Check in the scalariform formatted source

adam-cli/src/main/scala/org/bdgenomics/adam/cli/ADAMMain.scala

@@ -65,7 +65,7 @@ object ADAMMain extends Logging {
  printCommands()
  } else {
  commands.find(_.commandName == args(0)) match {
- case None => printCommands()
+ case None  => printCommands()
  case Some(cmd) => cmd.apply(args drop 1).run()
  }
  }

adam-cli/src/main/scala/org/bdgenomics/adam/cli/CompareADAM.scala

@@ -68,11 +68,11 @@ object CompareADAM extends ADAMCommandCompanion with Serializable {
  * @see CompareADAMArgs.recurse1, CompareADAMArgs.recurse2
  */
  def setupTraversalEngine(sc: SparkContext,
- input1Path: String,
- recurse1: String,
- input2Path: String,
- recurse2: String,
- generator: BucketComparisons[Any]): ComparisonTraversalEngine = {
+  input1Path: String,
+  recurse1: String,
+  input2Path: String,
+  recurse2: String,
+  generator: BucketComparisons[Any]): ComparisonTraversalEngine = {
 
  val schemas = Seq[FieldValue](
  recordGroupId,
@@ -88,7 +88,7 @@ object CompareADAM extends ADAMCommandCompanion with Serializable {
  def parseGenerators(nameList: String): Seq[BucketComparisons[Any]] = {
  nameList match {
  case null => DefaultComparisons.comparisons
- case s => parseGenerators(s.split(","))
+ case s  => parseGenerators(s.split(","))
  }
  }
 
@@ -146,9 +146,9 @@ class CompareADAM(protected val args: CompareADAMArgs) extends ADAMSparkCommand[
  * @param writer The PrintWriter to print the summary with.
  */
  def printSummary(engine: ComparisonTraversalEngine,
- generators: Seq[BucketComparisons[Any]],
- aggregateds: Seq[Histogram[Any]],
- writer: PrintWriter) {
+  generators: Seq[BucketComparisons[Any]],
+  aggregateds: Seq[Histogram[Any]],
+  writer: PrintWriter) {
 
  writer.println("%15s: %s".format("INPUT1", args.input1Path))
  writer.println("\t%15s: %d".format("total-reads", engine.named1.count()))

adam-cli/src/main/scala/org/bdgenomics/adam/cli/MpileupCommand.scala

@@ -57,7 +57,7 @@ class MpileupCommand(protected val args: MpileupArgs) extends ADAMSparkCommand[M
  // The reference base
  pileup.referenceBase match {
  case Some(base) => print(base)
- case None => print("?")
+ case None  => print("?")
  }
 
  // The number of reads

adam-cli/src/main/scala/org/bdgenomics/adam/cli/PileupAggregator.scala

@@ -43,7 +43,7 @@ class PileupAggregatorArgs extends Args4jBase with SparkArgs with ParquetArgs {
 }
 
 class PileupAggregator(protected val args: PileupAggregatorArgs)
- extends ADAMSparkCommand[PileupAggregatorArgs] {
+  extends ADAMSparkCommand[PileupAggregatorArgs] {
 
  val companion = PileupAggregator
 

adam-cli/src/main/scala/org/bdgenomics/adam/cli/PluginExecutor.scala

@@ -95,19 +95,19 @@ class PluginExecutor(protected val args: PluginExecutorArgs) extends ADAMSparkCo
  // see. This is related to Issue #62: Predicate to filter conversion.
  val filter = accessControl.predicate match {
  case None => plugin.predicate match {
- case None => None
+ case None  => None
  case Some(predicateFilter) => Some(predicateFilter)
  }
  case Some(accessControlPredicate) => plugin.predicate match {
- case None => Some(accessControlPredicate)
+ case None  => Some(accessControlPredicate)
  case Some(predicateFilter) => Some((value: ADAMRecord) => accessControlPredicate(value) && predicateFilter(value))
  }
  }
 
