.gitignore

@@ -2,3 +2,4 @@
 .idea/workspace.xml
 *.jar
 igv.sh
+/out/

build.xml

 <!--
-  ~ Copyright (c) 2007-2012 The Broad Institute, Inc.
-  ~ SOFTWARE COPYRIGHT NOTICE
-  ~ This software and its documentation are the copyright of the Broad Institute, Inc. All rights are reserved.
-  ~
-  ~ This software is supplied without any warranty or guaranteed support whatsoever. The Broad Institute is not responsible for its use, misuse, or functionality.
-  ~
-  ~ This software is licensed under the terms of the GNU Lesser General Public License (LGPL),
-  ~ Version 2.1 which is available at http://www.opensource.org/licenses/lgpl-2.1.php.
+ ~ The MIT License (MIT)
+ ~
+ ~ Copyright (c) 2007-2017 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.
   -->
 
 <project name="IGV" default="all" basedir=".">

build_macros.xml

 <!--
-  ~ Copyright (c) 2007-2012 The Broad Institute, Inc.
-  ~ SOFTWARE COPYRIGHT NOTICE
-  ~ This software and its documentation are the copyright of the Broad Institute, Inc. All rights are reserved.
-  ~
-  ~ This software is supplied without any warranty or guaranteed support whatsoever. The Broad Institute is not responsible for its use, misuse, or functionality.
-  ~
-  ~ This software is licensed under the terms of the GNU Lesser General Public License (LGPL),
-  ~ Version 2.1 which is available at http://www.opensource.org/licenses/lgpl-2.1.php.
+ ~ The MIT License (MIT)
+ ~
+ ~ Copyright (c) 2007-2017 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.
   -->
 
 <project name="macrodefs">

genomes/db/hg38/hg38.json

+{
+  "id": "hg38",
+  "ucscID": "hg38",
+  "name": "Human (hg38)",
+  "fastaURL": "http://s3.amazonaws.com/igv.broadinstitute.org/genomes/seq/hg38/hg38.fa",
+  "indexURL": "http://s3.amazonaws.com/igv.broadinstitute.org/genomes/seq/hg38/hg38.fa.fai",
+  "cytobandURL": "http://hgdownload.cse.ucsc.edu/goldenPath/hg38/database/cytoBandIdeo.txt.gz",
+  "aliasURL": "https://s3.amazonaws.com/igv.broadinstitute.org/annotations/hg38/hg38_alias.tab",
+  "annotations": [
+    {
+      "name": "Refseq Genes",
+      "url": "http://hgdownload.cse.ucsc.edu/goldenPath/hg38/database/refGene.txt.gz",
+      "indexed": false
+    }
+  ]
+}

genomes/db/ws235/ws235_dataServerRegistry.txt

+https://s3.amazonaws.com/igv.broadinstitute.org/annotations/WS235/WS235_annotations.xml

scripts/build-tools.xml

 <?xml version="1.0"?>
 <!--
-  ~ Copyright (c) 2007-2012 The Broad Institute, Inc.
-  ~ SOFTWARE COPYRIGHT NOTICE
-  ~ This software and its documentation are the copyright of the Broad Institute, Inc. All rights are reserved.
-  ~
-  ~ This software is supplied without any warranty or guaranteed support whatsoever. The Broad Institute is not responsible for its use, misuse, or functionality.
-  ~
-  ~ This software is licensed under the terms of the GNU Lesser General Public License (LGPL),
-  ~ Version 2.1 which is available at http://www.opensource.org/licenses/lgpl-2.1.php.
+ ~ The MIT License (MIT)
+ ~
+ ~ Copyright (c) 2007-2017 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.
   -->
 
 <project name="igvtools" basedir="../." default="deploy">

scripts/igv_build.xml

 <!--
-  ~ Copyright (c) 2007-2012 The Broad Institute, Inc.
-  ~ SOFTWARE COPYRIGHT NOTICE
-  ~ This software and its documentation are the copyright of the Broad Institute, Inc. All rights are reserved.
-  ~
-  ~ This software is supplied without any warranty or guaranteed support whatsoever. The Broad Institute is not responsible for its use, misuse, or functionality.
-  ~
-  ~ This software is licensed under the terms of the GNU Lesser General Public License (LGPL),
-  ~ Version 2.1 which is available at http://www.opensource.org/licenses/lgpl-2.1.php.
+ ~ The MIT License (MIT)
+ ~
+ ~ Copyright (c) 2007-2017 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.
   -->
 
