Default build to Spark 3/Scala 2.12.

bigdatagenomics · Aug 7, 2020 · beb7a4f · beb7a4f
1 parent 19f4c20
commit beb7a4f
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Showing 13 changed files with 89 additions and 69 deletions.
diff --git a/adam-apis/pom.xml b/adam-apis/pom.xml
@@ -3,12 +3,12 @@
   <modelVersion>4.0.0</modelVersion>
   <parent>
     <groupId>org.bdgenomics.adam</groupId>
-    <artifactId>adam-parent-spark2_2.11</artifactId>
+    <artifactId>adam-parent-spark3_2.12</artifactId>
     <version>0.33.0-SNAPSHOT</version>
     <relativePath>../pom.xml</relativePath>
   </parent>
 
-  <artifactId>adam-apis-spark2_2.11</artifactId>
+  <artifactId>adam-apis-spark3_2.12</artifactId>
   <packaging>jar</packaging>
   <name>ADAM_${scala.version.prefix}: APIs for Java, Python</name>
   <build>
@@ -107,7 +107,7 @@
     </dependency>
     <dependency>
       <groupId>org.bdgenomics.utils</groupId>
-      <artifactId>utils-misc-spark2_${scala.version.prefix}</artifactId>
+      <artifactId>utils-misc-spark3_${scala.version.prefix}</artifactId>
       <type>test-jar</type>
       <scope>test</scope>
     </dependency>
@@ -118,12 +118,12 @@
     </dependency>
     <dependency>
       <groupId>org.bdgenomics.adam</groupId>
-      <artifactId>adam-core-spark2_${scala.version.prefix}</artifactId>
+      <artifactId>adam-core-spark3_${scala.version.prefix}</artifactId>
       <scope>compile</scope>
     </dependency>
     <dependency>
       <groupId>org.bdgenomics.adam</groupId>
-      <artifactId>adam-core-spark2_${scala.version.prefix}</artifactId>
+      <artifactId>adam-core-spark3_${scala.version.prefix}</artifactId>
       <type>test-jar</type>
       <scope>test</scope>
     </dependency>

diff --git a/adam-assembly/pom.xml b/adam-assembly/pom.xml
@@ -3,12 +3,12 @@
   <modelVersion>4.0.0</modelVersion>
   <parent>
     <groupId>org.bdgenomics.adam</groupId>
-    <artifactId>adam-parent-spark2_2.11</artifactId>
+    <artifactId>adam-parent-spark3_2.12</artifactId>
     <version>0.33.0-SNAPSHOT</version>
     <relativePath>../pom.xml</relativePath>
   </parent>
 
-  <artifactId>adam-assembly-spark2_2.11</artifactId>
+  <artifactId>adam-assembly-spark3_2.12</artifactId>
   <packaging>jar</packaging>
   <name>ADAM_${scala.version.prefix}: Assembly</name>
   <build>
@@ -42,7 +42,7 @@
         <dependencies>
           <dependency>
             <groupId>org.bdgenomics.adam</groupId>
-            <artifactId>adam-shade-spark2_${scala.version.prefix}</artifactId>
+            <artifactId>adam-shade-spark3_${scala.version.prefix}</artifactId>
             <version>${project.version}</version>
           </dependency>
         </dependencies>
@@ -123,7 +123,7 @@
   <dependencies>
     <dependency>
       <groupId>org.bdgenomics.adam</groupId>
-      <artifactId>adam-cli-spark2_${scala.version.prefix}</artifactId>
+      <artifactId>adam-cli-spark3_${scala.version.prefix}</artifactId>
       <scope>compile</scope>
     </dependency>
   </dependencies>

diff --git a/adam-cli/pom.xml b/adam-cli/pom.xml
@@ -3,12 +3,12 @@
   <modelVersion>4.0.0</modelVersion>
   <parent>
     <groupId>org.bdgenomics.adam</groupId>
-    <artifactId>adam-parent-spark2_2.11</artifactId>
+    <artifactId>adam-parent-spark3_2.12</artifactId>
     <version>0.33.0-SNAPSHOT</version>
     <relativePath>../pom.xml</relativePath>
   </parent>
 
