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<?xml version="1.0" encoding="ISO-8859-1"?>
<!--
biojava-adam Biojava and ADAM integration.
Copyright (c) 2017-2022 held jointly by the individual authors.
This library is free software; you can redistribute it and/or modify it
under the terms of the GNU Lesser General Public License as published
by the Free Software Foundation; either version 3 of the License, or (at
your option) any later version.
This library is distributed in the hope that it will be useful, but WITHOUT
ANY WARRANTY; with out even the implied warranty of MERCHANTABILITY or
FITNESS FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public
License for more details.
You should have received a copy of the GNU Lesser General Public License
along with this library; if not, write to the Free Software Foundation,
Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
> http://www.fsf.org/licensing/licenses/lgpl.html
> http://www.opensource.org/licenses/lgpl-license.php
-->
<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/maven-v4_0_0.xsd">
<modelVersion>4.0.0</modelVersion>
<parent>
<groupId>org.sonatype.oss</groupId>
<artifactId>oss-parent</artifactId>
<version>9</version>
</parent>
<groupId>org.biojava</groupId>
<artifactId>biojava-adam</artifactId>
<packaging>jar</packaging>
<name>biojava-adam</name>
<version>1.0</version>
<description>Biojava and ADAM integration.</description>
<url>http://www.biojava.org</url>
<inceptionYear>2017</inceptionYear>
<scm>
<connection>scm:git:git@github.com:biojava/biojava-adam.git</connection>
<developerConnection>scm:git:git@github.com:biojava/biojava-adam.git</developerConnection>
<url>git@github.com:biojava/biojava-adam.git</url>
<tag>biojava-adam-1.0</tag>
</scm>
<developers>
<developer>
<id>heuermh</id>
<name>Michael Heuer</name>
</developer>
</developers>
<issueManagement>
<system>GitHub</system>
<url>https://github.com/biojava/biojava-adam/issues</url>
</issueManagement>
<licenses>
<license>
<name>GNU Lesser General Public License (LGPL)</name>
<url>http://www.gnu.org/licenses/lgpl.html</url>
<distribution>repo</distribution>
</license>
</licenses>
<properties>
<adam.version>1.0</adam.version>
<bdg-convert.version>1.0</bdg-convert.version>
<biojava.version>6.0.5</biojava.version>
<guava.version>31.1-jre</guava.version>
<jdk.version>1.8</jdk.version>
<junit.version>4.13.2</junit.version>
<maven.enforcer.jdk-version>[1.8,)</maven.enforcer.jdk-version>
<project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
<project.build.targetEncoding>UTF-8</project.build.targetEncoding>
<scala-guice.version>5.1.0</scala-guice.version>
<scala.version>2.12.15</scala.version>
<scala.version.prefix>2.12</scala.version.prefix>
<slf4j.version>1.7.30</slf4j.version>
<spark.version>3.2.1</spark.version>
</properties>
<build>
<pluginManagement>
<plugins>
<plugin>
<artifactId>maven-assembly-plugin</artifactId>
<version>3.3.0</version>
</plugin>
<plugin>
<artifactId>maven-clean-plugin</artifactId>
<version>3.1.0</version>
</plugin>
<plugin>
<artifactId>maven-compiler-plugin</artifactId>
<version>3.8.1</version>
<configuration>
<source>${jdk.version}</source>
<target>${jdk.version}</target>
</configuration>
</plugin>
<plugin>
<artifactId>maven-deploy-plugin</artifactId>
<version>3.0.0-M1</version>
</plugin>
<plugin>
<artifactId>maven-enforcer-plugin</artifactId>
<version>3.0.0-M3</version>
</plugin>
<plugin>
<artifactId>maven-gpg-plugin</artifactId>
<version>1.6</version>
</plugin>
<plugin>
<artifactId>maven-install-plugin</artifactId>
<version>3.0.0-M1</version>
</plugin>
<plugin>
<artifactId>maven-jar-plugin</artifactId>
<version>3.2.0</version>
</plugin>
<plugin>
<artifactId>maven-javadoc-plugin</artifactId>
<version>3.2.0</version>
</plugin>
<plugin>
<artifactId>maven-release-plugin</artifactId>
<version>3.0.0-M1</version>
</plugin>
<plugin>
<artifactId>maven-resources-plugin</artifactId>
<version>3.2.0</version>
</plugin>
<plugin>