 <project name="IGV" default="build" basedir="../.">

src/org/broad/igv/batch/CommandExecutor.java

@@ -335,7 +335,7 @@ public class CommandExecutor {
         }
     }
 
-    private String setSleepInterval(String param1) {
+    public String setSleepInterval(String param1) {
         try {
             sleepInterval = Integer.parseInt(param1.trim());
             return "OK";

src/org/broad/igv/feature/genome/Genome.java

@@ -40,6 +40,7 @@ import org.broad.igv.feature.Chromosome;
 import org.broad.igv.feature.Cytoband;
 import org.broad.igv.track.FeatureTrack;
 import org.broad.igv.ui.panel.ReferenceFrame;
+import org.broad.igv.util.ResourceLocator;
 
 import java.io.*;
 import java.util.*;
@@ -67,6 +68,7 @@ public class Genome {
     private String species;
     private String ucscID;
     private GenomeDescriptor descriptor;   // Can be null
+    private ArrayList<ResourceLocator> annotationResources;
 
 
     public Genome(String id, String displayName, Sequence sequence, boolean chromosOrdered, GenomeDescriptor descriptor) {
@@ -601,4 +603,12 @@ public class Genome {
     public boolean sequenceIsLoaded(ReferenceFrame frame) {
         return sequence.isLoaded(frame);
     }
+
+    public void setAnnotationResources(ArrayList<ResourceLocator> annotationResources) {
+        this.annotationResources = annotationResources;
+    }
+
+    public ArrayList<ResourceLocator> getAnnotationResources() {
+        return annotationResources;
+    }
 }

src/org/broad/igv/feature/genome/GenomeDescriptor.java

@@ -43,7 +43,6 @@ import java.io.InputStream;
 public abstract class GenomeDescriptor {
 
     private String name;
-    private boolean chrNamesAltered;
     private String id;
     protected String cytoBandFileName;
     protected String geneFileName;
@@ -55,11 +54,9 @@ public abstract class GenomeDescriptor {
     private boolean hasCustomSequencePath;
     private boolean chromosomesAreOrdered = false;
     private boolean fasta = false;
-    private boolean fastaDirectory = false;
     private String [] fastaFileNames;
 
     public GenomeDescriptor(String name,
-                            boolean chrNamesAltered,
                             String id,
                             String cytoBandFileName,
                             String geneFileName,
@@ -70,9 +67,7 @@ public abstract class GenomeDescriptor {
                             String compressedSequencePath,
                             boolean chromosomesAreOrdered,
                             boolean fasta,
-                            boolean fastaDirectory,
                             String fastaFileNameString) {
-        this.chrNamesAltered = chrNamesAltered;
         this.name = name;
         this.id = id;
         this.cytoBandFileName = cytoBandFileName;
@@ -84,7 +79,6 @@ public abstract class GenomeDescriptor {
         this.compressedSequencePath = compressedSequencePath;
         this.chromosomesAreOrdered = chromosomesAreOrdered;
         this.fasta = fasta;
-        this.fastaDirectory = fastaDirectory;
 
         if(fastaFileNameString != null) {
             fastaFileNames = fastaFileNameString.split(",");
@@ -109,8 +103,6 @@ public abstract class GenomeDescriptor {
         return id;
     }
 
-    // Used to determine feature file type, really only extension is needed
-
     public String getGeneFileName() {
         return geneFileName;
     }
@@ -123,12 +115,6 @@ public abstract class GenomeDescriptor {
         return fastaFileNames;
     }
 
-    public abstract InputStream getCytoBandStream() throws IOException;
-
-    public abstract InputStream getGeneStream() throws IOException;
-
-    public abstract InputStream getChrAliasStream() throws IOException;
-
     public String getSequencePath() {
         return compressedSequencePath == null ? sequencePath : compressedSequencePath;
     }
@@ -165,4 +151,10 @@ public abstract class GenomeDescriptor {
         return hasCustomSequencePath;
     }
 
+    public abstract InputStream getCytoBandStream() throws IOException;
+
+    public abstract InputStream getGeneStream() throws IOException;
+
+    public abstract InputStream getChrAliasStream() throws IOException;
+
 }

src/org/broad/igv/feature/genome/GenomeManager.java

@@ -34,6 +34,10 @@
 package org.broad.igv.feature.genome;
 
 
+import com.google.gson.JsonArray;
+import com.google.gson.JsonElement;
+import com.google.gson.JsonObject;
+import com.google.gson.JsonParser;
 import org.apache.log4j.Logger;
 import org.broad.igv.DirectoryManager;
 import org.broad.igv.Globals;
@@ -51,8 +55,10 @@ import org.broad.igv.track.*;
 import org.broad.igv.ui.IGV;
 import org.broad.igv.ui.commandbar.GenomeListManager;
 import org.broad.igv.ui.panel.FrameManager;
-import org.broad.igv.ui.util.*;
+import org.broad.igv.ui.util.MessageUtils;
+import org.broad.igv.ui.util.ProgressBar;
 import org.broad.igv.ui.util.ProgressMonitor;
+import org.broad.igv.ui.util.UIUtilities;
 import org.broad.igv.ui.util.download.Downloader;
 import org.broad.igv.util.*;
 
@@ -101,21 +107,10 @@ public class GenomeManager {
 
     private GenomeListManager genomeListManager;
 
-//    public static String getUserDefinedGenomeListFile() {
-//        if (Globals.isTesting()) {
-//            return TEST_USER_DEFINED_GENOME_LIST_FILE;
-//        } else {
-//            return ACT_USER_DEFINED_GENOME_LIST_FILE;
-//        }
-//
-//    }
-
     private static GenomeManager theInstance;
 
     private Genome currentGenome;
 
-    boolean serverGenomeListUnreachable = false;
-
     private Map<String, File> localSequenceMap;
 
