-Added VariantFiltration integration tests

-Added integration test for GLFs



git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2133 348d0f76-0448-11de-a6fe-93d51630548a

java/src/org/broadinstitute/sting/gatk/walkers/filters/VariantFiltrationWalker.java

@@ -177,8 +177,6 @@ public class VariantFiltrationWalker extends RodWalker<Integer, Integer> {
             filter();
         }
 
-        out.printf("Processed %d loci.\n", result);
-
         if ( writer != null )
             writer.close();
     }

java/test/org/broadinstitute/sting/gatk/walkers/filters/VariantFiltrationIntegrationTest.java

@@ -0,0 +1,54 @@
+package org.broadinstitute.sting.gatk.walkers.filters;
+
+import org.broadinstitute.sting.WalkerTest;
+import org.junit.Test;
+
+import java.util.Arrays;
+
+public class VariantFiltrationIntegrationTest extends WalkerTest {
+
+    public static String baseTestString() {
+        return "-T VariantFiltration -o %s -R /broad/1KG/reference/human_b36_both.fasta";
+    }
+
+
+    @Test
+    public void testNoAction() {
+        WalkerTestSpec spec = new WalkerTestSpec(
+                baseTestString() + " -B variant,VCF,/humgen/gsa-scr1/GATK_Data/Validation_Data/vcfexample2.vcf -L 1:10,020,000-10,021,000", 1,
+                Arrays.asList("2408d449fbe7bf74099cc53d2d97c248"));
+        executeTest("test no action", spec);
+    }
+
+    @Test
+    public void testClusteredSnps() {
+        WalkerTestSpec spec = new WalkerTestSpec(
+                baseTestString() + " -window 10 -B variant,VCF,/humgen/gsa-scr1/GATK_Data/Validation_Data/vcfexample2.vcf -L 1:10,020,000-10,021,000", 1,
+                Arrays.asList("58a2d4cd3d3ba1460833b45b9b8455c2"));
+        executeTest("test clustered SNPs", spec);
+    }
+
+    @Test
+    public void testMask() {
+        WalkerTestSpec spec = new WalkerTestSpec(
+                baseTestString() + " -mask foo -B mask,VCF,/humgen/gsa-scr1/GATK_Data/Validation_Data/vcfexample2.vcf -B variant,VCF,/humgen/gsa-scr1/GATK_Data/Validation_Data/vcfexample2.vcf -L 1:10,020,000-10,021,000", 1,
+                Arrays.asList("9fc2cb210b3595159f34ddfba5a2e572"));
+        executeTest("test mask", spec);
+    }
+
+    @Test
+    public void testFilter1() {
+        WalkerTestSpec spec = new WalkerTestSpec(
+                baseTestString() + " -filter 'DoC < 20 || FisherStrand > 20.0' -filterName foo -B variant,VCF,/humgen/gsa-scr1/GATK_Data/Validation_Data/vcfexample2.vcf -L 1:10,020,000-10,021,000", 1,
+                Arrays.asList("5effa4b4fdd4dd33a373561637a5d86e"));
+        executeTest("test filter #1", spec);
+    }
+
+    @Test
+    public void testFilter2() {
+        WalkerTestSpec spec = new WalkerTestSpec(
+                baseTestString() + " -filter 'AlleleBalance < 70.0 && FisherStrand == 1.4' -filterName bar -B variant,VCF,/humgen/gsa-scr1/GATK_Data/Validation_Data/vcfexample2.vcf -L 1:10,020,000-10,021,000", 1,
+                Arrays.asList("5e0077148eda3b4274fbef1048902d47"));
+        executeTest("test filter #2", spec);
+    }
+}

java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperIntegrationTest.java

@@ -101,6 +101,14 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
         executeTest("testSingleSamplePilot2 - Joint Estimate", spec);
     }
 
+    @Test
+    public void testGLF() {
+        WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
+                "-T UnifiedGenotyper -R /broad/1KG/reference/human_b36_both.fasta -I /humgen/gsa-scr1/GATK_Data/Validation_Data/NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -varout %s -L 1:10,000,000-10,050,000 -bm empirical -gm JOINT_ESTIMATE -confidence 10", 1,
+                Arrays.asList("c552f3adcad91ee5f3ce42c204026a68"));
+        executeTest("testGLF", spec);
+    }
+
     // --------------------------------------------------------------------------------------------------------------
     //
     // testing calls with SLX, 454, and SOLID data