From e4627ed5c3d6a5229d03caf50ebdff2447fc61ab Mon Sep 17 00:00:00 2001
From: meganshand <mshand@broadinstitute.org>
Date: Wed, 4 Nov 2015 11:00:01 -0500
Subject: [PATCH] Addressing comments

---
 .../variantutils/SelectVariantsIntegrationTest.java       | 2 ++
 .../gatk/tools/walkers/variantutils/SelectVariants.java   | 8 +++++++-
 2 files changed, 9 insertions(+), 1 deletion(-)

diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/SelectVariantsIntegrationTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/SelectVariantsIntegrationTest.java
index c1293b872..bfda18f16 100644
--- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/SelectVariantsIntegrationTest.java
+++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/SelectVariantsIntegrationTest.java
@@ -612,6 +612,8 @@ public class SelectVariantsIntegrationTest extends WalkerTest {
 
     /**
      * Test excluding variants with IDs
+     * Also tests --forceValidOutput flag, which changes the GQ from floats to ints to match
+     * header spec.
      */
     @Test
     public void testExcludeSelectionID() {
diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/variantutils/SelectVariants.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/variantutils/SelectVariants.java
index 9559e066e..022ef2e37 100644
--- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/variantutils/SelectVariants.java
+++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/variantutils/SelectVariants.java
@@ -574,7 +574,13 @@ public class SelectVariants extends RodWalker<Integer, Integer> implements TreeR
     @Argument(fullName="ALLOW_NONOVERLAPPING_COMMAND_LINE_SAMPLES", required=false, doc="Allow samples other than those in the VCF to be specified on the command line. These samples will be ignored.")
     private boolean allowNonOverlappingCommandLineSamples = false;
 
-    @Argument(fullName="forceValidOutput", required=false, doc="Forces output VCF to be compliant to up to date version")
+    /**
+     * If this argument is provided, the output will be compliant with the version in the header, however it will also
+     * cause the tool to run slower than without the argument. Without the argument the header will be compliant with
+     * the up-to-date version, but the output in the body may not be compliant. If an up-to-date input file is used,
+     * then the output will also be up-to-date regardless of this argument.
+     */
+    @Argument(fullName="forceValidOutput", required=false, doc="Forces output VCF to be compliant to up-to-date version")
     private boolean forceValidOutput = false;
 
     public enum NumberAlleleRestriction {