From 33462c7b5068acee1df53e9842bba3adc84917f2 Mon Sep 17 00:00:00 2001
From: Takuto Sato <tsato@broadinstitute.org>
Date: Tue, 20 Oct 2015 14:49:04 -0400
Subject: [PATCH] Removed the line that caused a null pointer, as the
 information it logged was not useful. Updated docs and added an integration
 test to ensure the code no longer throws the exception.

---
 .../VariantEvalIntegrationTest.java            | 18 ++++++++++++++++++
 .../evaluators/PrintMissingComp.java           |  8 ++++----
 2 files changed, 22 insertions(+), 4 deletions(-)

diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/varianteval/VariantEvalIntegrationTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/varianteval/VariantEvalIntegrationTest.java
index 82acc98b2..4cb123b63 100644
--- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/varianteval/VariantEvalIntegrationTest.java
+++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/varianteval/VariantEvalIntegrationTest.java
@@ -690,4 +690,22 @@ public class VariantEvalIntegrationTest extends WalkerTest {
         tests.add(new Object[]{"genotypes/genotypes", evalGenotypes, compGenotypes, "73790b530595fcbd467a88475ea9717f"});
         return tests.toArray(new Object[][]{});
     }
+
+
+    @Test
+    public void testPrintMissingComp() {
+        WalkerTestSpec spec = new WalkerTestSpec(
+                buildCommandLine(
+                        "-T VariantEval",
+                        "-R " + b37KGReference,
+                        "-eval " + privateTestDir + "validationReportEval.noGenotypes.vcf",
+                        "--comp " + privateTestDir + "validationReportComp.noGenotypes.vcf",
+                        "-L 20",
+                        "-EV PrintMissingComp"
+                ),
+                0,
+                Arrays.asList("d41d8cd98f00b204e9800998ecf8427e")); // sato: make sure it doesn't throw a null pointer exception.
+        executeTest("testPrintMissingComp", spec);
+
+    }
 }
diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/evaluators/PrintMissingComp.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/evaluators/PrintMissingComp.java
index 1a2251921..f9c67e872 100644
--- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/evaluators/PrintMissingComp.java
+++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/varianteval/evaluators/PrintMissingComp.java
@@ -25,6 +25,7 @@
 
 package org.broadinstitute.gatk.tools.walkers.varianteval.evaluators;
 
+import org.apache.commons.lang.ObjectUtils;
 import org.broadinstitute.gatk.utils.contexts.AlignmentContext;
 import org.broadinstitute.gatk.utils.contexts.ReferenceContext;
 import org.broadinstitute.gatk.utils.refdata.RefMetaDataTracker;
@@ -32,9 +33,9 @@ import org.broadinstitute.gatk.tools.walkers.varianteval.util.Analysis;
 import org.broadinstitute.gatk.tools.walkers.varianteval.util.DataPoint;
 import htsjdk.variant.variantcontext.VariantContext;
 
-@Analysis(name = "PrintMissingComp", description = "the overlap between eval and comp sites")
+@Analysis(name = "PrintMissingComp", description = "count the number of comp SNP sites that are not in eval")
 public class PrintMissingComp extends VariantEvaluator {
-    @DataPoint(description = "number of eval sites outside of comp sites", format = "%d")
+    @DataPoint(description = "number of comp SNP sites outside of eval sites", format = "%d")
     public long nMissing = 0;
 
     public String getName() {
@@ -49,9 +50,8 @@ public class PrintMissingComp extends VariantEvaluator {
         final boolean compIsGood = comp != null && comp.isNotFiltered() && comp.isSNP();
         final boolean evalIsGood = eval != null && eval.isSNP();
 
-        if ( compIsGood & ! evalIsGood ) {
+        if ( compIsGood && !evalIsGood ) {
             nMissing++;
-            super.getWalker().getLogger().info("MissingFrom" + eval.toString() + " is missing from " + comp.getSource());
         }
     }
 }
\ No newline at end of file