     /**
@@ -149,9 +144,6 @@ public class GenomeManager {
         }
     }
 
-    public boolean isServerGenomeListUnreachable() {
-        return serverGenomeListUnreachable;
-    }
 
     public void loadGenomeById(String genomeId) throws IOException {
 
@@ -214,7 +206,11 @@ public class GenomeManager {
             } else if (genomePath.endsWith(".chrom.sizes")) {
                 altGenomePath = genomePath;
                 newGenome = loadChromSizes(genomePath);
+            } else if (genomePath.endsWith(".json")) {
+                altGenomePath = genomePath;
+                newGenome = loadJsonFile(genomePath);
             } else {
+
                 // Assume a fasta file
                 altGenomePath = genomePath;
                 if (genomePath.endsWith(Globals.GZIP_FILE_EXTENSION)) {
@@ -262,8 +258,13 @@ public class GenomeManager {
             setCurrentGenome(newGenome);
 
             if (IGV.hasInstance()) {
-                FeatureTrack geneFeatureTrack = newGenome.getGeneTrack();
+                FeatureTrack geneFeatureTrack = newGenome.getGeneTrack();   // Can be null
                 IGV.getInstance().setGenomeTracks(geneFeatureTrack);
+
+                List<ResourceLocator> resources = newGenome.getAnnotationResources();
+                if (resources != null) {
+                    IGV.getInstance().loadResources(resources);
+                }
             }
 
 
@@ -384,6 +385,55 @@ public class GenomeManager {
         return newGenome;
     }
 
+    private Genome loadJsonFile(String genomePath) throws IOException {
+
+        Genome newGenome = null;
+
+        BufferedReader reader = ParsingUtils.openBufferedReader(genomePath);
+        JsonParser parser = new JsonParser();
+        JsonObject json = parser.parse(reader).getAsJsonObject();
+
+        String id = json.get("id").getAsString();
+        String name = json.get("name").getAsString();
+        String fastaPath = json.get("fastaURL").getAsString();
+        JsonElement indexPathObject = json.get("indexURL");
+        String indexPath = indexPathObject == null ? null : indexPathObject.getAsString();
+
+        FastaIndexedSequence sequence = fastaPath.endsWith(".gz") ?
+                new FastaBlockCompressedSequence(fastaPath, indexPath) :
+                new FastaIndexedSequence(fastaPath, indexPath);
+
+
+        ArrayList<ResourceLocator> tracks = new ArrayList<>();
+        JsonArray annotations = json.getAsJsonArray("annotations");
+        if (annotations != null) {
+            annotations.forEach((JsonElement jsonElement) -> {
+                JsonObject obj = jsonElement.getAsJsonObject();
+                String trackPath = obj.get("url").getAsString();
+                JsonElement trackName = obj.get("name");
+                JsonElement trackIndexPath = obj.get("indexURL");
+                JsonElement indexed = obj.get("indexed");
+                JsonElement aliasURL = obj.get("aliasURL");
+
+                ResourceLocator res = new ResourceLocator(trackPath);
+                if (trackName != null) res.setName(trackName.getAsString());
+                if (trackIndexPath != null) res.setIndexPath(trackIndexPath.getAsString());
+                if (indexed != null) res.setIndexed(indexed.getAsBoolean());
+                tracks.add(res);
+            });
+        }
+
+
+        newGenome = new Genome(id, name, sequence, true);
+
+        newGenome.setAnnotationResources(tracks);
+
+        // TODO -- set aliases
+
+        return newGenome;
+
+    }
+
     private Collection<Collection<String>> loadChrAliases(String path) {
 
         // String id = genome.getId();
@@ -720,7 +770,6 @@ public class GenomeManager {
                     // The new descriptor
                     genomeDescriptor = new GenomeZipDescriptor(
                             properties.getProperty(GENOME_ARCHIVE_NAME_KEY),
-                            chrNamesAltered,
                             properties.getProperty(GENOME_ARCHIVE_ID_KEY),
                             cytobandZipEntryName,
                             geneFileName,
@@ -733,7 +782,6 @@ public class GenomeManager {
                             zipEntries,
                             chromosomesAreOrdered,
                             fasta,
-                            fastaDirectory,
                             fastaFileNameString);
 
                     if (url != null) {

src/org/broad/igv/feature/genome/GenomeZipDescriptor.java

@@ -43,7 +43,6 @@ public class GenomeZipDescriptor extends GenomeDescriptor {
     private ZipFile genomeZipFile;
 
     public GenomeZipDescriptor(String name,
-                               boolean chrNamesAltered,
                                String id,
                                String cytoBandFileName,
                                String geneFileName,
@@ -56,12 +55,11 @@ public class GenomeZipDescriptor extends GenomeDescriptor {
                                Map<String, ZipEntry> zipEntries,
                                boolean chromosomesAreOrdered,
                                boolean fasta,
-                               boolean fastaDirectory,
                                String fastaFileNameString) {
 
