Description

<dependency>
    <groupId>org.disq-bio</groupId>
    <artifactId>disq</artifactId>
    <version>0.3.8</version>
</dependency>

<?xml version="1.0" encoding="UTF-8"?>
<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.disq-bio</groupId>
    <artifactId>disq</artifactId>
    <version>0.3.8</version>
    <name>Disq</name>
    <description>A library for manipulating bioinformatics sequencing formats in Apache Spark.</description>
    <url>https://github.com/disq-bio/disq</url>
    <inceptionYear>2018</inceptionYear>
    <licenses>
        <license>
            <name>MIT License</name>
            <url>https://opensource.org/licenses/MIT</url>
            <distribution>repo</distribution>
        </license>
    </licenses>
    <organization>
        <name>Disq contributors</name>
        <url>https://github.com/disq-bio</url>
    </organization>
    <developers>
        <developer>
            <id>tomwhite</id>
            <name>Tom White</name>
            <email>tom.e.white@gmail.com</email>
            <url>https://github.com/tomwhite</url>
        </developer>
    </developers>

    <properties>
        <java.release>8</java.release>
        <java.version>1.8</java.version>
        <maven.compiler.target>${java.version}</maven.compiler.target>
        <maven.compiler.source>${java.version}</maven.compiler.source>
        <htsjdk.version>2.24.1</htsjdk.version>
        <hadoop.version>3.2.1</hadoop.version>
        <mockito.version>3.7.7</mockito.version>
        <kryo-serializers.version>0.43</kryo-serializers.version>
        <slf4j.version>1.7.30</slf4j.version>
        <scala.version>2.12</scala.version>
        <spark.version>3.0.2</spark.version>
    </properties>

    <dependencies>
        <dependency>
            <groupId>com.github.samtools</groupId>
            <artifactId>htsjdk</artifactId>
            <version>${htsjdk.version}</version>
        </dependency>
        <dependency>
            <groupId>de.javakaffee</groupId>
            <artifactId>kryo-serializers</artifactId>
            <version>${kryo-serializers.version}</version>
        </dependency>
        <dependency>
            <groupId>org.slf4j</groupId>
            <artifactId>slf4j-api</artifactId>
            <version>${slf4j.version}</version>
            <scope>compile</scope>
        </dependency>
        <dependency>
            <groupId>org.slf4j</groupId>
            <artifactId>slf4j-simple</artifactId>
            <version>${slf4j.version}</version>
            <scope>test</scope>
        </dependency>
        <dependency>
            <groupId>org.slf4j</groupId>
            <artifactId>jul-to-slf4j</artifactId>
            <version>${slf4j.version}</version>
            <scope>test</scope>
        </dependency>
        <dependency>
            <groupId>org.slf4j</groupId>
            <artifactId>jcl-over-slf4j</artifactId>
            <version>${slf4j.version}</version>
            <scope>test</scope>
        </dependency>
        <dependency>
            <groupId>org.apache.hadoop</groupId>
            <artifactId>hadoop-client</artifactId>
            <version>${hadoop.version}</version>
            <scope>provided</scope>
            <exclusions>
              <exclusion>
                <groupId>commons-logging</groupId>
                <artifactId>*</artifactId>
              </exclusion>
              <exclusion>
                <groupId>org.slf4j</groupId>
                <artifactId>*</artifactId>
              </exclusion>
            </exclusions>
        </dependency>
        <dependency>
            <groupId>org.apache.spark</groupId>
            <artifactId>spark-core_${scala.version}</artifactId>
            <version>${spark.version}</version>
            <scope>provided</scope>
            <exclusions>
              <exclusion>
                <groupId>org.slf4j</groupId>
                <artifactId>*</artifactId>
              </exclusion>
            </exclusions>
        </dependency>
        <dependency>
            <groupId>org.mockito</groupId>
            <artifactId>mockito-core</artifactId>
            <version>${mockito.version}</version>
            <scope>test</scope>
        </dependency>
        <dependency>
            <groupId>junit</groupId>
            <artifactId>junit</artifactId>
            <version>4.13.1</version>
            <scope>test</scope>
        </dependency>
        <dependency>
            <groupId>pl.pragmatists</groupId>
            <artifactId>JUnitParams</artifactId>
            <version>1.1.1</version>
            <scope>test</scope>
        </dependency>
        <dependency>
            <groupId>org.apache.hadoop</groupId>
            <artifactId>hadoop-minicluster</artifactId>
            <version>${hadoop.version}</version>
            <scope>test</scope>
            <exclusions>
              <exclusion>
                <groupId>commons-logging</groupId>
                <artifactId>*</artifactId>
              </exclusion>
              <exclusion>
                <groupId>org.slf4j</groupId>
                <artifactId>*</artifactId>
              </exclusion>
            </exclusions>
        </dependency>
        <dependency>
            <groupId>org.apache.commons</groupId>
            <artifactId>commons-exec</artifactId>
            <version>1.3</version>
            <scope>test</scope>
        </dependency>
        <dependency>
            <groupId>com.google.cloud</groupId>
            <artifactId>google-cloud-nio</artifactId>
            <version>0.59.0-alpha</version>
            <classifier>shaded</classifier>
            <scope>test</scope>
        </dependency>
        <dependency>
            <groupId>com.github.jsr203hadoop</groupId>
            <artifactId>jsr203hadoop</artifactId>
            <version>1.0.3</version>
            <scope>test</scope>
        </dependency>
    </dependencies>

