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Fix failing unit tests

This commit is contained in:
David Roazen 2014-02-04 02:55:54 -05:00
parent 4eaa724be6
commit c9032f0b5c
3 changed files with 9 additions and 7 deletions
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2
public/gatk-framework/src/test/java/org/broadinstitute/sting/utils/MWUnitTest.java
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@ -93,7 +93,7 @@ public class MWUnitTest extends BaseTest {
// tests using the hypothesis that set 1 dominates set 2 (U value = 30) -- empirical should be identical, normall approx close, uniform way off // tests using the hypothesis that set 1 dominates set 2 (U value = 30) -- empirical should be identical, normall approx close, uniform way off
Assert.assertEquals(MannWhitneyU.calculatePNormalApproximation(sizes.second,sizes.first,30L,true).second,2.0*0.08216463976903321,1e-14); Assert.assertEquals(MannWhitneyU.calculatePNormalApproximation(sizes.second,sizes.first,30L,true).second,2.0*0.08216463976903321,1e-14);
Assert.assertEquals(MannWhitneyU.calculatePUniformApproximation(sizes.second,sizes.first,30L),0.0023473625009328147,1e-14); Assert.assertEquals(MannWhitneyU.calculatePUniformApproximation(sizes.second,sizes.first,30L),0.0023473625009559074,1e-14);
Assert.assertEquals(MannWhitneyU.calculatePRecursively(sizes.second,sizes.first,30L,false,pm).second,0.021756021756021756,1e-14); // note -- exactly same value as above Assert.assertEquals(MannWhitneyU.calculatePRecursively(sizes.second,sizes.first,30L,false,pm).second,0.021756021756021756,1e-14); // note -- exactly same value as above
Assert.assertEquals(MannWhitneyU.calculatePRecursively(sizes.second,sizes.first,29L,false,cm).second,1.0-0.08547008547008,1e-14); // r does a correction, subtracting 1 from U Assert.assertEquals(MannWhitneyU.calculatePRecursively(sizes.second,sizes.first,29L,false,cm).second,1.0-0.08547008547008,1e-14); // r does a correction, subtracting 1 from U
Assert.assertEquals(MannWhitneyU.calculatePRecursively(sizes.second,sizes.first,11L,false,cm).second,0.08547008547008,1e-14); // r does a correction, subtracting 1 from U Assert.assertEquals(MannWhitneyU.calculatePRecursively(sizes.second,sizes.first,11L,false,cm).second,0.08547008547008,1e-14); // r does a correction, subtracting 1 from U

12
public/gatk-framework/src/test/java/org/broadinstitute/sting/utils/io/IOUtilsUnitTest.java
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@ -160,7 +160,7 @@ public class IOUtilsUnitTest extends BaseTest {
public void testWriteSystemFile() throws IOException { public void testWriteSystemFile() throws IOException {
File temp = createTempFile("temp.", ".properties"); File temp = createTempFile("temp.", ".properties");
try { try {
IOUtils.writeResource(new Resource("StingText.properties", null), temp); IOUtils.writeResource(new Resource("testProperties.properties", null), temp);
} finally { } finally {
FileUtils.deleteQuietly(temp); FileUtils.deleteQuietly(temp);
} }
@ -168,9 +168,9 @@ public class IOUtilsUnitTest extends BaseTest {
@Test @Test
public void testWriteSystemTempFile() throws IOException { public void testWriteSystemTempFile() throws IOException {
File temp = IOUtils.writeTempResource(new Resource("StingText.properties", null)); File temp = IOUtils.writeTempResource(new Resource("testProperties.properties", null));
try { try {
Assert.assertTrue(temp.getName().startsWith("StingText"), "File does not start with 'StingText.': " + temp); Assert.assertTrue(temp.getName().startsWith("testProperties"), "File does not start with 'testProperties.': " + temp);
Assert.assertTrue(temp.getName().endsWith(".properties"), "File does not end with '.properties': " + temp); Assert.assertTrue(temp.getName().endsWith(".properties"), "File does not end with '.properties': " + temp);
} finally { } finally {
FileUtils.deleteQuietly(temp); FileUtils.deleteQuietly(temp);
@ -191,7 +191,7 @@ public class IOUtilsUnitTest extends BaseTest {
public void testWriteRelativeFile() throws IOException { public void testWriteRelativeFile() throws IOException {
File temp = createTempFile("temp.", ".properties"); File temp = createTempFile("temp.", ".properties");
try { try {
IOUtils.writeResource(new Resource("/StingText.properties", IOUtils.class), temp); IOUtils.writeResource(new Resource("/testProperties.properties", IOUtils.class), temp);
} finally { } finally {
FileUtils.deleteQuietly(temp); FileUtils.deleteQuietly(temp);
} }
@ -199,9 +199,9 @@ public class IOUtilsUnitTest extends BaseTest {
@Test @Test
public void testWriteRelativeTempFile() throws IOException { public void testWriteRelativeTempFile() throws IOException {
File temp = IOUtils.writeTempResource(new Resource("/StingText.properties", IOUtils.class)); File temp = IOUtils.writeTempResource(new Resource("/testProperties.properties", IOUtils.class));
try { try {
Assert.assertTrue(temp.getName().startsWith("StingText"), "File does not start with 'StingText.': " + temp); Assert.assertTrue(temp.getName().startsWith("testProperties"), "File does not start with 'testProperties.': " + temp);
Assert.assertTrue(temp.getName().endsWith(".properties"), "File does not end with '.properties': " + temp); Assert.assertTrue(temp.getName().endsWith(".properties"), "File does not end with '.properties': " + temp);
} finally { } finally {
FileUtils.deleteQuietly(temp); FileUtils.deleteQuietly(temp);

2
public/gatk-framework/src/test/resources/testProperties.properties 100644
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@ -0,0 +1,2 @@
foo=bar
version=1.0