }
+            seqLen = struct.length();
+
+        } finally {
+            if (br != null) br.close();
+        }
+
+        return new SeqLenAndPairs(seqLen, pairs);
+    }
+
+    static SeqLenAndPairs loadConnectTable(String inFile) throws
+            FileNotFoundException, IOException {
+        // TODO: add error messages for misformatted file
+        ArrayList<Point> pairs = new ArrayList<Point>();
+        int seqLen = 0;
+
+        BufferedReader br = null;
+
+        try {
+            br = new BufferedReader(new FileReader(inFile));
+            seqLen = Integer.parseInt(Globals.whitespacePattern.split(br.readLine().trim())[0]);
+
+            String nextLine;
+            int n = 1;
+            while ((nextLine = br.readLine()) != null && n <= seqLen) {
+                String[] s = Globals.whitespacePattern.split(nextLine.trim());
+                int left = Integer.parseInt(s[0]);
+                int right = Integer.parseInt(s[4]);
+                if (right > left) pairs.add(new Point(left, right));
+                n++;
+            }
+
+        } finally {
+            if (br != null) br.close();
+        }
+
+        return new SeqLenAndPairs(seqLen, pairs);
+    }
+
+    static SeqLenAndBinnedPairs loadPairingProb(String inFile) throws
+            FileNotFoundException, IOException {
+        // TODO: add probability threshold color legend to track dropdown menu
+        // TODO: support alternate thresholds, interactive threshold update from track UI?
+
+        ArrayList<ArrayList<Point>> binnedPairs = new ArrayList<ArrayList<Point>>();
+        int seqLen = 0;
+
+        double[] probThresh = {0.1, 0.3, 0.8};
+        double[] negLogTenProbThresh = {0, 0, 0};
+        for (int i = 0; i < probThresh.length; i++) {
+            negLogTenProbThresh[i] = -Math.log10(probThresh[i]);
+        }
+
+        for (int i = 0; i < probThresh.length; i++) binnedPairs.add(new ArrayList<java.awt.Point>());
+
+        BufferedReader br = null;
+
+        try {
+            br = new BufferedReader(new FileReader(inFile));
+            seqLen = Integer.parseInt(Globals.whitespacePattern.split(br.readLine().trim())[0]);
+            br.readLine();
+
+            String nextLine;
+            while ((nextLine = br.readLine()) != null) {
+                String[] s = Globals.whitespacePattern.split(nextLine.trim());
+                int left = Integer.parseInt(s[0]);
+                int right = Integer.parseInt(s[1]);
+                double negLogTenProb = Double.parseDouble(s[2]);
+                int binIndex = -1;
+                for (int i = probThresh.length - 1; i >= 0; i--) {
+                    if (negLogTenProb <= negLogTenProbThresh[i]) {
+                        binIndex = i;
+                        break;
+                    }
+                }
+                if (binIndex != -1) binnedPairs.get(binIndex).add(new Point(left, right));
+            }
+
+        } finally {
+            if (br != null) br.close();
+        }
+
+        return new SeqLenAndBinnedPairs(seqLen, binnedPairs);
+    }
+
+
+    static void writeBasePairFile(String bpFile,
+                                  ArrayList<Color> colors,
+                                  ArrayList<LinkedList<BasePairFeature>> groupedArcs) throws IOException {
+        PrintWriter pw = null;
+
+        try {
+            pw = new PrintWriter(new BufferedWriter(new FileWriter(bpFile)));
+            // first write enumerated colors header
+            for (Color color : colors) {
+                pw.println("color:\t" + color.getRed() + "\t" + color.getGreen() + "\t" + color.getBlue());
+            }
+
+            // then write arc coordinates
+            int colorIndex = 0;
+            for (LinkedList<BasePairFeature> colorGroup : groupedArcs) {
+                for (BasePairFeature arc : colorGroup) {
+                    pw.println(arc.toStringNoColor() + "\t" + colorIndex);
+                }
+                colorIndex++;
+            }
+        } finally {
+            if (pw != null) pw.close();
+        }
+    }
+
+    /**
+     * Merge adjacent basepairs into helices. This makes assumptions about input pair list order.
+     */
+    static LinkedList<BasePairFeature> pairsToHelices(ArrayList<Point> pairs,
+                                                      String chromosome) {
+        ArrayList<Point> bps = new ArrayList<Point>(pairs);
+        LinkedList<LinkedList<Point>> helixPairGroups = new LinkedList<LinkedList<Point>>();
+
+        // FIXME: there should be a much faster and more elegant way to do this
+        while (bps.size() > 0) {
+            Point bp = bps.get(0);
+            LinkedList<Point> helixPairs = new LinkedList<Point>();
+            boolean[] removePairs = new boolean[bps.size()];
+            helixPairs.add(bp);
+            removePairs[0] = true;
+            boolean endOfList = false;
+            /* - ignore other pairs starting with this left nuc
+             * - if any base pairs exist starting one nuc downstream of current left nuc
+             *   and ending one nuc upstream of current right nuc, store index to remove
+             *   and append to growing helix
+             */
+            int i = 1;
+            int skippedCount = 0;
+            if (i < bps.size()) {
+                while (bps.get(i).x == bp.x) {
+                    i++;
+                    skippedCount++;
+                    if (i >= bps.size()) {
+                        endOfList = true;
+                        break;
+                    }
+                }
+            } else {
+                endOfList = true;
+            }
+            while (i < bps.size()) {
+                if (bps.get(i).x - bp.x > 1) {
+                    // reached the end of the helix
+                    helixPairGroups.add(helixPairs);
+                    // remove helix pairs
+                    ArrayList<Point> tmpBps = new ArrayList<Point>();
+                    for (int k = 0; k < bps.size(); k++) {
+                        if (!removePairs[k]) tmpBps.add(bps.get(k));
+                    }
+                    bps = tmpBps;
+                    break;
+                } else if (bps.get(i).y - bp.y == -1) {
+                    bp = bps.get(i);
+                    helixPairs.add(bp);
+                    removePairs[i] = true;
+                }
+                i++;
+                if (i >= bps.size()) {
+                    endOfList = true;
+                    break;
+                }
+            }
+            if (endOfList) {
+                helixPairGroups.add(helixPairs);
+                // remove helix pairs
+                ArrayList<Point> tmpBps = new ArrayList<Point>();
+                for (int k = 0; k < bps.size(); k++) {
+                    if (!removePairs[k]) tmpBps.add(bps.get(k));
+                }
+                bps = tmpBps;
+            }
+        }
+
+        // convert lists of adjacent pairs to BasePairFeatures
+        LinkedList<BasePairFeature> helices = new LinkedList<BasePairFeature>();
+        for (LinkedList<Point> helixPairs : helixPairGroups) {
+            int startLeft = Integer.MAX_VALUE;
+            int startRight = 0;
+            int endLeft = Integer.MAX_VALUE;
+            int endRight = 0;
+
+            for (Point pair : helixPairs) {
+                if (pair.x < startLeft) startLeft = pair.x;
+                if (pair.x > startRight) startRight = pair.x;
+                if (pair.y < endLeft) endLeft = pair.y;
+                if (pair.y > endRight) endRight = pair.y;
+            }
+            helices.add(new BasePairFeature(chromosome,
+                    startLeft,
+                    startRight,
+                    endLeft,
+                    endRight,
+                    null));
+        }
+        return helices;
+    }
+
+    /**
+     * Convert a base pairing structure file in dot-bracket notation
+     * (also known as Vienna format) to an easily parseable .bp arcs file. Does not
+     * currently handle mapping coords to spliced transcripts.
+     */
+    public static void dotBracketToBasePairFile(String inFile,
+                                                String bpFile,
+                                                String chromosome,
+                                                String strand,
+                                                int left) throws
+            FileNotFoundException, IOException {
+
+        SeqLenAndPairs s = loadDotBracket(inFile);
+        ArrayList<Point> pairs = s.pairs;
+        int seqLen = s.seqLen;
+        LinkedList<BasePairFeature> arcs = pairsToHelices(pairs, chromosome);
+        arcs = transformArcs(arcs, seqLen, left, strand);
+        ArrayList<Color> colors = new ArrayList<Color>();
+        colors.add(Color.black);
+        ArrayList<LinkedList<BasePairFeature>> groupedArcs = new ArrayList<LinkedList<BasePairFeature>>();
+        groupedArcs.add(arcs); // list of length 1 for this case (arcs only have 1 color)
+        writeBasePairFile(bpFile, colors, groupedArcs);
+    }
+
+    /**
+     * Convert a connectivity table file as output by RNAStructure
+     * to an easily parseable .bp arcs file. Does not
+     * currently handle mapping coords to spliced transcripts.
+     */
+    public static void connectTableToBasePairFile(String inFile,
+                                                  String bpFile,
+                                                  String chromosome,
+                                                  String strand,
+                                                  int left) throws
+            FileNotFoundException, IOException {
+
+        SeqLenAndPairs s = loadConnectTable(inFile);
+        ArrayList<Point> pairs = s.pairs;
+        int seqLen = s.seqLen;
+        LinkedList<BasePairFeature> arcs = pairsToHelices(pairs, chromosome);
+        arcs = transformArcs(arcs, seqLen, left, strand);
+        ArrayList<Color> colors = new ArrayList<Color>();
+        colors.add(Color.black);
+        ArrayList<LinkedList<BasePairFeature>> groupedArcs = new ArrayList<LinkedList<BasePairFeature>>();
+        groupedArcs.add(arcs); // list of length 1 for this case (arcs only have 1 color)
+        writeBasePairFile(bpFile, colors, groupedArcs);
+    }
+
+    /**
+     * Convert a pairing probability file as output by RNAStructure
+     * and/or SuperFold to an easily parseable .bp arcs file. Does not
+     * currently handle mapping coords to spliced transcripts.
+     */
+    public static void pairingProbToBasePairFile(String inFile,
+                                                 String bpFile,
+                                                 String chromosome,
+                                                 String strand,
+                                                 int left) throws
+            FileNotFoundException, IOException {
+
+        SeqLenAndBinnedPairs s = loadPairingProb(inFile);
+        ArrayList<ArrayList<Point>> binnedPairs = s.binnedPairs;
+        int seqLen = s.seqLen;
+        ArrayList<LinkedList<BasePairFeature>> groupedArcs = new ArrayList<LinkedList<BasePairFeature>>();
+        for (ArrayList<Point> pairGroup : binnedPairs) {
+            groupedArcs.add(transformArcs(pairsToHelices(pairGroup, chromosome),
+                    seqLen, left, strand));
+        }
+        ArrayList<Color> colors = new ArrayList<Color>();
+        colors.add(new Color(255, 204, 0));
+        colors.add(new Color(72, 143, 205));
+        colors.add(new Color(81, 184, 72));
+        writeBasePairFile(bpFile, colors, groupedArcs);
+    }
+
+
+}
diff -Nru igv-2.3.88+dfsg/src/org/broad/igv/feature/Codon.java igv-2.3.90+dfsg/src/org/broad/igv/feature/Codon.java
--- igv-2.3.88+dfsg/src/org/broad/igv/feature/Codon.java	2016-11-07 10:42:41.000000000 +0000
+++ igv-2.3.90+dfsg/src/org/broad/igv/feature/Codon.java	2017-01-09 04:30:59.000000000 +0000
@@ -115,7 +115,7 @@
         }
 
         if (strand == Strand.NEGATIVE) {
-            aas = AminoAcidManager.getNucleotideComplement(aas);
+            aas = AminoAcidManager.getReverseComplement(aas);
         }
 
         this.sequence = aas;
diff -Nru igv-2.3.88+dfsg/src/org/broad/igv/feature/FeatureDB.java igv-2.3.90+dfsg/src/org/broad/igv/feature/FeatureDB.java
--- igv-2.3.88+dfsg/src/org/broad/igv/feature/FeatureDB.java	2016-11-07 10:42:41.000000000 +0000
+++ igv-2.3.90+dfsg/src/org/broad/igv/feature/FeatureDB.java	2017-01-09 04:30:59.000000000 +0000
@@ -363,7 +363,7 @@
                     }
                     tempNT = new String(nuclSequence);
                     if (bf.getStrand() == Strand.NEGATIVE) {
-                        tempNT = AminoAcidManager.getNucleotideComplement(tempNT);
+                        tempNT = AminoAcidManager.getReverseComplement(tempNT);
                     }
 
                     if (tempNT.toUpperCase().equals(brefNT)) {
diff -Nru igv-2.3.88+dfsg/src/org/broad/igv/feature/genome/GenomeManager.java igv-2.3.90+dfsg/src/org/broad/igv/feature/genome/GenomeManager.java
--- igv-2.3.88+dfsg/src/org/broad/igv/feature/genome/GenomeManager.java	2016-11-07 10:42:41.000000000 +0000
+++ igv-2.3.90+dfsg/src/org/broad/igv/feature/genome/GenomeManager.java	2017-01-09 04:30:59.000000000 +0000
@@ -147,7 +147,7 @@
             Genome newGenome = null;
 
             if (monitor != null) {
-                monitor.fireProgressChange(25);
+                monitor.fireProgress(25);
             }
 
             // Clear Feature DB
@@ -179,7 +179,7 @@
             if (aliases != null) newGenome.addChrAliases(aliases);
 
             if (monitor != null) {
-                monitor.fireProgressChange(25);
+                monitor.fireProgress(25);
             }
 
             setCurrentGenome(newGenome);
@@ -559,8 +559,10 @@
         // Look in cache first
         try {
             if (cachedFile.exists()) {
+
                 //Check to see cached version has a custom sequence
                 GenomeDescriptor cachedDescriptor = parseGenomeArchiveFile(cachedFile);
+
                 //File sizes won't be the same if the local version has a different sequence location
                 boolean remoteModfied = HttpUtils.getInstance().remoteIsNewer(cachedFile, genomeArchiveURL,
                         !cachedDescriptor.hasCustomSequenceLocation());
@@ -568,6 +570,7 @@
                 // Force an update of cached genome if file length does not equal remote content length
                 boolean forceUpdate = remoteModfied &&
                         PreferenceManager.getInstance().getAsBoolean(PreferenceManager.AUTO_UPDATE_GENOMES);
+
                 if (forceUpdate) {
                     log.info("Refreshing genome: " + genomeArchiveURL.toString());
                     File tmpFile = new File(cachedFile.getAbsolutePath() + ".tmp");
@@ -1212,7 +1215,7 @@
                                        String chrAliasFileName,
                                        String genomeDisplayName,
                                        String genomeId,
-                                       ProgressMonitor monitor)
+                                       javax.swing.ProgressMonitor monitor)
             throws IOException {
 
         File refFlatFile = null;
@@ -1235,15 +1238,18 @@
             chrAliasFile = new File(chrAliasFileName);
         }
 
-        if (monitor != null) monitor.fireProgressChange(25);
+        if (monitor != null) monitor.setProgress(25);
 
         (new GenomeImporter()).createGenomeArchive(genomeFile, genomeId,
                 genomeDisplayName, fastaFileName, refFlatFile, cytobandFile, chrAliasFile);
 
-        if (monitor != null) monitor.fireProgressChange(75);
+        if (monitor != null) monitor.setProgress(75);
 
         GenomeListItem newItem = new GenomeListItem(genomeDisplayName, genomeFile.getAbsolutePath(), genomeId);
         addGenomeItem(newItem, true);
+
+        if (monitor != null) monitor.setProgress(100);
+
         return newItem;
 
     }
@@ -1261,7 +1267,7 @@
 
         //Whether the srcGenome is simply a fasta file
         boolean isFastaFile = FastaUtils.isFastaPath(srcPath);
-        boolean showProgressDialog = !Globals.isHeadless() && !Globals.isBatch();
+
         String srcFileName = Utilities.getFileNameFromURL(srcPath);
 
         if (isFastaFile) {
@@ -1269,12 +1275,15 @@
             return downloadFasta(srcPath, targetDir, srcFileName, dialogsParent);
 
