pom.xml

<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>edu.rice.comp416</groupId>
    <artifactId>mapper</artifactId>
    <version>1.0.0</version>

    <properties>
        <maven.compiler.source>11</maven.compiler.source>
        <maven.compiler.target>11</maven.compiler.target>
        <project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
    </properties>

    <dependencies>
        <dependency>
            <groupId>junit</groupId>
            <artifactId>junit</artifactId>
            <version>4.13.2</version>
            <scope>test</scope>
        </dependency>
        <dependency>
            <groupId>org.biojava</groupId>
            <artifactId>biojava-core</artifactId>
            <version>6.0.0</version>
        </dependency>
        <dependency>
            <groupId>org.biojava</groupId>
            <artifactId>biojava-genome</artifactId>
            <version>6.0.0</version>
        </dependency>
        <dependency>
            <groupId>com.github.samtools</groupId>
            <artifactId>htsjdk</artifactId>
            <version>2.24.1</version>
        </dependency>
    </dependencies>

    <build>
        <pluginManagement>
            <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-jar-plugin</artifactId>
                    <version>3.2.0</version>
                    <configuration>
                        <archive>
                            <manifest>
                                <addClasspath>true</addClasspath>
                                <mainClass>edu.rice.comp416.mapper.Main</mainClass>
                            </manifest>
                        </archive>
                    </configuration>
                </plugin>
            </plugins>
        </pluginManagement>
        <plugins>
            <plugin>
                <artifactId>maven-assembly-plugin</artifactId>
                <configuration>
                    <archive>
                        <manifest>
                            <mainClass>edu.rice.comp416.mapper.Main</mainClass>
                        </manifest>
                    </archive>
                    <descriptorRefs>
                        <descriptorRef>jar-with-dependencies</descriptorRef>
                    </descriptorRefs>
                </configuration>
                <executions>
                    <execution>
                        <id>make-assembly</id> <!-- this is used for inheritance merges -->
                        <phase>package</phase> <!-- bind to the packaging phase -->
                        <goals>
                            <goal>single</goal>
                        </goals>
                    </execution>
                </executions>
            </plugin>
            <plugin>
                <groupId>com.diffplug.spotless</groupId>
                <artifactId>spotless-maven-plugin</artifactId>
                <version>2.17.1</version>
                <executions>
                    <execution>
                        <goals>
                            <goal>check</goal>
                        </goals>
                        <phase>compile</phase>
                    </execution>
                </executions>
                <configuration>
                    <formats>
                        <!-- you can define as many formats as you want, each is independent -->
                        <format>
                            <!-- define the files to apply to -->
                            <includes>
                                <include>*.md</include>
                                <include>.gitignore</include>
                            </includes>
                            <!-- define the steps to apply to those files -->
                            <trimTrailingWhitespace/>
                            <endWithNewline/>
                            <indent>
                                <tabs>true</tabs>
                                <spacesPerTab>4</spacesPerTab>
                            </indent>
                        </format>
                    </formats>
                    <!-- define a language-specific format -->
                    <java>
                        <!-- no need to specify files, inferred automatically, but you can if you want -->

                        <!-- apply a specific flavor of google-java-format and reflow long strings -->
                        <googleJavaFormat>
                            <version>1.8</version>
                            <style>AOSP</style>
                            <reflowLongStrings>true</reflowLongStrings>
                        </googleJavaFormat>
                    </java>
                </configuration>
            </plugin>
        </plugins>
    </build>
</project>