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

  <modelVersion>4.0.0</modelVersion>
  <groupId>org.bdgenomics.convert</groupId>
  <artifactId>convert-parent</artifactId>
  <version>0.5.0-SNAPSHOT</version>
  <packaging>pom</packaging>
  <name>Big Data Genomics: Convert Parent</name>
  <description>Convert Parent POM</description>
  <url>http://bdgenomics.org/</url>

  <properties>
    <java.version>1.8</java.version>
    <bdg-formats.version>0.11.3</bdg-formats.version>
    <commons-lang3.version>3.8.1</commons-lang3.version>
    <ga4gh.version>0.6.0a10</ga4gh.version>
    <guava.version>27.0-jre</guava.version>
    <guice.version>4.2.1</guice.version>
    <htsjdk.version>2.16.1</htsjdk.version>
    <jsr305.version>3.0.2</jsr305.version>
    <junit.version>4.12</junit.version>
    <protobuf.version>3.0.0-beta-3</protobuf.version>
    <slf4j.version>1.7.25</slf4j.version>
  </properties>

  <licenses>
    <license>
      <name>Apache License</name>
      <url>https://raw.github.com/bigdatagenomics/convert/master/LICENSE</url>
      <distribution>repo</distribution>
    </license>
  </licenses>
  <scm>
    <connection>scm:git:git<EMAIL>:bigdatagenomics/convert.git</connection>
    <developerConnection>scm:git:git<EMAIL>:bigdatagenomics/convert.git</developerConnection>
    <url>scm:git:git<EMAIL>:bigdatagenomics/convert.git</url>
    <tag>master</tag>
  </scm>
  <developers>
    <developer>
      <id>heuermh</id>
    </developer>
  </developers>
  <issueManagement>
    <system>github</system>
    <url>https://github.com/bigdatagenomics/convert/issues</url>
  </issueManagement>

  <build>
    <pluginManagement>
      <plugins>
        <plugin>
          <groupId>org.apache.maven.plugins</groupId>
          <artifactId>maven-assembly-plugin</artifactId>
          <version>3.1.0</version>
        </plugin>
        <plugin>
          <groupId>org.apache.maven.plugins</groupId>
          <artifactId>maven-javadoc-plugin</artifactId>
          <version>3.0.1</version>
        </plugin>
        <plugin>
          <groupId>org.apache.maven.plugins</groupId>
          <artifactId>maven-release-plugin</artifactId>
          <version>2.5.3</version>
          <configuration>
            <mavenExecutorId>forked-path</mavenExecutorId>
            <useReleaseProfile>false</useReleaseProfile>
            <arguments>-Psonatype-oss-release</arguments>
          </configuration>
        </plugin>
        <plugin>
          <groupId>org.apache.maven.plugins</groupId>
          <artifactId>maven-gpg-plugin</artifactId>
          <version>1.6</version>
        </plugin>
        <plugin>
          <groupId>org.apache.maven.plugins</groupId>
          <artifactId>maven-clean-plugin</artifactId>
          <version>3.1.0</version>
        </plugin>
        <plugin>
          <groupId>org.apache.maven.plugins</groupId>
          <artifactId>maven-compiler-plugin</artifactId>
          <version>3.8.0</version>
          <configuration>
            <source>${java.version}</source>
            <target>${java.version}</target>
          </configuration>
        </plugin>
        <plugin>
          <groupId>org.apache.maven.plugins</groupId>
          <artifactId>maven-deploy-plugin</artifactId>
          <version>2.8.2</version>
        </plugin>
        <plugin>
          <groupId>org.apache.maven.plugins</groupId>
          <artifactId>maven-enforcer-plugin</artifactId>
          <version>1.4.1</version>
          <executions>
            <execution>
              <id>enforce-versions</id>
              <goals>
                <goal>enforce</goal>
              </goals>
              <configuration>
                <rules>
                  <requireMavenVersion>
                    <version>[3.1.1,)</version>
                    <message>convert requires Maven 3.1.1 or greater</message>
                  </requireMavenVersion>
                  <requireJavaVersion>
                    <version>[1.8,)</version>
                    <message>convert requires Java 1.8 or greater</message>
                  </requireJavaVersion>
                </rules>
              </configuration>
            </execution>
          </executions>
        </plugin>
        <plugin>
          <groupId>org.apache.maven.plugins</groupId>
          <artifactId>maven-install-plugin</artifactId>
          <version>2.5.2</version>
        </plugin>
        <plugin>
          <groupId>org.apache.maven.plugins</groupId>
          <artifactId>maven-jar-plugin</artifactId>
          <version>3.1.0</version>
        </plugin>
        <plugin>
          <groupId>org.apache.maven.plugins</groupId>
          <artifactId>maven-resources-plugin</artifactId>
          <version>3.0.1</version>
        </plugin>
        <plugin>
          <groupId>org.apache.maven.plugins</groupId>
          <artifactId>maven-surefire-plugin</artifactId>
          <version>2.22.0</version>
        </plugin>
      </plugins>
    </pluginManagement>
  </build>

