fix some deprecation/style things and rename a pkg

fixes bigdatagenomics#984 and some of bigdatagenomics#985
ryan-williams · Mar 28, 2016 · 33eb79f · 33eb79f
1 parent 2e843de
commit 33eb79f
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Showing 4 changed files with 12 additions and 12 deletions.
diff --git a/.../src/main/scala/org/bdgenomics/adam/rdd/contig/NucleotideContigFragmentRDDFunctions.scala b/.../src/main/scala/org/bdgenomics/adam/rdd/contig/NucleotideContigFragmentRDDFunctions.scala
@@ -46,7 +46,7 @@ class NucleotideContigFragmentRDDFunctions(rdd: RDD[NucleotideContigFragment]) e
    *
    * @return Returns an RDD of reads.
    */
-  def toReads(): RDD[AlignmentRecord] = {
+  def toReads: RDD[AlignmentRecord] = {
     FragmentConverter.convertRdd(rdd)
   }
 
@@ -59,18 +59,18 @@ class NucleotideContigFragmentRDDFunctions(rdd: RDD[NucleotideContigFragment]) e
   def saveAsFasta(fileName: String, lineWidth: Int = 60) = {
 
     def isFragment(record: NucleotideContigFragment): Boolean = {
-      Option(record.fragmentNumber).isDefined && Option(record.numberOfFragmentsInContig).fold(false)(_ > 1)
+      Option(record.getFragmentNumber).isDefined && Option(record.getNumberOfFragmentsInContig).fold(false)(_ > 1)
     }
 
     def toFasta(record: NucleotideContigFragment): String = {
       val sb = new StringBuilder()
       sb.append(">")
-      sb.append(record.contig.contigName)
-      Option(record.description).foreach(n => sb.append(" ").append(n))
+      sb.append(record.getContig.getContigName)
+      Option(record.getDescription).foreach(n => sb.append(" ").append(n))
       if (isFragment(record)) {
-        sb.append(" fragment %d of %d".format(record.fragmentNumber + 1, record.numberOfFragmentsInContig))
+        sb.append(s" fragment ${record.getFragmentNumber + 1} of ${record.getNumberOfFragmentsInContig}")
       }
-      for (line <- Splitter.fixedLength(lineWidth).split(record.fragmentSequence)) {
+      for (line <- Splitter.fixedLength(lineWidth).split(record.getFragmentSequence)) {
         sb.append("\n")
         sb.append(line)
       }
@@ -90,15 +90,15 @@ class NucleotideContigFragmentRDDFunctions(rdd: RDD[NucleotideContigFragment]) e
         .setFragmentNumber(null)
         .setFragmentStartPosition(null)
         .setNumberOfFragmentsInContig(null)
-        .setFragmentSequence(first.fragmentSequence + second.fragmentSequence)
+        .setFragmentSequence(first.getFragmentSequence + second.getFragmentSequence)
         .build
 
       merged
     }
 
     rdd
-      .sortBy(fragment => (fragment.contig.contigName, Option(fragment.fragmentNumber).map(_.toInt).getOrElse(-1)))
-      .map(fragment => (fragment.contig.contigName, fragment))
+      .sortBy(fragment => (fragment.getContig.getContigName, Option(fragment.getFragmentNumber).map(_.toInt).getOrElse(-1)))
+      .map(fragment => (fragment.getContig.getContigName, fragment))
       .reduceByKey(merge)
       .values
   }

diff --git a/.../rdd/fragments/FragmentRDDFunctions.scala → ...m/rdd/fragment/FragmentRDDFunctions.scala b/.../rdd/fragments/FragmentRDDFunctions.scala → ...m/rdd/fragment/FragmentRDDFunctions.scala
diff --git a/adam-core/src/main/scala/org/bdgenomics/adam/rdd/variation/VariationRDDFunctions.scala b/adam-core/src/main/scala/org/bdgenomics/adam/rdd/variation/VariationRDDFunctions.scala
@@ -51,7 +51,7 @@ class VariantContextRDDFunctions(rdd: RDD[VariantContext]) extends ADAMSequenceD
 
   }
 
-  def getCallsetSamples(): List[String] = {
+  def getCallsetSamples: List[String] = {
     rdd.flatMap(c => c.genotypes.map(_.getSampleId).toSeq.distinct)
       .distinct
       .collect()
@@ -80,7 +80,7 @@ class VariantContextRDDFunctions(rdd: RDD[VariantContext]) extends ADAMSequenceD
     log.info(s"Writing $vcfFormat file to $filePath")
 
     // Initialize global header object required by Hadoop VCF Writer
-    val header = getCallsetSamples()
+    val header = getCallsetSamples
     val bcastHeader = rdd.context.broadcast(header)
     val mp = rdd.mapPartitionsWithIndex((idx, iter) => {
       log.info(s"Setting header for partition $idx")

diff --git a/adam-core/src/test/scala/org/bdgenomics/adam/rdd/variation/VariationRDDFunctionsSuite.scala b/adam-core/src/test/scala/org/bdgenomics/adam/rdd/variation/VariationRDDFunctionsSuite.scala
@@ -50,7 +50,7 @@ class ADAMVariationRDDFunctionsSuite extends ADAMFunSuite {
       .build()
 
     val vc = VariantContext.buildFromGenotypes(List(genotype0, genotype1))
-    val samples = sc.parallelize(List(vc)).getCallsetSamples()
+    val samples = sc.parallelize(List(vc)).getCallsetSamples
 
     assert(samples.count(_ == "you") === 1)
     assert(samples.count(_ == "me") === 1)