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Merge pull request #1422 from broadinstitute/rhl_htsjdk_picard_2.5.0 

Move htsjdk and picard to version 2.5.0
This commit is contained in:
Ron Levine 2016-06-28 12:16:04 -04:00 committed by GitHub
parent 23c48bcdb1 3c5eac8c17
commit b80a293848
5 changed files with 7 additions and 8 deletions
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3
public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/CommandLineGATK.java
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@ -178,8 +178,7 @@ public class CommandLineGATK extends CommandLineExecutable {
System.getProperty("os.name") + " " + System.getProperty("os.version") + System.getProperty("os.name") + " " + System.getProperty("os.version") +
" " + System.getProperty("os.arch")); " " + System.getProperty("os.arch"));
header.add( System.getProperty("java.vm.name") + header.add( System.getProperty("java.vm.name") +
" " + System.getProperty("java.runtime.version") + " " + System.getProperty("java.runtime.version"));
" " + (DeflaterFactory.usingIntelDeflater()? "IntelDeflater": "JdkDeflater"));
} }
catch (Exception e) { /* Unpossible! */ } catch (Exception e) { /* Unpossible! */ }

2
public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/arguments/IntervalIntegrationTest.java
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@ -89,7 +89,7 @@ public class IntervalIntegrationTest extends WalkerTest {
File baseOutputFile = createTempFile("testMultipleIntervalInclusionOnCRAM", ".cram"); File baseOutputFile = createTempFile("testMultipleIntervalInclusionOnCRAM", ".cram");
spec.setOutputFileLocation(baseOutputFile); spec.setOutputFileLocation(baseOutputFile);
spec.addAuxFile("", createTempFileFromBase(baseOutputFile.getAbsolutePath())); // Bypass MD5 check since the CRAM header stores the file name spec.addAuxFile("", createTempFileFromBase(baseOutputFile.getAbsolutePath())); // Bypass MD5 check since the CRAM header stores the file name
spec.addAuxFile("4bd9185ce1c7d2e97e8c131b77f76aef", createTempFileFromBase(baseOutputFile.getAbsolutePath() + ".bai")); spec.addAuxFile("019bc0dfad029bb86854a0dc6b149983", createTempFileFromBase(baseOutputFile.getAbsolutePath() + ".bai"));
executeTest("testMultipleIntervalInclusionOnCRAM", spec); executeTest("testMultipleIntervalInclusionOnCRAM", spec);
} }

4
public/gatk-root/pom.xml
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@ -44,8 +44,8 @@
<test.listeners>org.testng.reporters.FailedReporter,org.testng.reporters.JUnitXMLReporter,org.broadinstitute.gatk.utils.TestNGTestTransformer,org.broadinstitute.gatk.utils.GATKTextReporter,org.uncommons.reportng.HTMLReporter</test.listeners> <test.listeners>org.testng.reporters.FailedReporter,org.testng.reporters.JUnitXMLReporter,org.broadinstitute.gatk.utils.TestNGTestTransformer,org.broadinstitute.gatk.utils.GATKTextReporter,org.uncommons.reportng.HTMLReporter</test.listeners>
<!-- Version numbers for picard and htsjdk --> <!-- Version numbers for picard and htsjdk -->
<htsjdk.version>2.4.1</htsjdk.version> <htsjdk.version>2.5.0</htsjdk.version>
<picard.version>2.4.1</picard.version> <picard.version>2.5.0</picard.version>
</properties> </properties>
<!-- Dependency configuration (versions, etc.) --> <!-- Dependency configuration (versions, etc.) -->

2
public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/CNV/SymbolicAllelesIntegrationTest.java
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@ -57,7 +57,7 @@ public class SymbolicAllelesIntegrationTest extends WalkerTest {
WalkerTestSpec spec = new WalkerTestSpec( WalkerTestSpec spec = new WalkerTestSpec(
baseTestString(b36KGReference, "symbolic_alleles_2.vcf"), baseTestString(b36KGReference, "symbolic_alleles_2.vcf"),
1, 1,
Arrays.asList("c8b294089832bb1a2c450b550318a471")); Arrays.asList("3f97ed3243fad7f953f4859af92d227f"));
executeTest("Test symbolic alleles mixed in with non-symbolic alleles", spec); executeTest("Test symbolic alleles mixed in with non-symbolic alleles", spec);
} }
} }

4
public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/MannWhitneyU.java
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@ -503,7 +503,7 @@ public class MannWhitneyU {
* @return P-value based on histogram with u calculated for every possible permutation of group tag. * @return P-value based on histogram with u calculated for every possible permutation of group tag.
*/ */
public double permutationTest(final double[] series1, final double[] series2, final double testStatU) { public double permutationTest(final double[] series1, final double[] series2, final double testStatU) {
final Histogram<Double> histo = new Histogram<Double>(); final Histogram<Double> histo = new Histogram<>();
final int n1 = series1.length; final int n1 = series1.length;
final int n2 = series2.length; final int n2 = series2.length;
@ -555,7 +555,7 @@ public class MannWhitneyU {
*/ */
double sumOfAllSmallerBins = histo.get(testStatU).getValue() / 2.0; double sumOfAllSmallerBins = histo.get(testStatU).getValue() / 2.0;
for (final Histogram<Double>.Bin bin : histo.values()) { for (final Histogram.Bin<Double> bin : histo.values()) {
if (bin.getId() < testStatU) sumOfAllSmallerBins += bin.getValue(); if (bin.getId() < testStatU) sumOfAllSmallerBins += bin.getValue();
} }