         } else if (srcFileName.endsWith(Globals.GENOME_FILE_EXTENSION)) {
-            //Most useful case of a .genome file, which contains nearly everything in it, except the
-            //sequence which is a fasta file stored elsewhere
+
+            //A .genome file, which references a remote fasta file
+
             String genomeName = Utilities.getFileNameFromURL(srcPath);
             File srcGenomeArchive = new File(targetDir, genomeName);
             RunnableResult genomeResult = HttpUtils.getInstance().downloadFile(srcPath, srcGenomeArchive);
-            if (!genomeResult.isSuccess()) return genomeResult;
+            if (!genomeResult.isSuccess()) {
+                return genomeResult;
+            }
 
             GenomeDescriptor descriptor = parseGenomeArchiveFile(srcGenomeArchive);
 
@@ -1290,14 +1299,13 @@
             }
 
             String sequenceFileName = Utilities.getFileNameFromURL(sequencePath);
-            File localSequenceFile = new File(targetDir, sequenceFileName);
 
             // Copy file directly from the server to local area
             // Shows cancellable dialog
             RunnableResult fastaResult = downloadFasta(sequencePath, targetDir, sequenceFileName, dialogsParent);
             if (fastaResult.isSuccess()) {
                 //Rewrite properties file to point to local fasta
-                rewriteSequenceLocation(targetGenomeFile, localSequenceFile.getAbsolutePath());
+                rewriteSequenceLocation(targetGenomeFile, sequenceFileName);
             }
             return fastaResult;
         } else {
@@ -1362,11 +1370,10 @@
      * the specified {@code newSequencePath}. Works by creating a temp file and renaming
      *
      * @param targetFile      A .genome file, in zip format
-     * @param newSequencePath
      * @return boolean indicating success or failure.
      * @throws IOException
      */
-    static boolean rewriteSequenceLocation(File targetFile, String newSequencePath) throws IOException {
+    static boolean rewriteSequenceLocation(File targetFile, String sequenceFileName) throws IOException {
 
         ZipFile targetZipFile = new ZipFile(targetFile);
         boolean success = false;
@@ -1385,7 +1392,7 @@
 
             //Copy over property.txt, only replacing a few properties
             inputProperties.load(reader);
-            inputProperties.put(Globals.GENOME_ARCHIVE_SEQUENCE_FILE_LOCATION_KEY, newSequencePath);
+            inputProperties.put(Globals.GENOME_ARCHIVE_SEQUENCE_FILE_LOCATION_KEY, sequenceFileName);
             inputProperties.put(Globals.GENOME_ARCHIVE_CUSTOM_SEQUENCE_LOCATION_KEY, Boolean.TRUE.toString());
 
 
diff -Nru igv-2.3.88+dfsg/src/org/broad/igv/feature/ShapeFileUtils.java igv-2.3.90+dfsg/src/org/broad/igv/feature/ShapeFileUtils.java
--- igv-2.3.88+dfsg/src/org/broad/igv/feature/ShapeFileUtils.java	1970-01-01 00:00:00.000000000 +0000
+++ igv-2.3.90+dfsg/src/org/broad/igv/feature/ShapeFileUtils.java	2017-01-09 04:30:59.000000000 +0000
@@ -0,0 +1,162 @@
+/*
+ * The MIT License (MIT)
+ *
+ * Copyright (c) 2007-2015 Broad Institute
+ *
+ * Permission is hereby granted, free of charge, to any person obtaining a copy
+ * of this software and associated documentation files (the "Software"), to deal
+ * in the Software without restriction, including without limitation the rights
+ * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+ * copies of the Software, and to permit persons to whom the Software is
+ * furnished to do so, subject to the following conditions:
+ *
+ * The above copyright notice and this permission notice shall be included in
+ * all copies or substantial portions of the Software.
+ *
+ *
+ * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+ * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+ * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+ * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+ * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+ * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
+ * THE SOFTWARE.
+ */
+
+package org.broad.igv.feature;
+
+
+import org.broad.igv.Globals;
+
+
+import java.io.*;
+import java.lang.reflect.Array;
+import java.util.*;
+
+
+class LocAndVal {
+    public int loc;
+    public double val;
+    public LocAndVal(int loc, double val) {
+        this.loc = loc;
+        this.val = val;
+    }
+}
+
+
+
+/**
+ * @author sbusan
+ */
+public class ShapeFileUtils {
+
+    static LinkedList<LocAndVal> transformProfile(LinkedList<LocAndVal> profile,
+                                                  int seqLen,
+                                                  int newLeft,
+                                                  String strand){
+        LinkedList<LocAndVal> transProfile = new LinkedList<LocAndVal>();
+        for (LocAndVal d : profile){
+            int loc = d.loc;
+            double val = d.val;
+            if (strand == "+"){
+                loc = loc + newLeft - 1;
+            } else if (strand == "-"){
+                loc = seqLen - loc + newLeft;
+            } else {
+                throw new RuntimeException("Unrecognized strand (options: \"+\",\"-\")");
+            }
+            transProfile.add(new LocAndVal(loc, val));
+        }
+        return transProfile;
+    }
+
+    static LinkedList<LocAndVal> loadShape(String inFile) throws
+            FileNotFoundException, IOException {
+        // TODO: add error messages for misformatted file
+        LinkedList<LocAndVal> profile = new LinkedList<LocAndVal>();
+
+        BufferedReader br = null;
+
+        try {
+            br = new BufferedReader(new FileReader(inFile));
+
+            String nextLine;
+            while ((nextLine = br.readLine()) != null) {
+                String[] s = Globals.whitespacePattern.split(nextLine.trim());
+                int loc = Integer.parseInt(s[0]);
+                double val = Double.parseDouble(s[1]);
+                if (val < -998) {
+                    val = Double.NaN;
+                }
+                profile.add(new LocAndVal(loc, val));
+            }
+        } finally {
+            if (br != null) br.close();
+        }
+
+        return profile;
+    }
+
+
+    static void writeWigFile(String wigFile,
+                             String chrom,
+                             LinkedList<LocAndVal> profile) throws IOException {
+        PrintWriter pw = null;
+
+        try {
+            pw = new PrintWriter(new BufferedWriter(new FileWriter(wigFile)));
+            // write header
+            pw.println("variableStep chrom="+chrom);
+
+            // write locs and values
+            for (LocAndVal d : profile) {
+                int loc = d.loc;
+                double val = d.val;
+                if (!Double.isNaN(val)){
+                    pw.println(""+loc+"\t"+String.format("%.6f",val));
+                }
+            }
+        } finally {
+            if (pw != null) pw.close();
+        }
+    }
+
+
+    public static void shapeToWigFile(String inFile,
+                                      String wigFile,
+                                      String chromosome,
+                                      String strand,
+                                      int left) throws
+            FileNotFoundException, IOException {
+
+        LinkedList<LocAndVal> profile = loadShape(inFile);
+        profile = transformProfile(profile, profile.size(), left, strand);
+        writeWigFile(wigFile, chromosome, profile);
+    }
+
+    /**
+     * Convert a base pairing structure file in dot-bracket notation
+     * (also known as Vienna format) to an easily parseable .bp arcs file. Does not
+     * currently handle mapping coords to spliced transcripts.
+     *
+     * @param dbFile        Input file
+     * @param bpFile        Output file
+     * @param chromosome    Associated IGV chromosome
+     * @param strand        Associated strand ("+" or "-")
+     * @param left          Starting left-most position (0-based)
+     */
+
+
+    /**
+     * Convert a pairing probability file as output by RNAStructure
+     * and/or SuperFold to an easily parseable .bp arcs file. Does not
+     * currently handle mapping coords to spliced transcripts.
+     *
+     * @param dpFile        Input file
+     * @param bpFile        Output file
+     * @param chromosome    Associated IGV chromosome
+     * @param strand        Associated strand ("+" or "-")
+     * @param left          Starting left-most position (0-based)
+     */
+
+}
diff -Nru igv-2.3.88+dfsg/src/org/broad/igv/PreferenceManager.java igv-2.3.90+dfsg/src/org/broad/igv/PreferenceManager.java
--- igv-2.3.88+dfsg/src/org/broad/igv/PreferenceManager.java	2016-11-07 10:42:41.000000000 +0000
+++ igv-2.3.90+dfsg/src/org/broad/igv/PreferenceManager.java	2017-01-09 04:30:59.000000000 +0000
@@ -300,6 +300,8 @@
 
     public static final String SESSION_RELATIVE_PATH = "SESSION.RELATIVE_PATH";
 
+    public static final String CHECK_VERSION = "CHECK_VERSION";
+
     IGVPreferences preferences;
     Map<String, String> defaultValues;
 
@@ -1230,6 +1232,7 @@
 
         defaultValues.put(SHOW_LOS, "true");
 
+        defaultValues.put(CHECK_VERSION, "true");
     }
 
     /**
diff -Nru igv-2.3.88+dfsg/src/org/broad/igv/renderer/DataRenderer.java igv-2.3.90+dfsg/src/org/broad/igv/renderer/DataRenderer.java
--- igv-2.3.88+dfsg/src/org/broad/igv/renderer/DataRenderer.java	2016-11-07 10:42:41.000000000 +0000
+++ igv-2.3.90+dfsg/src/org/broad/igv/renderer/DataRenderer.java	2017-01-09 04:30:59.000000000 +0000
@@ -73,7 +73,10 @@
             // has caused concurrent modification exceptions.
             synchronized (scores) {
                 renderScores(track, scores, context, rect);
-                renderAxis(track, context, rect);
+
+                if(context.isMerged() == false) {
+                    renderAxis(track, context, rect);
+                }
             }
         }
         renderBorder(track, context, rect);
diff -Nru igv-2.3.88+dfsg/src/org/broad/igv/sam/AlignmentTrack.java igv-2.3.90+dfsg/src/org/broad/igv/sam/AlignmentTrack.java
--- igv-2.3.88+dfsg/src/org/broad/igv/sam/AlignmentTrack.java	2016-11-07 10:42:41.000000000 +0000
+++ igv-2.3.90+dfsg/src/org/broad/igv/sam/AlignmentTrack.java	2017-01-09 04:30:59.000000000 +0000
@@ -38,6 +38,7 @@
 import org.broad.igv.feature.FeatureUtils;
 import org.broad.igv.feature.Locus;
 import org.broad.igv.feature.Range;
+import org.broad.igv.feature.Strand;
 import org.broad.igv.feature.genome.ChromosomeNameComparator;
 import org.broad.igv.feature.genome.Genome;
 import org.broad.igv.lists.GeneList;
@@ -2058,6 +2059,8 @@
 
             item.addActionListener(new ActionListener() {
                 public void actionPerformed(ActionEvent aEvt) {
+                    String blatSeq = alignment.getReadStrand() == Strand.NEGATIVE ?
+                            SequenceTrack.getReverseComplement(seq) : seq;
                     BlatClient.doBlatQuery(seq);
                 }
             });
diff -Nru igv-2.3.88+dfsg/src/org/broad/igv/sam/BaseAlignmentCounts.java igv-2.3.90+dfsg/src/org/broad/igv/sam/BaseAlignmentCounts.java
--- igv-2.3.88+dfsg/src/org/broad/igv/sam/BaseAlignmentCounts.java	2016-11-07 10:42:41.000000000 +0000
+++ igv-2.3.90+dfsg/src/org/broad/igv/sam/BaseAlignmentCounts.java	2017-01-09 04:30:59.000000000 +0000
@@ -206,7 +206,6 @@
         Set<Integer> filteredSnps = knownSnps == null ? null : knownSnps.get(chr);
 
         if (filteredSnps == null || !filteredSnps.contains(pos + 1)) {
-
             float threshold = snpThreshold * (qualityWeight ? getTotalQuality(pos) : getTotalCount(pos));
             float mismatchQualitySum = 0;
 
@@ -218,7 +217,7 @@
                     }
 
                 }
-                return mismatchQualitySum >= threshold;
+                return (mismatchQualitySum >= threshold) && (threshold > 0); // (threshold > 0) avoids mismatch call in columns with all 0 quality
             }
         }
         return false;
diff -Nru igv-2.3.88+dfsg/src/org/broad/igv/sam/BisulfiteBaseInfo.java igv-2.3.90+dfsg/src/org/broad/igv/sam/BisulfiteBaseInfo.java
--- igv-2.3.88+dfsg/src/org/broad/igv/sam/BisulfiteBaseInfo.java	2016-11-07 10:42:41.000000000 +0000
+++ igv-2.3.90+dfsg/src/org/broad/igv/sam/BisulfiteBaseInfo.java	2017-01-09 04:30:59.000000000 +0000
@@ -80,7 +80,7 @@
 
         myContext = bisulfiteContext;
         byte[] inRead = block.getBases();
-        if(inRead != null) {
+        if (inRead != null) {
             int alignmentLen = inRead.length;
 
             // We will only need reverse complement if the strand and paired end status don't match (2nd ends are G->A)
@@ -113,6 +113,14 @@
                 byte readbase = read[idx];
                 if (readbase == '=') readbase = refbase;
 
+                // Force both bases to upper case
+                if (refbase > 90) {
+                    refbase = (byte) (refbase - 32);
+                }
+                if (readbase > 90) {
+                    readbase = (byte) (readbase - 32);
+                }
+
                 Color out = null;
                 boolean matchesContext = false;
 
@@ -195,13 +203,13 @@
      * @param idx
      * @param bisulfiteContext
      * @return Returns the context that matched (in the case of the base class, this is always the same
-     *         as the context passed in, derived classes might return a different context).
-     *         If we don't match, return null.
+     * as the context passed in, derived classes might return a different context).
+     * If we don't match, return null.
      */
     protected BisulfiteContext contextIsMatching(byte[] reference, byte[] read, int idx,
                                                  BisulfiteContext bisulfiteContext) {
 
-        if(BisulfiteContext.NONE == bisulfiteContext) {
+        if (BisulfiteContext.NONE == bisulfiteContext) {
             return bisulfiteContext;
         }
 
@@ -302,8 +310,8 @@
     /**
      * @param item
      * @return 0 if the cytosine context is not symmetric, else the number of
-     *         base pairs to shift the position by (caller must be careful to shift
-     *         relative to the strand the cytosine is on).
+     * base pairs to shift the position by (caller must be careful to shift
+     * relative to the strand the cytosine is on).
      */
     protected double getBisulfiteSymmetricCytosineShift(BisulfiteContext item) {
         double out = 0.0;
diff -Nru igv-2.3.88+dfsg/src/org/broad/igv/sam/BisulfiteCounts.java igv-2.3.90+dfsg/src/org/broad/igv/sam/BisulfiteCounts.java
--- igv-2.3.88+dfsg/src/org/broad/igv/sam/BisulfiteCounts.java	2016-11-07 10:42:41.000000000 +0000
+++ igv-2.3.90+dfsg/src/org/broad/igv/sam/BisulfiteCounts.java	2017-01-09 04:30:59.000000000 +0000
@@ -95,12 +95,21 @@
 
                 // The read base can be an equals sign, so change that to the actual ref base
                 byte refbase =  reference[idx];
-
+                if (refbase > 90) {
+                    refbase = (byte) (refbase - 32);     // Uppercase
+                }
 
                 // Strand has already been accounted for
                 if (refbase == 'C') {
                     byte readbase = read[idx];
-                    if (readbase == '=') readbase = refbase;
+                    if (readbase == '=') {
+                        readbase = refbase;
+                    }
+
+                    // Force both bases to upper case
+                    if (readbase > 90) {
+                        readbase = (byte) (readbase - 32);
+                    }
 
                     if (AlignmentUtils.compareBases((byte) 'C', readbase) || AlignmentUtils.compareBases((byte) 'T', readbase)) {
 
diff -Nru igv-2.3.88+dfsg/src/org/broad/igv/sam/DenseAlignmentCounts.java igv-2.3.90+dfsg/src/org/broad/igv/sam/DenseAlignmentCounts.java
--- igv-2.3.88+dfsg/src/org/broad/igv/sam/DenseAlignmentCounts.java	2016-11-07 10:42:41.000000000 +0000
+++ igv-2.3.90+dfsg/src/org/broad/igv/sam/DenseAlignmentCounts.java	2017-01-09 04:30:59.000000000 +0000
@@ -305,13 +305,9 @@
     protected void incrementInsertion(AlignmentBlock insBlock) {
         int pos = insBlock.getStart();
         int offset = pos - start;
-        // Insertions are between bases.  increment count on either side
+        // Insertions are between bases.  increment count at position just before insertion
         if (offset >= 0 && offset < ins.length) {
-            ins[offset] = ins[offset] + 1;
-            offset--;
-            if (offset >= 0) {
-                ins[offset] = ins[offset] + 1;
-            }
+           ins[offset] = ins[offset] + 1;
         }
     }
 
diff -Nru igv-2.3.88+dfsg/src/org/broad/igv/sam/reader/MergedAlignmentReader.java igv-2.3.90+dfsg/src/org/broad/igv/sam/reader/MergedAlignmentReader.java
--- igv-2.3.88+dfsg/src/org/broad/igv/sam/reader/MergedAlignmentReader.java	2016-11-07 10:42:41.000000000 +0000
+++ igv-2.3.90+dfsg/src/org/broad/igv/sam/reader/MergedAlignmentReader.java	2017-01-09 04:30:59.000000000 +0000
@@ -235,6 +235,8 @@
 