  val firstRdd: RDD[ADAMRecord] = load[ADAMRecord](sc, args.input, plugin.projection)
 
  val input = filter match {
- case None => firstRdd
+ case None  => firstRdd
  case Some(filterFunc) => firstRdd.filter(filterFunc)
  }
 

adam-cli/src/main/scala/org/bdgenomics/adam/cli/SummarizeGenotypes.scala

@@ -56,8 +56,8 @@ class SummarizeGenotypes(val args: SummarizeGenotypesArgs) extends ADAMSparkComm
  val stats = GenotypesSummary(adamGTs)
  val result = args.format match {
  case "human" => GenotypesSummaryFormatting.format_human_readable(stats)
- case "csv" => GenotypesSummaryFormatting.format_csv(stats)
- case _ => throw new IllegalArgumentException("Invalid -format: %s".format(args.format))
+ case "csv"  => GenotypesSummaryFormatting.format_csv(stats)
+ case _  => throw new IllegalArgumentException("Invalid -format: %s".format(args.format))
  }
  if (args.out.isEmpty) {
  println(result)

adam-core/src/main/scala/org/bdgenomics/adam/algorithms/smithwaterman/SmithWatermanConstantGapScoring.scala

@@ -33,10 +33,10 @@ object SmithWatermanConstantGapScoring {
 }
 
 abstract class SmithWatermanConstantGapScoring(xSequence: String,
- ySequence: String,
- wMatch: Double,
- wMismatch: Double,
- wInsert: Double,
- wDelete: Double)
- extends SmithWatermanGapScoringFromFn(xSequence, ySequence, SmithWatermanConstantGapScoring.constantGapFn(wMatch, wMismatch, wInsert, wDelete)) {
+  ySequence: String,
+  wMatch: Double,
+  wMismatch: Double,
+  wInsert: Double,
+  wDelete: Double)
+  extends SmithWatermanGapScoringFromFn(xSequence, ySequence, SmithWatermanConstantGapScoring.constantGapFn(wMatch, wMismatch, wInsert, wDelete)) {
 }

adam-core/src/main/scala/org/bdgenomics/adam/algorithms/smithwaterman/SmithWatermanGapScoringFromFn.scala

@@ -17,9 +17,9 @@
 package org.bdgenomics.adam.algorithms.smithwaterman
 
 abstract class SmithWatermanGapScoringFromFn(xSequence: String,
- ySequence: String,
- scoreFn: (Int, Int, Char, Char) => Double)
- extends SmithWaterman(xSequence, ySequence) {
+  ySequence: String,
+  scoreFn: (Int, Int, Char, Char) => Double)
+  extends SmithWaterman(xSequence, ySequence) {
 
  def buildScoringMatrix(): Array[Array[Double]] = {
 

adam-core/src/main/scala/org/bdgenomics/adam/converters/FastaConverter.scala

@@ -43,7 +43,7 @@ private[adam] object FastaConverter {
  * @return An RDD of ADAM FASTA data.
  */
  def apply(rdd: RDD[(Int, String)],
- maxFragmentLength: Long = 10000L): RDD[ADAMNucleotideContigFragment] = {
+  maxFragmentLength: Long = 10000L): RDD[ADAMNucleotideContigFragment] = {
  val filtered = rdd.map(kv => (kv._1, kv._2.trim()))
  .filter((kv: (Int, String)) => !kv._2.startsWith(";"))
 
@@ -164,9 +164,9 @@ private[converters] class FastaConverter(fragmentLength: Long) extends Serializa
  * @return The converted ADAM FASTA contig.
  */
  def convert(name: Option[String],
- id: Int,
- sequence: Seq[String],
- description: Option[String]): Seq[ADAMNucleotideContigFragment] = {
+  id: Int,
+  sequence: Seq[String],
+  description: Option[String]): Seq[ADAMNucleotideContigFragment] = {
 
