Fix GSA-515 Nanoscheduler GSA-573 -nt and -nct interact badly w.r.t. output

-- See https://jira.broadinstitute.org/browse/GSA-573
-- Uses InheritedThreadLocal storage so that children threads created by the NanoScheduler see the parent stubs in the main thread.
-- Added explicit integration test that checks that -nt 1, 2 and -nct 1, 2 give the same results for GLM BOTH with the UG over 1 MB.

public/java/src/org/broadinstitute/sting/gatk/executive/ShardTraverser.java

@@ -55,6 +55,10 @@ public class ShardTraverser implements Callable {
         try {
             final long startTime = System.currentTimeMillis();
 
+            // this is CRITICAL -- initializes the thread-local output maps in the parent thread,
+            // so that any subthreads created by the traversal itself are shared...
+            outputTracker.getStorageAndInitializeIfNecessary();
+
             Object accumulator = walker.reduceInit();
             final WindowMaker windowMaker = new WindowMaker(shard,microScheduler.getEngine().getGenomeLocParser(),
                     microScheduler.getReadIterator(shard),

public/java/src/org/broadinstitute/sting/gatk/io/ThreadLocalOutputTracker.java

@@ -39,14 +39,17 @@ import java.util.Map;
 /**
  * An output tracker that can either track its output per-thread or directly,
  *
- * @author mhanna
- * @version 0.1
+ * @author mhanna, depristo
+ * @version 0.2
  */
 public class ThreadLocalOutputTracker extends OutputTracker {
     /**
      * Thread-local storage for output streams.
+     *
+     * MUST BE A INHERITABLE THREAD LOCAL
+     * -- NanoScheduler creates subthreads, and these threads must inherit the binding from their parent
      */
-    private ThreadLocal<Map<Stub, Storage>> storage = new ThreadLocal<Map<Stub,Storage>>();
+    private ThreadLocal<Map<Stub, Storage>> storage = new InheritableThreadLocal<Map<Stub, Storage>>();
 
     /**
      * A total hack.  If bypass = true, bypass thread local storage and write directly
@@ -57,6 +60,29 @@ public class ThreadLocalOutputTracker extends OutputTracker {
         this.bypass = bypass;
     }
 
+    /**
+     * Initialize the storage map for this thread, if necessary.
+     *
+     * Checks if there's a thread local binding for this thread, and if
+     * not initializes it.
+     *
+     * Particularly useful in the case where we want to initialize the map in
+     * a parent thread but have it used available to all the children via
+     * the InheritedThreadLocal map.
+     *
+     * @return the storage
+     */
+    public Map<Stub,Storage> getStorageAndInitializeIfNecessary() {
+        Map<Stub,Storage> threadLocalOutputStreams = storage.get();
+
+        if( threadLocalOutputStreams == null ) {
+            threadLocalOutputStreams = new HashMap<Stub,Storage>();
+            storage.set( threadLocalOutputStreams );
+        }
+
+        return threadLocalOutputStreams;
+    }
+
     public <T> T getStorage( Stub<T> stub ) {
         Storage target;
 
@@ -68,12 +94,7 @@ public class ThreadLocalOutputTracker extends OutputTracker {
             }
         }
         else {
-            Map<Stub,Storage> threadLocalOutputStreams = storage.get();
-
-            if( threadLocalOutputStreams == null ) {
-                threadLocalOutputStreams = new HashMap<Stub,Storage>();
-                storage.set( threadLocalOutputStreams );
-            }
+            final Map<Stub,Storage> threadLocalOutputStreams = getStorageAndInitializeIfNecessary();
 
             target = threadLocalOutputStreams.get(stub);
             if( target == null ) {

public/java/test/org/broadinstitute/sting/utils/nanoScheduler/NanoSchedulerIntegrationTest.java

@@ -0,0 +1,52 @@
+package org.broadinstitute.sting.utils.nanoScheduler;
+
+import org.broadinstitute.sting.WalkerTest;
+import org.testng.annotations.DataProvider;
+import org.testng.annotations.Test;
+
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.List;
+
+// ********************************************************************************** //
+// Note that this class also serves as an integration test for the VariantAnnotator!  //
+// ********************************************************************************** //
+
+public class NanoSchedulerIntegrationTest extends WalkerTest {
+    @DataProvider(name = "NanoSchedulerUGTest")
+    public Object[][] createNanoSchedulerUGTest() {
+        List<Object[]> tests = new ArrayList<Object[]>();
+
+        for ( final int nt : Arrays.asList(1, 2) )
+            for ( final int nct : Arrays.asList(1, 2) ) {
+//                tests.add(new Object[]{ "SNP",   "a1c7546f32a8919a3f3a70a04b2e8322", nt, nct });
+//                tests.add(new Object[]{ "INDEL", "0a6d2be79f4f8a4b0eb788cc4751b31b", nt, nct });
+                tests.add(new Object[]{ "BOTH",  "1eaf8ac30cdefd573850e58c1ec38790", nt, nct });
+            }
+
+        return tests.toArray(new Object[][]{});
+    }
+
+    @Test(enabled = true, dataProvider = "NanoSchedulerUGTest")
+    private void testNanoSchedulerUGTest(final String glm, final String md5, final int nt, final int nct ) {
+        WalkerTestSpec spec = new WalkerTestSpec(
+                buildCommandLine(
+                        "-T UnifiedGenotyper -R " + b37KGReference,
+                        "-nosl --no_cmdline_in_header -G",
+                        //"--dbsnp " + b37dbSNP132,
+                        "-I " + privateTestDir + "NA12878.HiSeq.b37.chr20.10_11mb.bam",
+                        "-L 20:10,000,000-11,000,000",
+                        "-glm " + glm,
+                        "-nt " + nt,
+                        "-nct " + nct,
+                        "-o %s"
+                ),
+                1,
+                Arrays.asList(md5)
+        );
+        executeTest(String.format("testUG-glm:%s-nt%d-nct%d", glm, nt, nct), spec);
+    }
+
+
+
+}