<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">
  <modelVersion>4.0.0</modelVersion>
  <groupId>org.bdgenomics.avocado</groupId>
  <artifactId>avocado</artifactId>
  <version>0.0.2</version>
  <packaging>pom</packaging>
  <name>avocado: A Variant Caller, Distributed</name>

  <properties>
    <adam.version>0.8.1-SNAPSHOT</adam.version>
    <avro.version>1.7.4</avro.version>
    <java.version>1.6</java.version>
    <scala.version>2.10.3</scala.version>
    <scala.version.prefix>2.10</scala.version.prefix>
  </properties>

  <modules>
    <module>avocado-sufficient-statistics</module>
    <module>avocado-core</module>
  </modules>
  <licenses>
    <license>
      <name>Apache License</name>
      <url>https://raw.github.com/bigdatagenomics/adam/master/LICENSE.txt</url>
      <distribution>repo</distribution>
    </license>
  </licenses>

  <scm>
    <connection>scm:git:<EMAIL>:bigdatagenomics/avocado.git</connection>
    <developerConnection>scm:git:<EMAIL>:bigdatagenomics/avocado.git</developerConnection>
    <url>scm:git:<EMAIL>:bigdatagenomics/avocado.git</url>
    <tag>HEAD</tag>
  </scm>

  <developers>
    <developer>
      <id>fnothaft</id>
      <name><NAME></name>
      <email><EMAIL></email>
      <url>http://www.fnothaft.net</url>
      <organization>U.C. Berkeley, Department of Electrical Engineering and  Computer Science</organization>
      <organizationUrl>http://www.cs.berkeley.edu/</organizationUrl>
    </developer>
    <developer>
      <id>peterj</id>
      <name><NAME></name>
      <email><EMAIL></email>
      <url>http://www.eecs.berkeley.edu/~phj/</url>
      <organization>U.C. Berkeley, Department of Electrical Engineering and  Computer Science</organization>
      <organizationUrl>http://www.cs.berkeley.edu/</organizationUrl>
    </developer>
    <developer>
      <id>ehiunno</id>
      <name><NAME></name>
      <email><EMAIL></email>
      <url>http://www.eecs.berkeley.edu/~brielin</url>
      <organization>U.C. Berkeley, Department of Electrical Engineering and  Computer Science</organization>
      <organizationUrl>http://www.cs.berkeley.edu/</organizationUrl>
    </developer>
  </developers>

  <issueManagement>
    <system>github</system>
    <url>https://github.com/bigdatagenomics/avocado/issues</url>
  </issueManagement>

  <build>
    <outputDirectory>target/scala-${scala.version}/classes</outputDirectory>
    <testOutputDirectory>target/scala-${scala.version}/test-classes</testOutputDirectory>
    <plugins>
      <plugin>
        <groupId>org.apache.maven.plugins</groupId>
        <artifactId>maven-compiler-plugin</artifactId>
        <version>3.1</version>
        <configuration>
          <source>${java.version}</source>
          <target>${java.version}</target>
        </configuration>
      </plugin>
      <plugin>
        <groupId>net.alchim31.maven</groupId>
        <artifactId>scala-maven-plugin</artifactId>
        <version>3.1.5</version>
        <executions>
          <execution>
            <id>scala-compile-first</id>
            <phase>process-resources</phase>
            <goals>
              <goal>compile</goal>
            </goals>
          </execution>
          <execution>
            <id>scala-test-compile-first</id>
            <phase>process-test-resources</phase>
            <goals>
              <goal>testCompile</goal>
            </goals>
          </execution>
          <execution>
            <id>attach-scaladocs</id>
            <phase>verify</phase>
            <goals>
              <goal>doc-jar</goal>
            </goals>
          </execution>
        </executions>
        <configuration>
          <scalaVersion>${scala.version}</scalaVersion>
          <recompileMode>incremental</recompileMode>
          <useZincServer>true</useZincServer>
          <args>
            <arg>-unchecked</arg>
            <arg>-optimise</arg>
            <arg>-deprecation</arg>
          </args>
          <jvmArgs>
            <jvmArg>-Xms64m</jvmArg>
            <jvmArg>-Xms1024m</jvmArg>
            <jvmArg>-Xmx1024m</jvmArg>
          </jvmArgs>
          <javacArgs>
            <javacArg>-source</javacArg>
            <javacArg>${java.version}</javacArg>
            <javacArg>-target</javacArg>
            <javacArg>${java.version}</javacArg>
          </javacArgs>
        </configuration>
      </plugin>

