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>

    <!--
    **** NOTE: HTSJDK (formerly part of Picard/Samtools) is a
    **** third-party dependency of Hadoop-BAM. This artifact was
    **** released since currently there is no first-party artifact
    **** for HTSJDK available.
    ****
    ****       For further information on HTSJDK see:
    ****       https://github.com/samtools/htsjdk/
    ****
    **** This POM file is based on:
    **** https://github.com/azymer/htsjdk/blob/271692b2406b1ae980b43fa95981672798b4f295/pom.xml
    -->


    <!-- add this to your shell:
         export MAVEN_OPTS="-Xms256m -Xmx1g -XX:MaxPermSize=256m" -->

    <!-- when running tests from an intellij project that was setup
         via importing a project from maven, be sure to set the
         working directory to the top level htsjdk directory -->

    <parent>
        <groupId>org.sonatype.oss</groupId>
        <artifactId>oss-parent</artifactId>
        <version>7</version>
        <relativePath />
    </parent>

    <groupId>org.seqdoop</groupId>
    <artifactId>htsjdk</artifactId>
    <version>1.118</version>
    <packaging>jar</packaging>
    <name>HTS JDK</name>
    <description>A Java API for high-throughput sequencing data (HTS) formats.</description>
    <url>https://github.com/samtools/htsjdk/</url>

    <dependencies>
        <dependency>
            <groupId>org.apache.ant</groupId>
            <artifactId>ant</artifactId>
            <version>1.8.2</version>
        </dependency>

        <dependency>
            <groupId>org.apache.bcel</groupId>
            <artifactId>bcel</artifactId>
            <version>5.2</version>
        </dependency>

        <dependency>
            <groupId>org.seqdoop</groupId>
            <artifactId>cofoja</artifactId>
            <version>1.1-r150</version>
        </dependency>

        <dependency>
            <groupId>org.apache.commons</groupId>
            <artifactId>commons-jexl</artifactId>
            <version>2.1.1</version>
        </dependency>

        <dependency>
            <groupId>commons-logging</groupId>
            <artifactId>commons-logging</artifactId>
            <version>1.1.1</version>
        </dependency>

        <dependency>
            <groupId>org.xerial.snappy</groupId>
            <artifactId>snappy-java</artifactId>
            <version>1.0.3-rc3</version>
        </dependency>

        <dependency>
            <groupId>org.testng</groupId>
            <artifactId>testng</artifactId>
            <!-- was 5.5; this was failing to compile with maven-->
            <version>6.8.8</version>
            <scope>compile</scope>
        </dependency>

    </dependencies>

    <build>
        <sourceDirectory>src/java</sourceDirectory>
        <testSourceDirectory>src/tests/java</testSourceDirectory>

        <plugins>
            <plugin>
                <groupId>org.apache.maven.plugins</groupId>
                <artifactId>maven-gpg-plugin</artifactId>
                <version>1.5</version>
            </plugin>

            <plugin>
                <groupId>org.apache.maven.plugins</groupId>
                <artifactId>maven-deploy-plugin</artifactId>
                <version>2.7</version>
            </plugin>

            <plugin>
                <groupId>org.apache.maven.plugins</groupId>
                <artifactId>maven-javadoc-plugin</artifactId>
                <version>2.9.1</version>
                <executions>
                    <execution>
                        <id>attach-javadocs</id>
                        <goals>
                            <goal>jar</goal>
                        </goals>
                    </execution>
                </executions>
            </plugin>

            <plugin>
                <groupId>org.apache.maven.plugins</groupId>
                <artifactId>maven-source-plugin</artifactId>
                <version>2.2.1</version>
                <executions>
                    <execution>
                        <id>attach-sources</id>
                        <goals>
                            <goal>jar-no-fork</goal>
                        </goals>
                    </execution>
                </executions>
            </plugin> 

            <plugin>
                <groupId>org.apache.maven.plugins</groupId>
                <artifactId>maven-jar-plugin</artifactId>
                <version>2.5</version>
                <configuration>
                    <archive>
                        <addMavenDescriptor>false</addMavenDescriptor>
                        <manifestEntries>
                            <Implementation-Vendor>${project.groupId}</Implementation-Vendor>
                            <Implementation-Version>${project.version}</Implementation-Version>
                        </manifestEntries>
                    </archive>
                </configuration>
            </plugin>

            <plugin>
                <groupId>org.apache.maven.plugins</groupId>
                <artifactId>maven-compiler-plugin</artifactId>
                <version>3.1</version>
                <configuration>
                    <source>1.6</source>
                    <target>1.6</target>
                    <!-- not sure if this plays nice with cofoja but the build fails without it,
                     complaining about cofoja "error in contract"-->
                    <compilerArgument>-proc:none</compilerArgument>
                    <debug>true</debug>
                    <optimize>false</optimize>
                </configuration>
            </plugin>

            <plugin>
                <groupId>org.apache.maven.plugins</groupId>
                <artifactId>maven-surefire-plugin</artifactId>
                <version>2.17</version>
                <configuration>
                    <!-- without bumping up memory, maven tests fail -->
                    <argLine>-Xms256m -Xmx1g -XX:MaxPermSize=256m</argLine>
                </configuration>
            </plugin>
        </plugins>


    </build>
</project>