-        super(name, chrNamesAltered, id, cytoBandFileName, geneFileName, chrAliasFileName, geneTrackName,
+        super(name, id, cytoBandFileName, geneFileName, chrAliasFileName, geneTrackName,
                 sequenceLocation, hasCustomSequenceLocation, compressedSequencePath,
-                chromosomesAreOrdered, fasta, fastaDirectory, fastaFileNameString);
+                chromosomesAreOrdered, fasta, fastaFileNameString);
 
         this.zipEntries = zipEntries;
         this.genomeZipFile = genomeZipFile;

src/org/broad/igv/feature/genome/fasta/FastaBlockCompressedSequence.java

@@ -7,25 +7,31 @@ import org.broad.igv.util.LittleEndianInputStream;
 import org.broad.igv.util.ParsingUtils;
 import org.broad.igv.util.stream.IGVSeekableStreamFactory;
 
-import java.io.*;
-import java.util.ArrayList;
-import java.util.List;
+import java.io.BufferedInputStream;
+import java.io.EOFException;
+import java.io.IOException;
+import java.io.InputStream;
 
 /**
  * Created by jrobinso on 6/23/17.
  */
 public class FastaBlockCompressedSequence extends FastaIndexedSequence {
 
-    Mapping [] gziMappings;
+    Mapping[] gziMappings;
     Mapping zeroMapping = new Mapping(0, 0);
 
     public FastaBlockCompressedSequence(String path) throws IOException {
-        super(path);
 
-        String gziPath = path + ".gzi";
+        this(path, null);
+    }
+
+    public FastaBlockCompressedSequence(String path, String indexPath) throws IOException {
+
+        super(path);
 
-        readGziMappings(gziPath);
+        if(indexPath == null) indexPath = path + ".gzi";
 
+        readGziMappings(indexPath);
     }
 
     @Override
@@ -44,7 +50,7 @@ public class FastaBlockCompressedSequence extends FastaIndexedSequence {
         try {
             int nBytes = (int) (posEnd - posStart);
 
-            int bufferSize = Math.max(512000, nBytes/8);
+            int bufferSize = Math.max(512000, nBytes / 8);
 
             ss = new SeekableBufferedStream(IGVSeekableStreamFactory.getInstance().getStreamFor(path), bufferSize);
 
@@ -66,16 +72,15 @@ public class FastaBlockCompressedSequence extends FastaIndexedSequence {
     protected Mapping findBlockContaining(long uoffset) {
 
         int ilo = 0, ihi = gziMappings.length - 1;
-        while ( ilo<=ihi )
-        {
-            int i = (ilo+ihi) / 2;
+        while (ilo <= ihi) {
+            int i = (ilo + ihi) / 2;
             Mapping mapping = gziMappings[i];
-            if ( uoffset < mapping.uncompressedOffset ) ihi = i - 1;
-            else if ( uoffset >= mapping.uncompressedOffset ) ilo = i + 1;
+            if (uoffset < mapping.uncompressedOffset) ihi = i - 1;
+            else if (uoffset >= mapping.uncompressedOffset) ilo = i + 1;
             else break;
         }
 
-        return ilo == 0 ? zeroMapping : gziMappings[ilo-1];
+        return ilo == 0 ? zeroMapping : gziMappings[ilo - 1];
     }
 
 
@@ -99,13 +104,13 @@ public class FastaBlockCompressedSequence extends FastaIndexedSequence {
 
     private void readFully(byte[] b, InputStream is) throws IOException {
         int len = b.length;
-        if(len < 0) {
+        if (len < 0) {
             throw new IndexOutOfBoundsException();
         } else {
             int count;
-            for(int n = 0; n < len; n += count) {
+            for (int n = 0; n < len; n += count) {
                 count = is.read(b, n, len - n);
-                if(count < 0) {
+                if (count < 0) {
                     throw new EOFException();
                 }
             }

src/org/broad/igv/feature/genome/fasta/FastaIndexedSequence.java

@@ -25,12 +25,10 @@
 
 package org.broad.igv.feature.genome.fasta;
 
-import htsjdk.samtools.seekablestream.SeekableBufferedStream;
 import htsjdk.samtools.seekablestream.SeekableStream;
 import org.apache.log4j.Logger;
 import org.broad.igv.feature.genome.Sequence;
 import org.broad.igv.util.FileUtils;
-import org.broad.igv.util.HttpUtils;
 import org.broad.igv.util.ParsingUtils;
 import org.broad.igv.util.stream.IGVSeekableStreamFactory;
 
@@ -56,11 +54,15 @@ public class FastaIndexedSequence implements Sequence {
     private final ArrayList<String> chromoNamesList;
 
     public FastaIndexedSequence(String path) throws IOException {
+        this(path, null);
+    }
+
+    public FastaIndexedSequence(String path, String indexPath) throws IOException {
 
         this.path = path;
         contentLength = ParsingUtils.getContentLength(path);
 
-        String indexPath = path + ".fai";
+        if (indexPath == null) indexPath = path + ".fai";
 
         index = new FastaIndex(indexPath);
         chromoNamesList = new ArrayList<>(index.getSequenceNames());
@@ -95,6 +97,7 @@ public class FastaIndexedSequence implements Sequence {
         FastaIndex.FastaSequenceIndexEntry idxEntry = index.getIndexEntry(chr);
 
         if (idxEntry == null) {
+            log.info("No fasta sequence entry for: " + chr);
             return null;
         }
 
