Update ADAM dependency version to 0.32.0.

heuermh · heuermh · commit f47e15823959 · 2020-07-31T14:06:15.000-05:00
diff --git a/HEADER.txt b/HEADER.txt
@@ -1,7 +1,7 @@
 /*
 
     biojava-adam  BioJava and ADAM integration.
-    Copyright (c) 2017-2019 held jointly by the individual authors.
+    Copyright (c) 2017-2020 held jointly by the individual authors.
 
     This library is free software; you can redistribute it and/or modify it
     under the terms of the GNU Lesser General Public License as published
diff --git a/README.md b/README.md
@@ -13,8 +13,8 @@ Install
 
  * JDK 1.8 or later, http://openjdk.java.net
  * Apache Maven 3.3.9 or later, http://maven.apache.org
- * Apache Spark 2.4.5 or later, http://spark.apache.org
- * ADAM: Genomic Data System 0.31.0 or later, https://github.com/bigdatagenomics/adam
+ * Apache Spark 3.0.0 or later, http://spark.apache.org
+ * ADAM: Genomic Data System 0.32.0 or later, https://github.com/bigdatagenomics/adam
 
 To build
 
diff --git a/pom.xml b/pom.xml
@@ -2,7 +2,7 @@
 <!--
 
     biojava-adam  Biojava and ADAM integration.
-    Copyright (c) 2017-2019 held jointly by the individual authors.
+    Copyright (c) 2017-2020 held jointly by the individual authors.
 
     This library is free software; you can redistribute it and/or modify it
     under the terms of the GNU Lesser General Public License as published
@@ -61,19 +61,19 @@
     </license>
   </licenses>
   <properties>
-    <adam.version>0.31.0</adam.version>
-    <bdg-convert.version>0.9.0</bdg-convert.version>
+    <adam.version>0.32.0</adam.version>
+    <bdg-convert.version>0.10.0</bdg-convert.version>
     <biojava.version>5.3.0</biojava.version>
     <jdk.version>1.8</jdk.version>
     <junit.version>4.12</junit.version>
     <maven.enforcer.jdk-version>[1.8,)</maven.enforcer.jdk-version>
     <project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
     <project.build.targetEncoding>UTF-8</project.build.targetEncoding>
     <scala-guice.version>4.2.6</scala-guice.version>
-    <scala.version>2.11.12</scala.version>
-    <scala.version.prefix>2.11</scala.version.prefix>
+    <scala.version>2.12.8</scala.version>
+    <scala.version.prefix>2.12</scala.version.prefix>
     <slf4j.version>1.7.30</slf4j.version>
-    <spark.version>2.4.5</spark.version>
+    <spark.version>3.0.0</spark.version>
   </properties>
   <build>
     <pluginManagement>
diff --git a/scripts/loadFastaDna.scala b/scripts/loadFastaDna.scala
@@ -1,7 +1,7 @@
 /*
 
     biojava-adam  BioJava and ADAM integration.
-    Copyright (c) 2017-2019 held jointly by the individual authors.
+    Copyright (c) 2017-2020 held jointly by the individual authors.
 
     This library is free software; you can redistribute it and/or modify it
     under the terms of the GNU Lesser General Public License as published
diff --git a/scripts/loadFastaProtein.scala b/scripts/loadFastaProtein.scala
@@ -1,7 +1,7 @@
 /*
 
     biojava-adam  BioJava and ADAM integration.
-    Copyright (c) 2017-2019 held jointly by the individual authors.
+    Copyright (c) 2017-2020 held jointly by the individual authors.
 
     This library is free software; you can redistribute it and/or modify it
     under the terms of the GNU Lesser General Public License as published
diff --git a/scripts/loadFastaRna.scala b/scripts/loadFastaRna.scala
@@ -1,7 +1,7 @@
 /*
 
     biojava-adam  BioJava and ADAM integration.
-    Copyright (c) 2017-2019 held jointly by the individual authors.
+    Copyright (c) 2017-2020 held jointly by the individual authors.
 