  // get sequence length
  val sequenceLength = sequence.map(_.length).reduce(_ + _)

adam-core/src/main/scala/org/bdgenomics/adam/converters/GenotypesToVariantsConverter.scala

@@ -19,7 +19,7 @@ import org.bdgenomics.adam.util._
 import scala.math.{ pow, sqrt }
 
 private[adam] class GenotypesToVariantsConverter(validateSamples: Boolean = false,
- failOnValidationError: Boolean = false) extends Serializable {
+  failOnValidationError: Boolean = false) extends Serializable {
 
  /**
  * Computes root mean squared (RMS) values for a series of doubles.

adam-core/src/main/scala/org/bdgenomics/adam/converters/SAMRecordConverter.scala

@@ -124,7 +124,7 @@ class SAMRecordConverter extends Serializable {
  if (recordGroup != null) {
  Option(recordGroup.getRunDate) match {
  case Some(date) => builder.setRecordGroupRunDateEpoch(date.getTime)
- case None =>
+ case None  =>
  }
  recordGroup.getId
  builder.setRecordGroupId(readGroups(recordGroup.getReadGroupId))

adam-core/src/main/scala/org/bdgenomics/adam/converters/VariantAnnotationConverter.scala

@@ -26,18 +26,18 @@ import org.bdgenomics.adam.util.ImplicitJavaConversions._
 object VariantAnnotationConverter extends Serializable {
 
  private def attrAsInt(attr: Object): Object = attr match {
- case a: String => java.lang.Integer.valueOf(a)
+ case a: String  => java.lang.Integer.valueOf(a)
  case a: java.lang.Integer => a
- case a: java.lang.Number => java.lang.Integer.valueOf(a.intValue)
+ case a: java.lang.Number  => java.lang.Integer.valueOf(a.intValue)
  }
  private def attrAsLong(attr: Object): Object = attr match {
- case a: String => java.lang.Long.valueOf(a)
- case a: java.lang.Long => a
+ case a: String  => java.lang.Long.valueOf(a)
+ case a: java.lang.Long  => a
  case a: java.lang.Number => java.lang.Long.valueOf(a.longValue)
  }
  private def attrAsFloat(attr: Object): Object = attr match {
- case a: String => java.lang.Float.valueOf(a)
- case a: java.lang.Float => a
+ case a: String  => java.lang.Float.valueOf(a)
+ case a: java.lang.Float  => a
  case a: java.lang.Number => java.lang.Float.valueOf(a.floatValue)
  }
  private def attrAsString(attr: Object): Object = attr match {
@@ -46,7 +46,7 @@ object VariantAnnotationConverter extends Serializable {
 
  private def attrAsBoolean(attr: Object): Object = attr match {
  case a: java.lang.Boolean => a
- case a: String => java.lang.Boolean.valueOf(a)
+ case a: String  => java.lang.Boolean.valueOf(a)
  }
 
  private case class AttrKey(adamKey: String, attrConverter: (Object => Object), hdrLine: VCFCompoundHeaderLine) {

adam-core/src/main/scala/org/bdgenomics/adam/converters/VariantContextConverter.scala

@@ -48,8 +48,8 @@ object VariantContextConverter {
  private def convertAlleles(g: ADAMGenotype): java.util.List[Allele] = {
  g.getAlleles.map(a => a match {
  case ADAMGenotypeAllele.NoCall => Allele.NO_CALL
- case ADAMGenotypeAllele.Ref => Allele.create(g.getVariant.getReferenceAllele.toString, true)
- case ADAMGenotypeAllele.Alt => Allele.create(g.getVariant.getVariantAllele.toString)
+ case ADAMGenotypeAllele.Ref  => Allele.create(g.getVariant.getReferenceAllele.toString, true)
+ case ADAMGenotypeAllele.Alt  => Allele.create(g.getVariant.getVariantAllele.toString)
  })
  }
 }

adam-core/src/main/scala/org/bdgenomics/adam/metrics/aggregators/Aggregator.scala