                 Integer idx1 = chrNameIndex.get(a1.getChr());
                 Integer idx2 = chrNameIndex.get(a2.getChr());
+                if(idx1==null) idx1 = Integer.MAX_VALUE;
+                if(idx2== null) idx2 = Integer.MAX_VALUE;  // Put these records at the end.
                 if (idx1 > idx2) {
                     return 1;
                 } else if (idx1 < idx2) {
diff -Nru igv-2.3.88+dfsg/src/org/broad/igv/tdf/TDFDataSource.java igv-2.3.90+dfsg/src/org/broad/igv/tdf/TDFDataSource.java
--- igv-2.3.88+dfsg/src/org/broad/igv/tdf/TDFDataSource.java	2016-11-07 10:42:41.000000000 +0000
+++ igv-2.3.90+dfsg/src/org/broad/igv/tdf/TDFDataSource.java	2017-01-09 04:30:59.000000000 +0000
@@ -217,7 +217,7 @@
 
         } else {
 
-            if(querySeq.equals(genome.getHomeChromosome())) {
+            if(querySeq.equals(Globals.CHR_ALL)) {
                 scores = getWGRawScores();
             }
             else {
diff -Nru igv-2.3.88+dfsg/src/org/broad/igv/track/AbstractTrack.java igv-2.3.90+dfsg/src/org/broad/igv/track/AbstractTrack.java
--- igv-2.3.88+dfsg/src/org/broad/igv/track/AbstractTrack.java	2016-11-07 10:42:41.000000000 +0000
+++ igv-2.3.90+dfsg/src/org/broad/igv/track/AbstractTrack.java	2017-01-09 04:30:59.000000000 +0000
@@ -967,7 +967,15 @@
 
 
     public String getNameValueString(int y) {
-        return getName();
+
+        StringBuffer buffer = new StringBuffer();
+        buffer.append("<html>" + getName());
+
+        if(resourceLocator != null && resourceLocator.getPath() != null) {
+            buffer.append("<br>" + this.resourceLocator.getPath());
+        }
+
+        return buffer.toString();
     }
 
     /**
diff -Nru igv-2.3.88+dfsg/src/org/broad/igv/track/MergedTracks.java igv-2.3.90+dfsg/src/org/broad/igv/track/MergedTracks.java
--- igv-2.3.88+dfsg/src/org/broad/igv/track/MergedTracks.java	2016-11-07 10:42:41.000000000 +0000
+++ igv-2.3.90+dfsg/src/org/broad/igv/track/MergedTracks.java	2017-01-09 04:30:59.000000000 +0000
@@ -54,7 +54,7 @@
  * @date 2013-Nov-05
  */
 @XmlType(factoryMethod = "getNextTrack")
-public class MergedTracks extends DataTrack {
+public class MergedTracks extends DataTrack implements ScalableTrack {
 
     @XmlAttribute
     protected Class clazz = MergedTracks.class;
@@ -83,6 +83,18 @@
                 this.memberTracks.add(inputTrack);
             }
         }
+
+        // Set the group autoscale attribute only of all tracks are in the same group
+        this.removeAttribute(AttributeManager.GROUP_AUTOSCALE);
+        if (memberTracks.size() > 0) {
+            String group = memberTracks.iterator().next().getAttributeValue(AttributeManager.GROUP_AUTOSCALE);
+            if(group != null) {
+                for (Track t : memberTracks) {
+                    if(!group.equals(t.getAttributeValue(AttributeManager.GROUP_AUTOSCALE))) return;
+                }
+                this.setAttributeValue(AttributeManager.GROUP_AUTOSCALE, group);
+            }
+        }
     }
 
     @Override
@@ -95,7 +107,7 @@
     }
 
     @XmlElement(name = MEMBER_TRACK_TAG_NAME)
-    Collection<DataTrack> getMemberTracks() {
+    public Collection<DataTrack> getMemberTracks() {
         return this.memberTracks;
     }
 
@@ -110,6 +122,7 @@
     @Override
     public void render(RenderContext context, Rectangle rect) {
 
+        context.setMerged(true);
         for (Track track : memberTracks) {
             track.render(context, rect);
         }
@@ -178,7 +191,7 @@
 
     @Override
     public boolean getAutoScale() {
-        boolean autoScale = super.getAutoScale();
+        boolean autoScale = true;
         for (Track track : memberTracks) {
             autoScale &= track.getAutoScale();
         }
@@ -187,13 +200,33 @@
 
     @Override
     public void setAutoScale(boolean autoScale) {
-        super.setAutoScale(autoScale);
         for (Track track : memberTracks) {
             track.setAutoScale(autoScale);
         }
     }
 
     @Override
+    public void setAttributeValue(String name, String value) {
+        super.setAttributeValue(name, value);
+        if (name.equals(AttributeManager.GROUP_AUTOSCALE)) {
+            for (Track track : memberTracks) {
+                track.setAttributeValue(name, value);
+            }
+        }
+    }
+
+    @Override
+    public void removeAttribute(String name) {
+        super.removeAttribute(name);
+        if (name.equals(AttributeManager.GROUP_AUTOSCALE)) {
+            for (Track track : memberTracks) {
+                track.removeAttribute(name);
+            }
+        }
+    }
+
+
+    @Override
     public ContinuousColorScale getColorScale() {
         return super.getColorScale();
     }
@@ -267,13 +300,32 @@
         return menu;
     }
 
-    //Not clear whether this is necessary, don't think it is, the real problem is loading not saving
-//    public void marshalMemberTracks(Marshaller m, Element trackElement) throws JAXBException{
-//        for(DataTrack memberTrack: memberTracks){
-//            JAXBElement element = new JAXBElement<DataTrack>(new QName("", DataTrack.DATA_TRACK), DataTrack.class, memberTrack);
-//            m.marshal(element, trackElement);
-//        }
-//    }
+
+    @Override
+    public Range getInViewRange(ReferenceFrame referenceFrame) {
+
+        List<LocusScore> scores = new ArrayList<LocusScore>();
+        for (DataTrack track : memberTracks) {
+            scores.addAll(track.getInViewScores(referenceFrame));
+        }
+
+        if (scores.size() > 0) {
+            float min = Float.MAX_VALUE;
+            float max = -Float.MAX_VALUE;
+            for (LocusScore score : scores) {
+                float value = score.getScore();
+                if (!Float.isNaN(value)) {
+                    min = Math.min(value, min);
+                    max = Math.max(value, max);
+                }
+            }
+            return new Range(min, max);
+        } else {
+            return null;
+        }
+
+    }
+
 
     private enum ChangeTrackMethod {
         POSITIVE, NEGATIVE
diff -Nru igv-2.3.88+dfsg/src/org/broad/igv/track/RenderContextImpl.java igv-2.3.90+dfsg/src/org/broad/igv/track/RenderContextImpl.java
--- igv-2.3.88+dfsg/src/org/broad/igv/track/RenderContextImpl.java	2016-11-07 10:42:41.000000000 +0000
+++ igv-2.3.90+dfsg/src/org/broad/igv/track/RenderContextImpl.java	2017-01-09 04:30:59.000000000 +0000
@@ -47,6 +47,7 @@
     private ReferenceFrame referenceFrame;
     private JComponent panel;
     private Rectangle visibleRect;
+    boolean merged;
 
 
     public RenderContextImpl(JComponent panel, Graphics2D graphics, ReferenceFrame referenceFrame, Rectangle visibleRect) {
@@ -114,6 +115,15 @@
         return referenceFrame;
     }
 
+    @Override
+    public boolean isMerged() {
+        return merged;
+    }
+
+    public void setMerged(boolean merged) {
+        this.merged = merged;
+    }
+
     public int bpToScreenPixel(double location) {
         final double scale = getScale();
         final double origin = getOrigin();
@@ -132,6 +142,8 @@
         dispose();
     }
 
+
+
     public void dispose() {
         for (Graphics2D g : graphicCacheByColor.values()) {
             g.dispose();
diff -Nru igv-2.3.88+dfsg/src/org/broad/igv/track/RenderContext.java igv-2.3.90+dfsg/src/org/broad/igv/track/RenderContext.java
--- igv-2.3.88+dfsg/src/org/broad/igv/track/RenderContext.java	2016-11-07 10:42:41.000000000 +0000
+++ igv-2.3.90+dfsg/src/org/broad/igv/track/RenderContext.java	2017-01-09 04:30:59.000000000 +0000
@@ -58,6 +58,10 @@
 
     int bpToScreenPixel(double location);
 
+    void setMerged(boolean b);
+
+    boolean isMerged();
+
     void dispose();
 
 }
diff -Nru igv-2.3.88+dfsg/src/org/broad/igv/track/SequenceTrack.java igv-2.3.90+dfsg/src/org/broad/igv/track/SequenceTrack.java
--- igv-2.3.88+dfsg/src/org/broad/igv/track/SequenceTrack.java	2016-11-07 10:42:41.000000000 +0000
+++ igv-2.3.90+dfsg/src/org/broad/igv/track/SequenceTrack.java	2017-01-09 04:30:59.000000000 +0000
@@ -171,8 +171,9 @@
 
     private void flipStrand() {
         strand = (strand == Strand.POSITIVE ? Strand.NEGATIVE : Strand.POSITIVE);
-        repaint();
         IGV.getInstance().clearSelections();
+        repaint();
+
     }
 
     public void setShouldShowTranslation(boolean shouldShowTranslation) {
@@ -269,8 +270,7 @@
 
     public String getValueStringAt(String chr, double position, int y, ReferenceFrame frame) {
         if (sequenceVisible && !this.sequenceRenderer.hasSequence()) {
-            return "Sequence info not found. Make sure the server in question supports byte-range requests, and that "
-                    + "there are no firewalls which remove this information";
+            return "Sequence info not found";
         } else {
             return null;
         }
@@ -281,4 +281,43 @@
     }
 
 
+
+    public static String getReverseComplement(String sequence) {
+        char[] complement = new char[sequence.length()];
+        int jj = complement.length;
+        for (int ii = 0; ii < sequence.length(); ii++) {
+            char c = sequence.charAt(ii);
+            jj--;
+            switch (c) {
+                case 'T':
+                    complement[jj] = 'A';
+                    break;
+                case 'A':
+                    complement[jj] = 'T';
+                    break;
+                case 'C':
+                    complement[jj] = 'G';
+                    break;
+                case 'G':
+                    complement[jj] = 'C';
+                    break;
+                case 't':
+                    complement[jj] = 'a';
+                    break;
+                case 'a':
+                    complement[jj] = 't';
+                    break;
+                case 'c':
+                    complement[jj] = 'g';
+                    break;
+                case 'g':
+                    complement[jj] = 'c';
+                    break;
+                default:
+                    complement[jj] = c;
+            }
+        }
+        return new String(complement);
+    }
+
 }
diff -Nru igv-2.3.88+dfsg/src/org/broad/igv/track/TrackLoader.java igv-2.3.90+dfsg/src/org/broad/igv/track/TrackLoader.java
--- igv-2.3.88+dfsg/src/org/broad/igv/track/TrackLoader.java	2016-11-07 10:42:41.000000000 +0000
+++ igv-2.3.90+dfsg/src/org/broad/igv/track/TrackLoader.java	2017-01-09 04:30:59.000000000 +0000
@@ -47,7 +47,9 @@
 import org.broad.igv.dev.db.SampleInfoSQLReader;
 import org.broad.igv.dev.db.SegmentedSQLReader;
 import org.broad.igv.exceptions.DataLoadException;
-import org.broad.igv.feature.basepair.BasePairFileParser;
+import org.broad.igv.feature.basepair.BasePairTrack;
+import org.broad.igv.feature.BasePairFileUtils;
+import org.broad.igv.feature.ShapeFileUtils;
 import org.broad.igv.feature.CachingFeatureSource;
 import org.broad.igv.feature.GisticFileParser;
 import org.broad.igv.feature.MutationTrackLoader;
@@ -83,6 +85,8 @@
 import org.broad.igv.ui.IGV;
 import org.broad.igv.ui.util.ConfirmDialog;
 import org.broad.igv.ui.util.MessageUtils;
+import org.broad.igv.ui.util.ConvertFileDialog;
+import org.broad.igv.ui.util.ConvertOptions;
 import org.broad.igv.util.FileUtils;
 import org.broad.igv.util.HttpUtils;
 import org.broad.igv.util.ParsingUtils;
@@ -174,6 +178,8 @@
                 loadSyntentyMapping(locator, newTracks);
             } else if (isAlignmentTrack(typeString)) {
                 loadAlignmentsTrack(locator, newTracks, genome);
+            } else if (typeString.endsWith(".shape") || typeString.endsWith(".map")) {
+                convertLoadShapeFile(locator, newTracks, genome);
             } else if (typeString.endsWith(".wig") || typeString.endsWith(".bedgraph") || typeString.endsWith(".bdg") ||
                     typeString.endsWith("cpg.txt") || typeString.endsWith(".expr")) {
                 loadWigFile(locator, newTracks, genome);
@@ -202,6 +208,12 @@
             } else if (typeString.endsWith("mage-tab") || ExpressionFileParser.parsableMAGE_TAB(locator)) {
                 locator.setDescription("MAGE_TAB");
                 loadGctFile(locator, newTracks, genome);
+            } else if (typeString.endsWith(".db") || typeString.endsWith(".dbn")) {
+                convertLoadStructureFile(locator, newTracks, genome, "dotBracket");
+            } else if (typeString.endsWith(".ct")) {
+                convertLoadStructureFile(locator, newTracks, genome, "connectTable");
+            } else if (typeString.endsWith(".dp")) {
+                convertLoadStructureFile(locator, newTracks, genome, "pairingProb");
             } else if (typeString.endsWith(".bp")) {
                 loadBasePairFile(locator, newTracks, genome);
             } else if (GWASParser.isGWASFile(typeString)) {
@@ -1233,10 +1245,68 @@
         PedigreeUtils.parseTrioFile(locator.getPath());
     }
 
