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Add SortedGenomicRDD trait, refactor shuffle joins and pipe #1590

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Add SortedGenomicRDD trait, refactor shuffle joins and pipe #1590

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6ca3c6f
Revert slf4j dependency changes from 9505d47e881305367fbad4bdfb8f189c…
fnothaft Jun 26, 2017
56eca25
Flesh out Java APIs in GenomicRDDs.
fnothaft Feb 9, 2017
fee9263
[ADAM-538] Add support for an adam-python API.
fnothaft Feb 9, 2017
f430899
[ADAM-1018] Add support for Spark SQL Datasets.
fnothaft Feb 9, 2017
9ee0375
Add Dataset based k-mer counter.
fnothaft May 12, 2017
dea5fa0
[ADAM-882] Add R API.
fnothaft Feb 21, 2017
7b9b329
[ADAM-1584] Add SortedGenomicRDD trait, support for sorted legacy files.
fnothaft Jun 27, 2017
f03ba95
[ADAM-1583] Accelerate sorted pipe commands by leveraging sorted know…
fnothaft Jul 6, 2017
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4 changes: 4 additions & 0 deletions adam-apis/pom.xml
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Expand Up @@ -142,5 +142,9 @@
<artifactId>scalatest_${scala.version.prefix}</artifactId>
<scope>test</scope>
</dependency>
<dependency>
<groupId>org.apache.spark</groupId>
<artifactId>spark-sql_${scala.version.prefix}</artifactId>
</dependency>
</dependencies>
</project>
15 changes: 0 additions & 15 deletions adam-assembly/pom.xml
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Expand Up @@ -116,20 +116,5 @@
<artifactId>adam-cli_${scala.version.prefix}</artifactId>
<scope>compile</scope>
</dependency>
<dependency>
<groupId>org.slf4j</groupId>
<artifactId>jcl-over-slf4j</artifactId>
<scope>runtime</scope>
</dependency>
<dependency>
<groupId>org.slf4j</groupId>
<artifactId>jul-to-slf4j</artifactId>
<scope>runtime</scope>
</dependency>
<dependency>
<groupId>org.slf4j</groupId>
<artifactId>slf4j-log4j12</artifactId>
<scope>runtime</scope>
</dependency>
</dependencies>
</project>
4 changes: 4 additions & 0 deletions adam-cli/pom.xml
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Expand Up @@ -193,5 +193,9 @@
<artifactId>scala-guice_${scala.version.prefix}</artifactId>
<scope>compile</scope>
</dependency>
<dependency>
<groupId>org.apache.spark</groupId>
<artifactId>spark-sql_${scala.version.prefix}</artifactId>
</dependency>
</dependencies>
</project>
114 changes: 114 additions & 0 deletions adam-codegen/pom.xml
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@@ -0,0 +1,114 @@
<?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>
<parent>
<groupId>org.bdgenomics.adam</groupId>
<artifactId>adam-parent_2.10</artifactId>
<version>0.23.0-SNAPSHOT</version>
<relativePath>../pom.xml</relativePath>
</parent>

<artifactId>adam-codegen_2.10</artifactId>
<packaging>jar</packaging>
<name>ADAM_${scala.version.prefix}: Avro-to-Dataset codegen utils</name>
<properties>
<timestamp>${maven.build.timestamp}</timestamp>
<maven.build.timestamp.format>yyyy-MM-dd</maven.build.timestamp.format>
</properties>
<build>
<plugins>
<!-- disable surefire -->
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-surefire-plugin</artifactId>
<configuration>
<skipTests>true</skipTests>
</configuration>
</plugin>
<plugin>
<groupId>org.codehaus.mojo</groupId>
<artifactId>build-helper-maven-plugin</artifactId>
<executions>
<execution>
<id>add-source</id>
<phase>generate-sources</phase>
<goals>
<goal>add-source</goal>
</goals>
<configuration>
<sources>
<source>src/main/scala</source>
</sources>
</configuration>
</execution>
<execution>
<id>add-test-source</id>
<phase>generate-test-sources</phase>
<goals>
<goal>add-test-source</goal>
</goals>
<configuration>
<sources>
<source>src/test/scala</source>
</sources>
</configuration>
</execution>
</executions>
</plugin>
<plugin>
<groupId>org.scalatest</groupId>
<artifactId>scalatest-maven-plugin</artifactId>
<configuration>
<reportsDirectory>${project.build.directory}/scalatest-reports</reportsDirectory>
<junitxml>.</junitxml>
<filereports>ADAMTestSuite.txt</filereports>
<!--
As explained here: http://stackoverflow.com/questions/1660441/java-flag-to-enable-extended-serialization-debugging-info
The second option allows us better debugging for serialization-based errors.
-->
<argLine>-Xmx1024m -Dsun.io.serialization.extendedDebugInfo=true</argLine>
<stdout>F</stdout>
</configuration>
<executions>
<execution>
<id>test</id>
<goals>
<goal>test</goal>
</goals>
</execution>
</executions>
</plugin>
</plugins>
</build>
<dependencies>
<dependency>
<groupId>org.scala-lang</groupId>
<artifactId>scala-library</artifactId>
</dependency>
<dependency>
<groupId>org.apache.avro</groupId>
<artifactId>avro</artifactId>
</dependency>
<dependency>
<groupId>org.scalatest</groupId>
<artifactId>scalatest_${scala.version.prefix}</artifactId>
<scope>test</scope>
</dependency>
</dependencies>
<profiles>
<profile>
<id>coverage</id>
<build>
<plugins>
<plugin>
<groupId>org.scoverage</groupId>
<artifactId>scoverage-maven-plugin</artifactId>
<configuration>
<excludedPackages>org.bdgenomics.adam.codegen</excludedPackages>
</configuration>
</plugin>
</plugins>
</build>
</profile>
</profiles>
</project>
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