      <!-- disable surefire -->
      <plugin>
        <groupId>org.apache.maven.plugins</groupId>
        <artifactId>maven-surefire-plugin</artifactId>
        <version>2.7</version>
        <configuration>
          <skipTests>true</skipTests>
        </configuration>
      </plugin>
      <!-- enable scalatest -->
      <plugin>
        <groupId>org.scalatest</groupId>
        <artifactId>scalatest-maven-plugin</artifactId>
        <version>1.0-RC2</version>
        <configuration>
          <reportsDirectory>${project.build.directory}/surefire-reports</reportsDirectory>
          <junitxml>.</junitxml>
          <filereports>ADAMTestSuite.txt</filereports>
          <argLine>-Xmx1024m</argLine>
        </configuration>
        <executions>
          <execution>
            <id>test</id>
            <goals>
              <goal>test</goal>
            </goals>
          </execution>
        </executions>
      </plugin>
      <plugin>
        <groupId>org.scalariform</groupId>
        <artifactId>scalariform-maven-plugin</artifactId>
        <version>0.1.4</version>
        <executions>
          <execution>
            <phase>process-sources</phase>
            <goals>
              <goal>format</goal>
            </goals>
            <configuration>
              <alignParameters>true</alignParameters>
              <alignSingleLineCaseStatements>true</alignSingleLineCaseStatements>
              <compactControlReadability>true</compactControlReadability>
              <doubleIndentClassDeclaration>true</doubleIndentClassDeclaration>
            </configuration>
          </execution>
        </executions>
      </plugin>
    </plugins>
  </build>

  <repositories>
    <repository>
      <id>Sonatype</id>
      <url>http://oss.sonatype.org/content/repositories/snapshots/</url>
    </repository>
    <repository>
      <id>hadoop-bam</id>
      <url>http://hadoop-bam.sourceforge.net/maven/</url>
    </repository>
    <repository>
      <id>Apache</id>
      <url>http://people.apache.org/repo/m2-snapshot-repository</url>
    </repository>
  </repositories>

  <dependencies>
    <dependency>
      <groupId>org.bdgenomics.adam</groupId>
      <artifactId>adam-format</artifactId>
      <version>${adam.version}</version>
    </dependency>
    <dependency><commit_msg>Update Scalariform to be consistent with ADAM<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">
  <modelVersion>4.0.0</modelVersion>
  <groupId>org.bdgenomics.avocado</groupId>
  <artifactId>avocado</artifactId>
  <version>0.0.2</version>
  <packaging>pom</packaging>
  <name>avocado: A Variant Caller, Distributed</name>

  <properties>
    <adam.version>0.8.1-SNAPSHOT</adam.version>
    <avro.version>1.7.4</avro.version>
    <java.version>1.6</java.version>
    <scala.version>2.10.3</scala.version>
    <scala.version.prefix>2.10</scala.version.prefix>
  </properties>

  <modules>
    <module>avocado-sufficient-statistics</module>
    <module>avocado-core</module>
  </modules>
  <licenses>
    <license>
      <name>Apache License</name>
      <url>https://raw.github.com/bigdatagenomics/adam/master/LICENSE.txt</url>
      <distribution>repo</distribution>
    </license>
  </licenses>

  <scm>
    <connection>scm:git:<EMAIL>:bigdatagenomics/avocado.git</connection>
    <developerConnection>scm:git:<EMAIL>:bigdatagenomics/avocado.git</developerConnection>
    <url>scm:git:<EMAIL>:bigdatagenomics/avocado.git</url>
    <tag>HEAD</tag>
  </scm>

  <developers>
    <developer>
      <id>fnothaft</id>
      <name><NAME></name>
      <email><EMAIL></email>
      <url>http://www.fnothaft.net</url>
      <organization>U.C. Berkeley, Department of Electrical Engineering and  Computer Science</organization>
      <organizationUrl>http://www.cs.berkeley.edu/</organizationUrl>
    </developer>
    <developer>
      <id>peterj</id>
      <name><NAME></name>
      <email><EMAIL></email>
      <url>http://www.eecs.berkeley.edu/~phj/</url>
      <organization>U.C. Berkeley, Department of Electrical Engineering and  Computer Science</organization>
      <organizationUrl>http://www.cs.berkeley.edu/</organizationUrl>
    </developer>
    <developer>
      <id>ehiunno</id>
      <name><NAME></name>
      <email><EMAIL></email>
      <url>http://www.eecs.berkeley.edu/~brielin</url>
      <organization>U.C. Berkeley, Department of Electrical Engineering and  Computer Science</organization>
      <organizationUrl>http://www.cs.berkeley.edu/</organizationUrl>
    </developer>
  </developers>

  <issueManagement>
    <system>github</system>
    <url>https://github.com/bigdatagenomics/avocado/issues</url>
  </issueManagement>