+    /**
+     * Convert an RNA chemical reactivity file (.shape, .map) into a .wig file
+     * and load.
+
+     */
+    private void convertLoadShapeFile(ResourceLocator locator,
+                                      List<Track> newTracks,
+                                      Genome genome) throws IOException {
+        String inPath = locator.getPath();
+        String fileName = locator.getFileName();
+        String outPath = inPath + ".wig";
+        String message = "The chemical reactivity file <br> &nbsp;&nbsp;" + fileName + "<br> needs to be converted to IGV chromosome <br>" +
+                         "coordinates and .wig format before loading. <br><br>Click <b>Continue</b> " +
+                         "to save converted file to <br> &nbsp;&nbsp;" + fileName+".wig" +
+                         "<br>and load with the selected options, or <b>Cancel</b> to skip this<br>file.";
+
+        ConvertOptions opts =  ConvertFileDialog.showConvertFileDialog(message);
+        if (opts.doConvert) {
+            ShapeFileUtils.shapeToWigFile(inPath, outPath, opts.chrom, opts.strand, opts.start);
+            loadWigFile(new ResourceLocator(outPath), newTracks, genome);
+        }
+    }
+
+    /**
+     * Convert various RNA structure formats to a more easily parseable format
+     * in genomic coordinates, then load converted file.
+
+     */
+    private void convertLoadStructureFile(ResourceLocator locator,
+                                          List<Track> newTracks,
+                                          Genome genome,
+                                          String fileType) throws IOException {
+        String inPath = locator.getPath();
+        String fileName = locator.getFileName();
+        String outPath = inPath + ".bp";
+
+        String message = "The RNA structure file <br> &nbsp;&nbsp;" + fileName + "<br> needs to be converted to IGV chromosome <br>" +
+                         "coordinates and .bp format before loading. <br><br>Click <b>Continue</b> " +
+                         "to save converted file to <br> &nbsp;&nbsp;" + fileName+".bp" +
+                         "<br>and load with the selected options, or <b>Cancel</b> to skip this<br>file.";
+
+        ConvertOptions opts =  ConvertFileDialog.showConvertFileDialog(message);
+
+        if (opts.doConvert){
+            if (fileType == "connectTable") {
+                BasePairFileUtils.connectTableToBasePairFile(inPath, outPath, opts.chrom, opts.strand, opts.start);
+            } else if (fileType == "pairingProb") {
+                BasePairFileUtils.pairingProbToBasePairFile(inPath, outPath, opts.chrom, opts.strand, opts.start);
+            } else if (fileType == "dotBracket") {
+                BasePairFileUtils.dotBracketToBasePairFile(inPath, outPath, opts.chrom, opts.strand, opts.start);
+            }
+            loadBasePairFile(new ResourceLocator(outPath), newTracks, genome);
+        }
+    }
 
-    private void loadBasePairFile(ResourceLocator locator, List<Track> newTracks, Genome genome) throws IOException {
-        BasePairFileParser parser = new BasePairFileParser();
-        newTracks.add(parser.loadTrack(locator, genome)); // should create one track from the given file
+    private void loadBasePairFile(ResourceLocator locator,
+                                  List<Track> newTracks,
+                                  Genome genome) throws IOException {
+        String name = locator.getTrackName();
+        String path = locator.getPath();
+        String id = path + "_" + name;
+        newTracks.add(new BasePairTrack(locator, id, name, genome));
     }
 
     public static boolean isIndexed(ResourceLocator locator, Genome genome) {
diff -Nru igv-2.3.88+dfsg/src/org/broad/igv/track/TrackMenuUtils.java igv-2.3.90+dfsg/src/org/broad/igv/track/TrackMenuUtils.java
--- igv-2.3.88+dfsg/src/org/broad/igv/track/TrackMenuUtils.java	2016-11-07 10:42:41.000000000 +0000
+++ igv-2.3.90+dfsg/src/org/broad/igv/track/TrackMenuUtils.java	2017-01-09 04:30:59.000000000 +0000
@@ -34,9 +34,7 @@
 import org.broad.igv.PreferenceManager;
 import org.broad.igv.data.AbstractDataSource;
 import org.broad.igv.data.CombinedDataSource;
-import org.broad.igv.feature.Exon;
-import org.broad.igv.feature.FeatureUtils;
-import org.broad.igv.feature.IGVFeature;
+import org.broad.igv.feature.*;
 import org.broad.igv.feature.Range;
 import org.broad.igv.feature.basepair.BasePairTrack;
 import org.broad.igv.feature.genome.Genome;
@@ -333,7 +331,7 @@
 
         menu.add(getAutoscaleItem(tracks));
 
-        if (tracks.size() > 1) {
+        if (tracks.size() > 1 || (tracks.size() == 1 && tracks.iterator().next() instanceof MergedTracks)) {
             menu.add(getGroupAutoscaleItem(tracks));
         }
 
@@ -884,9 +882,6 @@
                             t.removeAttribute(AttributeManager.GROUP_AUTOSCALE);
                         }
                     }
-
-                    DataPanelContainer.resetStateHash();
-
                     IGV.getInstance().repaint();
                 }
             });
@@ -901,15 +896,15 @@
         autoscaleItem.addActionListener(new ActionListener() {
 
             public void actionPerformed(ActionEvent evt) {
+
                 int nextAutoscaleGroup = IGV.getInstance().getSession().getNextAutoscaleGroup();
+
                 for (Track t : selectedTracks) {
                     t.setAttributeValue(AttributeManager.GROUP_AUTOSCALE, String.valueOf(nextAutoscaleGroup));
                     t.setAutoScale(false);
                 }
                 IGV.getInstance().getSession().incrementNextAutoscaleGroup();
 
-                DataPanelContainer.resetStateHash();
-
                 PreferenceManager.getInstance().setShowAttributeView(true);
                 IGV.getInstance().getMainPanel().invalidate();
                 IGV.getInstance().doRefresh();
@@ -1068,7 +1063,6 @@
             return;
         }
 
-        DataPanelContainer.resetStateHash();
         IGV.getInstance().removeTracks(selectedTracks);
         IGV.getInstance().doRefresh();
     }
@@ -1349,12 +1343,19 @@
 
 
     public static JMenuItem getCopySequenceItem(final Feature f) {
+
+        final Strand strand;
+        if(f instanceof IGVFeature) {
+            strand = ((IGVFeature) f).getStrand();
+        } else {
+           strand = Strand.NONE;
+        }
+
         JMenuItem item = new JMenuItem("Copy Sequence");
         item.addActionListener(new ActionListener() {
-
             public void actionPerformed(ActionEvent evt) {
                 Genome genome = GenomeManager.getInstance().getCurrentGenome();
-                IGV.copySequenceToClipboard(genome, f.getChr(), f.getStart(), f.getEnd());
+                IGV.copySequenceToClipboard(genome, f.getChr(), f.getStart(), f.getEnd(), strand);
             }
         });
         return item;
@@ -1366,7 +1367,15 @@
         item.addActionListener(new ActionListener() {
 
             public void actionPerformed(ActionEvent evt) {
-                BlatClient.doBlatQuery(f.getChr(), f.getStart(), f.getEnd());
+
+                final Strand strand;
+                if(f instanceof IGVFeature) {
+                    strand = ((IGVFeature) f).getStrand();
+                } else {
+                    strand = Strand.NONE;
+                }
+
+                BlatClient.doBlatQuery(f.getChr(), f.getStart(), f.getEnd(), strand);
             }
         });
         return item;
diff -Nru igv-2.3.88+dfsg/src/org/broad/igv/ui/GenomeSelectionDialog.java igv-2.3.90+dfsg/src/org/broad/igv/ui/GenomeSelectionDialog.java
--- igv-2.3.88+dfsg/src/org/broad/igv/ui/GenomeSelectionDialog.java	2016-11-07 10:42:41.000000000 +0000
+++ igv-2.3.90+dfsg/src/org/broad/igv/ui/GenomeSelectionDialog.java	2017-01-09 04:30:59.000000000 +0000
@@ -162,6 +162,7 @@
     }
 
     static void downloadGenome(final Frame dialogsParent, final GenomeListItem genomeListItem) {
+
         final File targetDir = DirectoryManager.getGenomeCacheDirectory();
         if(!targetDir.exists()){
             targetDir.mkdirs();
diff -Nru igv-2.3.88+dfsg/src/org/broad/igv/ui/IGV.java igv-2.3.90+dfsg/src/org/broad/igv/ui/IGV.java
--- igv-2.3.88+dfsg/src/org/broad/igv/ui/IGV.java	2016-11-07 10:42:41.000000000 +0000
+++ igv-2.3.90+dfsg/src/org/broad/igv/ui/IGV.java	2017-01-09 04:30:59.000000000 +0000
@@ -39,6 +39,7 @@
 import com.google.common.eventbus.Subscribe;
 import com.jidesoft.swing.JideSplitPane;
 import htsjdk.samtools.seekablestream.SeekableFileStream;
+import htsjdk.samtools.util.StringUtil;
 import org.apache.log4j.Logger;
 import org.broad.igv.DirectoryManager;
 import org.broad.igv.Globals;
@@ -48,9 +49,7 @@
 import org.broad.igv.batch.CommandListener;
 import org.broad.igv.dev.api.IGVPlugin;
 import org.broad.igv.exceptions.DataLoadException;
-import org.broad.igv.feature.Locus;
-import org.broad.igv.feature.MaximumContigGenomeException;
-import org.broad.igv.feature.RegionOfInterest;
+import org.broad.igv.feature.*;
 import org.broad.igv.feature.genome.*;
 import org.broad.igv.lists.GeneList;
 import org.broad.igv.lists.Preloader;
@@ -481,7 +480,7 @@
     }
 
 
-    public void doDefineGenome(ProgressMonitor monitor) {
+    public void doDefineGenome(javax.swing.ProgressMonitor monitor) {
 
         ProgressBar.ProgressDialog progressDialog = null;
         File archiveFile = null;
@@ -496,9 +495,6 @@
                 return;
             }
 
-            if (monitor != null) {
-                progressDialog = ProgressBar.showProgressDialog(mainFrame, "Defining Genome...", monitor, false);
-            }
 
             String cytobandFileName = genomeBuilderDialog.getCytobandFileName();
             String geneAnnotFileName = genomeBuilderDialog.getGeneAnnotFileName();
@@ -517,7 +513,7 @@
                 contentPane.getCommandBar().selectGenome(genomeListItem.getId());
             }
             if (monitor != null) {
-                monitor.fireProgressChange(100);
+                monitor.setProgress(100);
             }
 
         } catch (MaximumContigGenomeException e) {
@@ -568,11 +564,10 @@
         Runnable showDialog = new Runnable() {
             @Override
             public void run() {
+
                 Collection<GenomeListItem> inputListItems = GenomeManager.getInstance().getServerGenomeArchiveList();
                 if (inputListItems == null) {
-                    //Not necessary to display a message, getServerGenomeArchiveList does it already
-                    //IOException exc = new IOException("Unable to reach genome server");
-                    //MessageUtils.showErrorMessage(exc.getMessage(), exc);
+                    //Could not reach genome server.  Not necessary to display a message, getServerGenomeArchiveList does it already
                     return;
                 }
 
@@ -583,7 +578,9 @@
                 if (selectedValues != null && selectedValues.size() >= 1) {
 
                     if (selectedValues.size() == 1 && dialog.downloadSequence()) {
+
                         GenomeListItem oldItem = selectedValues.get(0);
+
                         GenomeSelectionDialog.downloadGenome(getMainFrame(), oldItem);
 
                         File newLocation = new File(DirectoryManager.getGenomeCacheDirectory().getAbsolutePath(), Utilities.getFileNameFromURL(oldItem.getLocation()));
@@ -653,9 +650,15 @@
     }
 
     public void loadGenomeById(String genomeId) {
+
+        final Genome currentGenome = genomeManager.getCurrentGenome();
+        if(currentGenome != null && genomeId.equals(currentGenome.getId())) {
+            return; // Already loaded
+        }
+
         if (ParsingUtils.pathExists(genomeId)) {
             try {
-                IGV.getInstance().loadGenome(genomeId, null, false);
+                loadGenome(genomeId, null, false);
             } catch (IOException e) {
                 log.error("Error loading genome file: " + genomeId, e);
             }
@@ -2703,21 +2706,20 @@
 
     }
 
-    public static void copySequenceToClipboard(Genome genome, String chr, int start, int end) {
+    public static void copySequenceToClipboard(Genome genome, String chr, int start, int end, Strand strand) {
         try {
             IGV.getMainFrame().setCursor(Cursor.getPredefinedCursor(Cursor.WAIT_CURSOR));
             byte[] seqBytes = genome.getSequence(chr, start, end);
 
             if (seqBytes == null) {
-                MessageUtils.showMessage("Sequence not available. Try enabling http byte-range requests");
+                MessageUtils.showMessage("Sequence not available");
             } else {
                 String sequence = new String(seqBytes);
-                //TODO This will complement sequence if sequence track is flipped
-                //Might be un-intuitive to user if they do it from region dialog
-//                SequenceTrack sequenceTrack = IGV.getInstance().getSequenceTrack();
-//                if(sequenceTrack != null && sequenceTrack.getStrand() == Strand.NEGATIVE){
-//                    sequence = AminoAcidManager.getNucleotideComplement(sequence);
-//                }
+
+                SequenceTrack sequenceTrack = IGV.getInstance().getSequenceTrack();
+                if(strand == Strand.NEGATIVE || (sequenceTrack != null && sequenceTrack.getStrand() == Strand.NEGATIVE)){
+                    sequence = AminoAcidManager.getReverseComplement(sequence);
+                }
                 StringUtils.copyTextToClipboard(sequence);
             }
 
diff -Nru igv-2.3.88+dfsg/src/org/broad/igv/ui/IGVMenuBar.java igv-2.3.90+dfsg/src/org/broad/igv/ui/IGVMenuBar.java
--- igv-2.3.88+dfsg/src/org/broad/igv/ui/IGVMenuBar.java	2016-11-07 10:42:41.000000000 +0000
+++ igv-2.3.90+dfsg/src/org/broad/igv/ui/IGVMenuBar.java	2017-01-09 04:30:59.000000000 +0000
@@ -579,7 +579,8 @@
                 new MenuAction("Create .genome File...", null, KeyEvent.VK_D) {
                     @Override
                     public void actionPerformed(ActionEvent event) {
-                        org.broad.igv.ui.util.ProgressMonitor monitor = new org.broad.igv.ui.util.ProgressMonitor();
+                        javax.swing.ProgressMonitor monitor = new javax.swing.ProgressMonitor(IGV.getInstance().getMainPanel(),
+                                "Creating genome", null, 0, 100);
                         igv.doDefineGenome(monitor);
                     }
                 };
@@ -597,9 +598,9 @@
                 dialog2.setVisible(true);
                 boolean cancelled = dialog2.isCancelled();
                 List<GenomeListItem> removedValuesList = dialog2.getRemovedValuesList();
+
                 if (!cancelled) {
-                    GenomeManager.getInstance().buildGenomeItemList();
-                    igv.getContentPane().getCommandBar().refreshGenomeListComboBox();
+
                     if (removedValuesList != null && !removedValuesList.isEmpty()) {
                         try {
                             GenomeManager.getInstance().deleteDownloadedGenomes(removedValuesList);
@@ -608,7 +609,20 @@
                         }
                         GenomeManager.getInstance().updateImportedGenomePropertyFile();
                         notifyGenomesAddedRemoved(removedValuesList, false);
+
+                        String defaultGenomeKey = PreferenceManager.getInstance().get(PreferenceManager.DEFAULT_GENOME_KEY);
+                        for (GenomeListItem item : removedValuesList) {
+                            if (defaultGenomeKey.equals(item.getId())) {
+                                PreferenceManager.getInstance().remove(PreferenceManager.DEFAULT_GENOME_KEY);
+                                break;
+                            }
+                        }
                     }
+
+                    GenomeManager.getInstance().buildGenomeItemList();
+
+                    igv.getContentPane().getCommandBar().refreshGenomeListComboBox();
+
                 }
             }
         };
diff -Nru igv-2.3.88+dfsg/src/org/broad/igv/ui/Main.java igv-2.3.90+dfsg/src/org/broad/igv/ui/Main.java
--- igv-2.3.88+dfsg/src/org/broad/igv/ui/Main.java	2016-11-07 10:42:41.000000000 +0000
+++ igv-2.3.90+dfsg/src/org/broad/igv/ui/Main.java	2017-01-09 04:30:59.000000000 +0000
@@ -145,6 +145,7 @@
         System.setProperty("awt.useSystemAAFontSettings", "on");
         System.setProperty("swing.aatext", "true");
 
+
         checkVersion();
 
 
@@ -161,47 +162,47 @@
 
     private static void checkVersion() {
 
-        int readTimeout = Globals.READ_TIMEOUT;
-        int connectTimeout = Globals.CONNECT_TIMEOUT;
 