@@ -149,8 +152,7 @@ public class FastaIndexedSequence implements Sequence {
             return bos.toByteArray();
 
         } catch (IOException e) {
-            e.printStackTrace();  //To change body of catch statement use File | Settings | File Templates.
-
+            log.error("Error loading sequence " + chr + ":" + qstart + "-" + qend, e);
             return null;
         }
     }
@@ -171,7 +173,7 @@ public class FastaIndexedSequence implements Sequence {
 
         SeekableStream ss = null;
         try {
-            ss =  IGVSeekableStreamFactory.getInstance().getStreamFor(path);
+            ss = IGVSeekableStreamFactory.getInstance().getStreamFor(path);
             int nBytes = (int) (posEnd - posStart);
             byte[] bytes = new byte[nBytes];
             ss.seek(posStart);

src/org/broad/igv/ga4gh/OAuthUtils.java

@@ -37,12 +37,17 @@ import org.broad.igv.util.FileUtils;
 import org.broad.igv.util.HttpUtils;
 
 import java.awt.*;
+import java.io.BufferedReader;
+import java.io.File;
+import java.io.FileReader;
 import java.io.IOException;
 import java.net.URI;
 import java.net.URISyntaxException;
 import java.net.URL;
 import java.util.HashMap;
+import java.util.HashSet;
 import java.util.Map;
+import java.util.Set;
 import java.util.prefs.Preferences;
 
 /**
@@ -66,7 +71,7 @@ public class OAuthUtils {
     private static final String PROPERTIES_URL = "https://igvdata.broadinstitute.org/app/oauth_native.json";
     private String genomicsScope = "https://www.googleapis.com/auth/genomics";
     private String gsScope = "https://www.googleapis.com/auth/devstorage.read_write";
-    private String profileScope = "https://www.googleapis.com/auth/userinfo.profile";
+    private String emailScope = "https://www.googleapis.com/auth/userinfo.email";
     private String state = "%2Fprofile";
     private String redirectURI = "http%3A%2F%2Flocalhost%3A60151%2FoauthCallback";
     private String oobURI = "urn%3Aietf%3Awg%3Aoauth%3A2.0%3Aoob";
@@ -84,19 +89,23 @@ public class OAuthUtils {
 
     private static OAuthUtils theInstance;
     private String currentUserName;
+    private String currentUserEmail;
+    private String currentUserID;
+
 
     // dwm08
     // by default this is the google scope
-    private String scope = genomicsScope + "%20" + gsScope + "%20" + profileScope;
+    private String scope = genomicsScope + "%20" + gsScope + "%20" + emailScope;
 
-    // Construct OAuthUtils earcly so Google menu can be updated to the 
+    // Construct OAuthUtils earcly so Google menu can be updated to the
     // correct oauth provider. dwm08
     static {
-    	if (theInstance == null) {
+        if (theInstance == null) {
             theInstance = new OAuthUtils();
         }
     }
 
+
     public static synchronized OAuthUtils getInstance() {
 
         if (theInstance == null) {
@@ -169,7 +178,7 @@ public class OAuthUtils {
      * @throws URISyntaxException
      */
     public void openAuthorizationPage() throws IOException, URISyntaxException {
-		Desktop desktop = Desktop.getDesktop();
+        Desktop desktop = Desktop.getDesktop();
 
         // properties moved to early init dwm08
         //if (clientId == null) fetchOauthProperties();
@@ -208,13 +217,13 @@ public class OAuthUtils {
 //        	throw new IOException("Either scope or resource must be provided to authenticate.");
 //        }
 
-		// check if the "browse" Desktop action is suppported (many Linux DEs cannot directly 
-		// launch browsers!)
-		if(desktop.isSupported(Desktop.Action.BROWSE)) {
-			desktop.browse(new URI(url));
-		} else { // otherwise, display a dialog box for the user to copy the URL manually.
-			MessageUtils.showMessage("Copy this authorization URL into your web browser: " + url);
-		}
+        // check if the "browse" Desktop action is suppported (many Linux DEs cannot directly
+        // launch browsers!)
+        if (desktop.isSupported(Desktop.Action.BROWSE)) {
+            desktop.browse(new URI(url));
+        } else { // otherwise, display a dialog box for the user to copy the URL manually.
+            MessageUtils.showMessage("Copy this authorization URL into your web browser: " + url);
+        }
 
         // if the listener is not active, prompt the user
         // for the access token
@@ -330,29 +339,26 @@ public class OAuthUtils {
      *
      * @throws IOException
      */
-    private void fetchUserProfile() throws IOException {
-
-// dwm08 - removing functionality to get user profile info from microsoft oauth. Just not worth the trouble
-//            JWT jwt = JWT.decode(accessToken);
-//            Map<String, Claim> claims = jwt.getClaims();
-//            for (String claim: claims.keySet()) {
-//            	System.out.println(claim + " = " + claims.get(claim).asString());
-//            }
-//            currentUserName = claims.get("unique_name").asString();
+    public JsonObject fetchUserProfile() throws IOException {
+
         try {
-            URL url = new URL("https://www.googleapis.com/plus/v1/people/me?access_token=" + accessToken);
+
+            URL url = new URL("https://www.googleapis.com/oauth2/v1/userinfo?access_token=" + accessToken);
             String response = HttpUtils.getInstance().getContentsAsJSON(url);
             JsonParser parser = new JsonParser();
             JsonObject obj = parser.parse(response).getAsJsonObject();
-            currentUserName = obj.get("displayName").getAsString();
 
