Update avro dependency version to 1.10.1, parquet to 1.11.1, spark to 3.2.0-SNAPSHOT

Author: heuermh

adam-assembly/pom.xml

@@ -39,13 +39,6 @@
       <plugin>
         <groupId>org.apache.maven.plugins</groupId>
         <artifactId>maven-shade-plugin</artifactId>
-        <dependencies>
-          <dependency>
-            <groupId>org.bdgenomics.adam</groupId>
-            <artifactId>adam-shade-spark3_${scala.version.prefix}</artifactId>
-            <version>${project.version}</version>
-          </dependency>
-        </dependencies>
         <configuration>
           <createDependencyReducedPom>false</createDependencyReducedPom>
           <filters>
@@ -58,12 +51,6 @@
               </excludes>
             </filter>
           </filters>
-          <relocations>
-            <relocation>
-              <pattern>org.apache.parquet.avro</pattern>
-              <shadedPattern>org.bdgenomics.adam.shaded.org.apache.parquet.avro</shadedPattern>
-            </relocation>
-          </relocations>
         </configuration>
         <executions>
           <execution>
@@ -72,7 +59,6 @@
               <goal>shade</goal>
             </goals>
             <configuration>
-              <shaderHint>workaround</shaderHint>
               <transformers>
                 <transformer implementation="org.apache.maven.plugins.shade.resource.ServicesResourceTransformer" />
               </transformers>

adam-cli/src/main/scala/org/bdgenomics/adam/cli/PrintADAM.scala

@@ -83,9 +83,6 @@ class PrintADAM(protected val args: PrintADAMArgs) extends BDGSparkCommand[Print
               val schema = hd.getSchema
               val writer = new GenericDatumWriter[Object](schema)
               val encoder = EncoderFactory.get().jsonEncoder(schema, out)
-              val jg = new org.codehaus.jackson.JsonFactory().createJsonGenerator(out)
-              jg.useDefaultPrettyPrinter()
-              encoder.configure(jg)
               it.foreach(pileup => {
                 writer.write(pileup, encoder)
               })