-        try {
-            Version thisVersion = Version.getVersion(Globals.VERSION);
-            if (thisVersion == null) return;  // Can't compare
-
-            Globals.CONNECT_TIMEOUT = 5000;
-            Globals.READ_TIMEOUT = 1000;
-            final String serverVersionString = HttpUtils.getInstance().getContentsAsString(new URL(Globals.getVersionURL())).trim();
-            // See if user has specified to skip this update
-
-            final String skipString = PreferenceManager.getInstance().get(PreferenceManager.SKIP_VERSION);
-            HashSet<String> skipVersion = new HashSet<String>(Arrays.asList(skipString.split(",")));
-            if (skipVersion.contains(serverVersionString)) return;
-
-            Version serverVersion = Version.getVersion(serverVersionString.trim());
-            if (serverVersion == null) return;
-
-            if (thisVersion.lessThan(serverVersion)) {
-
-                log.info("A later version of IGV is available (" + serverVersionString + ")");
-//                final VersionUpdateDialog dlg = new VersionUpdateDialog(serverVersionString);
-//                SwingUtilities.invokeAndWait(new Runnable() {
-//                    public void run() {
-//                        dlg.setVisible(true);
-//                        if (dlg.isSkipVersion()) {
-//                            String newSkipString = skipString + "," + serverVersionString;
-//                            PreferenceManager.getInstance().put(PreferenceManager.SKIP_VERSION, newSkipString);
-//                        }
-//                    }
-//                });
+        Runnable runnable = new Runnable() {
+            public void run() {
+                try {
+                    Version thisVersion = Version.getVersion(Globals.VERSION);
+                    if (thisVersion == null) return;  // Can't compare
+
+                    final String serverVersionString = HttpUtils.getInstance().getContentsAsString(new URL(Globals.getVersionURL())).trim();
+                    // See if user has specified to skip this update
+
+                    final String skipString = PreferenceManager.getInstance().get(PreferenceManager.SKIP_VERSION);
+                    HashSet<String> skipVersion = new HashSet<String>(Arrays.asList(skipString.split(",")));
+                    if (skipVersion.contains(serverVersionString)) return;
+
+                    Version serverVersion = Version.getVersion(serverVersionString.trim());
+                    if (serverVersion == null) return;
+
+                    if (thisVersion.lessThan(serverVersion)) {
+
+                        log.info("A later version of IGV is available (" + serverVersionString + ")");
+        //                final VersionUpdateDialog dlg = new VersionUpdateDialog(serverVersionString);
+        //                SwingUtilities.invokeAndWait(new Runnable() {
+        //                    public void run() {
+        //                        dlg.setVisible(true);
+        //                        if (dlg.isSkipVersion()) {
+        //                            String newSkipString = skipString + "," + serverVersionString;
+        //                            PreferenceManager.getInstance().put(PreferenceManager.SKIP_VERSION, newSkipString);
+        //                        }
+        //                    }
+        //                });
+                    }
+
+                } catch (Exception e) {
+                    log.error("Error checking version", e);
+                } finally {
 
+                }
             }
+        };
 
-        } catch (Exception e) {
-            log.error("Error checking version", e);
-        } finally {
-            Globals.CONNECT_TIMEOUT = connectTimeout;
-            Globals.READ_TIMEOUT = readTimeout;
-        }
+        (new Thread(runnable)).start();
 
     }
 
diff -Nru igv-2.3.88+dfsg/src/org/broad/igv/ui/ManageGenomesDialog.java igv-2.3.90+dfsg/src/org/broad/igv/ui/ManageGenomesDialog.java
--- igv-2.3.88+dfsg/src/org/broad/igv/ui/ManageGenomesDialog.java	2016-11-07 10:42:41.000000000 +0000
+++ igv-2.3.90+dfsg/src/org/broad/igv/ui/ManageGenomesDialog.java	2017-01-09 04:30:59.000000000 +0000
@@ -108,12 +108,6 @@
                     countHasSeq++;
                 }
             }
-
-            if(countHasSeq > 0){
-                String msg = String.format("%d of the genomes you chose to remove have downloaded sequences. Those will be deleted as well. Are you sure?", countHasSeq);
-                boolean sure = MessageUtils.confirm(msg);
-                if(!sure) return;
-            }
         }
 
         cancelled = false;
diff -Nru igv-2.3.88+dfsg/src/org/broad/igv/ui/panel/DataPanelContainer.java igv-2.3.90+dfsg/src/org/broad/igv/ui/panel/DataPanelContainer.java
--- igv-2.3.88+dfsg/src/org/broad/igv/ui/panel/DataPanelContainer.java	2016-11-07 10:42:41.000000000 +0000
+++ igv-2.3.90+dfsg/src/org/broad/igv/ui/panel/DataPanelContainer.java	2017-01-09 04:30:59.000000000 +0000
@@ -27,8 +27,6 @@
 
 import org.apache.log4j.Logger;
 import org.broad.igv.exceptions.DataLoadException;
-import org.broad.igv.feature.FeatureUtils;
-import org.broad.igv.feature.LocusScore;
 import org.broad.igv.renderer.DataRange;
 import org.broad.igv.track.*;
 import org.broad.igv.ui.IGV;
@@ -53,16 +51,9 @@
 
     private static Logger log = Logger.getLogger(DataPanelContainer.class);
 
-    static int lastStateHash = 0;   // TODO -- could synchronization be an issue?
-
     TrackPanel parent;
 
 
-    public static void resetStateHash() {
-        lastStateHash = 0;
-    }
-
-
     public DataPanelContainer(TrackPanel trackPanel) {
         super(trackPanel);
 
@@ -261,28 +252,36 @@
 
     private void autoscale() {
 
-        int stateHash = FrameManager.getStateHash();
-
-        //if(lastStateHash == stateHash) return;
-
-        lastStateHash = stateHash;
-
         final Collection<Track> trackList = IGV.getInstance().getAllTracks();
 
         Map<String, List<Track>> autoscaleGroups = new HashMap<String, List<Track>>();
 
         for (Track track : trackList) {
 
-            if(!track.isVisible()) continue;
+            if (!track.isVisible()) continue;
 
             String asGroup = track.getAttributeValue(AttributeManager.GROUP_AUTOSCALE);
             if (asGroup != null) {
                 if (!autoscaleGroups.containsKey(asGroup)) {
                     autoscaleGroups.put(asGroup, new ArrayList<Track>());
                 }
-                autoscaleGroups.get(asGroup).add(track);
+
+                if (track instanceof MergedTracks) {
+                    for (Track mt : ((MergedTracks) track).getMemberTracks()) {
+                        autoscaleGroups.get(asGroup).add(track);
+                    }
+                } else {
+                    autoscaleGroups.get(asGroup).add(track);
+                }
             } else if (track.getAutoScale()) {
-                autoscaleGroup(Arrays.asList(track));
+
+                if (track instanceof MergedTracks) {
+                    for (Track mt : ((MergedTracks) track).getMemberTracks()) {
+                        autoscaleGroup(Arrays.asList(mt));
+                    }
+                } else {
+                    autoscaleGroup(Arrays.asList(track));
+                }
             }
 
 
diff -Nru igv-2.3.88+dfsg/src/org/broad/igv/ui/panel/RegionNavigatorDialog.java igv-2.3.90+dfsg/src/org/broad/igv/ui/panel/RegionNavigatorDialog.java
--- igv-2.3.88+dfsg/src/org/broad/igv/ui/panel/RegionNavigatorDialog.java	2016-11-07 10:42:41.000000000 +0000
+++ igv-2.3.90+dfsg/src/org/broad/igv/ui/panel/RegionNavigatorDialog.java	2017-01-09 04:30:59.000000000 +0000
@@ -30,6 +30,7 @@
 import org.apache.log4j.Logger;
 import org.broad.igv.feature.Range;
 import org.broad.igv.feature.RegionOfInterest;
+import org.broad.igv.feature.Strand;
 import org.broad.igv.feature.genome.GenomeManager;
 import org.broad.igv.lists.GeneList;
 import org.broad.igv.ui.IGV;
@@ -817,7 +818,7 @@
                                 JOptionPane.showMessageDialog(RegionNavigatorDialog.this, "Region is to large to copy sequence data.");
                             } else {
                                 IGV.copySequenceToClipboard(GenomeManager.getInstance().getCurrentGenome(),
-                                        chr, start, end);
+                                        chr, start, end, Strand.NONE);
                             }
                         }
                     });
diff -Nru igv-2.3.88+dfsg/src/org/broad/igv/ui/panel/RegionOfInterestPanel.java igv-2.3.90+dfsg/src/org/broad/igv/ui/panel/RegionOfInterestPanel.java
--- igv-2.3.88+dfsg/src/org/broad/igv/ui/panel/RegionOfInterestPanel.java	2016-11-07 10:42:41.000000000 +0000
+++ igv-2.3.90+dfsg/src/org/broad/igv/ui/panel/RegionOfInterestPanel.java	2017-01-09 04:30:59.000000000 +0000
@@ -30,6 +30,7 @@
 package org.broad.igv.ui.panel;
 
 import org.broad.igv.Globals;
+import org.broad.igv.feature.Strand;
 import org.broad.igv.util.blat.BlatClient;
 import org.broad.igv.feature.RegionOfInterest;
 import org.broad.igv.feature.genome.Genome;
@@ -182,7 +183,7 @@
 
                     public void run() {
                         Genome genome = GenomeManager.getInstance().getCurrentGenome();
-                        IGV.copySequenceToClipboard(genome, roi.getChr(), roi.getStart(), roi.getEnd());
+                        IGV.copySequenceToClipboard(genome, roi.getChr(), roi.getStart(), roi.getEnd(), Strand.NONE);
                     }
                 });
             }
@@ -198,7 +199,7 @@
         item.addActionListener(new ActionListener() {
 
             public void actionPerformed(ActionEvent e) {
-                BlatClient.doBlatQuery(roi.getChr(), roi.getStart(), roi.getEnd());
+                BlatClient.doBlatQuery(roi.getChr(), roi.getStart(), roi.getEnd(), Strand.NONE);
             }
         });
         popupMenu.add(item);
diff -Nru igv-2.3.88+dfsg/src/org/broad/igv/ui/panel/TrackNamePanel.java igv-2.3.90+dfsg/src/org/broad/igv/ui/panel/TrackNamePanel.java
--- igv-2.3.88+dfsg/src/org/broad/igv/ui/panel/TrackNamePanel.java	2016-11-07 10:42:41.000000000 +0000
+++ igv-2.3.90+dfsg/src/org/broad/igv/ui/panel/TrackNamePanel.java	2017-01-09 04:30:59.000000000 +0000
@@ -540,37 +540,22 @@
 
 
         /**
-         * Mouse was clicked.  Delegate single-click action to the track(s) clicked on.   We won't know if this
-         * is a double click or not until the double-click interval has passed, so defer the action with a
-         * TimerTask.  If a second click arrives it will be canceled.
+         * Mouse was clicked.  Delegate single-click action to the track(s) clicked on.
          *
          * @param e
          */
         @Override
         public void mouseClicked(final MouseEvent e) {
 
-            // If this is the second click of a double click, cancel the scheduled single click task.
-            if (e.getClickCount() > 1) {
-                clickScheduler.cancelClickTask();
-                return;
-            }
-
-            TimerTask clickTask = new TimerTask() {
-
-                @Override
-                public void run() {
-                    for (MouseableRegion mouseRegion : mouseRegions) {
-                        if (mouseRegion.containsPoint(e.getX(), e.getY())) {
-                            for (Track t : mouseRegion.getTracks()) {
-                                t.handleNameClick(e);
-                            }
-                            return;
-                        }
-                    }//To change body of implemented methods use File | Settings | File Templates.
+            for (MouseableRegion mouseRegion : mouseRegions) {
+                if (mouseRegion.containsPoint(e.getX(), e.getY())) {
+                    for (Track t : mouseRegion.getTracks()) {
+                        t.handleNameClick(e);
+                    }
+                    return;
                 }
-            };
-            //clickScheduler.scheduleClickTask(clickTask);
-            clickTask.run();
+            }//To change body of implemented methods use File | Settings | File Templates.
+
         }
 
         protected void fireGhostDropEvent(GhostDropEvent evt) {
diff -Nru igv-2.3.88+dfsg/src/org/broad/igv/ui/util/CancellableProgressDialog.java igv-2.3.90+dfsg/src/org/broad/igv/ui/util/CancellableProgressDialog.java
--- igv-2.3.88+dfsg/src/org/broad/igv/ui/util/CancellableProgressDialog.java	2016-11-07 10:42:41.000000000 +0000
+++ igv-2.3.90+dfsg/src/org/broad/igv/ui/util/CancellableProgressDialog.java	2017-01-09 04:30:59.000000000 +0000
@@ -172,7 +172,10 @@
      * @param monitor Optional (may be null). Status text is updated based on monitor.updateStatus
      * @return
      */
-    public static CancellableProgressDialog showCancellableProgressDialog(Frame dialogsParent, String title, final ActionListener buttonActionListener, final boolean autoClose, ProgressMonitor monitor){
+    public static CancellableProgressDialog showCancellableProgressDialog(Frame dialogsParent,
+                                                                          String title, final
+                                                                          ActionListener buttonActionListener,
+                                                                          final boolean autoClose, ProgressMonitor monitor){
         final CancellableProgressDialog progressDialog = new CancellableProgressDialog(dialogsParent);
 