    <build>
        <plugins>
            <plugin>
                <groupId>org.apache.maven.plugins</groupId>
                <artifactId>maven-compiler-plugin</artifactId>
                <version>3.8.1</version>
            </plugin>
            <plugin>
                <groupId>org.apache.maven.plugins</groupId>
                <artifactId>maven-enforcer-plugin</artifactId>
                <version>3.0.0-M3</version>
                <executions>
                    <execution>
                        <id>enforce-versions</id>
                        <goals>
                            <goal>enforce</goal>
                        </goals>
                        <configuration>
                            <rules>
                                <requireMavenVersion>
                                    <version>[3.3.9,)</version>
                                    <message>Maven 3.3.9 or greater is required</message>
                                </requireMavenVersion>
                                <requireJavaVersion>
                                    <version>[1.8,)</version>
                                    <message>Java 1.8 or greater is required</message>
                                </requireJavaVersion>
                            </rules>
                        </configuration>
                    </execution>
                </executions>
            </plugin>
            <plugin>
                <groupId>org.apache.maven.plugins</groupId>
                <artifactId>maven-surefire-plugin</artifactId>
                <version>3.0.0-M5</version>
                <configuration>
                    <trimStackTrace>false</trimStackTrace>
                </configuration>
            </plugin>
            <plugin>
                <groupId>org.codehaus.mojo</groupId>
                <artifactId>build-helper-maven-plugin</artifactId>
                <version>3.0.0</version>
                <executions>
                    <execution>
                        <id>add-source</id>
                        <phase>generate-sources</phase>
                        <goals>
                            <goal>add-source</goal>
                        </goals>
                        <configuration>
                            <sources>
                                <source>src/htsjdk/java</source>
                            </sources>
                        </configuration>
                    </execution>
                </executions>
            </plugin>
            <plugin>
                <!-- If this fails the build, type 'mvn fmt:format' from the command line to reformat code. -->
                <groupId>com.coveo</groupId>
                <artifactId>fmt-maven-plugin</artifactId>
                <version>2.9</version>
                <executions>
                    <execution>
                        <goals>
                            <goal>check</goal>
                        </goals>
                    </execution>
                </executions>
            </plugin>
            <plugin>
                <!-- Run 'mvn license:format' to add new headers. -->
                <groupId>com.mycila</groupId>
                <artifactId>license-maven-plugin</artifactId>
                <version>4.0.rc2</version>
                <configuration>
                    <header>LICENSE_header.txt</header>
                    <strictCheck>true</strictCheck>
                    <properties>
                        <owner>Disq contributors</owner>
                    </properties>
                    <includes>
                        <include>**/src/main/java/**</include>
                        <include>**/src/test/java/**</include>
                    </includes>
                    <mapping>
                        <!-- Don't use the default javadoc comments, since fmt-maven-plugin will try to reformat -->
                        <java>SLASHSTAR_STYLE</java>
                    </mapping>
                </configuration>
                <executions>
                    <execution>
                        <phase>validate</phase>
                        <goals>
                            <goal>check</goal>
                        </goals>
                    </execution>
                </executions>
            </plugin>
            <plugin>
                <groupId>org.jacoco</groupId>
                <artifactId>jacoco-maven-plugin</artifactId>
                <version>0.8.6</version>
                <executions>
                    <execution>
                        <id>jacoco-initialize</id>
                        <goals>
                            <goal>prepare-agent</goal>
                        </goals>
                    </execution>
                    <execution>
                        <id>jacoco-report</id>
                        <phase>test</phase>
                        <goals>
                            <goal>report</goal>
                        </goals>
                    </execution>
                </executions>
            </plugin>
            <plugin>
                <groupId>com.github.spotbugs</groupId>
                <artifactId>spotbugs-maven-plugin</artifactId>
                <version>4.2.0</version>
                <configuration>
                    <excludeFilterFile>src/build/conf/spotbugs-exclude.xml</excludeFilterFile>
                    <onlyAnalyze>org.disq_bio.disq.-</onlyAnalyze>
                    <xmlOutput>true</xmlOutput>
                </configuration>
                <executions>
                    <execution>
                        <goals>
                            <goal>check</goal>
                        </goals>
                    </execution>
                </executions>
            </plugin>
            <plugin>
                <groupId>org.apache.maven.plugins</groupId>
                <artifactId>maven-failsafe-plugin</artifactId>
                <version>3.0.0-M4</version>
                <executions>
                    <execution>
                        <goals>
                            <goal>integration-test</goal>
                            <goal>verify</goal>
                        </goals>
                    </execution>
                </executions>
            </plugin>
            <plugin>
                <groupId>org.apache.maven.plugins</groupId>
                <artifactId>maven-release-plugin</artifactId>
                <version>3.0.0-M1</version>
                <configuration>
                    <autoVersionSubmodules>true</autoVersionSubmodules>
                    <useReleaseProfile>false</useReleaseProfile>
                    <releaseProfiles>release</releaseProfiles>
                    <goals>deploy</goals>
                </configuration>
            </plugin>
        </plugins>
    </build>

