upgrade parent plugin

build.sbt

@@ -1,53 +1,41 @@
 organization := "org.hammerlab.adam"
 
-name := ParentPlugin.sparkName("adam-core")
+name := sparkName("adam-core")
 
 version := "0.20.4-SNAPSHOT"
 
-val utilsVersion = "0.2.10"
-
 hadoopVersion := "2.7.3"
 
 scalatestVersion := "2.2.1"
 
 addSparkDeps
+publishTestJar
+enableScalariform
 
 // Using ":=" here to clobber the usual default hammerlab-test-libs that are added by parent-plugin, which use
 // Scalatest 3.0.0.
 testDeps := Seq(
-  "org.bdgenomics.utils" %% "utils-misc" % utilsVersion classifier("tests") exclude("org.apache.spark", "*"),
   "org.mockito" % "mockito-core" % "1.10.19"
 )
 
+testJarTestDeps += (libraries.value('bdg_utils_misc) exclude("org.apache.spark", "*"))
+
 libraryDependencies ++= Seq(
   libraries.value('bdg_formats),
-  libraries.value('hadoop_bam) exclude("com.github.samtools", "htsjdk"),
-  "org.bdgenomics.utils" %% "utils-metrics" % utilsVersion,
-  "org.bdgenomics.utils" %% "utils-misc" % utilsVersion,
-  "org.bdgenomics.utils" %% "utils-io" % utilsVersion exclude("com.fasterxml.jackson.core", "*"),
-  "org.bdgenomics.utils" %% "utils-cli" % utilsVersion,
-  "org.bdgenomics.utils" %% "utils-intervalrdd" % utilsVersion,
+  libraries.value('bdg_utils_cli),
+  libraries.value('bdg_utils_intervalrdd),
+  libraries.value('bdg_utils_io),
+  libraries.value('bdg_utils_metrics),
+  libraries.value('bdg_utils_misc),
   libraries.value('commons_io),
+  libraries.value('hadoop_bam) exclude("com.github.samtools", "htsjdk"),
+  libraries.value('log4j),
+  "com.github.samtools" % "htsjdk" % "2.5.0",
+  "com.netflix.servo" % "servo-core" % "0.10.0",
   "it.unimi.dsi" % "fastutil" % "6.6.5",
   "org.apache.avro" % "avro" % "1.8.0",
-  "org.slf4j" % "slf4j-log4j12" % "1.7.21",
+  "org.apache.httpcomponents" % "httpclient" % "4.5.2",
   "org.apache.parquet" % "parquet-avro" % "1.8.1",
   "org.apache.parquet" % "parquet-scala_2.10" % "1.8.1" exclude("org.scala-lang", "scala-library"),
-  "com.github.samtools" % "htsjdk" % "2.5.0",
-  "org.apache.httpcomponents" % "httpclient" % "4.5.2",
-  "com.netflix.servo" % "servo-core" % "0.10.0",
-  libraries.value('loci) exclude("com.github.samtools", "htsjdk")
+  "org.hammerlab" %% "genomic-loci" % "1.4.4" exclude("com.github.samtools", "htsjdk")
 )
-
-import scalariform.formatter.preferences._
-import com.typesafe.sbt.SbtScalariform
-import com.typesafe.sbt.SbtScalariform.ScalariformKeys
-
-SbtScalariform.defaultScalariformSettings
-
-ScalariformKeys.preferences := ScalariformKeys.preferences.value
-                               .setPreference(AlignParameters, true)
-                               .setPreference(CompactStringConcatenation, false)
-                               .setPreference(AlignSingleLineCaseStatements, true)
-                               .setPreference(DoubleIndentClassDeclaration, true)
-                               .setPreference(PreserveDanglingCloseParenthesis, true)

project/plugins.sbt

@@ -1,2 +1 @@
-addSbtPlugin("org.hammerlab" % "sbt-parent" % "1.3.5-SNAPSHOT")
-addSbtPlugin("com.typesafe.sbt" % "sbt-scalariform" % "1.3.0")
+addSbtPlugin("org.hammerlab" % "sbt-parent" % "1.4.0")

src/main/scala/org/bdgenomics/adam/serialization/ADAMKryoRegistrator.scala

@@ -23,7 +23,7 @@ import it.unimi.dsi.fastutil.io.{ FastByteArrayInputStream, FastByteArrayOutputS
 import org.apache.avro.io.{ BinaryDecoder, BinaryEncoder, DecoderFactory, EncoderFactory }
 import org.apache.avro.specific.{ SpecificDatumReader, SpecificDatumWriter, SpecificRecord }
 import org.apache.spark.serializer.KryoRegistrator
-import org.hammerlab.genomics.loci.kryo.Registrar
+import org.hammerlab.genomics.kryo.Registrar
 
 import scala.reflect.ClassTag