     This library is free software; you can redistribute it and/or modify it
     under the terms of the GNU Lesser General Public License as published
diff --git a/scripts/loadFastqReads.scala b/scripts/loadFastqReads.scala
@@ -1,7 +1,7 @@
 /*
 
     biojava-adam  BioJava and ADAM integration.
-    Copyright (c) 2017-2019 held jointly by the individual authors.
+    Copyright (c) 2017-2020 held jointly by the individual authors.
 
     This library is free software; you can redistribute it and/or modify it
     under the terms of the GNU Lesser General Public License as published
diff --git a/scripts/loadGenbankDna.scala b/scripts/loadGenbankDna.scala
@@ -1,7 +1,7 @@
 /*
 
     biojava-adam  BioJava and ADAM integration.
-    Copyright (c) 2017-2019 held jointly by the individual authors.
+    Copyright (c) 2017-2020 held jointly by the individual authors.
 
     This library is free software; you can redistribute it and/or modify it
     under the terms of the GNU Lesser General Public License as published
diff --git a/scripts/loadGenbankDnaFeatures.scala b/scripts/loadGenbankDnaFeatures.scala
@@ -1,7 +1,7 @@
 /*
 
     biojava-adam  BioJava and ADAM integration.
-    Copyright (c) 2017-2019 held jointly by the individual authors.
+    Copyright (c) 2017-2020 held jointly by the individual authors.
 
     This library is free software; you can redistribute it and/or modify it
     under the terms of the GNU Lesser General Public License as published
diff --git a/scripts/loadGenbankProtein.scala b/scripts/loadGenbankProtein.scala
@@ -1,7 +1,7 @@
 /*
 
     biojava-adam  BioJava and ADAM integration.
-    Copyright (c) 2017-2019 held jointly by the individual authors.
+    Copyright (c) 2017-2020 held jointly by the individual authors.
 
     This library is free software; you can redistribute it and/or modify it
     under the terms of the GNU Lesser General Public License as published
diff --git a/scripts/loadGenbankProteinFeatures.scala b/scripts/loadGenbankProteinFeatures.scala
@@ -1,7 +1,7 @@
 /*
 
     biojava-adam  BioJava and ADAM integration.
-    Copyright (c) 2017-2019 held jointly by the individual authors.
+    Copyright (c) 2017-2020 held jointly by the individual authors.
 
     This library is free software; you can redistribute it and/or modify it
     under the terms of the GNU Lesser General Public License as published
diff --git a/scripts/loadGenbankRna.scala b/scripts/loadGenbankRna.scala
@@ -1,7 +1,7 @@
 /*
 
     biojava-adam  BioJava and ADAM integration.
-    Copyright (c) 2017-2019 held jointly by the individual authors.
+    Copyright (c) 2017-2020 held jointly by the individual authors.
 
     This library is free software; you can redistribute it and/or modify it
     under the terms of the GNU Lesser General Public License as published
diff --git a/scripts/loadGenbankRnaFeatures.scala b/scripts/loadGenbankRnaFeatures.scala
@@ -1,7 +1,7 @@
 /*
 
     biojava-adam  BioJava and ADAM integration.
-    Copyright (c) 2017-2019 held jointly by the individual authors.
+    Copyright (c) 2017-2020 held jointly by the individual authors.
 
     This library is free software; you can redistribute it and/or modify it
     under the terms of the GNU Lesser General Public License as published
diff --git a/src/main/java/org/biojava/nbio/adam/BiojavaKryoRegistrator.java b/src/main/java/org/biojava/nbio/adam/BiojavaKryoRegistrator.java
@@ -1,7 +1,7 @@
 /*
 
     biojava-adam  Biojava and ADAM integration.
-    Copyright (c) 2017-2019 held jointly by the individual authors.
+    Copyright (c) 2017-2020 held jointly by the individual authors.
 
     This library is free software; you can redistribute it and/or modify it
     under the terms of the GNU Lesser General Public License as published
diff --git a/src/main/java/org/biojava/nbio/adam/UnmodifiableCollectionsSerializer.java b/src/main/java/org/biojava/nbio/adam/UnmodifiableCollectionsSerializer.java
@@ -1,7 +1,7 @@
 /*
 
     biojava-adam  Biojava and ADAM integration.
-    Copyright (c) 2017-2019 held jointly by the individual authors.
+    Copyright (c) 2017-2020 held jointly by the individual authors.
 
