From ca874650af5c6ec13c04d3f6489fa1dcbb0f57cb Mon Sep 17 00:00:00 2001
From: Nick Booher <njbooher@iastate.edu>
Date: Tue, 8 Feb 2022 15:38:14 -0600
Subject: [PATCH] update igv

---
 igv                |  2 +-
 scanfoldmenu.patch | 29 +++++++++++++++++++----------
 2 files changed, 20 insertions(+), 11 deletions(-)

diff --git a/igv b/igv
index be9ae95..104b3d9 160000
--- a/igv
+++ b/igv
@@ -1 +1 @@
-Subproject commit be9ae95457ea66cbdad257408af52d30b6b73f3a
+Subproject commit 104b3d97b0e9ded9ae1a18d7c5ba030a14c12917
diff --git a/scanfoldmenu.patch b/scanfoldmenu.patch
index 1eb905a..f7326f0 100644
--- a/scanfoldmenu.patch
+++ b/scanfoldmenu.patch
@@ -1,8 +1,8 @@
 diff --git a/src/main/java/org/broad/igv/track/TrackLoader.java b/src/main/java/org/broad/igv/track/TrackLoader.java
-index ff9de8abc..ed1924f90 100644
+index f09591e39..f87d019b6 100644
 --- a/src/main/java/org/broad/igv/track/TrackLoader.java
 +++ b/src/main/java/org/broad/igv/track/TrackLoader.java
-@@ -75,6 +75,8 @@ import org.broad.igv.renderer.MutationRenderer;
+@@ -76,6 +76,8 @@ import org.broad.igv.renderer.MutationRenderer;
  import org.broad.igv.renderer.PointsRenderer;
  import org.broad.igv.sam.*;
  import org.broad.igv.sam.reader.IndexNotFoundException;
@@ -11,7 +11,7 @@ index ff9de8abc..ed1924f90 100644
  import org.broad.igv.tdf.TDFDataSource;
  import org.broad.igv.tdf.TDFReader;
  import org.broad.igv.ui.IGV;
-@@ -210,6 +212,10 @@ public class TrackLoader {
+@@ -207,6 +209,10 @@ public class TrackLoader {
                  loadMutFile(locator, newTracks, genome); // Must be tried before ".maf" test below
              } else if (format.equals("maf")) {
                  loadMultipleAlignmentTrack(locator, newTracks, genome);
@@ -23,10 +23,10 @@ index ff9de8abc..ed1924f90 100644
                  //if a url, try htsget
                  boolean isHtsget = tryHtsget(locator, newTracks, genome);
 diff --git a/src/main/java/org/broad/igv/ui/IGVMenuBar.java b/src/main/java/org/broad/igv/ui/IGVMenuBar.java
-index 3b6dd0880..594f2208e 100644
+index 4d46a5a26..2c7ec796d 100644
 --- a/src/main/java/org/broad/igv/ui/IGVMenuBar.java
 +++ b/src/main/java/org/broad/igv/ui/IGVMenuBar.java
-@@ -60,6 +60,10 @@ import org.broad.igv.util.HttpUtils;
+@@ -62,6 +62,10 @@ import org.broad.igv.util.HttpUtils;
  import org.broad.igv.util.LongRunningTask;
  import org.broad.igv.util.blat.BlatClient;
  import org.broad.igv.util.encode.EncodeFileBrowser;
@@ -37,7 +37,7 @@ index 3b6dd0880..594f2208e 100644
  
  import javax.swing.*;
  import javax.swing.event.MenuEvent;
-@@ -171,6 +175,7 @@ public class IGVMenuBar extends JMenuBar implements IGVEventObserver {
+@@ -173,6 +177,7 @@ public class IGVMenuBar extends JMenuBar implements IGVEventObserver {
          menus.add(createViewMenu());
          menus.add(createTracksMenu());
          menus.add(createRegionsMenu());
@@ -45,7 +45,16 @@ index 3b6dd0880..594f2208e 100644
  
          refreshToolsMenu();
          menus.add(toolsMenu);
-@@ -1224,4 +1229,46 @@ public class IGVMenuBar extends JMenuBar implements IGVEventObserver {
+@@ -437,7 +442,7 @@ public class IGVMenuBar extends JMenuBar implements IGVEventObserver {
+         menuAction.setToolTipText("Load a FASTA, .json, or .genome file...");
+         menuItems.add(MenuAndToolbarUtils.createMenuItem(menuAction));
+ 
+-        // Download genome from server 
++        // Download genome from server
+         menuAction = new MenuAction("Select Hosted Genome...", null) {
+             @Override
+             public void actionPerformed(ActionEvent event) {
+@@ -1221,4 +1226,46 @@ public class IGVMenuBar extends JMenuBar implements IGVEventObserver {
  
          return menuItem;
      }
@@ -60,7 +69,7 @@ index 3b6dd0880..594f2208e 100644
 +                String chr = defaultFrame.getChrName();
 +                int start = (int) defaultFrame.getOrigin();
 +                int end = (int) defaultFrame.getEnd();
-+                String sequence = ScanFoldGui.extractSequence(igv.getGenomeManager().getCurrentGenome(), chr, start, end, Strand.NONE);
++                String sequence = ScanFoldGui.extractSequence(GenomeManager.getInstance().getCurrentGenome(), chr, start, end, Strand.NONE);
 +                ScanFoldGui.launch(chr, start, sequence, false, "main");
 +            }
 +        };
@@ -72,7 +81,7 @@ index 3b6dd0880..594f2208e 100644
 +                String chr = defaultFrame.getChrName();
 +                int start = (int) defaultFrame.getOrigin();
 +                int end = (int) defaultFrame.getEnd();
-+                String sequence = RNAFoldGui.extractSequence(igv.getGenomeManager().getCurrentGenome(), chr, start, end, Strand.NONE);
++                String sequence = RNAFoldGui.extractSequence(GenomeManager.getInstance().getCurrentGenome(), chr, start, end, Strand.NONE);
 +                RNAFoldGui.launch(chr, start, sequence, false, "main");
 +            }
 +        };
@@ -84,7 +93,7 @@ index 3b6dd0880..594f2208e 100644
 +                String chr = defaultFrame.getChrName();
 +                int start = (int) defaultFrame.getOrigin();
 +                int end = (int) defaultFrame.getEnd();
-+                String sequence = RNAStructureGui.extractSequence(igv.getGenomeManager().getCurrentGenome(), chr, start, end, Strand.NONE);
++                String sequence = RNAStructureGui.extractSequence(GenomeManager.getInstance().getCurrentGenome(), chr, start, end, Strand.NONE);
 +                RNAStructureGui.launch(chr, start, sequence, false, "main");
 +            }
 +        };