@@ -55,8 +55,8 @@ trait Aggregated[+T] extends Writable with Serializable {
 }
 
 class AggregatedCollection[T, U <: Aggregated[T]](val values: Seq[U])
- extends Aggregated[metrics.Collection[Seq[T]]]
- with Serializable {
+  extends Aggregated[metrics.Collection[Seq[T]]]
+  with Serializable {
 
  def count(): Long = values.map(_.count()).reduce(_ + _)
  def countIdentical(): Long =
@@ -72,7 +72,7 @@ object AggregatedCollection {
 }
 
 class CombinedAggregator[Single, Agg <: Aggregated[Single]](aggs: Seq[Aggregator[Single, Agg]])
- extends Aggregator[metrics.Collection[Seq[Single]], AggregatedCollection[Single, Agg]] {
+  extends Aggregator[metrics.Collection[Seq[Single]], AggregatedCollection[Single, Agg]] {
 
  def initialValue: AggregatedCollection[Single, Agg] = AggregatedCollection(aggs.map(_.initialValue))
 

adam-core/src/main/scala/org/bdgenomics/adam/models/ADAMVariantContext.scala

@@ -78,10 +78,10 @@ object ADAMVariantContext {
 }
 
 class ADAMVariantContext(
- val position: ReferencePosition,
- val variant: RichADAMVariant,
- val genotypes: Seq[ADAMGenotype],
- val databases: Option[ADAMDatabaseVariantAnnotation] = None) {
+  val position: ReferencePosition,
+  val variant: RichADAMVariant,
+  val genotypes: Seq[ADAMGenotype],
+  val databases: Option[ADAMDatabaseVariantAnnotation] = None) {
  def this(variant: RichADAMVariant, genotypes: Seq[ADAMGenotype], database: Option[ADAMDatabaseVariantAnnotation] = None) = {
  this(ReferencePosition(variant), variant, genotypes, database)
  }

adam-core/src/main/scala/org/bdgenomics/adam/models/ReadBucket.scala

@@ -29,12 +29,12 @@ import com.esotericsoftware.kryo.io.{ Input, Output }
  * This is useful as this will usually map a single read in any of the sequences.
  */
 case class ReadBucket(unpairedPrimaryMappedReads: Seq[ADAMRecord] = Seq.empty,
- pairedFirstPrimaryMappedReads: Seq[ADAMRecord] = Seq.empty,
- pairedSecondPrimaryMappedReads: Seq[ADAMRecord] = Seq.empty,
- unpairedSecondaryMappedReads: Seq[ADAMRecord] = Seq.empty,
- pairedFirstSecondaryMappedReads: Seq[ADAMRecord] = Seq.empty,
- pairedSecondSecondaryMappedReads: Seq[ADAMRecord] = Seq.empty,
- unmappedReads: Seq[ADAMRecord] = Seq.empty) {
+  pairedFirstPrimaryMappedReads: Seq[ADAMRecord] = Seq.empty,
+  pairedSecondPrimaryMappedReads: Seq[ADAMRecord] = Seq.empty,
+  unpairedSecondaryMappedReads: Seq[ADAMRecord] = Seq.empty,
+  pairedFirstSecondaryMappedReads: Seq[ADAMRecord] = Seq.empty,
+  pairedSecondSecondaryMappedReads: Seq[ADAMRecord] = Seq.empty,
+  unmappedReads: Seq[ADAMRecord] = Seq.empty) {
  def allReads(): Seq[ADAMRecord] =
  unpairedPrimaryMappedReads ++
  pairedFirstPrimaryMappedReads ++

