Finally found the bug that everyone is reporting on GS. Iterators on PriorityQueues aren't guaranteed to return elements in sorted order (a pretty stupid contract) - so we were passing items to the constrained writer out of order. Just do a Collections.sort instead (1 line of code). Happy father's day!

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5476 348d0f76-0448-11de-a6fe-93d51630548a

java/src/org/broadinstitute/sting/gatk/walkers/indels/IndelRealigner.java

@@ -402,9 +402,10 @@ public class IndelRealigner extends ReadWalker<Integer, Integer> {
     }
 
     private void emitReadLists() {
-        // pre-merge lists with priority queue for constrained SAMFileWriter
+        // pre-merge lists to sort them in preparation for constrained SAMFileWriter
         readsNotToClean.addAll(readsToClean.getReads());
-        for ( SAMRecord read : ReadUtils.coordinateSortReads(readsNotToClean) )
+        ReadUtils.coordinateSortReads(readsNotToClean);
+        for ( SAMRecord read : readsNotToClean )
             emit(read);
         readsToClean.clear();
         readsNotToClean.clear();

java/src/org/broadinstitute/sting/utils/sam/ReadUtils.java

@@ -216,17 +216,9 @@ public class ReadUtils {
      * @param reads
      * @return
      */
-    public final static List<SAMRecord> coordinateSortReads(Collection<SAMRecord> reads) {
+    public final static void coordinateSortReads(List<SAMRecord> reads) {
-        final int n = reads.size();
+        final SAMRecordComparator comparer = new SAMRecordCoordinateComparator();
-
+        Collections.sort(reads, comparer);
-        if ( n > 0 ) {
-            final SAMRecordComparator comparer = new SAMRecordCoordinateComparator();
-            final Queue<SAMRecord> sorted = new PriorityQueue<SAMRecord>(reads.size(), comparer);
-            sorted.addAll(reads);
-            return new ArrayList<SAMRecord>(sorted);
-        } else {
-            return Collections.emptyList();
-        }
     }
 
     public final static int getFirstInsertionOffset(SAMRecord read) {

java/test/org/broadinstitute/sting/gatk/walkers/indels/IndelRealignerIntegrationTest.java

@@ -117,13 +117,4 @@ public class IndelRealignerIntegrationTest extends WalkerTest {
             executeTest(String.format("realigner [%s]", entry.getKey()), spec);
         }
     }
-
-    @Test(expectedExceptions = { RuntimeException.class }, dependsOnMethods = { "testMaxReadsInMemory" })
-    public void testFailure() {
-        WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
-                baseCommand + "--maxReadsInMemory 1000",
-                1,
-                Arrays.asList(""));
-        executeTest("realigner failure", spec);
-    }
 }