-        } catch (Throwable exception){
-            
-        }
+            currentUserName = obj.get("name").getAsString();
+            currentUserEmail = obj.get("email").getAsString();
+            currentUserID = obj.get("id").getAsString();
 
+            return obj;
+        } catch (Throwable exception) {
+            log.error(exception);
+            return null;
+        }
     }
 
-
     public String getAccessToken() {
 
         // Check expiration time, with 1 minute cushion
@@ -428,4 +434,89 @@ public class OAuthUtils {
 
         }
     }
+
+    /**
+     * Try to login to secure server. dwm08
+     */
+    public static void doSecureLogin() {
+        // if user is not currently logged in, attempt to
+        // log in user if not logged in dwm08
+        if (!OAuthUtils.getInstance().isLoggedIn()) {
+            try {
+                OAuthUtils.getInstance().openAuthorizationPage();
+            } catch (Exception ex) {
+                MessageUtils.showErrorMessage("Error fetching oAuth tokens.  See log for details", ex);
+                log.error("Error fetching oAuth tokens", ex);
+            }
+
+        }
+        // wait until authentication successful or 1 minute -
+        // dwm08
+        int i = 0;
+        while (!OAuthUtils.getInstance().isLoggedIn() && i < 600) {
+            ++i;
+            try {
+                Thread.sleep(100);
+            } catch (InterruptedException e1) {
+                e1.printStackTrace();
+            }
+        }
+    }
+
+    /**
+     * Generate a set of all urls in the sessino file
+     *
+     * @param sessionPath
+     * @return list of urls
+     */
+    public static Set<String> findUrlsInSessionFile(String sessionPath) {
+        BufferedReader br = null;
+        HashSet<String> urlSet = new HashSet<>();
+        try {
+            br = new BufferedReader(new FileReader(new File(sessionPath)));
+            String line;
+            while ((line = br.readLine()) != null) {
+                int start = line.indexOf("http");
+                if (start != -1) {
+                    int mid = line.indexOf("://", start);
+                    int end = line.indexOf("/", mid + 3);
+                    String url = line.substring(start, end);
+                    urlSet.add(url);
+                }
+            }
+
+        } catch (Exception e) {
+            e.printStackTrace();
+        } finally {
+            if (br != null) {
+                try {
+                    br.close();
+                } catch (IOException e) {
+                }
+            }
+        }
+        return urlSet;
+    }
+
+    /**
+     * Check if any reference in the session file refers to a server protected
+     * by the oauth protocol. If so, check to see if the user is logged in. If
+     * user is not logged in, put up login prompt.
+     *
+     * @param sessionPath
+     */
+    public static void checkServerLogin(String sessionPath) {
+        Set<String> urlSet = findUrlsInSessionFile(sessionPath);
+        if (urlSet.size() > 0) {
+            for (String url : urlSet) {
+                if (OAuthUtils.isGoogleCloud(url)) {
+
+                    OAuthUtils.doSecureLogin();
+
+                    // user is logged in. Can proceed with the load
+                    return;
+                }
+            }
+        }
+    }
 }

src/org/broad/igv/prefs/Constants.java

@@ -7,7 +7,6 @@ import java.util.Arrays;
  */
 final public class Constants {
 
-
     private Constants() {}  // Prevent instantiation
 
     // Preference sets
@@ -248,6 +247,10 @@ final public class Constants {
     // Letter of support dialog
     public static final String SHOW_LOS = "showLOS";
 
+    // Experimental
+    public static final String SCORE_VARIANTS = "SCORE_VARIANTS";
+
+
     /**
      * List of keys that affect the alignments loaded.  This list is used to trigger a reload, if required.
      * Not all alignment preferences need trigger a reload, this is a subset.

src/org/broad/igv/prefs/PreferencesManager.java

@@ -25,13 +25,16 @@ public class PreferencesManager implements IGVEventObserver {
 
     private static List<PreferenceGroup> preferenceGroupList;
     private static Logger log = Logger.getLogger(PreferencesManager.class);
-
     private static Map<String, IGVPreferences> preferencesMap = Collections.synchronizedMap(new HashMap<>());
+    private static IGVPreferences genericDefaults;
+
+    public static boolean forceDefaults = false;
 
     private static String prefFile;  // User preferences file
 
     static Hashtable<String, String> aliasTable = new Hashtable<String, String>();
 
+
     static {
         aliasTable.put("SAM>SORT_OPTION", "SAM.SORT_OPTION");
         aliasTable.put("FLAKING_REGIONS", "FLANKING_REGION");
@@ -49,7 +52,9 @@ public class PreferencesManager implements IGVEventObserver {
         if (preferenceGroupList == null) {
             init();
         }
-        if (preferencesMap.containsKey(category)) {
+        if (forceDefaults) {
+            return genericDefaults;
+        } else if (preferencesMap.containsKey(category)) {
             return preferencesMap.get(category);
         } else {
             return preferencesMap.get(NULL_CATEGORY);
@@ -80,7 +85,7 @@ public class PreferencesManager implements IGVEventObserver {
                 }
             }
 