adam-core/src/main/scala/org/bdgenomics/adam/models/ReferencePosition.scala

@@ -43,7 +43,7 @@ object ReferencePositionWithOrientation {
 }
 
 case class ReferencePositionWithOrientation(refPos: Option[ReferencePosition], negativeStrand: Boolean)
- extends Ordered[ReferencePositionWithOrientation] {
+  extends Ordered[ReferencePositionWithOrientation] {
  override def compare(that: ReferencePositionWithOrientation): Int = {
  val posCompare = refPos.compare(that.refPos)
  if (posCompare != 0) {

adam-core/src/main/scala/org/bdgenomics/adam/models/ReferencePositionPair.scala

@@ -48,7 +48,7 @@ object ReferencePositionPair extends Logging {
 }
 
 case class ReferencePositionPair(read1refPos: Option[ReferencePositionWithOrientation],
- read2refPos: Option[ReferencePositionWithOrientation])
+  read2refPos: Option[ReferencePositionWithOrientation])
 
 class ReferencePositionPairSerializer extends Serializer[ReferencePositionPair] {
  val rps = new ReferencePositionWithOrientationSerializer()

adam-core/src/main/scala/org/bdgenomics/adam/models/ReferenceRegion.scala

@@ -122,7 +122,7 @@ case class ReferenceRegion(refId: Int, start: Long, end: Long) extends Ordered[R
  */
  def isAdjacent(region: ReferenceRegion): Boolean = distance(region) match {
  case Some(d) => d == 1
- case None => false
+ case None  => false
  }
 
  /**

adam-core/src/main/scala/org/bdgenomics/adam/models/SequenceDictionary.scala

@@ -208,7 +208,7 @@ class SequenceDictionary(val recordsIn: Array[SequenceRecord]) extends Serializa
  def records: Set[SequenceRecord] = recordIndices.values.toSet
 
  private[models] def cleanAndMerge(a1: Array[SequenceRecord],
- a2: Array[SequenceRecord]): Array[SequenceRecord] = {
+  a2: Array[SequenceRecord]): Array[SequenceRecord] = {
  val a2filt = a2.filter(k => !a1.contains(k))
 
  a1 ++ a2filt

adam-core/src/main/scala/org/bdgenomics/adam/models/SingleReadBucket.scala

@@ -36,8 +36,8 @@ object SingleReadBucket extends Logging {
 }
 
 case class SingleReadBucket(primaryMapped: Seq[ADAMRecord] = Seq.empty,
- secondaryMapped: Seq[ADAMRecord] = Seq.empty,
- unmapped: Seq[ADAMRecord] = Seq.empty) {
+  secondaryMapped: Seq[ADAMRecord] = Seq.empty,
+  unmapped: Seq[ADAMRecord] = Seq.empty) {
  // Note: not a val in order to save serialization/memory cost
  def allReads = {
  primaryMapped ++ secondaryMapped ++ unmapped

adam-core/src/main/scala/org/bdgenomics/adam/rdd/ADAMContext.scala

@@ -113,12 +113,12 @@ object ADAMContext {
  * @return Returns a properly configured Spark Context.
  */
  def createSparkContext(name: String,
- master: String,
- sparkHome: String,
- sparkJars: Seq[String],
- sparkEnvVars: Seq[String],
- sparkAddStatsListener: Boolean = false,
- sparkKryoBufferSize: Int = 4): SparkContext = {
+  master: String,
+  sparkHome: String,
+  sparkJars: Seq[String],
+  sparkEnvVars: Seq[String],
+  sparkAddStatsListener: Boolean = false,
+  sparkKryoBufferSize: Int = 4): SparkContext = {
  ADAMKryoProperties.setupContextProperties(sparkKryoBufferSize)
  val appName = "adam: " + name
  val environment: Map[String, String] = if (sparkEnvVars.isEmpty) {

adam-core/src/main/scala/org/bdgenomics/adam/rdd/ADAMRDDFunctions.scala

@@ -52,8 +52,8 @@ import scala.math.{ min, max }
 class ADAMRDDFunctions[T <% SpecificRecord: Manifest](rdd: RDD[T]) extends Serializable {
 
