pom.xml

<?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.bgi.flexlab</groupId>
    <artifactId>vcfstats</artifactId>
    <name>vcfstats</name>
    <version>1.0</version>
    <build>
        <resources>
            <resource>
                <directory>src/main/resources</directory>
                <filtering>true</filtering>
            </resource>
        </resources>
        <plugins>
            <plugin>
                <groupId>org.apache.maven.plugins</groupId>
                <artifactId>maven-compiler-plugin</artifactId>
                <configuration>
                    <source>8</source>
                    <target>8</target>
                </configuration>
            </plugin>
            <plugin>
                <artifactId>maven-assembly-plugin</artifactId>
                <configuration>
                    <archive>
                        <manifest>
                            <mainClass>org.bgi.flexlab.vcfstats.Main</mainClass>
                        </manifest>
                    </archive>
                    <descriptorRefs>
                        <descriptorRef>jar-with-dependencies</descriptorRef>
                    </descriptorRefs>
                </configuration>
            </plugin>
        </plugins>
    </build>
    <dependencies>
        <dependency>
            <groupId>commons-cli</groupId>
            <artifactId>commons-cli</artifactId>
            <version>1.4</version>
        </dependency>
        <dependency>
            <groupId>com.github.samtools</groupId>
            <artifactId>htsjdk</artifactId>
            <version>2.23.0</version>
        </dependency>
    </dependencies>
    <packaging>jar</packaging>




    <properties>
        <project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
    </properties>


</project>