Fix compile errors due to upstream commit 0afbda96.

bigdatagenomics · Jul 13, 2017 · 560789a · 560789a
1 parent 7a098f6
commit 560789a
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Showing 3 changed files with 14 additions and 5 deletions.
diff --git a/pom.xml b/pom.xml
@@ -360,6 +360,11 @@
           </exclusion>
         </exclusions>
       </dependency>
+      <dependency>
+        <groupId>org.apache.spark</groupId>
+        <artifactId>spark-sql_${scala.version.prefix}</artifactId>
+        <version>${spark.version}</version>
+      </dependency>
       <dependency>
         <groupId>org.scalatest</groupId>
         <artifactId>scalatest_${scala.version.prefix}</artifactId>
@@ -373,6 +378,11 @@
       <artifactId>spark-core_${scala.version.prefix}</artifactId>
       <scope>provided</scope>
     </dependency>
+    <dependency>
+      <groupId>org.apache.spark</groupId>
+      <artifactId>spark-sql_${scala.version.prefix}</artifactId>
+      <scope>provided</scope>
+    </dependency>
     <dependency>
       <groupId>org.bdgenomics.adam</groupId>
       <artifactId>adam-cli_${scala.version.prefix}</artifactId>

diff --git a/src/main/scala/org/bdgenomics/cannoli/Bwa.scala b/src/main/scala/org/bdgenomics/cannoli/Bwa.scala
@@ -196,11 +196,11 @@ class Bwa(protected val args: BwaArgs) extends BDGSparkCommand[BwaArgs] with Log
     }
 
     val output: AlignmentRecordRDD = input.pipe[AlignmentRecord, AlignmentRecordRDD, InterleavedFASTQInFormatter](bwaCommand)
-      .copy(recordGroups = RecordGroupDictionary(Seq(RecordGroup(sample, sample))))
+      .replaceRecordGroups(RecordGroupDictionary(Seq(RecordGroup(sample, sample))))
 
     val outputMaybeWithSequences = Option(args.sequenceDictionary).fold(output)(sdPath => {
       val sequences = SequenceDictionaryReader(sdPath, sc)
-      output.copy(sequences = sequences)
+      output.replaceSequences(sequences)
     })
 
     if (!args.asFragments) {

diff --git a/src/main/scala/org/bdgenomics/cannoli/util/QuerynameGrouper.scala b/src/main/scala/org/bdgenomics/cannoli/util/QuerynameGrouper.scala
@@ -29,9 +29,8 @@ private[cannoli] object QuerynameGrouper extends Serializable {
   }
 
   def apply(rdd: AlignmentRecordRDD): FragmentRDD = {
-    new FragmentRDD(apply(rdd.rdd),
+    FragmentRDD(apply(rdd.rdd),
       rdd.sequences,
-      rdd.recordGroups,
-      optPartitionMap = None)
+      rdd.recordGroups)
   }
 }