hadoop-bam cleanup cont.

biodatageeks · Sep 22, 2014 · c9b497a · c9b497a
1 parent de093f3
commit c9b497a
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Showing 3 changed files with 5 additions and 4 deletions.
diff --git a/sparkseq-core/lib/hadoop-bam-6.1.jar b/sparkseq-core/lib/hadoop-bam-6.1.jar
diff --git a/sparkseq-core/src/main/scala/pl/elka/pw/sparkseq/SparkSeqDERFinder.scala b/sparkseq-core/src/main/scala/pl/elka/pw/sparkseq/SparkSeqDERFinder.scala
@@ -29,7 +29,8 @@ import org.apache.spark.SparkContext
 import org.apache.spark.SparkContext._
 import collection.mutable.ArrayBuffer
 import org.apache.hadoop.io.LongWritable
-import fi.tkk.ics.hadoop.bam.{BAMInputFormat, SAMRecordWritable}
+import org.seqdoop.hadoop_bam.BAMInputFormat
+import org.seqdoop.hadoop_bam.SAMRecordWritable
 import pl.elka.pw.sparkseq.conversions.SparkSeqConversions
 import pl.elka.pw.sparkseq.util.SparkSeqContexProperties
 import scala.util.control._

diff --git a/sparkseq-core/src/main/scala/pl/elka/pw/sparkseq/serialization/SparkSeqKryoRegistrator.scala b/sparkseq-core/src/main/scala/pl/elka/pw/sparkseq/serialization/SparkSeqKryoRegistrator.scala
@@ -26,13 +26,13 @@ class SparkSeqKryoRegistrator extends org.apache.spark.serializer.KryoRegistrato
    * @param kryo
    */
   override def registerClasses(kryo: Kryo) {
-    kryo.register(classOf[fi.tkk.ics.hadoop.bam.SAMRecordWritable])
+    kryo.register(classOf[org.seqdoop.hadoop_bam.SAMRecordWritable])
     kryo.register(classOf[htsjdk.samtools.Cigar])
-    kryo.register(classOf[fi.tkk.ics.hadoop.bam.BAMInputFormat])
+    kryo.register(classOf[org.seqdoop.hadoop_bam.BAMInputFormat])
     kryo.register(classOf[org.apache.hadoop.io.LongWritable])
     kryo.register(classOf[htsjdk.samtools.BAMRecord])
     //kryo.register(classOf[pl.elka.pw.sparkseq.differentialExpression.SparkSeqDiffExpr])
     //kryo.register(classOf[scala.collection.Traversable[_]], new ScalaCollectionSerializer(kryo))
     //kryo.register(classOf[scala.Product], new ScalaProductSerializer(kryo))
    }
-}
+}