    <scm>
        <connection>scm:git:https://github.com/disq-bio/disq</connection>
        <developerConnection>scm:git:https://github.com/disq-bio/disq</developerConnection>
        <url>https://github.com/disq-bio/disq</url>
        <tag>disq-0.3.8</tag>
    </scm>

    <distributionManagement>
        <snapshotRepository>
            <id>ossrh</id>
            <url>https://oss.sonatype.org/content/repositories/snapshots</url>
        </snapshotRepository>
        <repository>
            <id>ossrh</id>
            <url>https://oss.sonatype.org/service/local/staging/deploy/maven2/</url>
        </repository>
    </distributionManagement>

    <profiles>
        <profile>
            <id>java11</id>
            <activation>
                <jdk>11</jdk>
            </activation>
            <build>
                <plugins>
                    <plugin>
                        <groupId>org.apache.maven.plugins</groupId>
                        <artifactId>maven-compiler-plugin</artifactId>
                        <version>3.8.1</version>
                        <configuration>
                            <release>${java.release}</release>
                        </configuration>
                    </plugin>
                </plugins>
            </build>
        </profile>
        <profile>
            <id>release</id>
            <build>
                <plugins>
                    <plugin>
                        <groupId>org.apache.maven.plugins</groupId>
                        <artifactId>maven-source-plugin</artifactId>
                        <version>3.2.1</version>
                        <executions>
                            <execution>
                                <id>attach-source</id>
                                <goals>
                                    <goal>jar</goal>
                                </goals>
                            </execution>
                        </executions>
                    </plugin>
                    <plugin>
                        <groupId>org.apache.maven.plugins</groupId>
                        <artifactId>maven-javadoc-plugin</artifactId>
                        <version>3.2.0</version>
                        <configuration>
                            <excludePackageNames>org.disq_bio.disq.impl.*,htsjdk.*</excludePackageNames>
                            <failOnError>true</failOnError>
                        </configuration>
                        <executions>
                            <execution>
                                <id>attach-javadocs</id>
                                <goals>
                                    <goal>jar</goal>
                                </goals>
                            </execution>
                        </executions>
                    </plugin>
                    <plugin>
                        <groupId>org.apache.maven.plugins</groupId>
                        <artifactId>maven-gpg-plugin</artifactId>
                        <version>1.6</version>
                        <executions>
                            <execution>
                                <id>sign-artifacts</id>
                                <phase>verify</phase>
                                <goals>
                                    <goal>sign</goal>
                                </goals>
                            </execution>
                        </executions>
                    </plugin>
                </plugins>
            </build>
        </profile>
    </profiles>
</project>