Merge pull request #1031 from broadinstitute/lb_update_for_java8
Updated gatk so it compiles with java 8
This commit is contained in:
Louis Bergelson
commit
9d9827f176
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@ -59,6 +59,7 @@ import org.testng.annotations.Test;
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import java.util.ArrayList;
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import java.util.Arrays;
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import java.util.List;
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import java.util.Set;
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/**
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* Created with IntelliJ IDEA.
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@ -102,7 +103,10 @@ public class InbreedingCoeffUnitTest {
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private VariantContext makeVC(String source, List<Allele> alleles, Genotype... genotypes) {
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int start = 10;
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int stop = start; // alleles.contains(ATC) ? start + 3 : start;
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return new VariantContextBuilder(source, "1", start, stop, alleles).genotypes(Arrays.asList(genotypes)).filters(null).make();
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return new VariantContextBuilder(source, "1", start, stop, alleles)
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.genotypes(Arrays.asList(genotypes))
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.filters((String)null)
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.make();
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}
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@Test
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@ -134,7 +134,7 @@ public class PosteriorLikelihoodsUtilsUnitTest extends BaseTest {
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private VariantContext makeVC(String source, List<Allele> alleles, Genotype... genotypes) {
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int start = 10;
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int stop = start; // alleles.contains(ATC) ? start + 3 : start;
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return new VariantContextBuilder(source, "1", start, stop, alleles).genotypes(Arrays.asList(genotypes)).filters(null).make();
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return new VariantContextBuilder(source, "1", start, stop, alleles).genotypes(Arrays.asList(genotypes)).filters((String)null).make();
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}
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@Test
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@ -64,7 +64,7 @@
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<dependency>
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<groupId>com.google.code.cofoja</groupId>
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<artifactId>cofoja</artifactId>
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<version>1.0-r139</version>
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<version>1.2-20140817</version>
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</dependency>
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<dependency>
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<groupId>com.github.samtools</groupId>
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@ -133,7 +133,7 @@ public class AnnotationInterfaceManager {
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// note that technically an annotation can work on both the INFO and FORMAT fields
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for ( Class c : classes )
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annotations.add(pluginManager.createByType(c));
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annotations.add((T)pluginManager.createByType(c));
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return annotations;
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}
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@ -1,9 +0,0 @@
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<project xmlns="http://maven.apache.org/POM/4.0.0"
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xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
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xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/maven-v4_0_0.xsd">
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<modelVersion>4.0.0</modelVersion>
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<groupId>com.google.code.cofoja</groupId>
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<artifactId>cofoja</artifactId>
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<name>cofoja</name>
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<version>1.0-r139</version>
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</project>
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@ -0,0 +1,89 @@
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<project xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd" xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance">
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<modelVersion>4.0.0</modelVersion>
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<groupId>com.google.java.contract</groupId>
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<artifactId>cofoja</artifactId>
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<version>1.2-20140817</version>
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<name>Contracts for Java</name>
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<description>Contracts for Java is a contract programming framework for Java.</description>
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<url>http://code.google.com/p/cofoja</url>
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<issueManagement>
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<system>code.google.com</system>
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<url>http://code.google.com/p/cofoja/issues</url>
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</issueManagement>
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<inceptionYear>2010</inceptionYear>
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<licenses>
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<license>
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<name>GNU Lesser General Public License, version 2.1 or later</name>
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<url>http://www.gnu.org/licenses/lgpl-2.1.html</url>
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<distribution>repo</distribution>
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</license>
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</licenses>
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<scm>
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<connection>scm:svn:http://cofoja.googlecode.com/svn/trunk/</connection>
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<developerConnection>scm:svn:https://cofoja.googlecode.com/svn/trunk/</developerConnection>
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<url>http://code.google.com/p/cofoja/source/browse</url>
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</scm>
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<properties>
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<project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
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</properties>
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<developers>
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<developer>
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<id>andreasleitner</id>
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<name>Andreas Leitner</name>
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<email>andreasleitner@google.com</email>
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<organization>Google</organization>
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<organizationUrl>http://www.google.com</organizationUrl>
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<roles>
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<role>Developer</role>
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</roles>
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</developer>
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<developer>
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<id>davidmorgan</id>
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<name>David Morgan</name>
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<email>davidmorgan@google.com</email>
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<organization>Google</organization>
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<organizationUrl>http://www.google.com</organizationUrl>
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<roles>
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<role>Developer</role>
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</roles>
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</developer>
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<developer>
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<id>lenh</id>
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<name>Nhat Minh Lê</name>
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<email>nhat.minh.le@huoc.org</email>
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<roles>
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<role>Developer</role>
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</roles>
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</developer>
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</developers>
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<dependencies>
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<dependency>
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<groupId>org.ow2.asm</groupId>
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<artifactId>asm-all</artifactId>
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<version>5.0.4</version>
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<scope>compile</scope>
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</dependency>
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<dependency>
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<groupId>junit</groupId>
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<artifactId>junit</artifactId>
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<version>4.8.2</version>
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<scope>test</scope>
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</dependency>
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<dependency>
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<groupId>com.sun</groupId>
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<artifactId>tools</artifactId>
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<version>1.5.0</version>
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<scope>system</scope>
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<systemPath>${toolsjar}</systemPath>
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</dependency>
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</dependencies>
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</project>
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