Merge 9694465 into 4cea777

bigdatagenomics · Nov 13, 2018 · 463dfed · 463dfed
2 parents 4cea777 + 9694465
commit 463dfed
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Showing 2 changed files with 29 additions and 18 deletions.
diff --git a/avocado-core/src/test/scala/org/bdgenomics/avocado/genotyping/BiallelicGenotyperSuite.scala b/avocado-core/src/test/scala/org/bdgenomics/avocado/genotyping/BiallelicGenotyperSuite.scala
@@ -153,7 +153,7 @@ class BiallelicGenotyperSuite extends AvocadoFunSuite {
         Seq.empty),
       CopyNumberMap(2,
         FeatureRDD(sc.parallelize(Seq(cnvDup)),
-          SequenceDictionary.empty)),
+          SequenceDictionary.empty, Seq.empty)),
       false,
       maxQuality = 40,
       maxMapQ = 40)
@@ -189,7 +189,7 @@ class BiallelicGenotyperSuite extends AvocadoFunSuite {
         Seq.empty),
       CopyNumberMap(2,
         FeatureRDD(sc.parallelize(Seq(cnvDel)),
-          SequenceDictionary.empty)),
+          SequenceDictionary.empty, Seq.empty)),
       false,
       maxQuality = 40,
       maxMapQ = 40)

diff --git a/pom.xml b/pom.xml
@@ -15,15 +15,15 @@
   <name>avocado: A Variant Caller, Distributed</name>
 
   <properties>
-    <adam.version>0.24.0</adam.version>
-    <avro.version>1.8.0</avro.version>
+    <adam.version>0.25.0</adam.version>
+    <avro.version>1.8.2</avro.version>
     <java.version>1.8</java.version>
-    <scala.version>2.11.4</scala.version>
+    <scala.version>2.11.12</scala.version>
     <scala.version.prefix>2.11</scala.version.prefix>
-    <spark.version>2.2.0</spark.version>
+    <spark.version>2.3.2</spark.version>
     <!-- Edit the following line to configure the Hadoop (HDFS) version. -->
-    <hadoop.version>2.6.0</hadoop.version>
-    <utils.version>0.2.11</utils.version>
+    <hadoop.version>2.7.5</hadoop.version>
+    <utils.version>0.2.13</utils.version>
     <scoverage.plugin.version>1.1.1</scoverage.plugin.version>
   </properties>
 
@@ -71,7 +71,7 @@
         <plugin>
           <groupId>org.apache.maven.plugins</groupId>
           <artifactId>maven-assembly-plugin</artifactId>
-          <version>2.4.1</version>
+          <version>3.1.0</version>
         </plugin>
         <plugin>
           <groupId>org.apache.maven.plugins</groupId>
@@ -86,7 +86,7 @@
         <plugin>
           <groupId>pl.project13.maven</groupId>
           <artifactId>git-commit-id-plugin</artifactId>
-          <version>2.2.1</version>
+          <version>2.2.2</version>
           <configuration>
             <gitDescribe>
               <always>true</always>
@@ -122,7 +122,7 @@
         <plugin>
           <groupId>org.apache.maven.plugins</groupId>
           <artifactId>maven-compiler-plugin</artifactId>
-          <version>3.5.1</version>
+          <version>3.8.0</version>
           <configuration>
             <source>${java.version}</source>
             <target>${java.version}</target>
@@ -137,7 +137,7 @@
         <plugin>
           <groupId>org.apache.maven.plugins</groupId>
           <artifactId>maven-surefire-plugin</artifactId>
-          <version>2.7</version>
+          <version>2.22.1</version>
         </plugin>
         <!-- enable scalatest -->
         <plugin>
@@ -153,12 +153,12 @@
         <plugin>
           <artifactId>exec-maven-plugin</artifactId>
           <groupId>org.codehaus.mojo</groupId>
-          <version>1.3.2</version>
+          <version>1.5.0</version>
         </plugin>
         <plugin>
           <groupId>org.codehaus.mojo</groupId>
           <artifactId>build-helper-maven-plugin</artifactId>
-          <version>1.10</version>
+          <version>1.12</version>
         </plugin>
         <plugin>
           <groupId>org.apache.maven.plugins</groupId>
@@ -170,6 +170,11 @@
             <arguments>-Psonatype-oss-release -DskipTests</arguments>
           </configuration>
         </plugin>
+        <plugin>
+          <groupId>org.apache.maven.plugins</groupId>
+          <artifactId>maven-jar-plugin</artifactId>
+          <version>3.1.0</version>
+        </plugin>
       </plugins>
     </pluginManagement>
     <plugins>
@@ -312,6 +317,12 @@
         <version>${utils.version}</version>
         <type>test-jar</type>
         <scope>test</scope>        
+        <exclusions>
+          <exclusion>
+            <groupId>org.apache.spark</groupId>
+            <artifactId>*</artifactId>
+          </exclusion>
+        </exclusions>
       </dependency>
       <dependency>
         <groupId>org.bdgenomics.utils</groupId>
@@ -384,7 +395,7 @@
       <dependency>
         <groupId>args4j</groupId>
         <artifactId>args4j</artifactId>
-        <version>2.0.23</version>
+        <version>2.0.31</version>
       </dependency>
       <dependency>
         <groupId>org.apache.spark</groupId>
@@ -426,7 +437,7 @@
           <plugin>
             <groupId>org.apache.maven.plugins</groupId>
             <artifactId>maven-source-plugin</artifactId>
-            <version>2.2.1</version>
+            <version>3.0.1</version>
             <executions>
               <execution>
                 <id>attach-sources</id>
@@ -440,7 +451,7 @@
           <plugin>
             <groupId>org.apache.maven.plugins</groupId>
             <artifactId>maven-javadoc-plugin</artifactId>
-            <version>2.9.1</version>
+            <version>3.0.1</version>
             <executions>
               <execution>
                 <id>attach-javadocs</id>
@@ -495,7 +506,7 @@
             <artifactId>scoverage-maven-plugin</artifactId>
             <version>${scoverage.plugin.version}</version>
             <configuration>
-              <scalaVersion>2.11.4</scalaVersion>
+              <scalaVersion>2.11.12</scalaVersion>
               <excludedPackages>org.bdgenomics.avocado.Timers</excludedPackages>
               <aggregate>true</aggregate>
               <minimumCoverage>90</minimumCoverage>