Added integration tests for ReadBackedPhasing

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4446 348d0f76-0448-11de-a6fe-93d51630548a
2010-10-06 20:50:32 +00:00 · 2010-10-06 20:50:32 +00:00 · 652a3e8de5
parent f8f1cc45a3
commit 652a3e8de5
1 changed files with 72 additions and 0 deletions
--- a/java/test/org/broadinstitute/sting/gatk/walkers/phasing/ReadBackedPhasingIntegrationTest.java
+++ b/java/test/org/broadinstitute/sting/gatk/walkers/phasing/ReadBackedPhasingIntegrationTest.java
@ -0,0 +1,72 @@
+package org.broadinstitute.sting.gatk.walkers.phasing;
+
+import org.broadinstitute.sting.WalkerTest;
+import org.junit.Test;
+
+import java.util.Arrays;
+
+public class ReadBackedPhasingIntegrationTest extends WalkerTest {
+
+    public static String baseTestString(String reference, String reads, String VCF, int cacheWindowSize, int maxPhaseSites, double phaseQualityThresh) {
+        return "-T ReadBackedPhasing" +
+                " -R " + reference +
+                " -I " + validationDataLocation + reads +
+                " -B:variant,VCF " + validationDataLocation + VCF +
+                " --cacheWindowSize " + cacheWindowSize +
+                " --maxPhaseSites " + maxPhaseSites +
+                " --phaseQualityThresh " + phaseQualityThresh +
+                " -o %s";
+    }
+
+
+    @Test
+    public void test1() {
+        WalkerTestSpec spec = new WalkerTestSpec(
+                baseTestString(hg18Reference, "phasing_test_chr20_332341_1332503.bam", "phasing_test_chr20_332341_1332503.vcf", 20000, 10, 10)
+                        + " -L chr20:332341-382503",
+                1,
+                Arrays.asList("7ea69a898890b7bea53477547ae5580a"));
+        executeTest("MAX 10 het sites [TEST ONE]; require PQ >= 10", spec);
+    }
+
+    @Test
+    public void test2() {
+        WalkerTestSpec spec = new WalkerTestSpec(
+                baseTestString(hg18Reference, "phasing_test_chr20_332341_1332503.bam", "phasing_test_chr20_332341_1332503.vcf", 20000, 10, 10)
+                        + " -L chr20:1232503-1332503",
+                1,
+                Arrays.asList("9a8f9beb94b204332d0a32a3af0d4118"));
+        executeTest("MAX 10 het sites [TEST TWO]; require PQ >= 10", spec);
+    }
+
+    @Test
+    public void test3() {
+        WalkerTestSpec spec = new WalkerTestSpec(
+                baseTestString(hg18Reference, "phasing_test_chr20_332341_1332503.bam", "phasing_test_chr20_332341_1332503.vcf", 20000, 2, 30)
+                        + " -L chr20:332341-382503",
+                1,
+                Arrays.asList("3d2973ca1f6d26062fa7f0d795faa216"));
+        executeTest("MAX 2 het sites [TEST THREE]; require PQ >= 30", spec);
+    }
+
+    @Test
+    public void test4() {
+        WalkerTestSpec spec = new WalkerTestSpec(
+                baseTestString(hg18Reference, "phasing_test_chr20_332341_1332503.bam", "phasing_test_chr20_332341_1332503.vcf", 20000, 5, 100)
+                        + " -L chr20:332341-382503",
+                1,
+                Arrays.asList("13c66ff8448a8c3b1e3db4f7881f871d"));
+        executeTest("MAX 5 het sites [TEST FOUR]; require PQ >= 100", spec);
+    }
+
+    @Test
+    public void test5() {
+        WalkerTestSpec spec = new WalkerTestSpec(
+                baseTestString(hg18Reference, "phasing_test_chr20_332341_1332503.bam", "phasing_test_chr20_332341_1332503.vcf", 1000, 7, 10)
+                        + " -L chr20:332341-482503",
+                1,
+                Arrays.asList("3d35745e1cf40c892a8e793b141dbf20"));
+        executeTest("MAX 7 het sites [TEST FIVE]; require PQ >= 10; cacheWindow = 1000", spec);
+    }
+
+}