Remove "snappy" dependency

Author: jrobinso

Diff for: build.gradle

@@ -111,7 +111,6 @@ dependencies {
             [group: 'org.apache.commons', name: 'commons-math3', version: '3.6.1'],
             [group: 'commons-io', name: 'commons-io', version: '2.7'],
             [group: 'org.apache.commons', name: 'commons-compress', version: '1.26.0'],
-            [group: 'org.xerial.snappy', name: 'snappy-java', version: '1.1.10.4'],
             [group: 'org.apache.commons', name: 'commons-jexl', version: '2.1.1'],
             [group: 'org.apache.commons', name: 'commons-lang3', version: '3.9'],
             [group: 'com.github.samtools', name: 'htsjdk', version: '4.1.1'],
@@ -186,7 +185,6 @@ tasks.withType(Test) {
     systemProperties['make.fail'] = 'false'
     systemProperties['include.longrunning'] = 'false'
     systemProperties['ignore.ioexceptions'] = 'false'
-    systemProperties['org.xerial.snappy.tempdir'] = 'build/tmp'
     maxHeapSize = '2g'
     maxParallelForks = Runtime.runtime.availableProcessors().intdiv(2) ?: 1
     useJUnitPlatform()

Diff for: src/main/java/org/broad/igv/tools/sort/AsciiSorter.java

@@ -68,7 +68,6 @@ public AsciiSorter(File inputFile, File outputFile) {
         this.writeStdOut = outputFile == null;
         this.tmpDir = new File(System.getProperty("java.io.tmpdir"), System.getProperty("user.name"));
 
-        System.setProperty("snappy.disable", "true");
         if (!tmpDir.exists()) {
             tmpDir.mkdir();
         }

Diff for: src/main/java/org/broad/igv/ui/IGV.java

@@ -1884,6 +1884,9 @@ 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);