  <dependencyManagement>
    <dependencies>
      <dependency>
        <groupId>com.github.samtools</groupId>
        <artifactId>htsjdk</artifactId>
        <version>${htsjdk.version}</version>
      </dependency>
      <dependency>
        <groupId>com.google.code.findbugs</groupId>
        <artifactId>jsr305</artifactId>
        <version>${jsr305.version}</version>
      </dependency>
      <dependency>
        <groupId>com.google.inject</groupId>
        <artifactId>guice</artifactId>
        <version>${guice.version}</version>
      </dependency>
      <dependency>
        <groupId>com.google.guava</groupId>
        <artifactId>guava</artifactId>
        <version>${guava.version}</version>
      </dependency>
      <dependency>
        <groupId>junit</groupId>
        <artifactId>junit</artifactId>
        <version>${junit.version}</version>
      </dependency>
      <dependency>
        <groupId>com.google.protobuf</groupId>
        <artifactId>protobuf-java</artifactId>
        <version>${protobuf.version}</version>
      </dependency>
      <dependency>
        <groupId>com.google.protobuf</groupId>
        <artifactId>protobuf-java-util</artifactId>
        <version>${protobuf.version}</version>
      </dependency>
      <dependency>
        <groupId>org.apache.commons</groupId>
        <artifactId>commons-lang3</artifactId>
        <version>${commons-lang3.version}</version>
      </dependency>
      <dependency>
        <groupId>org.bdgenomics.bdg-formats</groupId>
        <artifactId>bdg-formats</artifactId>
        <version>${bdg-formats.version}</version>
      </dependency>
      <dependency>
        <groupId>org.ga4gh</groupId>
        <artifactId>ga4gh-schemas</artifactId>
        <version>${ga4gh.version}</version>
      </dependency>
      <dependency>
        <groupId>org.slf4j</groupId>
        <artifactId>slf4j-api</artifactId>
        <version>${slf4j.version}</version>
      </dependency>
      <dependency>
        <groupId>org.slf4j</groupId>
        <artifactId>slf4j-simple</artifactId>
        <version>${slf4j.version}</version>
      </dependency>
    </dependencies>
  </dependencyManagement>

  <modules>
    <module>convert</module>
    <module>convert-htsjdk</module>
    <module>convert-ga4gh</module>
  </modules>

  <profiles>
    <!-- Only sign artifacts when we are performing a release, not snapshots -->
    <profile>
      <id>sonatype-oss-release</id>
      <build>
        <plugins>
          <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>
          <plugin>
            <artifactId>maven-jar-plugin</artifactId>
            <version>3.1.0</version>
          </plugin>
          <plugin>
            <artifactId>maven-javadoc-plugin</artifactId>
            <version>3.0.1</version>
          </plugin>
          <plugin>
            <artifactId>maven-source-plugin</artifactId>
            <version>3.0.1</version>
          </plugin>
        </plugins>
      </build>
    </profile>
  </profiles>
</project>
<commit_msg>Update bdg-formats dependency version to 0.11.4.<commit_after><?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">
  <parent>
    <groupId>org.sonatype.oss</groupId>
    <artifactId>oss-parent</artifactId>
    <version>7</version>
    <relativePath />
  </parent>