-  <artifactId>adam-cli-spark2_2.11</artifactId>
+  <artifactId>adam-cli-spark3_2.12</artifactId>
   <packaging>jar</packaging>
   <name>ADAM_${scala.version.prefix}: CLI</name>
   <build>
@@ -124,23 +124,23 @@
     </dependency>
     <dependency>
       <groupId>org.bdgenomics.utils</groupId>
-      <artifactId>utils-misc-spark2_${scala.version.prefix}</artifactId>
+      <artifactId>utils-misc-spark3_${scala.version.prefix}</artifactId>
       <type>test-jar</type>
       <scope>test</scope>
     </dependency>
     <dependency>
       <groupId>org.bdgenomics.utils</groupId>
-      <artifactId>utils-misc-spark2_${scala.version.prefix}</artifactId>
+      <artifactId>utils-misc-spark3_${scala.version.prefix}</artifactId>
       <scope>compile</scope>
     </dependency>
     <dependency>
       <groupId>org.bdgenomics.utils</groupId>
-      <artifactId>utils-io-spark2_${scala.version.prefix}</artifactId>
+      <artifactId>utils-io-spark3_${scala.version.prefix}</artifactId>
       <scope>compile</scope>
     </dependency>
     <dependency>
       <groupId>org.bdgenomics.utils</groupId>
-      <artifactId>utils-cli-spark2_${scala.version.prefix}</artifactId>
+      <artifactId>utils-cli-spark3_${scala.version.prefix}</artifactId>
       <scope>compile</scope>
     </dependency>
     <dependency>
@@ -150,23 +150,23 @@
     </dependency>
     <dependency>
       <groupId>org.bdgenomics.adam</groupId>
-      <artifactId>adam-core-spark2_${scala.version.prefix}</artifactId>
+      <artifactId>adam-core-spark3_${scala.version.prefix}</artifactId>
       <scope>compile</scope>
     </dependency>
     <dependency>
       <groupId>org.bdgenomics.adam</groupId>
-      <artifactId>adam-core-spark2_${scala.version.prefix}</artifactId>
+      <artifactId>adam-core-spark3_${scala.version.prefix}</artifactId>
       <type>test-jar</type>
       <scope>test</scope>
     </dependency>
     <dependency>
       <groupId>org.bdgenomics.adam</groupId>
-      <artifactId>adam-apis-spark2_${scala.version.prefix}</artifactId>
+      <artifactId>adam-apis-spark3_${scala.version.prefix}</artifactId>
       <scope>compile</scope>
     </dependency>
     <dependency>
       <groupId>org.bdgenomics.adam</groupId>
-      <artifactId>adam-apis-spark2_${scala.version.prefix}</artifactId>
+      <artifactId>adam-apis-spark3_${scala.version.prefix}</artifactId>
       <type>test-jar</type>
       <scope>test</scope>
     </dependency>

diff --git a/adam-codegen/pom.xml b/adam-codegen/pom.xml
@@ -3,12 +3,12 @@
   <modelVersion>4.0.0</modelVersion>
   <parent>
     <groupId>org.bdgenomics.adam</groupId>
-    <artifactId>adam-parent-spark2_2.11</artifactId>
+    <artifactId>adam-parent-spark3_2.12</artifactId>
     <version>0.33.0-SNAPSHOT</version>
     <relativePath>../pom.xml</relativePath>
   </parent>
 