         progressDialog.setTitle(title);
diff -Nru igv-2.3.88+dfsg/src/org/broad/igv/ui/util/ConvertFileDialog.java igv-2.3.90+dfsg/src/org/broad/igv/ui/util/ConvertFileDialog.java
--- igv-2.3.88+dfsg/src/org/broad/igv/ui/util/ConvertFileDialog.java	1970-01-01 00:00:00.000000000 +0000
+++ igv-2.3.90+dfsg/src/org/broad/igv/ui/util/ConvertFileDialog.java	2017-01-09 04:30:59.000000000 +0000
@@ -0,0 +1,257 @@
+/*
+ * The MIT License (MIT)
+ *
+ * Copyright (c) 2007-2015 Broad Institute
+ *
+ * Permission is hereby granted, free of charge, to any person obtaining a copy
+ * of this software and associated documentation files (the "Software"), to deal
+ * in the Software without restriction, including without limitation the rights
+ * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+ * copies of the Software, and to permit persons to whom the Software is
+ * furnished to do so, subject to the following conditions:
+ *
+ * The above copyright notice and this permission notice shall be included in
+ * all copies or substantial portions of the Software.
+ *
+ *
+ * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+ * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+ * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+ * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+ * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+ * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
+ * THE SOFTWARE.
+ */
+
+/*
+ * Created by JFormDesigner on Tue Nov 15 14:22:59 EST 2016
+ */
+
+package org.broad.igv.ui.util;
+
+import org.broad.igv.Globals;
+import org.broad.igv.PreferenceManager;
+import org.broad.igv.ui.IGV;
+
+import java.awt.*;
+import java.awt.event.*;
+import java.text.NumberFormat;
+import javax.swing.*;
+import javax.swing.border.*;
+import javax.swing.text.DefaultFormatterFactory;
+import javax.swing.text.NumberFormatter;
+
+import java.util.*;
+
+/**
+ * Before converting .shape, .map, .ct, .db, or .dp files (associated with individual RNAs)
+ * to IGV-loadable formats, allow the user to select the applicable chromosome,
+ * coordinate offset, and strand, since that information is not present in those files.
+ *
+ * @author sbusan
+ */
+public class ConvertFileDialog extends JDialog {
+
+    ConvertOptions opts = new ConvertOptions();
+
+    private ConvertFileDialog(Frame owner, String message, java.util.List<String> chromosomes) {
+        super(owner);
+        this.setModal(true);
+        initComponents();
+        label.setText("<html>" + message + "</html>");
+        okButton.setText("Continue");
+
+        // FIXME: limit input to empty string or integer
+        /*NumberFormat format = NumberFormat.getInstance();
+        NumberFormatter formatter = new NumberFormatter(format);
+        formatter.setValueClass(Integer.class);
+        formatter.setMinimum(0);
+        formatter.setMaximum(Integer.MAX_VALUE);
+        formatter.setAllowsInvalid(false);
+        DefaultFormatterFactory factory = new DefaultFormatterFactory(formatter);
+        startTextField.setFormatterFactory(factory);*/
+
+        DefaultComboBoxModel boxModel = new DefaultComboBoxModel();
+        for (String chrom : chromosomes) {
+            boxModel.addElement(chrom);
+        }
+        chromBox.setModel(boxModel);
+
+        getRootPane().setDefaultButton(okButton);
+    }
+
+    public static ConvertOptions showConvertFileDialog(String message) {
+        ConvertFileDialog dlg = new ConvertFileDialog(IGV.getMainFrame(),
+                message,
+                IGV.getInstance().getGenomeManager().getCurrentGenome().getAllChromosomeNames());
+        dlg.setVisible(true);
+        dlg.opts.chrom = dlg.chromBox.getSelectedItem().toString();
+        dlg.opts.start = Integer.parseInt(dlg.startTextField.getText());
+        if (dlg.reverseRadio.isSelected()) dlg.opts.strand = "-";
+        return dlg.opts;
+    }
+
+    private void cancelButtonActionPerformed(ActionEvent e) {
+        opts.doConvert = false;
+        setVisible(false);
+    }
+
+    private void okButtonActionPerformed(ActionEvent e) {
+        opts.doConvert = true;
+        setVisible(false);
+    }
+
+    private void initComponents() {
+        // JFormDesigner - Component initialization - DO NOT MODIFY  //GEN-BEGIN:initComponents
+        // Generated using JFormDesigner non-commercial license
+        dialogPane = new JPanel();
+        contentPanel = new JPanel();
+        label = new JLabel();
+        forwardRadio = new JRadioButton();
+        reverseRadio = new JRadioButton();
+        label1 = new JLabel();
+        label2 = new JLabel();
+        label3 = new JLabel();
+        startTextField = new JFormattedTextField();
+        chromBox = new JComboBox();
+        buttonBar = new JPanel();
+        cancelButton = new JButton();
+        okButton = new JButton();
+
+        //======== this ========
+        setDefaultCloseOperation(WindowConstants.DISPOSE_ON_CLOSE);
+        setResizable(false);
+        Container contentPane = getContentPane();
+        contentPane.setLayout(new BorderLayout());
+
+        //======== dialogPane ========
+        {
+            dialogPane.setBorder(new EmptyBorder(12, 12, 12, 12));
+            dialogPane.setLayout(new BorderLayout());
+
+            //======== contentPanel ========
+            {
+                contentPanel.setLayout(null);
+
+                //---- label ----
+                label.setText("text");
+                label.setFont(label.getFont().deriveFont(label.getFont().getStyle() & ~Font.BOLD));
+                contentPanel.add(label);
+                label.setBounds(0, 0, 415, 140);
+
+                //---- forwardRadio ----
+                forwardRadio.setText("Forward");
+                forwardRadio.setSelected(true);
+                contentPanel.add(forwardRadio);
+                forwardRadio.setBounds(65, 180, forwardRadio.getPreferredSize().width, 23);
+
+                //---- reverseRadio ----
+                reverseRadio.setText("Reverse");
+                contentPanel.add(reverseRadio);
+                reverseRadio.setBounds(145, 180, reverseRadio.getPreferredSize().width, 23);
+
+                //---- label1 ----
+                label1.setText("Strand:");
+                label1.setHorizontalAlignment(SwingConstants.RIGHT);
+                contentPanel.add(label1);
+                label1.setBounds(5, 185, label1.getPreferredSize().width, 15);
+
+                //---- label2 ----
+                label2.setText("Chr:");
+                label2.setHorizontalAlignment(SwingConstants.RIGHT);
+                contentPanel.add(label2);
+                label2.setBounds(10, 155, 42, 15);
+
+                //---- label3 ----
+                label3.setText("Start:");
+                label3.setHorizontalAlignment(SwingConstants.RIGHT);
+                contentPanel.add(label3);
+                label3.setBounds(5, 215, 49, 15);
+
+                //---- startTextField ----
+                startTextField.setText("1");
+                contentPanel.add(startTextField);
+                startTextField.setBounds(65, 210, 165, startTextField.getPreferredSize().height);
+
+                //---- chromBox ----
+                chromBox.setMaximumRowCount(100);
+                contentPanel.add(chromBox);
+                chromBox.setBounds(65, 150, 165, chromBox.getPreferredSize().height);
+
+                { // compute preferred size
+                    Dimension preferredSize = new Dimension();
+                    for (int i = 0; i < contentPanel.getComponentCount(); i++) {
+                        Rectangle bounds = contentPanel.getComponent(i).getBounds();
+                        preferredSize.width = Math.max(bounds.x + bounds.width, preferredSize.width);
+                        preferredSize.height = Math.max(bounds.y + bounds.height, preferredSize.height);
+                    }
+                    Insets insets = contentPanel.getInsets();
+                    preferredSize.width += insets.right;
+                    preferredSize.height += insets.bottom;
+                    contentPanel.setMinimumSize(preferredSize);
+                    contentPanel.setPreferredSize(preferredSize);
+                }
+            }
+            dialogPane.add(contentPanel, BorderLayout.CENTER);
+
+            //======== buttonBar ========
+            {
+                buttonBar.setBorder(new EmptyBorder(12, 0, 0, 0));
+                buttonBar.setLayout(new GridBagLayout());
+                ((GridBagLayout) buttonBar.getLayout()).columnWidths = new int[]{0, 0, 80};
+                ((GridBagLayout) buttonBar.getLayout()).columnWeights = new double[]{1.0, 0.0, 0.0};
+
+                //---- cancelButton ----
+                cancelButton.setText("Cancel");
+                cancelButton.addActionListener(new ActionListener() {
+                    @Override
+                    public void actionPerformed(ActionEvent e) {
+                        cancelButtonActionPerformed(e);
+                    }
+                });
+                buttonBar.add(cancelButton, new GridBagConstraints(1, 0, 1, 1, 0.0, 0.0,
+                        GridBagConstraints.CENTER, GridBagConstraints.BOTH,
+                        new Insets(0, 0, 5, 5), 0, 0));
+
+                //---- okButton ----
+                okButton.setText("OK");
+                okButton.addActionListener(new ActionListener() {
+                    @Override
+                    public void actionPerformed(ActionEvent e) {
+                        okButtonActionPerformed(e);
+                    }
+                });
+                buttonBar.add(okButton, new GridBagConstraints(2, 0, 1, 1, 0.0, 0.0,
+                        GridBagConstraints.CENTER, GridBagConstraints.BOTH,
+                        new Insets(0, 0, 5, 0), 0, 0));
+            }
+            dialogPane.add(buttonBar, BorderLayout.SOUTH);
+        }
+        contentPane.add(dialogPane, BorderLayout.CENTER);
+        setSize(450, 355);
+        setLocationRelativeTo(getOwner());
+
+        //---- buttonGroup1 ----
+        ButtonGroup buttonGroup1 = new ButtonGroup();
+        buttonGroup1.add(forwardRadio);
+        buttonGroup1.add(reverseRadio);
+        // JFormDesigner - End of component initialization  //GEN-END:initComponents
+    }
+
+    // JFormDesigner - Variables declaration - DO NOT MODIFY  //GEN-BEGIN:variables
+    // Generated using JFormDesigner non-commercial license
+    private JPanel dialogPane;
+    private JPanel contentPanel;
+    private JLabel label;
+    private JRadioButton forwardRadio;
+    private JRadioButton reverseRadio;
+    private JLabel label1;
+    private JLabel label2;
+    private JLabel label3;
+    private JFormattedTextField startTextField;
+    private JComboBox chromBox;
+    private JPanel buttonBar;
+    private JButton cancelButton;
+    private JButton okButton;
+    // JFormDesigner - End of variables declaration  //GEN-END:variables
+}
diff -Nru igv-2.3.88+dfsg/src/org/broad/igv/ui/util/ConvertFileDialog.jfd igv-2.3.90+dfsg/src/org/broad/igv/ui/util/ConvertFileDialog.jfd
--- igv-2.3.88+dfsg/src/org/broad/igv/ui/util/ConvertFileDialog.jfd	1970-01-01 00:00:00.000000000 +0000
+++ igv-2.3.90+dfsg/src/org/broad/igv/ui/util/ConvertFileDialog.jfd	2017-01-09 04:30:59.000000000 +0000
@@ -0,0 +1,481 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<java version="1.8.0_76-release" class="java.beans.XMLDecoder">
+ <object class="com.jformdesigner.model.FormModel">
+  <void property="contentType">
+   <string>form/swing</string>
+  </void>
+  <void property="root">
+   <object class="com.jformdesigner.model.FormRoot">
+    <void method="add">
+     <object class="com.jformdesigner.model.FormWindow">
+      <string>javax.swing.JDialog</string>
+      <object class="com.jformdesigner.model.FormLayoutManager">
+       <class>java.awt.BorderLayout</class>
+      </object>
+      <void method="setProperty">
+       <string>defaultCloseOperation</string>
+       <int>2</int>
+      </void>
+      <void method="setProperty">
+       <string>$sizePolicy</string>
+       <int>1</int>
+      </void>
+      <void method="setProperty">
+       <string>resizable</string>
+       <boolean>false</boolean>
+      </void>
+      <void method="add">
+       <object class="com.jformdesigner.model.FormContainer">
+        <string>javax.swing.JPanel</string>
+        <object class="com.jformdesigner.model.FormLayoutManager">
+         <class>java.awt.BorderLayout</class>
+        </object>
+        <void method="setProperty">
+         <string>border</string>
+         <object class="javax.swing.border.EmptyBorder">
+          <int>12</int>
+          <int>12</int>
+          <int>12</int>
+          <int>12</int>
+         </object>
+        </void>
+        <void property="name">
+         <string>dialogPane</string>
+        </void>
+        <void method="add">
+         <object class="com.jformdesigner.model.FormContainer">
+          <string>javax.swing.JPanel</string>
+          <object class="com.jformdesigner.model.FormLayoutManager">
+           <class>com.jformdesigner.runtime.NullLayout</class>
+          </object>
+          <void property="name">
+           <string>contentPanel</string>
+          </void>
+          <void method="add">
+           <object class="com.jformdesigner.model.FormComponent">
+            <string>javax.swing.JLabel</string>
+            <void method="setProperty">
+             <string>text</string>
+             <string>text</string>
+            </void>
+            <void method="setProperty">
+             <string>font</string>
+             <object class="com.jformdesigner.model.SwingDerivedFont">
+              <null/>
+              <int>65536</int>
+              <int>0</int>
+              <boolean>false</boolean>
+             </object>
+            </void>
+            <void property="name">
+             <string>label</string>
+            </void>
+           </object>
+           <object class="com.jformdesigner.model.FormLayoutConstraints">
+            <class>com.jformdesigner.runtime.NullConstraints</class>
+            <void method="setProperty">
+             <string>x</string>
+             <int>0</int>
+            </void>
+            <void method="setProperty">
+             <string>y</string>
+             <int>0</int>
+            </void>
+            <void method="setProperty">
+             <string>width</string>
+             <int>415</int>
+            </void>
+            <void method="setProperty">
+             <string>height</string>
+             <int>140</int>
+            </void>
+           </object>
+          </void>
+          <void method="add">
+           <object class="com.jformdesigner.model.FormComponent">
+            <string>javax.swing.JRadioButton</string>
+            <void method="setProperty">
+             <string>text</string>
+             <string>Forward</string>
+            </void>
+            <void method="setProperty">
+             <string>selected</string>
+             <boolean>true</boolean>
+            </void>
+            <void method="setProperty">
+             <string>$buttonGroup</string>
+             <object class="com.jformdesigner.model.FormReference">
+              <string>buttonGroup1</string>
+             </object>
+            </void>
+            <void property="name">
+             <string>forwardRadio</string>
+            </void>
+           </object>
+           <object class="com.jformdesigner.model.FormLayoutConstraints">
+            <class>com.jformdesigner.runtime.NullConstraints</class>
+            <void method="setProperty">
+             <string>x</string>
+             <int>65</int>
+            </void>
+            <void method="setProperty">
+             <string>y</string>
+             <int>180</int>
+            </void>
+            <void method="setProperty">
+             <string>height</string>
+             <int>23</int>
+            </void>
+           </object>
+          </void>
+          <void method="add">
+           <object class="com.jformdesigner.model.FormComponent">
+            <string>javax.swing.JRadioButton</string>
+            <void method="setProperty">
+             <string>text</string>
+             <string>Reverse</string>
+            </void>
+            <void method="setProperty">
+             <string>$buttonGroup</string>
+             <object class="com.jformdesigner.model.FormReference">
+              <string>buttonGroup1</string>
+             </object>
+            </void>
+            <void property="name">
+             <string>reverseRadio</string>
+            </void>
+           </object>
+           <object class="com.jformdesigner.model.FormLayoutConstraints">
+            <class>com.jformdesigner.runtime.NullConstraints</class>
+            <void method="setProperty">
+             <string>x</string>
+             <int>145</int>
+            </void>
+            <void method="setProperty">
+             <string>y</string>
+             <int>180</int>
+            </void>
+            <void method="setProperty">
+             <string>height</string>
+             <int>23</int>
+            </void>
+           </object>
+          </void>
+          <void method="add">
+           <object class="com.jformdesigner.model.FormComponent">
+            <string>javax.swing.JLabel</string>
+            <void method="setProperty">
+             <string>text</string>
+             <string>Strand:</string>
+            </void>
+            <void method="setProperty">
+             <string>horizontalAlignment</string>
+             <int>4</int>
+            </void>
+            <void property="name">
+             <string>label1</string>
+            </void>
+           </object>
+           <object class="com.jformdesigner.model.FormLayoutConstraints">
+            <class>com.jformdesigner.runtime.NullConstraints</class>
+            <void method="setProperty">
+             <string>x</string>
+             <int>5</int>
+            </void>
+            <void method="setProperty">
+             <string>y</string>
+             <int>185</int>
+            </void>
+            <void method="setProperty">
+             <string>height</string>
+             <int>15</int>
+            </void>
+           </object>
+          </void>
+          <void method="add">
+           <object class="com.jformdesigner.model.FormComponent">
+            <string>javax.swing.JLabel</string>
+            <void method="setProperty">
+             <string>text</string>
+             <string>Chr:</string>
+            </void>
+            <void method="setProperty">
+             <string>horizontalAlignment</string>
+             <int>4</int>
+            </void>
+            <void property="name">
+             <string>label2</string>
+            </void>
+           </object>
+           <object class="com.jformdesigner.model.FormLayoutConstraints">
+            <class>com.jformdesigner.runtime.NullConstraints</class>
+            <void method="setProperty">
+             <string>width</string>
+             <int>42</int>
+            </void>
+            <void method="setProperty">
+             <string>height</string>
+             <int>15</int>
+            </void>
+            <void method="setProperty">
+             <string>x</string>
+             <int>10</int>
+            </void>
+            <void method="setProperty">
+             <string>y</string>
+             <int>155</int>
+            </void>
+           </object>
+          </void>
+          <void method="add">
+           <object class="com.jformdesigner.model.FormComponent">
+            <string>javax.swing.JLabel</string>
+            <void method="setProperty">
+             <string>text</string>
+             <string>Start:</string>
+            </void>
+            <void method="setProperty">
+             <string>horizontalAlignment</string>
+             <int>4</int>
+            </void>
+            <void property="name">
+             <string>label3</string>
+            </void>
+           </object>
+           <object class="com.jformdesigner.model.FormLayoutConstraints">
+            <class>com.jformdesigner.runtime.NullConstraints</class>
+            <void method="setProperty">
+             <string>width</string>
+             <int>49</int>
+            </void>
+            <void method="setProperty">
+             <string>height</string>
+             <int>15</int>
+            </void>
+            <void method="setProperty">
+             <string>x</string>
+             <int>5</int>
+            </void>
+            <void method="setProperty">
+             <string>y</string>
+             <int>215</int>
+            </void>
+           </object>
+          </void>
+          <void method="add">
+           <object class="com.jformdesigner.model.FormComponent">
+            <string>javax.swing.JFormattedTextField</string>
+            <void method="setProperty">
+             <string>text</string>
+             <string>1</string>
+            </void>
+            <void property="name">
+             <string>startTextField</string>
+            </void>
+           </object>
+           <object class="com.jformdesigner.model.FormLayoutConstraints">
+            <class>com.jformdesigner.runtime.NullConstraints</class>
+            <void method="setProperty">
+             <string>x</string>
+             <int>65</int>
+            </void>
+            <void method="setProperty">
+             <string>y</string>
+             <int>210</int>
+            </void>
+            <void method="setProperty">
+             <string>width</string>
+             <int>165</int>
+            </void>
+           </object>
+          </void>
+          <void method="add">
+           <object class="com.jformdesigner.model.FormComponent">
+            <string>javax.swing.JComboBox</string>
+            <void method="setProperty">
+             <string>maximumRowCount</string>
+             <int>100</int>
+            </void>
+            <void property="name">
+             <string>chromBox</string>
+            </void>
+           </object>
+           <object class="com.jformdesigner.model.FormLayoutConstraints">
+            <class>com.jformdesigner.runtime.NullConstraints</class>
+            <void method="setProperty">
+             <string>x</string>
+             <int>65</int>
+            </void>
+            <void method="setProperty">
+             <string>y</string>
+             <int>150</int>
+            </void>
+            <void method="setProperty">
+             <string>width</string>
+             <int>165</int>
+            </void>
+           </object>
+          </void>
+         </object>
+         <object class="com.jformdesigner.model.FormLayoutConstraints">
+          <class>java.lang.String</class>
+          <void method="setProperty">
+           <string>value</string>
+           <string>Center</string>
+          </void>
+         </object>
+        </void>
+        <void method="add">
+         <object class="com.jformdesigner.model.FormContainer">
+          <string>javax.swing.JPanel</string>
+          <object class="com.jformdesigner.model.FormLayoutManager">
+           <class>java.awt.GridBagLayout</class>
+           <void method="setProperty">
+            <string>$columnSpecs</string>
+            <string>0:1.0, 0, 80</string>
+           </void>
+           <void method="setProperty">
+            <string>$rowSpecs</string>
+            <string>0, 0</string>
+           </void>
+           <void method="setProperty">
+            <string>$hGap</string>
+            <int>5</int>
+           </void>
+           <void method="setProperty">
+            <string>$vGap</string>
+            <int>5</int>
+           </void>
+          </object>
+          <void method="setProperty">
+           <string>border</string>
+           <object class="javax.swing.border.EmptyBorder">
+            <int>12</int>
+            <int>0</int>
+            <int>0</int>
+            <int>0</int>
+           </object>
+          </void>
+          <void property="name">
+           <string>buttonBar</string>
+          </void>
+          <void method="add">
+           <object class="com.jformdesigner.model.FormComponent">
+            <string>javax.swing.JButton</string>
+            <void method="setProperty">
+             <string>text</string>
+             <string>Cancel</string>
+            </void>
+            <void property="name">
+             <string>cancelButton</string>
+            </void>
+            <void method="addEvent">
+             <object class="com.jformdesigner.model.FormEvent">
+              <string>java.awt.event.ActionListener</string>
+              <string>actionPerformed</string>
+              <string>cancelButtonActionPerformed</string>
+              <boolean>true</boolean>
+             </object>
+            </void>
+           </object>
+           <object class="com.jformdesigner.model.FormLayoutConstraints">
+            <class>com.jformdesigner.runtime.GridBagConstraintsEx</class>
+            <void method="setProperty">
+             <string>gridx</string>
+             <int>1</int>
+            </void>
+           </object>
+          </void>
+          <void method="add">
+           <object class="com.jformdesigner.model.FormComponent">
+            <string>javax.swing.JButton</string>
+            <void method="setProperty">
+             <string>text</string>
+             <string>OK</string>
+            </void>
+            <void property="name">
+             <string>okButton</string>
+            </void>
+            <void method="addEvent">
+             <object class="com.jformdesigner.model.FormEvent">
+              <string>java.awt.event.ActionListener</string>
+              <string>actionPerformed</string>
+              <string>okButtonActionPerformed</string>
+              <boolean>true</boolean>
+             </object>
+            </void>
+           </object>
+           <object class="com.jformdesigner.model.FormLayoutConstraints">
+            <class>com.jformdesigner.runtime.GridBagConstraintsEx</class>
+            <void method="setProperty">
+             <string>gridx</string>
+             <int>2</int>
+            </void>
+            <void method="setProperty">
+             <string>gridy</string>
+             <int>0</int>
+            </void>
+           </object>
+          </void>
+         </object>
+         <object class="com.jformdesigner.model.FormLayoutConstraints">
+          <class>java.lang.String</class>
+          <void method="setProperty">
+           <string>value</string>
+           <string>South</string>
+          </void>
+         </object>
+        </void>
+       </object>
+       <object class="com.jformdesigner.model.FormLayoutConstraints">
+        <class>java.lang.String</class>
+        <void method="setProperty">
+         <string>value</string>
+         <string>Center</string>
+        </void>
+       </object>
+      </void>
+      <void property="name">
+       <string>this</string>
+      </void>
+     </object>
+     <object class="com.jformdesigner.model.FormLayoutConstraints">
+      <null/>
+      <void method="setProperty">
+       <string>location</string>
+       <object class="java.awt.Point">
+        <int>0</int>
+        <int>0</int>
+       </object>
+      </void>
+      <void method="setProperty">
+       <string>size</string>
+       <object class="java.awt.Dimension">
+        <int>450</int>
+        <int>355</int>
+       </object>
+      </void>
+     </object>
+    </void>
+    <void method="add">
+     <object class="com.jformdesigner.model.FormNonVisual">
+      <string>javax.swing.ButtonGroup</string>
+      <void property="name">
+       <string>buttonGroup1</string>
+      </void>
+     </object>
+     <object class="com.jformdesigner.model.FormLayoutConstraints">
+      <null/>
+      <void method="setProperty">
+       <string>location</string>
+       <object class="java.awt.Point">
+        <int>0</int>
+        <int>316</int>
+       </object>
+      </void>
+     </object>
+    </void>
+   </object>
+  </void>
+ </object>
+</java>
diff -Nru igv-2.3.88+dfsg/src/org/broad/igv/ui/util/ConvertOptions.java igv-2.3.90+dfsg/src/org/broad/igv/ui/util/ConvertOptions.java
--- igv-2.3.88+dfsg/src/org/broad/igv/ui/util/ConvertOptions.java	1970-01-01 00:00:00.000000000 +0000
+++ igv-2.3.90+dfsg/src/org/broad/igv/ui/util/ConvertOptions.java	2017-01-09 04:30:59.000000000 +0000
@@ -0,0 +1,34 @@
+/*
+ * The MIT License (MIT)
+ *
+ * Copyright (c) 2007-2015 Broad Institute
+ *
+ * Permission is hereby granted, free of charge, to any person obtaining a copy
+ * of this software and associated documentation files (the "Software"), to deal
+ * in the Software without restriction, including without limitation the rights
+ * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+ * copies of the Software, and to permit persons to whom the Software is
+ * furnished to do so, subject to the following conditions:
+ *
+ * The above copyright notice and this permission notice shall be included in
+ * all copies or substantial portions of the Software.
+ *
+ *
+ * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+ * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+ * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+ * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+ * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+ * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
+ * THE SOFTWARE.
+ */
+
+
+package org.broad.igv.ui.util;
+
+public class ConvertOptions {
+    public boolean doConvert = false;
+    public String chrom = "";
+    public String strand = "+";
+    public int start = 1;
+}
diff -Nru igv-2.3.88+dfsg/src/org/broad/igv/ui/util/ProgressBar.java igv-2.3.90+dfsg/src/org/broad/igv/ui/util/ProgressBar.java
--- igv-2.3.88+dfsg/src/org/broad/igv/ui/util/ProgressBar.java	2016-11-07 10:42:41.000000000 +0000
+++ igv-2.3.90+dfsg/src/org/broad/igv/ui/util/ProgressBar.java	2017-01-09 04:30:59.000000000 +0000
@@ -78,7 +78,7 @@
                 progressBar.setValue(progress);
 
