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<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
<modelVersion>4.0.0</modelVersion>
<groupId>org.snpeff</groupId>
<artifactId>snpeff</artifactId>
<version>5.2</version>
<packaging>jar</packaging>
<name>SnpEff</name>
<description>Variant annotation and effect prediction package.</description>
<url>https://pcingola.github.io/SnpEff/</url>
<licenses>
<license>
<name>GNU LESSER GENERAL PUBLIC LICENSE, Version 3.0</name>
<url>http://www.gnu.org/licenses/lgpl-3.0.txt</url>
<distribution>repo</distribution>
</license>
</licenses>
<developers>
<developer>
<id>pcingola</id>
<name>Pablo Cingolani</name>
</developer>
</developers>
<dependencyManagement>
<dependencies>
<dependency>
<groupId>org.junit</groupId>
<artifactId>junit-bom</artifactId>
<version>5.8.2</version>
<type>pom</type>
<scope>import</scope>
</dependency>
</dependencies>
</dependencyManagement>
<dependencies>
<dependency>
<groupId>org.apfloat</groupId>
<artifactId>apfloat</artifactId>
<version>1.10.1</version>
</dependency>
<dependency>
<groupId>com.googlecode.charts4j</groupId>
<artifactId>charts4j</artifactId>
<version>1.3</version>
</dependency>
<dependency>
<groupId>commons-cli</groupId>
<artifactId>commons-cli</artifactId>
<version>1.5.0</version>
</dependency>
<dependency>
<groupId>org.junit.jupiter</groupId>
<artifactId>junit-jupiter-api</artifactId>
</dependency>
<dependency>
<groupId>org.junit.jupiter</groupId>
<artifactId>junit-jupiter-engine</artifactId>
</dependency>
<dependency>
<groupId>org.junit.platform</groupId>
<artifactId>junit-platform-suite-api</artifactId>
<version>1.8.2</version>
</dependency>
<dependency>
<groupId>org.junit.platform</groupId>
<artifactId>junit-platform-suite-engine</artifactId>
<version>1.8.2</version>
</dependency>
<dependency>
<groupId>net.sf.trove4j</groupId>
<artifactId>trove4j</artifactId>
<version>3.0.2</version>
</dependency>
<dependency>
<groupId>org.freemarker</groupId>
<artifactId>freemarker</artifactId>
<version>2.3.31</version>
</dependency>
<dependency>
<groupId>distlib</groupId>
<artifactId>distlib</artifactId>
<version>0.9.1</version>
</dependency>
<dependency>
<groupId>org.apache.commons</groupId>
<artifactId>commons-math3</artifactId>
<version>3.6.1</version>
</dependency>
<dependency>
<groupId>commons-io</groupId>
<artifactId>commons-io</artifactId>
<version>2.11.0</version>
</dependency>
<dependency>
<groupId>commons-codec</groupId>
<artifactId>commons-codec</artifactId>
<version>1.15</version>
</dependency>
<dependency>
<groupId>org.biojava</groupId>
<artifactId>biojava-core</artifactId>
<version>6.0.4</version>
</dependency>
<dependency>
<groupId>org.biojava</groupId>
<artifactId>biojava-structure</artifactId>
<version>6.0.4</version>
</dependency>
<dependency>
<groupId>org.biojava</groupId>
<artifactId>biojava-genome</artifactId>
<version>5.x</version>
</dependency>
<dependency>
<groupId>com.github.samtools</groupId>
<artifactId>htsjdk</artifactId>
<version>2.24.1</version>
</dependency>
<dependency>
<groupId>javax.xml.bind</groupId>
<artifactId>jaxb-api</artifactId>
<version>2.3.1</version>
</dependency>
</dependencies>
<repositories>
<repository>
<id>maven</id>
<name>Maven Repository</name>
<url>https://repo1.maven.org/maven2/</url>
<layout>default</layout>
<snapshots>
<enabled>false</enabled>
</snapshots>
</repository>
<repository>
<id>central</id>
<name>Central Repository</name>
<url>https://repo.maven.apache.org/maven2</url>
<layout>default</layout>
<snapshots>
<enabled>false</enabled>
</snapshots>
</repository>
<repository>
<id>hadoop-bam</id>
<name>Hadoop-BAM</name>
<url>https://hadoop-bam.sourceforge.net/maven/</url>
</repository>
<repository>
<id>ncimvn-public</id>
<name>Public NIH repository</name>
<url>https://ncimvn.nci.nih.gov/nexus/content/groups/public/</url>
</repository>
<repository>
<id>typesafe</id>
<name>Typesafe Repository</name>
<url>https://repo.typesafe.com/typesafe/releases/</url>
</repository>
</repositories>
<build>
<plugins>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-compiler-plugin</artifactId>
<version>3.8.1</version>
<configuration>
<release>21</release>
<encoding>ISO-8859-1</encoding>
<showDeprecation>true</showDeprecation>
<showWarnings>true</showWarnings>
<excludes>
<exclude>**/snpEffect/testCases/**</exclude>
</excludes>
</configuration>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-resources-plugin</artifactId>
<version>3.2.0</version>
<configuration>
<encoding>ISO-8859-1</encoding>
</configuration>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-assembly-plugin</artifactId>
<version>3.3.0</version>
<configuration>
<descriptorRefs>
<descriptorRef>jar-with-dependencies</descriptorRef>
</descriptorRefs>
<archive>
<manifest>
<mainClass>org.snpeff.SnpEff</mainClass>
</manifest>
</archive>
</configuration>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-javadoc-plugin</artifactId>
<version>2.8.1</version>
<configuration>
<encoding>ISO-8859-1</encoding>
</configuration>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-surefire-plugin</artifactId>
<version>2.22.0</version>
<configuration>
<excludes>
<exclude>**/integration/**</exclude>
</excludes>
</configuration>
</plugin>
</plugins>
</build>
</project>
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