  <modelVersion>4.0.0</modelVersion>
  <groupId>org.bdgenomics.convert</groupId>
  <artifactId>convert-parent</artifactId>
  <version>0.5.0-SNAPSHOT</version>
  <packaging>pom</packaging>
  <name>Big Data Genomics: Convert Parent</name>
  <description>Convert Parent POM</description>
  <url>http://bdgenomics.org/</url>

  <properties>
    <java.version>1.8</java.version>
    <bdg-formats.version>0.11.4</bdg-formats.version>
    <commons-lang3.version>3.8.1</commons-lang3.version>
    <ga4gh.version>0.6.0a10</ga4gh.version>
    <guava.version>27.0-jre</guava.version>
    <guice.version>4.2.1</guice.version>
    <htsjdk.version>2.16.1</htsjdk.version>
    <jsr305.version>3.0.2</jsr305.version>
    <junit.version>4.12</junit.version>
    <protobuf.version>3.0.0-beta-3</protobuf.version>
    <slf4j.version>1.7.25</slf4j.version>
  </properties>

  <licenses>
    <license>
      <name>Apache License</name>
      <url>https://raw.github.com/bigdatagenomics/convert/master/LICENSE</url>
      <distribution>repo</distribution>
    </license>
  </licenses>
  <scm>
    <connection>scm:git:git@github.<EMAIL>:bigdatagenomics/convert.git</connection>
    <developerConnection>scm:git:git@github.com:bigdatagenomics/convert.git</developerConnection>
    <url>scm:git:git@github.com:bigdatagenomics/convert.git</url>
    <tag>master</tag>
  </scm>
  <developers>
    <developer>
      <id>heuermh</id>
    </developer>
  </developers>
  <issueManagement>
    <system>github</system>
    <url>https://github.com/bigdatagenomics/convert/issues</url>
  </issueManagement>

  <build>
    <pluginManagement>
      <plugins>
        <plugin>
          <groupId>org.apache.maven.plugins</groupId>
          <artifactId>maven-assembly-plugin</artifactId>
          <version>3.1.0</version>
        </plugin>
        <plugin>
          <groupId>org.apache.maven.plugins</groupId>
          <artifactId>maven-javadoc-plugin</artifactId>
          <version>3.0.1</version>
        </plugin>
        <plugin>
          <groupId>org.apache.maven.plugins</groupId>
          <artifactId>maven-release-plugin</artifactId>
          <version>2.5.3</version>
          <configuration>
            <mavenExecutorId>forked-path</mavenExecutorId>
            <useReleaseProfile>false</useReleaseProfile>
            <arguments>-Psonatype-oss-release</arguments>
          </configuration>
        </plugin>
        <plugin>
          <groupId>org.apache.maven.plugins</groupId>
          <artifactId>maven-gpg-plugin</artifactId>
          <version>1.6</version>
        </plugin>
        <plugin>
          <groupId>org.apache.maven.plugins</groupId>
          <artifactId>maven-clean-plugin</artifactId>
          <version>3.1.0</version>
        </plugin>
        <plugin>
          <groupId>org.apache.maven.plugins</groupId>
          <artifactId>maven-compiler-plugin</artifactId>
          <version>3.8.0</version>
          <configuration>
            <source>${java.version}</source>
            <target>${java.version}</target>
          </configuration>
        </plugin>
        <plugin>
          <groupId>org.apache.maven.plugins</groupId>
          <artifactId>maven-deploy-plugin</artifactId>
          <version>2.8.2</version>
        </plugin>
        <plugin>
          <groupId>org.apache.maven.plugins</groupId>
          <artifactId>maven-enforcer-plugin</artifactId>
          <version>1.4.1</version>
          <executions>
            <execution>
              <id>enforce-versions</id>
              <goals>
                <goal>enforce</goal>
              </goals>
              <configuration>
                <rules>
                  <requireMavenVersion>
                    <version>[3.1.1,)</version>
                    <message>convert requires Maven 3.1.1 or greater</message>
                  </requireMavenVersion>
                  <requireJavaVersion>
                    <version>[1.8,)</version>
                    <message>convert requires Java 1.8 or greater</message>
                  </requireJavaVersion>
                </rules>
              </configuration>
            </execution>
          </executions>
        </plugin>
        <plugin>
          <groupId>org.apache.maven.plugins</groupId>
          <artifactId>maven-install-plugin</artifactId>
          <version>2.5.2</version>
        </plugin>
        <plugin>
          <groupId>org.apache.maven.plugins</groupId>
          <artifactId>maven-jar-plugin</artifactId>
          <version>3.1.0</version>
        </plugin>
        <plugin>
          <groupId>org.apache.maven.plugins</groupId>
          <artifactId>maven-resources-plugin</artifactId>
          <version>3.0.1</version>
        </plugin>
        <plugin>
          <groupId>org.apache.maven.plugins</groupId>
          <artifactId>maven-surefire-plugin</artifactId>
          <version>2.22.0</version>
        </plugin>
      </plugins>
    </pluginManagement>
  </build>