 
-                if (progress > 99 && closeOnCompletion) {
+                if (progress == 100 && closeOnCompletion) {
                     setReady(false); // Accept no more input
                     progressParentWindow.setVisible(false);
                 }
@@ -237,4 +237,4 @@
         return isReady;
     }
 
-}
\ No newline at end of file
+}
diff -Nru igv-2.3.88+dfsg/src/org/broad/igv/ui/util/ProgressMonitor.java igv-2.3.90+dfsg/src/org/broad/igv/ui/util/ProgressMonitor.java
--- igv-2.3.88+dfsg/src/org/broad/igv/ui/util/ProgressMonitor.java	2016-11-07 10:42:41.000000000 +0000
+++ igv-2.3.90+dfsg/src/org/broad/igv/ui/util/ProgressMonitor.java	2017-01-09 04:30:59.000000000 +0000
@@ -76,6 +76,26 @@
         }
     }
 
+    /**
+     * Sends an event to update the listening progress bar.
+     *
+     * @param newValue This value is the percent amount completed (which goes from 0 to 100).
+     */
+    public void fireProgress(final int newValue) {
+
+        if (isReady) {
+
+            PropertyChangeEvent event =
+                    new PropertyChangeEvent(
+                            this,
+                            PROGRESS_PROPERTY,
+                            oldValue,
+                            newValue);
+            propertyChangeSupport.firePropertyChange(event);
+            oldValue = newValue;
+        }
+    }
+
     public void updateStatus(String newStatus){
         if(isReady){
             PropertyChangeEvent event = new PropertyChangeEvent(this, STATUS_PROPERTY,
@@ -102,4 +122,4 @@
     public boolean isReady() {
         return isReady;
     }
-}
\ No newline at end of file
+}
diff -Nru igv-2.3.88+dfsg/src/org/broad/igv/util/blat/BlatClient.java igv-2.3.90+dfsg/src/org/broad/igv/util/blat/BlatClient.java
--- igv-2.3.88+dfsg/src/org/broad/igv/util/blat/BlatClient.java	2016-11-07 10:42:41.000000000 +0000
+++ igv-2.3.90+dfsg/src/org/broad/igv/util/blat/BlatClient.java	2017-01-09 04:30:59.000000000 +0000
@@ -28,13 +28,11 @@
 import org.broad.igv.Globals;
 import org.broad.igv.PreferenceManager;
 import org.broad.igv.feature.PSLRecord;
+import org.broad.igv.feature.Strand;
 import org.broad.igv.feature.genome.Genome;
 import org.broad.igv.feature.genome.GenomeManager;
 import org.broad.igv.feature.tribble.PSLCodec;
-import org.broad.igv.track.FeatureCollectionSource;
-import org.broad.igv.track.FeatureSource;
-import org.broad.igv.track.FeatureTrack;
-import org.broad.igv.track.Track;
+import org.broad.igv.track.*;
 import org.broad.igv.ui.IGV;
 import org.broad.igv.ui.util.MessageUtils;
 import org.broad.igv.util.HttpUtils;
@@ -221,7 +219,7 @@
         return records;
     }
 
-    public static void doBlatQuery(final String chr, final int start, final int end) {
+    public static void doBlatQuery(final String chr, final int start, final int end, Strand strand) {
 
         if((end - start) > 8000) {
             MessageUtils.showMessage("BLAT searches are limited to 8kb.  Please try a shorter sequence.");
@@ -232,6 +230,10 @@
         final byte[] seqBytes = genome.getSequence(chr, start, end);
         String userSeq = new String(seqBytes);
 
+        if(strand == Strand.NEGATIVE) {
+            userSeq = SequenceTrack.getReverseComplement(userSeq);
+        }
+
         doBlatQuery(userSeq);
     }
 
diff -Nru igv-2.3.88+dfsg/src/org/broad/igv/util/HttpUtils.java igv-2.3.90+dfsg/src/org/broad/igv/util/HttpUtils.java
--- igv-2.3.88+dfsg/src/org/broad/igv/util/HttpUtils.java	2016-11-07 10:42:41.000000000 +0000
+++ igv-2.3.90+dfsg/src/org/broad/igv/util/HttpUtils.java	2017-01-09 04:30:59.000000000 +0000
@@ -458,7 +458,7 @@
             urlDownloader.run();
             return urlDownloader;
         } else {
-            ProgressMonitor monitor = new ProgressMonitor();
+            javax.swing.ProgressMonitor monitor = new javax.swing.ProgressMonitor(IGV.getInstance().getMainPanel(), "Downloading " + outputFile.getName(), "", 0, 100);
             urlDownloader.setMonitor(monitor);
             ActionListener buttonListener = new ActionListener() {
                 @Override
@@ -466,15 +466,15 @@
                     urlDownloader.cancel(true);
                 }
             };
-            String permText = "Downloading " + url;
-            String title = dialogTitle != null ? dialogTitle : permText;
-            CancellableProgressDialog dialog = CancellableProgressDialog.showCancellableProgressDialog(dialogsParent, title, buttonListener, false, monitor);
-            dialog.setPermText(permText);
+          //  String permText = "Downloading " + url;
+          //  String title = dialogTitle != null ? dialogTitle : permText;
+          //  CancellableProgressDialog dialog = CancellableProgressDialog.showCancellableProgressDialog(dialogsParent, title, buttonListener, false, monitor);
+          //  dialog.setPermText(permText);
 
-            Dimension dms = new Dimension(600, 150);
-            dialog.setPreferredSize(dms);
-            dialog.setSize(dms);
-            dialog.validate();
+          //  Dimension dms = new Dimension(600, 150);
+          //  dialog.setPreferredSize(dms);
+          //  dialog.setSize(dms);
+          //  dialog.validate();
 
             LongRunningTask.submit(urlDownloader);
             return urlDownloader;
diff -Nru igv-2.3.88+dfsg/src/org/broad/igv/util/URLDownloader.java igv-2.3.90+dfsg/src/org/broad/igv/util/URLDownloader.java
--- igv-2.3.88+dfsg/src/org/broad/igv/util/URLDownloader.java	2016-11-07 10:42:41.000000000 +0000
+++ igv-2.3.90+dfsg/src/org/broad/igv/util/URLDownloader.java	2017-01-09 04:30:59.000000000 +0000
@@ -42,7 +42,7 @@
 
     private static Logger log = Logger.getLogger(URLDownloader.class);
 
-    private ProgressMonitor monitor = null;
+    private javax.swing.ProgressMonitor monitor = null;
 
     private final URL srcUrl;
     private final File outputFile;
@@ -100,7 +100,6 @@
         OutputStream out = null;
 
         long downloaded = 0;
-        long downSinceLast = 0;
         String curStatus;
         String msg1 = String.format("downloaded of %s total", contentLength >= 0 ? bytesToByteCountString(contentLength) : "unknown");
         int perc = 0;
@@ -111,21 +110,26 @@
             byte[] buf = new byte[64 * 1024];
             int counter = 0;
             int interval = 100;
-            int bytesRead = 0;
+            int bytesRead;
             while (!this.cancelled && (bytesRead = is.read(buf)) != -1) {
                 out.write(buf, 0, bytesRead);
                 downloaded += bytesRead;
-                downSinceLast += bytesRead;
                 counter = (counter + 1) % interval;
                 if (counter == 0 && this.monitor != null) {
                     curStatus = String.format("%s %s", bytesToByteCountString(downloaded), msg1);
-                    this.monitor.updateStatus(curStatus);
+                    this.monitor.setNote(curStatus);
                     if (contentLength >= 0) {
-                        perc = (int) ((downSinceLast * 100) / contentLength);
-                        this.monitor.fireProgressChange(perc);
-                        if (perc >= 1) downSinceLast = 0;
+                        perc = (int) ((downloaded * 100) / contentLength);
+                        this.monitor.setProgress(perc);
                     }
                 }
+
+                if(this.monitor != null && this.monitor.isCanceled()) {
+                    is.close();
+                    outputFile.delete();
+                    this.cancelled = true;
+                }
+
             }
             log.info("Download complete.  Total bytes downloaded = " + downloaded);
         } catch (IOException e) {
@@ -140,14 +144,15 @@
         }
         long fileLength = outputFile.length();
 