-  <artifactId>adam-codegen-spark2_2.11</artifactId>
+  <artifactId>adam-codegen-spark3_2.12</artifactId>
   <packaging>jar</packaging>
   <name>ADAM_${scala.version.prefix}: Avro-to-Dataset codegen utils</name>
   <properties>

diff --git a/adam-core/pom.xml b/adam-core/pom.xml
@@ -3,12 +3,12 @@
   <modelVersion>4.0.0</modelVersion>
   <parent>
     <groupId>org.bdgenomics.adam</groupId>
-    <artifactId>adam-parent-spark2_2.11</artifactId>
+    <artifactId>adam-parent-spark3_2.12</artifactId>
     <version>0.33.0-SNAPSHOT</version>
     <relativePath>../pom.xml</relativePath>
   </parent>
 
-  <artifactId>adam-core-spark2_2.11</artifactId>
+  <artifactId>adam-core-spark3_2.12</artifactId>
   <packaging>jar</packaging>
   <name>ADAM_${scala.version.prefix}: Core</name>
   <build>
@@ -160,28 +160,28 @@
   <dependencies>
     <dependency>
       <groupId>org.bdgenomics.utils</groupId>
-      <artifactId>utils-misc-spark2_${scala.version.prefix}</artifactId>
+      <artifactId>utils-misc-spark3_${scala.version.prefix}</artifactId>
       <type>test-jar</type>
       <scope>test</scope>
     </dependency>
     <dependency>
       <groupId>org.bdgenomics.utils</groupId>
-      <artifactId>utils-misc-spark2_${scala.version.prefix}</artifactId>
+      <artifactId>utils-misc-spark3_${scala.version.prefix}</artifactId>
       <scope>compile</scope>
     </dependency>
     <dependency>
       <groupId>org.bdgenomics.utils</groupId>
-      <artifactId>utils-io-spark2_${scala.version.prefix}</artifactId>
+      <artifactId>utils-io-spark3_${scala.version.prefix}</artifactId>
       <scope>compile</scope>
     </dependency>
     <dependency>
       <groupId>org.bdgenomics.utils</groupId>
-      <artifactId>utils-cli-spark2_${scala.version.prefix}</artifactId>
+      <artifactId>utils-cli-spark3_${scala.version.prefix}</artifactId>
       <scope>compile</scope>
     </dependency>
     <dependency>
       <groupId>org.bdgenomics.utils</groupId>
-      <artifactId>utils-intervalrdd-spark2_${scala.version.prefix}</artifactId>
+      <artifactId>utils-intervalrdd-spark3_${scala.version.prefix}</artifactId>
       <scope>compile</scope>
     </dependency>
     <dependency>
@@ -275,7 +275,7 @@
     </dependency>
     <dependency>
       <groupId>org.bdgenomics.adam</groupId>
-      <artifactId>adam-codegen-spark2_${scala.version.prefix}</artifactId>
+      <artifactId>adam-codegen-spark3_${scala.version.prefix}</artifactId>
     </dependency>
   </dependencies>
   <profiles>

diff --git a/adam-distribution/pom.xml b/adam-distribution/pom.xml
@@ -3,12 +3,12 @@
   <modelVersion>4.0.0</modelVersion>
   <parent>
     <groupId>org.bdgenomics.adam</groupId>
-    <artifactId>adam-parent-spark2_2.11</artifactId>
+    <artifactId>adam-parent-spark3_2.12</artifactId>
     <version>0.33.0-SNAPSHOT</version>
     <relativePath>../pom.xml</relativePath>
   </parent>
 
-  <artifactId>adam-distribution-spark2_2.11</artifactId>
+  <artifactId>adam-distribution-spark3_2.12</artifactId>
   <packaging>pom</packaging>
   <name>ADAM_${scala.version.prefix}: Distribution</name>
   <build>

diff --git a/adam-python/pom.xml b/adam-python/pom.xml
@@ -3,12 +3,12 @@
   <modelVersion>4.0.0</modelVersion>
   <parent>
     <groupId>org.bdgenomics.adam</groupId>
-    <artifactId>adam-parent-spark2_2.11</artifactId>
+    <artifactId>adam-parent-spark3_2.12</artifactId>
     <version>0.33.0-SNAPSHOT</version>
     <relativePath>../pom.xml</relativePath>
   </parent>
 