  <dependencyManagement>
    <dependencies>
      <dependency>
        <groupId>com.github.samtools</groupId>
        <artifactId>htsjdk</artifactId>
        <version>${htsjdk.version}</version>
      </dependency>
      <dependency>
        <groupId>com.google.code.findbugs</groupId>
        <artifactId>jsr305</artifactId>
        <version>${jsr305.version}</version>
      </dependency>
      <dependency>
        <groupId>com.google.inject</groupId>
        <artifactId>guice</artifactId>
        <version>${guice.version}</version>
      </dependency>
      <dependency>
        <groupId>com.google.guava</groupId>
        <artifactId>guava</artifactId>
        <version>${guava.version}</version>
      </dependency>
      <dependency>
        <groupId>junit</groupId>
        <artifactId>junit</artifactId>
        <version>${junit.version}</version>
      </dependency>
      <dependency>
        <groupId>com.google.protobuf</groupId>
        <artifactId>protobuf-java</artifactId>
        <version>${protobuf.version}</version>
      </dependency>
      <dependency>
        <groupId>com.google.protobuf</groupId>
        <artifactId>protobuf-java-util</artifactId>
        <version>${protobuf.version}</version>
      </dependency>
      <dependency>
        <groupId>org.apache.commons</groupId>
        <artifactId>commons-lang3</artifactId>
        <version>${commons-lang3.version}</version>
      </dependency>
      <dependency>
        <groupId>org.bdgenomics.bdg-formats</groupId>
        <artifactId>bdg-formats</artifactId>
        <version>${bdg-formats.version}</version>
      </dependency>
      <dependency>
        <groupId>org.ga4gh</groupId>
        <artifactId>ga4gh-schemas</artifactId>
        <version>${ga4gh.version}</version>
      </dependency>
      <dependency>
        <groupId>org.slf4j</groupId>
        <artifactId>slf4j-api</artifactId>
        <version>${slf4j.version}</version>
      </dependency>
      <dependency>
        <groupId>org.slf4j</groupId>
        <artifactId>slf4j-simple</artifactId>
        <version>${slf4j.version}</version>
      </dependency>
    </dependencies>
  </dependencyManagement>

  <modules>
    <module>convert</module>
    <module>convert-htsjdk</module>
    <module>convert-ga4gh</module>
  </modules>

  <profiles>
    <!-- Only sign artifacts when we are performing a release, not snapshots -->
    <profile>
      <id>sonatype-oss-release</id>
      <build>
        <plugins>
          <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>
          <plugin>
            <artifactId>maven-jar-plugin</artifactId>
            <version>3.1.0</version>
          </plugin>
          <plugin>
            <artifactId>maven-javadoc-plugin</artifactId>
            <version>3.0.1</version>
          </plugin>
          <plugin>
            <artifactId>maven-source-plugin</artifactId>
            <version>3.0.1</version>
          </plugin>
        </plugins>
      </build>
    </profile>
  </profiles>
</project>

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{'dir': 'git-commits-cleaned', 'id': '1926743', 'n_tokens_mistral': 5889, 'n_tokens_neox': 5253, 'n_words': 575}