From 489e5cffc17f7aa00584a1fa6329bcfc354f69c7 Mon Sep 17 00:00:00 2001
From: Eric Banks <ebanks@broadinstitute.org>
Date: Tue, 9 Aug 2011 14:29:15 -0400
Subject: [PATCH] Missed a few 'variants'

---
 .../gatk/walkers/beagle/BeagleOutputToVCFWalker.java   |  2 +-
 .../annotator/VariantAnnotatorIntegrationTest.java     | 10 +++++-----
 2 files changed, 6 insertions(+), 6 deletions(-)

diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/beagle/BeagleOutputToVCFWalker.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/beagle/BeagleOutputToVCFWalker.java
index 1c155e786..a34dfd080 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/beagle/BeagleOutputToVCFWalker.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/beagle/BeagleOutputToVCFWalker.java
@@ -54,7 +54,7 @@ import static java.lang.Math.log10;
  */
 @Requires(value={})
 public class BeagleOutputToVCFWalker  extends RodWalker<Integer, Integer> {
-    @Input(fullName="variants", shortName = "V", doc="Input VCF file", required=true)
+    @Input(fullName="variant", shortName = "V", doc="Input VCF file", required=true)
     public RodBinding<VariantContext> variants;
 
     @Input(fullName="comp", shortName = "comp", doc="Comparison VCF file", required=false)
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 492651635..596ac5c36 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
@@ -86,7 +86,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
     @Test
     public void testNoReads() {
         WalkerTestSpec spec = new WalkerTestSpec(
-                baseTestString() + " -G \"Standard\" --variant:VCF3 " + validationDataLocation + "vcfexample3empty.vcf -BTI variants", 1,
+                baseTestString() + " -G \"Standard\" --variant:VCF3 " + validationDataLocation + "vcfexample3empty.vcf -BTI variant", 1,
                 Arrays.asList("16e3a1403fc376320d7c69492cad9345"));
         executeTest("not passing it any reads", spec);
     }
@@ -94,7 +94,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
     @Test
     public void testDBTagWithDbsnp() {
         WalkerTestSpec spec = new WalkerTestSpec(
-                baseTestString() + " -B:dbsnp,vcf " + b36dbSNP129 + " -G \"Standard\" --variant:VCF3 " + validationDataLocation + "vcfexample3empty.vcf -BTI variants", 1,
+                baseTestString() + " -B:dbsnp,vcf " + b36dbSNP129 + " -G \"Standard\" --variant:VCF3 " + validationDataLocation + "vcfexample3empty.vcf -BTI variant", 1,
                 Arrays.asList("3da8ca2b6bdaf6e92d94a8c77a71313d"));
         executeTest("getting DB tag with dbSNP", spec);
     }
@@ -102,7 +102,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
     @Test
     public void testDBTagWithHapMap() {
         WalkerTestSpec spec = new WalkerTestSpec(
-                baseTestString() + " -B:compH3,VCF " + validationDataLocation + "fakeHM3.vcf -G \"Standard\" --variant:VCF3 " + validationDataLocation + "vcfexample3empty.vcf -BTI variants", 1,
+                baseTestString() + " -B:compH3,VCF " + validationDataLocation + "fakeHM3.vcf -G \"Standard\" --variant:VCF3 " + validationDataLocation + "vcfexample3empty.vcf -BTI variant", 1,
                 Arrays.asList("1bc01c5b3bd0b7aef75230310c3ce688"));
         executeTest("getting DB tag with HM3", spec);
     }
@@ -110,7 +110,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
     @Test
     public void testUsingExpression() {
         WalkerTestSpec spec = new WalkerTestSpec(
-                baseTestString() + " -B:foo,VCF " + validationDataLocation + "targetAnnotations.vcf -G \"Standard\" --variant:VCF3 " + validationDataLocation + "vcfexample3empty.vcf -E foo.AF -BTI variants", 1,
+                baseTestString() + " -B:foo,VCF " + validationDataLocation + "targetAnnotations.vcf -G \"Standard\" --variant:VCF3 " + validationDataLocation + "vcfexample3empty.vcf -E foo.AF -BTI variant", 1,
                 Arrays.asList("e9c0d832dc6b4ed06c955060f830c140"));
         executeTest("using expression", spec);
     }
@@ -120,7 +120,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
         final String MD5 = "13269d5a2e16f06fd755cc0fb9271acf";
         for ( String file : Arrays.asList("CEU.exon.2010_03.sites.vcf", "CEU.exon.2010_03.sites.vcf.gz")) {
             WalkerTestSpec spec = new WalkerTestSpec(
-                    baseTestString() + " -A HomopolymerRun --variant:VCF " + validationDataLocation + "/" + file + " -BTI variants -NO_HEADER", 1,
+                    baseTestString() + " -A HomopolymerRun --variant:VCF " + validationDataLocation + "/" + file + " -BTI variant -NO_HEADER", 1,
                     Arrays.asList(MD5));
             executeTest("Testing lookup vcf tabix vs. vcf tribble", spec);
         }