  <build>
    <outputDirectory>target/scala-${scala.version}/classes</outputDirectory>
    <testOutputDirectory>target/scala-${scala.version}/test-classes</testOutputDirectory>
    <plugins>
      <plugin>
        <groupId>org.apache.maven.plugins</groupId>
        <artifactId>maven-compiler-plugin</artifactId>
        <version>3.1</version>
        <configuration>
          <source>${java.version}</source>
          <target>${java.version}</target>
        </configuration>
      </plugin>
      <plugin>
        <groupId>net.alchim31.maven</groupId>
        <artifactId>scala-maven-plugin</artifactId>
        <version>3.1.5</version>
        <executions>
          <execution>
            <id>scala-compile-first</id>
            <phase>process-resources</phase>
            <goals>
              <goal>compile</goal>
            </goals>
          </execution>
          <execution>
            <id>scala-test-compile-first</id>
            <phase>process-test-resources</phase>
            <goals>
              <goal>testCompile</goal>
            </goals>
          </execution>
          <execution>
            <id>attach-scaladocs</id>
            <phase>verify</phase>
            <goals>
              <goal>doc-jar</goal>
            </goals>
          </execution>
        </executions>
        <configuration>
          <scalaVersion>${scala.version}</scalaVersion>
          <recompileMode>incremental</recompileMode>
          <useZincServer>true</useZincServer>
          <args>
            <arg>-unchecked</arg>
            <arg>-optimise</arg>
            <arg>-deprecation</arg>
          </args>
          <jvmArgs>
            <jvmArg>-Xms64m</jvmArg>
            <jvmArg>-Xms1024m</jvmArg>
            <jvmArg>-Xmx1024m</jvmArg>
          </jvmArgs>
          <javacArgs>
            <javacArg>-source</javacArg>
            <javacArg>${java.version}</javacArg>
            <javacArg>-target</javacArg>
            <javacArg>${java.version}</javacArg>
          </javacArgs>
        </configuration>
      </plugin>

      <!-- disable surefire -->
      <plugin>
        <groupId>org.apache.maven.plugins</groupId>
        <artifactId>maven-surefire-plugin</artifactId>
        <version>2.7</version>
        <configuration>
          <skipTests>true</skipTests>
        </configuration>
      </plugin>
      <!-- enable scalatest -->
      <plugin>
        <groupId>org.scalatest</groupId>
        <artifactId>scalatest-maven-plugin</artifactId>
        <version>1.0-RC2</version>
        <configuration>
          <reportsDirectory>${project.build.directory}/surefire-reports</reportsDirectory>
          <junitxml>.</junitxml>
          <filereports>ADAMTestSuite.txt</filereports>
          <argLine>-Xmx1024m</argLine>
        </configuration>
        <executions>
          <execution>
            <id>test</id>
            <goals>
              <goal>test</goal>
            </goals>
          </execution>
        </executions>
      </plugin>
      <plugin>
        <groupId>org.scalariform</groupId>
        <artifactId>scalariform-maven-plugin</artifactId>
        <version>0.1.4</version>
        <executions>
          <execution>
            <phase>process-sources</phase>
            <goals>
              <goal>format</goal>
            </goals>
            <configuration>
              <alignParameters>true</alignParameters>
              <alignSingleLineCaseStatements>true</alignSingleLineCaseStatements>
              <doubleIndentClassDeclaration>true</doubleIndentClassDeclaration>
            </configuration>
          </execution>
        </executions>
      </plugin>
    </plugins>
  </build>

  <repositories>
    <repository>
      <id>Sonatype</id>
      <url>http://oss.sonatype.org/content/repositories/snapshots/</url>
    </repository>
    <repository>
      <id>hadoop-bam</id>
      <url>http://hadoop-bam.sourceforge.net/maven/</url>
    </repository>
    <repository>
      <id>Apache</id>
      <url>http://people.apache.org/repo/m2-snapshot-repository</url>
    </repository>
  </repositories>

  <dependencies>
    <dependency>
      <groupId>org.bdgenomics.adam</groupId>
      <artifactId>adam-format</artifactId>
      <version>${adam.version}</version>
    </dependency>
    <dependency>
{'fraction_non_alphanumeric': 0.15650584795321637, 'fraction_numerical': 0.009941520467836258, 'mean_word_length': 2.35236461651556, 'pattern_counts': {'":': 0, '<': 615, '<?xml version=': 2, '>': 615, 'https://': 4, 'lorem ipsum': 0, 'www.': 14, 'xml': 10}, 'pii_count': 0, 'substrings_counts': 0, 'word_list_counts': {'cursed_substrings.json': 0, 'profanity_word_list.json': 0, 'sexual_word_list.json': 0, 'zh_pornsignals.json': 0}}
{'dir': 'git-commits-cleaned', 'id': '6750877', 'n_tokens_mistral': 4626, 'n_tokens_neox': 4239, 'n_words': 468}