<artifactId>maven-shade-plugin</artifactId>
<version>3.2.4</version>
</plugin>
<plugin>
<artifactId>maven-site-plugin</artifactId>
<version>3.9.1</version>
</plugin>
<plugin>
<artifactId>maven-source-plugin</artifactId>
<version>3.2.1</version>
</plugin>
<plugin>
<artifactId>maven-surefire-plugin</artifactId>
<version>3.0.0-M5</version>
</plugin>
<plugin>
<groupId>net.alchim31.maven</groupId>
<artifactId>scala-maven-plugin</artifactId>
<version>4.5.6</version>
</plugin>
<plugin>
<groupId>org.codehaus.mojo</groupId>
<artifactId>templating-maven-plugin</artifactId>
<version>1.0.0</version>
</plugin>
<plugin>
<groupId>pl.project13.maven</groupId>
<artifactId>git-commit-id-plugin</artifactId>
<version>2.2.2</version>
</plugin>
</plugins>
</pluginManagement>
<plugins>
<plugin>
<artifactId>maven-enforcer-plugin</artifactId>
<executions>
<execution>
<id>enforce-java</id>
<goals>
<goal>enforce</goal>
</goals>
<configuration>
<rules>
<requireJavaVersion>
<version>${maven.enforcer.jdk-version}</version>
</requireJavaVersion>
</rules>
</configuration>
</execution>
</executions>
</plugin>
<plugin>
<artifactId>maven-shade-plugin</artifactId>
<configuration>
<createDependencyReducedPom>false</createDependencyReducedPom>
<filters>
<filter>
<artifact>*:*</artifact>
<excludes>
<exclude>META-INF/*.SF</exclude>
<exclude>META-INF/*.DSA</exclude>
<exclude>META-INF/*.RSA</exclude>
</excludes>
</filter>
</filters>
<relocations>
<relocation>
<pattern>com.google.common</pattern>
<shadedPattern>org.biojava.nbio.adam.shaded.com.google.common</shadedPattern>
</relocation>
</relocations>
</configuration>
<executions>
<execution>
<phase>package</phase>
<goals>
<goal>shade</goal>
</goals>
<configuration>
<transformers>
<transformer implementation="org.apache.maven.plugins.shade.resource.ServicesResourceTransformer" />
</transformers>
</configuration>
</execution>
</executions>
</plugin>
<plugin>
<groupId>net.alchim31.maven</groupId>
<artifactId>scala-maven-plugin</artifactId>
<executions>
<execution>
<id>scala-compile-first</id>
<phase>process-resources</phase>
<goals>
<goal>compile</goal>
</goals>
<configuration>
<args>
<arg>-g:vars</arg>
</args>
</configuration>
</execution>
<execution>
<id>scala-test-compile-first</id>
<phase>process-test-resources</phase>
<goals>
<goal>testCompile</goal>
</goals>
</execution>
<execution>
<id>attach-scaladocs</id>
<phase>verify</phase>
<goals>
<goal>doc-jar</goal>
</goals>
</execution>
</executions>
<configuration>
<scalaVersion>${scala.version}</scalaVersion>
<useZincServer>true</useZincServer>
<args>
<arg>-unchecked</arg>
<arg>-deprecation</arg>
</args>
<jvmArgs>
<jvmArg>-Xms64m</jvmArg>
<jvmArg>-Xms1024m</jvmArg>
<jvmArg>-Xmx1024m</jvmArg>
</jvmArgs>
<javacArgs>
<javacArg>-source</javacArg>
<javacArg>${jdk.version}</javacArg>
<javacArg>-target</javacArg>
<javacArg>${jdk.version}</javacArg>
</javacArgs>
</configuration>
</plugin>
</plugins>
<resources>
<resource>
<directory>${basedir}/src/main/resources</directory>
<filtering>false</filtering>
</resource>
<resource>
<targetPath>META-INF</targetPath>
<filtering>false</filtering>
<directory>${basedir}</directory>
<includes>
<include>COPYING</include>
<include>COPYING.LESSER</include>
</includes>
</resource>
</resources>
</build>
<dependencyManagement>
<dependencies>
<dependency>
<groupId>junit</groupId>
<artifactId>junit</artifactId>
<version>${junit.version}</version>
</dependency>
<dependency>
<groupId>org.apache.spark</groupId>
<artifactId>spark-core_${scala.version.prefix}</artifactId>
<version>${spark.version}</version>
<exclusions>
<exclusion>
<groupId>com.google.code.findbugs</groupId>
<artifactId>jsr305</artifactId>
</exclusion>
<exclusion>
<groupId>org.apache.avro</groupId>
<artifactId>avro</artifactId>
</exclusion>
<exclusion>
<groupId>org.apache.hadoop</groupId>
<artifactId>hadoop-client</artifactId>
</exclusion>
<exclusion>
<groupId>org.apache.hadoop</groupId>
<artifactId>hadoop-mapreduce</artifactId>
</exclusion>