     This library is free software; you can redistribute it and/or modify it
     under the terms of the GNU Lesser General Public License as published
diff --git a/src/main/java/org/biojava/nbio/adam/convert/BiojavaModule.java b/src/main/java/org/biojava/nbio/adam/convert/BiojavaModule.java
@@ -1,7 +1,7 @@
 /*
 
     biojava-adam  Biojava and ADAM integration.
-    Copyright (c) 2017-2019 held jointly by the individual authors.
+    Copyright (c) 2017-2020 held jointly by the individual authors.
 
     This library is free software; you can redistribute it and/or modify it
     under the terms of the GNU Lesser General Public License as published
diff --git a/src/main/java/org/biojava/nbio/adam/convert/BiojavaStrandToBdgenomicsStrand.java b/src/main/java/org/biojava/nbio/adam/convert/BiojavaStrandToBdgenomicsStrand.java
@@ -1,7 +1,7 @@
 /*
 
     biojava-adam  Biojava and ADAM integration.
-    Copyright (c) 2017-2019 held jointly by the individual authors.
+    Copyright (c) 2017-2020 held jointly by the individual authors.
 
     This library is free software; you can redistribute it and/or modify it
     under the terms of the GNU Lesser General Public License as published
diff --git a/src/main/java/org/biojava/nbio/adam/convert/ConvertUtils.java b/src/main/java/org/biojava/nbio/adam/convert/ConvertUtils.java
@@ -1,7 +1,7 @@
 /*
 
     biojava-adam  Biojava and ADAM integration.
-    Copyright (c) 2017-2019 held jointly by the individual authors.
+    Copyright (c) 2017-2020 held jointly by the individual authors.
 
     This library is free software; you can redistribute it and/or modify it
     under the terms of the GNU Lesser General Public License as published
diff --git a/src/main/java/org/biojava/nbio/adam/convert/DnaSequenceToFeatures.java b/src/main/java/org/biojava/nbio/adam/convert/DnaSequenceToFeatures.java
@@ -1,7 +1,7 @@
 /*
 
     biojava-adam  Biojava and ADAM integration.
-    Copyright (c) 2017-2019 held jointly by the individual authors.
+    Copyright (c) 2017-2020 held jointly by the individual authors.
 
     This library is free software; you can redistribute it and/or modify it
     under the terms of the GNU Lesser General Public License as published
diff --git a/src/main/java/org/biojava/nbio/adam/convert/DnaSequenceToSequence.java b/src/main/java/org/biojava/nbio/adam/convert/DnaSequenceToSequence.java
@@ -1,7 +1,7 @@
 /*
 
     biojava-adam  Biojava and ADAM integration.
-    Copyright (c) 2017-2019 held jointly by the individual authors.
+    Copyright (c) 2017-2020 held jointly by the individual authors.
 
     This library is free software; you can redistribute it and/or modify it
     under the terms of the GNU Lesser General Public License as published
diff --git a/src/main/java/org/biojava/nbio/adam/convert/FastqToRead.java b/src/main/java/org/biojava/nbio/adam/convert/FastqToRead.java
@@ -1,7 +1,7 @@
 /*
 
     biojava-adam  Biojava and ADAM integration.
-    Copyright (c) 2017-2019 held jointly by the individual authors.
+    Copyright (c) 2017-2020 held jointly by the individual authors.
 
     This library is free software; you can redistribute it and/or modify it
     under the terms of the GNU Lesser General Public License as published
diff --git a/src/main/java/org/biojava/nbio/adam/convert/ProteinSequenceToFeatures.java b/src/main/java/org/biojava/nbio/adam/convert/ProteinSequenceToFeatures.java
@@ -1,7 +1,7 @@
 /*
 
     biojava-adam  Biojava and ADAM integration.
-    Copyright (c) 2017-2019 held jointly by the individual authors.
+    Copyright (c) 2017-2020 held jointly by the individual authors.
 
     This library is free software; you can redistribute it and/or modify it
     under the terms of the GNU Lesser General Public License as published
diff --git a/src/main/java/org/biojava/nbio/adam/convert/ProteinSequenceToSequence.java b/src/main/java/org/biojava/nbio/adam/convert/ProteinSequenceToSequence.java
@@ -1,7 +1,7 @@
 /*
 
     biojava-adam  Biojava and ADAM integration.
-    Copyright (c) 2017-2019 held jointly by the individual authors.
+    Copyright (c) 2017-2020 held jointly by the individual authors.
 