+
         if (this.cancelled) return RunnableResult.CANCELLED;
 
         boolean knownComplete = contentLength == fileLength;
         //Assume success if file length not known
         if (knownComplete || contentLength < 0) {
             if (this.monitor != null) {
-                this.monitor.fireProgressChange(100);
-                this.monitor.updateStatus("Done");
+                this.monitor.setProgress(100);
+                this.monitor.setNote("Done");
             }
             return RunnableResult.SUCCESS;
         } else {
@@ -178,7 +183,7 @@
         return true;
     }
 
-    public void setMonitor(ProgressMonitor monitor) {
+    public void setMonitor(javax.swing.ProgressMonitor monitor) {
         this.monitor = monitor;
     }
 
diff -Nru igv-2.3.88+dfsg/src/org/broad/igv/util/Utilities.java igv-2.3.90+dfsg/src/org/broad/igv/util/Utilities.java
--- igv-2.3.88+dfsg/src/org/broad/igv/util/Utilities.java	2016-11-07 10:42:41.000000000 +0000
+++ igv-2.3.90+dfsg/src/org/broad/igv/util/Utilities.java	2017-01-09 04:30:59.000000000 +0000
@@ -245,4 +245,23 @@
         }
 
     }
+
+    public static boolean isAllLetters(String s) {
+         byte [] bytes = s.getBytes();
+         for(int i=0; i<bytes.length; i++) {
+             if(!isLetter(bytes[i])) {
+                 return false;
+             }
+         }
+         return true;
+     }
+
+    public  static boolean isLetter(int codePoint) {
+         return ((((1 << Character.UPPERCASE_LETTER) |
+                 (1 << Character.LOWERCASE_LETTER) |
+                 (1 << Character.TITLECASE_LETTER) |
+                 (1 << Character.MODIFIER_LETTER) |
+                 (1 << Character.OTHER_LETTER)) >> Character.getType(codePoint)) & 1)
+                 != 0;
+     }
 }
diff -Nru igv-2.3.88+dfsg/src/org/broad/igv/variant/VariantRenderer.java igv-2.3.90+dfsg/src/org/broad/igv/variant/VariantRenderer.java
--- igv-2.3.88+dfsg/src/org/broad/igv/variant/VariantRenderer.java	2016-11-07 10:42:41.000000000 +0000
+++ igv-2.3.90+dfsg/src/org/broad/igv/variant/VariantRenderer.java	2017-01-09 04:30:59.000000000 +0000
@@ -222,11 +222,6 @@
 
         Genotype genotype = variant.getGenotype(sampleName);
 
-        if (sampleName.equals("CYP26B1-B12")) {
-            System.out.println(genotype.getTypeString() + "   " + genotype.getGenotypeString() + "  " + isFiltered);
-        }
-
-
         if (genotype == null) {
             log.error("Genotype not found for sample " + sampleName);
         } else {
diff -Nru igv-2.3.88+dfsg/test/src/org/broad/igv/util/SeekableServiceStreamTest.java igv-2.3.90+dfsg/test/src/org/broad/igv/util/SeekableServiceStreamTest.java
--- igv-2.3.88+dfsg/test/src/org/broad/igv/util/SeekableServiceStreamTest.java	2016-11-07 10:42:41.000000000 +0000
+++ igv-2.3.90+dfsg/test/src/org/broad/igv/util/SeekableServiceStreamTest.java	2017-01-09 04:30:59.000000000 +0000
@@ -48,7 +48,7 @@
     @Test
     public void testRead() throws Exception {
 
-        String tdfFile = "http://data.broadinstitute.org/igvdata/annotations/hg18/conservation/omega.12mer.tdf";
+        String tdfFile = "https://data.broadinstitute.org/igvdata/annotations/hg18/conservation/omega.12mer.tdf";
 
         HttpUtils.getInstance().updateProxySettings();
 
diff -Nru igv-2.3.88+dfsg/test/src/org/broad/igv/util/TestByteRange.java igv-2.3.90+dfsg/test/src/org/broad/igv/util/TestByteRange.java
--- igv-2.3.88+dfsg/test/src/org/broad/igv/util/TestByteRange.java	2016-11-07 10:42:41.000000000 +0000
+++ igv-2.3.90+dfsg/test/src/org/broad/igv/util/TestByteRange.java	1970-01-01 00:00:00.000000000 +0000
@@ -1,73 +0,0 @@
-/*
- * The MIT License (MIT)
- *
- * Copyright (c) 2007-2015 Broad Institute
- *
- * Permission is hereby granted, free of charge, to any person obtaining a copy
- * of this software and associated documentation files (the "Software"), to deal
- * in the Software without restriction, including without limitation the rights
- * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
- * copies of the Software, and to permit persons to whom the Software is
- * furnished to do so, subject to the following conditions:
- *
- * The above copyright notice and this permission notice shall be included in
- * all copies or substantial portions of the Software.
- *
- *
- * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
- * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
- * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
- * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
- * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
- * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
- * THE SOFTWARE.
- */
-
-package org.broad.igv.util;
-
-import org.junit.Test;
-
-import java.io.BufferedReader;
-import java.io.IOException;
-import java.io.InputStream;
-import java.io.InputStreamReader;
-import java.net.HttpURLConnection;
-import java.net.URL;
-
-import static org.junit.Assert.assertTrue;
-
-
-/**
- * @author Jim Robinson
- * @date 12/21/11
- */
-public class TestByteRange {
-
-    @Test
-    public void testByteRange() throws Exception {
-
-        String urlString = "http://www.broadinstitute.org/igv/projects/dev/echo.php";
-        String byteRange = "bytes=" + 5 + "-" + 10;
-        HttpURLConnection conn = (HttpURLConnection) (new URL(urlString)).openConnection();
-        conn.setRequestMethod("GET");
-        conn.setRequestProperty("Range", byteRange);
-
-        InputStream is = null;
-
-        int lines = 0;
-        try {
-            is = conn.getInputStream();
-            BufferedReader br = new BufferedReader(new InputStreamReader(is));
-            String nextLine;
-            while ((nextLine = br.readLine()) != null) {
-                lines++;
-            }
-
-        } finally {
-            if (is != null) {
-                is.close();
-            }
-        }
-        assertTrue(lines > 0);
-    }
-}
diff -Nru igv-2.3.88+dfsg/test/src/org/broad/igv/util/TestS3Access.java igv-2.3.90+dfsg/test/src/org/broad/igv/util/TestS3Access.java
--- igv-2.3.88+dfsg/test/src/org/broad/igv/util/TestS3Access.java	2016-11-07 10:42:41.000000000 +0000
+++ igv-2.3.90+dfsg/test/src/org/broad/igv/util/TestS3Access.java	1970-01-01 00:00:00.000000000 +0000
@@ -1,82 +0,0 @@
-/*
- * The MIT License (MIT)
- *
- * Copyright (c) 2007-2015 Broad Institute
- *
- * Permission is hereby granted, free of charge, to any person obtaining a copy
- * of this software and associated documentation files (the "Software"), to deal
- * in the Software without restriction, including without limitation the rights
- * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
- * copies of the Software, and to permit persons to whom the Software is
- * furnished to do so, subject to the following conditions:
- *
- * The above copyright notice and this permission notice shall be included in
- * all copies or substantial portions of the Software.
- *
- *
- * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
- * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
- * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
- * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
- * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
- * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
- * THE SOFTWARE.
- */
-
-
-package org.broad.igv.util;
-
-import org.junit.Ignore;
-import org.junit.Test;
-
-import java.io.*;
-import java.net.URL;
-import java.util.Arrays;
-
-import static org.junit.Assert.assertTrue;
-
-/**
- * Timing test for S3 storage files
- */
-@Ignore //Not sure about URLs
-public class TestS3Access {
-
-    public static void main(String[] args) {
-        try {
-            testAsciiDownloadStatic();
-        } catch (IOException e) {
-            e.printStackTrace();  //To change body of catch statement use File | Settings | File Templates.
-        }
-    }
-
-    @Test
-    public void testAsciiDownload() throws Exception{
-        testAsciiDownloadStatic();
-    }
-    public static void testAsciiDownloadStatic() throws IOException {
-
-        String broadURL = "http://data.broadinstitute.org/igvdata/annotations/hg18/refGene.txt";
-        String s3URL = "http://s3.amazonaws.com/genomespace-igv/refGene.txt";
-
-        try {
-
-
-            for (int i = 0; i < 10; i++) {
-                for (String url : Arrays.asList(broadURL, s3URL)) {
-
-                    InputStream inputStream = HttpUtils.getInstance().openConnectionStream(new URL(url));
-                    BufferedReader reader = new BufferedReader(new InputStreamReader(inputStream));
-                    int nLines = 0;
-                    long t0 = System.currentTimeMillis();
-                    while (reader.readLine() != null) {
-                        nLines++;
-                    }
-                    //System.out.println(url + " read " + nLines + " in " + (System.currentTimeMillis() - t0) + " ms ");
-                    reader.close();
-                    assertTrue(nLines > 0);
-                }
-            }
-        } finally {
-        }
-    }
-}
diff -Nru igv-2.3.88+dfsg/test/src/org/broad/igv/util/UtilitiesTest.java igv-2.3.90+dfsg/test/src/org/broad/igv/util/UtilitiesTest.java
--- igv-2.3.88+dfsg/test/src/org/broad/igv/util/UtilitiesTest.java	1970-01-01 00:00:00.000000000 +0000
+++ igv-2.3.90+dfsg/test/src/org/broad/igv/util/UtilitiesTest.java	2017-01-09 04:30:59.000000000 +0000
@@ -0,0 +1,24 @@
+package org.broad.igv.util;
+
+import org.junit.Test;
+
+import static org.junit.Assert.*;
+
+/**
+ * Created by jrobinso on 12/17/16.
+ */
+public class UtilitiesTest {
+    @Test
+    public void isAllLetters() throws Exception {
+
+        boolean b = Utilities.isAllLetters("StringWithNothingButLetters");
+        assertTrue(b);
+
+        b = Utilities.isAllLetters("StringWithNumbers123");
+        assertFalse(b);
+
+        b = Utilities.isAllLetters("String with spaces");
+        assertFalse(b);
+    }
+
+}
\ No newline at end of file
diff -Nru igv-2.3.88+dfsg/web/StaticLinkExamples.html igv-2.3.90+dfsg/web/StaticLinkExamples.html
--- igv-2.3.88+dfsg/web/StaticLinkExamples.html	2016-11-07 10:42:41.000000000 +0000
+++ igv-2.3.90+dfsg/web/StaticLinkExamples.html	2017-01-09 04:30:59.000000000 +0000
@@ -6,27 +6,31 @@
     <title></title>
 </head>
 <body>
-<p><a href="http://www.broadinstitute.org/igv/projects/dev/launch.php?sessionURL=http://www.broadinstitute.org/igvdata/encode/hg19/broadEncode/wgEncodeBroadHistoneGm12878ControlStdSig.bigWig&amp;genome=hg19&amp;name=Gm12878&amp;merge=false">
-     Dev launch link with name, merge = false</a></p>
-<p><a href="http://www.broadinstitute.org/igv/projects/current/launch.php?sessionURL=http://www.broadinstitute.org/igvdata/encode/hg19/broadEncode/wgEncodeBroadHistoneGm12878ControlStdSig.bigWig&amp;genome=hg19&amp;name=Gm12878">
-     Prod launch link with name</a></p>
-<p><a href="http://www.broadinstitute.org/igv/projects/current/launch.php?sessionURL=http://www.broadinstitute.org/igvdata/encode/hg19/broadEncode/wgEncodeBroadHistoneGm12878ControlStdSig.bigWig&amp;genome=hg19&amp;name=Gm12878&amp;merge=false">
-     Prod launch link with name, merge = false</a></p>
-<p><a href="http://www.broadinstitute.org/igv/projects/current/igv.php?sessionURL=http://www.broadinstitute.org/igvdata/encode/hg19/broadEncode/wgEncodeBroadHistoneGm12878ControlStdSig.bigWig&amp;genome=hg19&amp;name=Gm12878">
-     Prod igv.php link with name</a></p>
-<p><a href="http://localhost:60151/load?file=http://www.broadinstitute.org/igvdata/annotations/hg18/conservation/pi.12mer.wig.tdf&amp;locus=egfr&amp;name=CONS">
-    Direct load with name</a></p>
-<p><a href="http://localhost:60151/load?file=http://www.broadinstitute.org/igvdata/annotations/hg18/conservation/pi.12mer.wig.tdf&amp;locus=egfr&amp;name=CONS&amp;merge=false">
-    Direct load with name, merge = false</a></p>
-<p><a href="http://localhost:60151/load?file=http://www.broadinstitute.org/igvdata/annotations/hg18/conservation/pi.12mer.wig.tdf">
-    Direct load no name</a></p>
+<p>
+    <a href="http://www.broadinstitute.org/igv/projects/current/launch.php?sessionURL=http://www.broadinstitute.org/igvdata/encode/hg19/broadEncode/wgEncodeBroadHistoneGm12878ControlStdSig.bigWig&amp;genome=hg19&amp;name=Gm12878">
+        Launch link with name</a></p>
+<p>
+    <a href="http://www.broadinstitute.org/igv/projects/current/launch.php?sessionURL=http://www.broadinstitute.org/igvdata/encode/hg19/broadEncode/wgEncodeBroadHistoneGm12878ControlStdSig.bigWig&amp;genome=hg19&amp;name=Gm12878&amp;merge=false">
+        Launch link with name, merge = false</a></p>
+<p>
+    <a href="http://localhost:60151/load?file=http://www.broadinstitute.org/igvdata/annotations/hg18/conservation/pi.12mer.wig.tdf&amp;locus=egfr&amp;name=CONS">
+        Direct load with name</a></p>
+<p>
+    <a href="http://localhost:60151/load?file=http://www.broadinstitute.org/igvdata/annotations/hg18/conservation/pi.12mer.wig.tdf&amp;locus=egfr&amp;name=CONS&amp;merge=false">
+        Direct load with name, merge = false</a></p>
+<p>
+    <a href="http://localhost:60151/load?file=http://www.broadinstitute.org/igvdata/annotations/hg18/conservation/pi.12mer.wig.tdf&amp;locus=egfr&amp;name=CONS&amp;merge=true">
+        Direct load with name, merge = true</a></p>
+<p>
+    <a href="http://localhost:60151/load?file=http://www.broadinstitute.org/igvdata/annotations/hg18/conservation/pi.12mer.wig.tdf">
+        Direct load no name</a></p>
+<p><a href="http://localhost:60151/load?genome=http://s3.amazonaws.com/igv.broadinstitute.org/genomes/seq/hg18/hg18.fasta">
+    Load fasta</a></p>
+<p>
+    <a href="http://localhost:60151/load?file=http://www.broadinstitute.org/igvdata/annotations/hg18/conservation/pi.12mer.wig.tdf&amp;genome=http://s3.amazonaws.com/igv.broadinstitute.org/genomes/seq/hg18/hg18.fasta">
+        Direct load with fasta, merge=true</a></p>
 <p><a href="http://localhost:60151/execute?command=sort+yourTack">
     Batch sort</a></p>
 
-<p>
-    <a href="http://www.broadinstitute.org/igv/projects/dev/launch.php?sessionURL=http://1000genomes.s3.amazonaws.com/data/NA12878/high_coverage_alignment/NA12878.mapped.ILLUMINA.bwa.CEU.high_coverage_pcr_free.20130520.bam,http://www.broadinstitute.org/igvdata/annotations/hg19/EnsemblGenes.ensGene,http://www.broadinstitute.org/igvdata/annotations/hg19/dbSnp/snp137.hg19.bed.gz&amp;index=http://1000genomes.s3.amazonaws.com/data/NA12878/high_coverage_alignment/NA12878.mapped.ILLUMINA.bwa.CEU.high_coverage_pcr_free.20130520.bam.bai,,http://www.broadinstitute.org/igvdata/annotations/hg19/dbSnp/snp137.hg19.bed.gz.tbi&amp;genome=hg19>
-    Dev launch link with name, merge = false</a></p>
-
-</p>
 </body>
-</html>
\ No newline at end of file
+</html>