<exclusion>
<groupId>org.slf4j</groupId>
<artifactId>slf4j-api</artifactId>
</exclusion>
<exclusion>
<groupId>org.xerial.snappy</groupId>
<artifactId>snappy-java</artifactId>
</exclusion>
</exclusions>
</dependency>
<dependency>
<groupId>org.apache.spark</groupId>
<artifactId>spark-sql_${scala.version.prefix}</artifactId>
<version>${spark.version}</version>
<exclusions>
<exclusion>
<groupId>com.google.code.findbugs</groupId>
<artifactId>jsr305</artifactId>
</exclusion>
</exclusions>
</dependency>
<dependency>
<groupId>org.bdgenomics.adam</groupId>
<artifactId>adam-assembly-spark3_${scala.version.prefix}</artifactId>
<version>${adam.version}</version>
</dependency>
<dependency>
<groupId>org.bdgenomics.convert</groupId>
<artifactId>convert</artifactId>
<version>${bdg-convert.version}</version>
<exclusions>
<exclusion>
<groupId>com.google.code.findbugs</groupId>
<artifactId>jsr305</artifactId>
</exclusion>
<exclusion>
<groupId>org.apache.avro</groupId>
<artifactId>avro</artifactId>
</exclusion>
<exclusion>
<groupId>org.slf4j</groupId>
<artifactId>slf4j-api</artifactId>
</exclusion>
</exclusions>
</dependency>
<dependency>
<groupId>org.biojava</groupId>
<artifactId>biojava-core</artifactId>
<exclusions>
<exclusion>
<groupId>org.apache.logging.log4j</groupId>
<artifactId>*</artifactId>
</exclusion>
<exclusion>
<groupId>org.slf4j</groupId>
<artifactId>slf4j-api</artifactId>
</exclusion>
</exclusions>
<version>${biojava.version}</version>
</dependency>
<dependency>
<groupId>org.biojava</groupId>
<artifactId>biojava-genome</artifactId>
<exclusions>
<exclusion>
<groupId>com.google.guava</groupId>
<artifactId>*</artifactId>
</exclusion>
<exclusion>
<groupId>org.apache.logging.log4j</groupId>
<artifactId>*</artifactId>
</exclusion>
<exclusion>
<groupId>org.slf4j</groupId>
<artifactId>slf4j-api</artifactId>
</exclusion>
</exclusions>
<version>${biojava.version}</version>
</dependency>
<dependency>
<groupId>org.slf4j</groupId>
<artifactId>slf4j-log4j12</artifactId>
<version>${slf4j.version}</version>
</dependency>
<dependency>
<groupId>com.google.guava</groupId>
<artifactId>guava</artifactId>
<version>${guava.version}</version>
</dependency>
</dependencies>
</dependencyManagement>
<dependencies>
<dependency>
<groupId>junit</groupId>
<artifactId>junit</artifactId>
<scope>test</scope>
</dependency>
<dependency>
<groupId>org.apache.spark</groupId>
<artifactId>spark-core_${scala.version.prefix}</artifactId>
<scope>provided</scope>
</dependency>
<dependency>
<groupId>org.apache.spark</groupId>
<artifactId>spark-sql_${scala.version.prefix}</artifactId>
<scope>provided</scope>
</dependency>
<dependency>
<groupId>org.bdgenomics.adam</groupId>
<artifactId>adam-assembly-spark3_${scala.version.prefix}</artifactId>
<scope>provided</scope>
</dependency>
<dependency>
<groupId>org.bdgenomics.convert</groupId>
<artifactId>convert</artifactId>
<scope>compile</scope>
</dependency>
<dependency>
<groupId>org.biojava</groupId>
<artifactId>biojava-core</artifactId>
<scope>compile</scope>
</dependency>
<dependency>
<groupId>org.biojava</groupId>
<artifactId>biojava-genome</artifactId>
<scope>compile</scope>
</dependency>
<dependency>
<groupId>org.slf4j</groupId>
<artifactId>slf4j-log4j12</artifactId>
<scope>test</scope>
</dependency>
</dependencies>
<profiles>
<profile>
<!-- Override maven plugin versions in release profile -->
<id>sonatype-oss-release</id>
<build>
<plugins>
<plugin>
<artifactId>maven-enforcer-plugin</artifactId>
<version>3.0.0-M3</version>
</plugin>
<plugin>
<artifactId>maven-gpg-plugin</artifactId>
<version>1.6</version>
</plugin>
<plugin>
<artifactId>maven-jar-plugin</artifactId>
<version>3.2.0</version>
</plugin>
<plugin>
<artifactId>maven-javadoc-plugin</artifactId>
<version>3.2.0</version>
</plugin>
<plugin>
<artifactId>maven-source-plugin</artifactId>
<version>3.2.1</version>
</plugin>
</plugins>
</build>
</profile>
</profiles>
</project>
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