From 4f7fa3009a4adb8617501f35d61730f62b6ca0b1 Mon Sep 17 00:00:00 2001
From: Eric Banks <ebanks@broadinstitute.org>
Date: Mon, 26 Nov 2012 11:34:59 -0500
Subject: [PATCH] I forget why I thought that the VariantAnnotator couldn't run
 multi-threaded because it works just fine.  Now you can specify -nt with VA.

---
 .../walkers/annotator/VariantAnnotator.java   | 28 +++++++------------
 .../VariantAnnotatorIntegrationTest.java      |  8 +++++-
 2 files changed, 17 insertions(+), 19 deletions(-)

diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotator.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotator.java
index c4de9ed45..92060b4a3 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotator.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotator.java
@@ -82,7 +82,7 @@ import java.util.*;
 @Allows(value={DataSource.READS, DataSource.REFERENCE})
 @Reference(window=@Window(start=-50,stop=50))
 @By(DataSource.REFERENCE)
-public class VariantAnnotator extends RodWalker<Integer, Integer> implements AnnotatorCompatible {
+public class VariantAnnotator extends RodWalker<Integer, Integer> implements AnnotatorCompatible, TreeReducible<Integer> {
 
     @ArgumentCollection
     protected StandardVariantContextInputArgumentCollection variantCollection = new StandardVariantContextInputArgumentCollection();
@@ -275,14 +275,6 @@ public class VariantAnnotator extends RodWalker<Integer, Integer> implements Ann
         return true;
     }
 
-    /**
-     * Initialize the number of loci processed to zero.
-     *
-     * @return 0
-     */
-    public Integer reduceInit() { return 0; }
-
-
     /**
      * We want reads that span deletions
      *
@@ -323,15 +315,15 @@ public class VariantAnnotator extends RodWalker<Integer, Integer> implements Ann
         return 1;
     }
 
-    /**
-     * Increment the number of loci processed.
-     *
-     * @param value result of the map.
-     * @param sum   accumulator for the reduce.
-     * @return the new number of loci processed.
-     */
-    public Integer reduce(Integer value, Integer sum) {
-        return sum + value;
+    @Override
+    public Integer reduceInit() { return 0; }
+
+    @Override
+    public Integer reduce(Integer value, Integer sum) { return value + sum; }
+
+    @Override
+    public Integer treeReduce(Integer lhs, Integer rhs) {
+        return lhs + rhs;
     }
 
     /**
diff --git a/public/java/test/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotatorIntegrationTest.java b/public/java/test/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotatorIntegrationTest.java
index 01dff0089..b097e3d34 100755
--- a/public/java/test/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotatorIntegrationTest.java
+++ b/public/java/test/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotatorIntegrationTest.java
@@ -151,7 +151,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
     }
 
     @Test
-    public void testTabixAnnotations() {
+    public void testTabixAnnotationsAndParallelism() {
         final String MD5 = "99938d1e197b8f10c408cac490a00a62";
         for ( String file : Arrays.asList("CEU.exon.2010_03.sites.vcf", "CEU.exon.2010_03.sites.vcf.gz")) {
             WalkerTestSpec spec = new WalkerTestSpec(
@@ -159,6 +159,12 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
                     Arrays.asList(MD5));
             executeTest("Testing lookup vcf tabix vs. vcf tribble", spec);
         }
+
+        WalkerTestSpec spec = new WalkerTestSpec(
+                baseTestString() + " -A HomopolymerRun -nt 2 --variant:vcf " + validationDataLocation + "CEU.exon.2010_03.sites.vcf -L " + validationDataLocation + "CEU.exon.2010_03.sites.vcf --no_cmdline_in_header", 1,
+                Arrays.asList(MD5));
+
+        executeTest("Testing lookup vcf tabix vs. vcf tribble plus parallelism", spec);
     }
 
     @Test