Fix gCNV retry seed being deterministic and potentially negative

src/main/java/org/broadinstitute/hellbender/tools/copynumber/GermlineCNVCaller.java

@@ -371,8 +371,7 @@ protected Object doWork() {
         if (pythonProcessOutput.getExitValue() != 0) {
             // We restart once if the inference diverged
             if (pythonProcessOutput.getExitValue() == DIVERGED_INFERENCE_EXIT_CODE) {
-                final Random generator = new Random(STARTING_SEED);
-                final int nextGCNVSeed = generator.nextInt();
+                final int nextGCNVSeed = generateRetrySeed();
                 logger.info("The inference failed to converge and will be restarted once with a different random seed.");
                 pythonProcessOutput = executor.executeScriptAndGetOutput(
                         new Resource(script, GermlineCNVCaller.class),
@@ -478,6 +477,10 @@ private List<File> writeIntervalSubsetReadCountFiles() {
         return intervalSubsetReadCountFiles;
     }
 
+    static int generateRetrySeed() {
+        return new Random().nextInt(Integer.MAX_VALUE);
+    }
+
     private List<String> composePythonArguments(final List<File> intervalSubsetReadCountFiles, final int randomSeed) {
         final String outputDirArg = CopyNumberArgumentValidationUtils.addTrailingSlashIfNecessary(outputDir.getAbsolutePath());
 

src/test/java/org/broadinstitute/hellbender/tools/copynumber/GermlineCNVCallerUnitTest.java

@@ -0,0 +1,39 @@
+package org.broadinstitute.hellbender.tools.copynumber;
+
+import org.broadinstitute.hellbender.GATKBaseTest;
+import org.testng.Assert;
+import org.testng.annotations.Test;
+
+import java.util.HashSet;
+import java.util.Set;
+
+/**
+ * Unit tests for {@link GermlineCNVCaller}.
+ */
+public final class GermlineCNVCallerUnitTest extends GATKBaseTest {
+
+    @Test
+    public void testGenerateRetrySeedIsNonNegative() {
+        for (int i = 0; i < 1000; i++) {
+            final int seed = GermlineCNVCaller.generateRetrySeed();
+            Assert.assertTrue(seed >= 0, "Retry seed must be non-negative (valid for numpy RandomState), but got: " + seed);
+        }
+    }
+
+    @Test
+    public void testGenerateRetrySeedIsLessThanMaxInt() {
+        for (int i = 0; i < 1000; i++) {
+            final int seed = GermlineCNVCaller.generateRetrySeed();
+            Assert.assertTrue(seed < Integer.MAX_VALUE, "Retry seed must be less than Integer.MAX_VALUE, but got: " + seed);
+        }
+    }
+
+    @Test
+    public void testGenerateRetrySeedIsNonDeterministic() {
+        final Set<Integer> seeds = new HashSet<>();
+        for (int i = 0; i < 100; i++) {
+            seeds.add(GermlineCNVCaller.generateRetrySeed());
+        }
+        Assert.assertTrue(seeds.size() > 1, "Retry seeds should not all be identical across calls");
+    }
+}