Address review comments.

bigdatagenomics · Jun 14, 2017 · c6af112 · c6af112
1 parent 540e83e
commit c6af112
Showing 1 changed file with 4 additions and 5 deletions.
diff --git a/adam-core/src/main/scala/org/bdgenomics/adam/rdd/ADAMContext.scala b/adam-core/src/main/scala/org/bdgenomics/adam/rdd/ADAMContext.scala
@@ -44,7 +44,6 @@ import org.apache.spark.rdd.MetricsContext._
 import org.apache.spark.rdd.RDD
 import org.apache.spark.storage.StorageLevel
 import org.bdgenomics.adam.converters._
-import org.bdgenomics.adam.converters.VariantContextConverter._
 import org.bdgenomics.adam.instrumentation.Timers._
 import org.bdgenomics.adam.io._
 import org.bdgenomics.adam.models._
@@ -219,7 +218,7 @@ class ADAMContext(@transient val sc: SparkContext) extends Serializable with Log
  .setSampleId(s)
  .build()
  }).toSeq
- (sd, samples, headerLines(vcfHeader))
+ (sd, samples, VariantContextConverter.headerLines(vcfHeader))
  }
 
  headerToMetadata(readVcfHeader(pathName))
@@ -232,7 +231,7 @@ class ADAMContext(@transient val sc: SparkContext) extends Serializable with Log
 
  private def loadHeaderLines(pathName: String): Seq[VCFHeaderLine] = {
  getFsAndFilesWithFilter(pathName, new FileFilter("_header"))
- .map(p => headerLines(readVcfHeader(p.toString)))
+ .map(p => VariantContextConverter.headerLines(readVcfHeader(p.toString)))
  .flatten
  .distinct
  }
@@ -1073,7 +1072,7 @@ class ADAMContext(@transient val sc: SparkContext) extends Serializable with Log
  VariantContextRDD(records.flatMap(p => vcc.convert(p._2.get)),
  sd,
  samples,
- cleanAndMixInSupportedLines(headers, stringency, log))
+ VariantContextConverter.cleanAndMixInSupportedLines(headers, stringency, log))
  }
 
  /**
@@ -1119,7 +1118,7 @@ class ADAMContext(@transient val sc: SparkContext) extends Serializable with Log
  VariantContextRDD(records.flatMap(p => vcc.convert(p._2.get)),
  sd,
  samples,
- cleanAndMixInSupportedLines(headers, stringency, log))
+ VariantContextConverter.cleanAndMixInSupportedLines(headers, stringency, log))
  }
 
  /**