  def adamSave(filePath: String, blockSize: Int = 128 * 1024 * 1024,
- pageSize: Int = 1 * 1024 * 1024, compressCodec: CompressionCodecName = CompressionCodecName.GZIP,
- disableDictionaryEncoding: Boolean = false): RDD[T] = {
+  pageSize: Int = 1 * 1024 * 1024, compressCodec: CompressionCodecName = CompressionCodecName.GZIP,
+  disableDictionaryEncoding: Boolean = false): RDD[T] = {
  val job = new Job(rdd.context.hadoopConfiguration)
  ParquetLogger.hadoopLoggerLevel(Level.SEVERE)
  ParquetOutputFormat.setWriteSupportClass(job, classOf[AvroWriteSupport])
@@ -131,7 +131,7 @@ abstract class ADAMSequenceDictionaryRDDAggregator[T](rdd: RDD[T]) extends Seria
  * @param rdd RDD over which aggregation is supported.
  */
 class ADAMSpecificRecordSequenceDictionaryRDDAggregator[T <% SpecificRecord: Manifest](rdd: RDD[T])
- extends ADAMSequenceDictionaryRDDAggregator[T](rdd) {
+  extends ADAMSequenceDictionaryRDDAggregator[T](rdd) {
 
  def getSequenceRecordsFromElement(elem: T): Set[SequenceRecord] = {
  Set(SequenceRecord.fromSpecificRecord(elem))
@@ -223,7 +223,7 @@ class ADAMRecordRDDFunctions(rdd: RDD[ADAMRecord]) extends ADAMSequenceDictionar
  * @return RDD of ADAMRods.
  */
  def adamRecords2Rods(bucketSize: Int = 1000,
- secondaryAlignments: Boolean = false): RDD[ADAMRod] = {
+  secondaryAlignments: Boolean = false): RDD[ADAMRod] = {
 
  /**
  * Maps a read to one or two buckets. A read maps to a single bucket if both
@@ -458,7 +458,7 @@ class ADAMNucleotideContigFragmentRDDFunctions(rdd: RDD[ADAMNucleotideContigFrag
  }
 
  def reducePairs(kv1: (ReferenceRegion, String),
- kv2: (ReferenceRegion, String)): (ReferenceRegion, String) = {
+  kv2: (ReferenceRegion, String)): (ReferenceRegion, String) = {
  assert(kv1._1.isAdjacent(kv2._1), "Regions being joined must be adjacent. For: " +
  kv1 + ", " + kv2)
 

adam-core/src/main/scala/org/bdgenomics/adam/rdd/FlagStat.scala

@@ -56,10 +56,10 @@ case class DuplicateMetrics(total: Long, bothMapped: Long, onlyReadMapped: Long,
 }
 
 case class FlagStatMetrics(total: Long, duplicatesPrimary: DuplicateMetrics, duplicatesSecondary: DuplicateMetrics,
- mapped: Long, pairedInSequencing: Long,
- read1: Long, read2: Long, properlyPaired: Long, withSelfAndMateMapped: Long,
- singleton: Long, withMateMappedToDiffChromosome: Long,
- withMateMappedToDiffChromosomeMapQ5: Long, failedQuality: Boolean) {
+  mapped: Long, pairedInSequencing: Long,
+  read1: Long, read2: Long, properlyPaired: Long, withSelfAndMateMapped: Long,
+  singleton: Long, withMateMappedToDiffChromosome: Long,
+  withMateMappedToDiffChromosomeMapQ5: Long, failedQuality: Boolean) {
  def +(that: FlagStatMetrics): FlagStatMetrics = {
  assert(failedQuality == that.failedQuality, "Can't reduce passedVendorQuality with different failedQuality values")
  new FlagStatMetrics(total + that.total,