From 4521c92408bdc6c74276b861f9bc2c25ff2e5157 Mon Sep 17 00:00:00 2001
From: jrobinso <933148+jrobinso@users.noreply.github.com>
Date: Mon, 9 Sep 2024 15:06:55 -0700
Subject: [PATCH] disable snappy, second attempt

---
 scripts/igv.sh                          | 2 ++
 scripts/igvtools                        | 4 ++--
 src/main/java/org/broad/igv/ui/IGV.java | 3 ---
 3 files changed, 4 insertions(+), 5 deletions(-)

diff --git a/scripts/igv.sh b/scripts/igv.sh
index 22d2d5792d..41ea0ec06c 100755
--- a/scripts/igv.sh
+++ b/scripts/igv.sh
@@ -26,6 +26,7 @@ java -version
 if [ -e "$HOME/.igv/java_arguments" ]; then
     java --module-path="${prefix}/lib" -Xmx8g \
         @"${prefix}/igv.args" \
+        -Dsamjdk.snappy.disable=true \
         -Dapple.laf.useScreenMenuBar=true \
         -Djava.net.preferIPv4Stack=true \
         -Djava.net.useSystemProxies=true \
@@ -34,6 +35,7 @@ if [ -e "$HOME/.igv/java_arguments" ]; then
 else
     java --module-path="${prefix}/lib" -Xmx8g \
         @"${prefix}/igv.args" \
+        -Dsamjdk.snappy.disable=true \
         -Dapple.laf.useScreenMenuBar=true \
         -Djava.net.preferIPv4Stack=true \
         -Djava.net.useSystemProxies=true \
diff --git a/scripts/igvtools b/scripts/igvtools
index 2de1d72471..4c55f1dc5a 100755
--- a/scripts/igvtools
+++ b/scripts/igvtools
@@ -12,12 +12,12 @@ fi
 
 # Check if there is a user-specified Java arguments file
 if [ -e "$HOME/.igv/java_arguments" ]; then
-    java -showversion -Djava.awt.headless=true --module-path="${prefix}/lib" -Xmx1500m \
+    java -showversion -Djava.awt.headless=true -Dsamjdk.snappy.disable=true --module-path="${prefix}/lib" -Xmx1500m \
         @"${prefix}/igv.args" \
         @"$HOME/.igv/java_arguments" \
         --module=org.igv/org.broad.igv.tools.IgvTools  "$@"
 else
-    java -showversion -Djava.awt.headless=true --module-path="${prefix}/lib" -Xmx1500m \
+    java -showversion -Djava.awt.headless=true -Dsamjdk.snappy.disable=true --module-path="${prefix}/lib" -Xmx1500m \
         @"${prefix}/igv.args" \
         --module=org.igv/org.broad.igv.tools.IgvTools  "$@"
 fi
diff --git a/src/main/java/org/broad/igv/ui/IGV.java b/src/main/java/org/broad/igv/ui/IGV.java
index a0de4ccd06..63344ddc6b 100644
--- a/src/main/java/org/broad/igv/ui/IGV.java
+++ b/src/main/java/org/broad/igv/ui/IGV.java
@@ -1884,9 +1884,6 @@ public void run() {
 
             final IGVPreferences preferences = PreferencesManager.getPreferences();
 
-            // Disable "snappy", used by htsjdk for sorting but not supported by IGV
-            System.setProperty("snappy.disable", "true");
-
             // Start CommandsServer **before** loading the initial genome, as credentials might need to be set for
             // privately hosted genomes.
             startCommandsServer(igvArgs, preferences);