-            IGVPreferences genericDefaults = new IGVPreferences(defaultPreferences.get(NULL_CATEGORY), null);
+            genericDefaults = new IGVPreferences(defaultPreferences.get(NULL_CATEGORY), null);
             IGVPreferences rnaDefaults = new IGVPreferences(defaultPreferences.get(RNA), genericDefaults);
             IGVPreferences thirdGenDefaults = new IGVPreferences(defaultPreferences.get(THIRD_GEN), genericDefaults);
 
@@ -101,7 +106,7 @@ public class PreferencesManager implements IGVEventObserver {
     }
 
     public static IGVPreferences getPreferences() {
-        return getPreferences(NULL_CATEGORY);
+        return forceDefaults ? genericDefaults : getPreferences(NULL_CATEGORY);
     }
 
     public static Collection<IGVPreferences> getAllPreferences() {

src/org/broad/igv/prefs/preferences.tab

@@ -142,6 +142,7 @@ CRAM.CACHE_SEQUENCES	Cache reference sequences	boolean	TRUE
 CRAM.CACHE_SIZE	Cache size (MB)	integer	500
 
 #Proxy
+PROXY.DISABLE_CHECK	Disable check for system proxy	boolean	FALSE
 PROXY.USE	Use proxy	boolean	FALSE
 PROXY.HOST	Proxy host	string	null
 PROXY.PORT	Proxy port	integer	0
@@ -168,6 +169,8 @@ TOOLTIP.DISMISS_DELAY	Tooltip dismiss delay (ms)	integer	60000
 ---
 
 #Hidden
+SCORE_VARIANTS	FALSE
+
 SAM.COLOR_BY	UNEXPECTED_PAIR
 SAM.AUTOSORT	FALSE
 SAM.SHADE_CENTER	TRUE

src/org/broad/igv/sam/AlignmentDataManager.java

@@ -41,6 +41,7 @@ import org.broad.igv.track.Track;
 import org.broad.igv.ui.panel.FrameManager;
 import org.broad.igv.ui.panel.ReferenceFrame;
 import org.broad.igv.util.ResourceLocator;
+import org.broad.igv.util.collections.IntArrayList;
 
 import java.io.IOException;
 import java.util.*;
@@ -57,7 +58,7 @@ public class AlignmentDataManager implements IGVEventObserver {
     private static Logger log = Logger.getLogger(AlignmentDataManager.class);
 
 
-    private Collection<AlignmentInterval> intervalCache;
+    private List<AlignmentInterval> intervalCache;
     private ResourceLocator locator;
     private HashMap<String, String> chrMappings = new HashMap();
     private Set<Range> isLoading = new HashSet<>();
@@ -66,7 +67,6 @@ public class AlignmentDataManager implements IGVEventObserver {
     private Map<String, PEStats> peStats;
     private SpliceJunctionHelper.LoadOptions loadOptions;
     private Object loadLock = new Object();
-    private boolean showAlignments = true;
     private AlignmentTrack.ExperimentType inferredExperimentType;
     private Set<Track> subscribedTracks;
 
@@ -86,21 +86,7 @@ public class AlignmentDataManager implements IGVEventObserver {
     public void receiveEvent(Object event) {
 
         if (event instanceof FrameManager.ChangeEvent) {
-
-            Collection<ReferenceFrame> frames = ((FrameManager.ChangeEvent) event).getFrames();
-            Collection<AlignmentInterval> newCache = Collections.synchronizedList(new ArrayList<>());
-
-            // Trim cache to include only current frames
-
-            for (ReferenceFrame f : frames) {
-                AlignmentInterval i = getLoadedInterval(f);
-                if (i != null) {
-                    newCache.add(i);
-                }
-            }
-            intervalCache = newCache;
-
-
+            trimCache();
         } else if (event instanceof RefreshEvent) {
             clear();
         } else {
@@ -206,7 +192,6 @@ public class AlignmentDataManager implements IGVEventObserver {
             }
         }
 
-
         return null;
     }
 
@@ -306,7 +291,11 @@ public class AlignmentDataManager implements IGVEventObserver {
 
             log.debug("Loading alignments: " + chr + ":" + adjustedStart + "-" + adjustedEnd + " for " + AlignmentDataManager.this);
 
+
             AlignmentInterval loadedInterval = loadInterval(chr, adjustedStart, adjustedEnd, renderOptions);
+
+            trimCache();
+
             intervalCache.add(loadedInterval);
 
             packAlignments(renderOptions);
@@ -318,6 +307,25 @@ public class AlignmentDataManager implements IGVEventObserver {
     }
 
 
+    /**
+     * Remove out-of-view intervals from the cache.  This is O(N) where N = #frames X #intervals.   It is assumed
+     * that N is small
+     */
+    private synchronized void trimCache() {
+
+       Iterator<AlignmentInterval> iter =  intervalCache.iterator();
+        while(iter.hasNext()) {
+            AlignmentInterval interval = iter.next();
+            for (ReferenceFrame frame : FrameManager.getFrames()) {
+                if (!interval.contains(frame.getCurrentRange())) {
+                    iter.remove();
+                }
+            }
+
+        }
+    }
+
+
     AlignmentInterval loadInterval(String chr, int start, int end, AlignmentTrack.RenderOptions renderOptions) {
 