     This library is free software; you can redistribute it and/or modify it
     under the terms of the GNU Lesser General Public License as published
diff --git a/src/main/java/org/biojava/nbio/adam/convert/ReadToFastq.java b/src/main/java/org/biojava/nbio/adam/convert/ReadToFastq.java
@@ -1,7 +1,7 @@
 /*
 
     biojava-adam  Biojava and ADAM integration.
-    Copyright (c) 2017-2019 held jointly by the individual authors.
+    Copyright (c) 2017-2020 held jointly by the individual authors.
 
     This library is free software; you can redistribute it and/or modify it
     under the terms of the GNU Lesser General Public License as published
diff --git a/src/main/java/org/biojava/nbio/adam/convert/RnaSequenceToFeatures.java b/src/main/java/org/biojava/nbio/adam/convert/RnaSequenceToFeatures.java
@@ -1,7 +1,7 @@
 /*
 
     biojava-adam  Biojava and ADAM integration.
-    Copyright (c) 2017-2019 held jointly by the individual authors.
+    Copyright (c) 2017-2020 held jointly by the individual authors.
 
     This library is free software; you can redistribute it and/or modify it
     under the terms of the GNU Lesser General Public License as published
diff --git a/src/main/java/org/biojava/nbio/adam/convert/RnaSequenceToSequence.java b/src/main/java/org/biojava/nbio/adam/convert/RnaSequenceToSequence.java
@@ -1,7 +1,7 @@
 /*
 
     biojava-adam  Biojava and ADAM integration.
-    Copyright (c) 2017-2019 held jointly by the individual authors.
+    Copyright (c) 2017-2020 held jointly by the individual authors.
 
     This library is free software; you can redistribute it and/or modify it
     under the terms of the GNU Lesser General Public License as published
diff --git a/src/main/java/org/biojava/nbio/adam/convert/package-info.java b/src/main/java/org/biojava/nbio/adam/convert/package-info.java
@@ -1,7 +1,7 @@
 /*
 
     biojava-adam  Biojava and ADAM integration.
-    Copyright (c) 2017-2019 held jointly by the individual authors.
+    Copyright (c) 2017-2020 held jointly by the individual authors.
 
     This library is free software; you can redistribute it and/or modify it
     under the terms of the GNU Lesser General Public License as published
diff --git a/src/main/java/org/biojava/nbio/adam/package-info.java b/src/main/java/org/biojava/nbio/adam/package-info.java
@@ -1,7 +1,7 @@
 /*
 
     biojava-adam  Biojava and ADAM integration.
-    Copyright (c) 2017-2019 held jointly by the individual authors.
+    Copyright (c) 2017-2020 held jointly by the individual authors.
 
     This library is free software; you can redistribute it and/or modify it
     under the terms of the GNU Lesser General Public License as published
diff --git a/src/main/scala/org/biojava/nbio/adam/BiojavaAdamContext.scala b/src/main/scala/org/biojava/nbio/adam/BiojavaAdamContext.scala
diff --git a/src/main/scala/org/biojava/nbio/adam/TryWith.scala b/src/main/scala/org/biojava/nbio/adam/TryWith.scala
diff --git a/src/test/java/org/biojava/nbio/adam/convert/BiojavaModuleTest.java b/src/test/java/org/biojava/nbio/adam/convert/BiojavaModuleTest.java
diff --git a/src/test/java/org/biojava/nbio/adam/convert/BiojavaStrandToBdgenomicsStrandTest.java b/src/test/java/org/biojava/nbio/adam/convert/BiojavaStrandToBdgenomicsStrandTest.java
diff --git a/src/test/java/org/biojava/nbio/adam/convert/FastqToReadTest.java b/src/test/java/org/biojava/nbio/adam/convert/FastqToReadTest.java
diff --git a/src/test/java/org/biojava/nbio/adam/convert/ReadToFastqTest.java b/src/test/java/org/biojava/nbio/adam/convert/ReadToFastqTest.java