-  <artifactId>adam-python-spark2_2.11</artifactId>
+  <artifactId>adam-python-spark3_2.12</artifactId>
   <packaging>jar</packaging>
   <name>ADAM_${scala.version.prefix}: Python APIs</name>
   <properties>

diff --git a/adam-r/bdgenomics.adam/DESCRIPTION b/adam-r/bdgenomics.adam/DESCRIPTION
@@ -22,4 +22,4 @@ Collate:
     'generics.R'
     'adam-context.R'
     'rdd.R'
-RoxygenNote: 6.1.1
+RoxygenNote: 7.1.1
diff --git a/adam-r/bdgenomics.adam/NAMESPACE b/adam-r/bdgenomics.adam/NAMESPACE
@@ -40,14 +40,15 @@ export(saveAsVcf)
 export(shuffleRegionJoin)
 export(shuffleRegionJoinAndGroupByLeft)
 export(sort)
+export(sortByReadName)
+export(sortByReferencePosition)
+export(sortByReferencePositionAndIndex)
 export(sortLexicographically)
-export(sortReadsByReferencePosition)
-export(sortReadsByReferencePositionAndIndex)
+export(toAlignments)
 export(toCoverage)
 export(toDF)
 export(toFeatures)
 export(toFragments)
-export(toReads)
 export(toVariantContexts)
 export(toVariants)
 export(transform)
@@ -102,14 +103,15 @@ exportMethods(saveAsVcf)
 exportMethods(shuffleRegionJoin)
 exportMethods(shuffleRegionJoinAndGroupByLeft)
 exportMethods(sort)
+exportMethods(sortByReadName)
+exportMethods(sortByReferencePosition)
+exportMethods(sortByReferencePositionAndIndex)
 exportMethods(sortLexicographically)
-exportMethods(sortReadsByReferencePosition)
-exportMethods(sortReadsByReferencePositionAndIndex)
+exportMethods(toAlignments)
 exportMethods(toCoverage)
 exportMethods(toDF)
 exportMethods(toFeatures)
 exportMethods(toFragments)
-exportMethods(toReads)
 exportMethods(toVariantContexts)
 exportMethods(toVariants)
 exportMethods(transform)

diff --git a/adam-r/pom.xml b/adam-r/pom.xml
@@ -3,12 +3,12 @@
   <modelVersion>4.0.0</modelVersion>
   <parent>
     <groupId>org.bdgenomics.adam</groupId>
-    <artifactId>adam-parent-spark2_2.11</artifactId>
+    <artifactId>adam-parent-spark3_2.12</artifactId>
     <version>0.33.0-SNAPSHOT</version>
     <relativePath>../pom.xml</relativePath>
   </parent>
 
-  <artifactId>adam-r-spark2_2.11</artifactId>
+  <artifactId>adam-r-spark3_2.12</artifactId>
   <packaging>jar</packaging>
   <name>ADAM_${scala.version.prefix}: R APIs</name>
   <properties>

diff --git a/adam-shade/pom.xml b/adam-shade/pom.xml
@@ -3,12 +3,12 @@
   <modelVersion>4.0.0</modelVersion>
   <parent>
     <groupId>org.bdgenomics.adam</groupId>
-    <artifactId>adam-parent-spark2_2.11</artifactId>
+    <artifactId>adam-parent-spark3_2.12</artifactId>
     <version>0.33.0-SNAPSHOT</version>
     <relativePath>../pom.xml</relativePath>
   </parent>
 
-  <artifactId>adam-shade-spark2_2.11</artifactId>
+  <artifactId>adam-shade-spark3_2.12</artifactId>
   <packaging>jar</packaging>
   <name>ADAM_${scala.version.prefix}: Shader workaround</name>