         String sequence = chrMappings.containsKey(chr) ? chrMappings.get(chr) : chr;
@@ -332,8 +340,8 @@ public class AlignmentDataManager implements IGVEventObserver {
         ReadStats readStats = new ReadStats();
 
         AlignmentTileLoader.AlignmentTile t = reader.loadTile(sequence, start, end, spliceJunctionHelper,
-                downsampleOptions, readStats, peStats, bisulfiteContext, showAlignments);
-
+                downsampleOptions, readStats, peStats, bisulfiteContext);
+//
         if (inferredExperimentType == null && !Globals.VERSION.contains("2.4")) {
             readStats.compute();
             inferType(readStats);
@@ -476,19 +484,6 @@ public class AlignmentDataManager implements IGVEventObserver {
         coverageTrack.setSnpThreshold(PreferencesManager.getPreferences().getAsFloat(SAM_ALLELE_THRESHOLD));
     }
 
-    public void setShowAlignments(boolean showAlignments) {
-        if (showAlignments != this.showAlignments) {
-            this.showAlignments = showAlignments;
-            if (showAlignments == false) {
-                dumpAlignments();
-            } else {
-                // Change from false => true,  need to reload
-                intervalCache.clear();
-            }
-        }
-
-    }
-
     public boolean isTenX() {
         return reader.isTenX();
     }

src/org/broad/igv/sam/AlignmentTileLoader.java

@@ -121,8 +121,7 @@ public class AlignmentTileLoader implements IGVEventObserver {
                            SpliceJunctionHelper spliceJunctionHelper,
                            AlignmentDataManager.DownsampleOptions downsampleOptions,
                            ReadStats readStats, Map<String, PEStats> peStats,
-                           AlignmentTrack.BisulfiteContext bisulfiteContext,
-                           boolean showAlignments) {
+                           AlignmentTrack.BisulfiteContext bisulfiteContext) {
 
         final IGVPreferences prefMgr = PreferencesManager.getPreferences();
         boolean filterFailedReads = prefMgr.getAsBoolean(SAM_FILTER_FAILED_READS);
@@ -134,7 +133,7 @@ public class AlignmentTileLoader implements IGVEventObserver {
 
         boolean reducedMemory = prefMgr.getAsBoolean(SAM_REDUCED_MEMORY_MODE);
 
-        AlignmentTile t = new AlignmentTile(start, end, spliceJunctionHelper, downsampleOptions, bisulfiteContext, showAlignments, reducedMemory);
+        AlignmentTile t = new AlignmentTile(start, end, spliceJunctionHelper, downsampleOptions, bisulfiteContext, reducedMemory);
 
 
         //assert (tiles.size() > 0);
@@ -392,7 +391,6 @@ public class AlignmentTileLoader implements IGVEventObserver {
         private static final Random RAND = new Random();
 
         private boolean downsample;
-        private boolean showAlignments;
         private int samplingWindowSize;
         private int samplingDepth;
 
@@ -417,14 +415,12 @@ public class AlignmentTileLoader implements IGVEventObserver {
                       SpliceJunctionHelper spliceJunctionHelper,
                       AlignmentDataManager.DownsampleOptions downsampleOptions,
                       AlignmentTrack.BisulfiteContext bisulfiteContext,
-                      boolean showAlignments,
                       boolean reducedMemory) {
             this.start = start;
             this.end = end;
             this.downsampledIntervals = new ArrayList<DownsampledInterval>();
 
             this.indelLimit = PreferencesManager.getPreferences().getAsInt(SAM_SMALL_INDEL_BP_THRESHOLD);
-            this.showAlignments = showAlignments;
 
             long seed = System.currentTimeMillis();
             //System.out.println("seed: " + seed);
@@ -485,19 +481,17 @@ public class AlignmentTileLoader implements IGVEventObserver {
                 spliceJunctionHelper.addAlignment(alignment);
             }
 
-            if (showAlignments) {
-                if (downsample) {
-                    final int alignmentStart = alignment.getAlignmentStart();
-                    int currentSamplingBucketEnd = currentSamplingWindowStart + samplingWindowSize;
-                    if (currentSamplingWindowStart < 0 || alignmentStart >= currentSamplingBucketEnd) {
-                        setCurrentSamplingBucket(alignmentStart);
-                    }
+            if (downsample) {
+                final int alignmentStart = alignment.getAlignmentStart();
+                int currentSamplingBucketEnd = currentSamplingWindowStart + samplingWindowSize;
+                if (currentSamplingWindowStart < 0 || alignmentStart >= currentSamplingBucketEnd) {
+                    setCurrentSamplingBucket(alignmentStart);
+                }
 
-                    attemptAddRecordDownsampled(alignment);
+                attemptAddRecordDownsampled(alignment);
 
-                } else {
-                    alignments.add(alignment);
-                }
+            } else {
+                alignments.add(alignment);
             }
 
             alignment.finish();