Replaced Contig with ContigName in AlignmentRecord and related changes

Contig factor out project, cleaning up some comments

clean up some unintended whitespace arbitrary diffs

Removed subproject POM changes and other small issues

adam-cli/src/main/scala/org/bdgenomics/adam/cli/Fragments2Reads.scala

@@ -54,4 +54,4 @@ class Fragments2Reads(protected val args: Fragments2ReadsArgs) extends BDGSparkC
  SequenceDictionary.empty,
  RecordGroupDictionary.empty)
  }
-}
+}

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

@@ -32,7 +32,7 @@ import org.bdgenomics.adam.models.{
 import org.bdgenomics.adam.projections.{ AlignmentRecordField, Filter }
 import org.bdgenomics.adam.rdd.ADAMContext._
 import org.bdgenomics.adam.rdd.ADAMSaveAnyArgs
-import org.bdgenomics.adam.rdd.read.MDTagging
+import org.bdgenomics.adam.rdd.read.{ AlignmentRecordRDD, MDTagging }
 import org.bdgenomics.adam.rich.RichVariant
 import org.bdgenomics.formats.avro.AlignmentRecord
 import org.bdgenomics.utils.cli._
@@ -267,7 +267,7 @@ class Transform(protected val args: TransformArgs) extends BDGSparkCommand[Trans
  )
  }
 
- val aRdd =
+ val aRdd: AlignmentRecordRDD =
  if (args.forceLoadBam) {
  sc.loadBam(args.inputPath)
  } else if (args.forceLoadFastq) {

adam-core/src/main/scala/org/bdgenomics/adam/algorithms/consensus/ConsensusGeneratorFromKnowns.scala

@@ -70,7 +70,7 @@ class ConsensusGeneratorFromKnowns(file: String, @transient sc: SparkContext) ex
  // get region
  val start = reads.map(_.record.getStart).min
  val end = reads.map(_.getEnd).max
- val refId = reads.head.record.getContig.getContigName
+ val refId = reads.head.record.getContigName
 
  val region = ReferenceRegion(refId, start, end + 1)
 

adam-core/src/main/scala/org/bdgenomics/adam/algorithms/consensus/ConsensusGeneratorFromReads.scala

@@ -78,7 +78,7 @@ class ConsensusGeneratorFromReads extends ConsensusGenerator {
  Consensus.generateAlternateConsensus(
  r.getSequence,
  ReferencePosition(
- r.getContig.getContigName,
+ r.getContigName,
  r.getStart
  ),
  r.samtoolsCigar

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

@@ -118,8 +118,7 @@ class AlignmentRecordConverter extends Serializable {
  })
 
  // set the reference name, and alignment position, for mate
- Option(adamRecord.getMateContig)
- .map(_.getContigName)
+ Option(adamRecord.getMateContigName)
  .foreach(builder.setMateReferenceName)
  Option(adamRecord.getMateAlignmentStart)
  .foreach(s => builder.setMateAlignmentStart(s.toInt + 1))
@@ -155,8 +154,8 @@ class AlignmentRecordConverter extends Serializable {
  // only set alignment flags if read is aligned
  if (m) {
  // if we are aligned, we must have a reference
- assert(adamRecord.getContig != null, "Cannot have null contig if aligned.")
- builder.setReferenceName(adamRecord.getContig.getContigName)
+ require(adamRecord.getContigName != null, "Cannot have null contig if aligned.")
+ builder.setReferenceName(adamRecord.getContigName)
 
  // set the cigar, if provided
  Option(adamRecord.getCigar).foreach(builder.setCigarString)

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

@@ -93,7 +93,7 @@ object FragmentConverter extends Serializable {
 
  // build record
  AlignmentRecord.newBuilder()
- .setContig(contig)
+ .setContigName(contig.getContigName)
  .setStart(fragmentRegion.start)
  .setEnd(fragmentRegion.end)
  .setSequence(fragmentString)

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

@@ -80,9 +80,7 @@ class SAMRecordConverter extends Serializable with Logging {
  // This prevents looking up a -1 in the sequence dictionary
  val readReference: Int = samRecord.getReferenceIndex
  if (readReference != SAMRecord.NO_ALIGNMENT_REFERENCE_INDEX) {
- dict(samRecord.getReferenceName).foreach { (rec) =>
- builder.setContig(SequenceRecord.toADAMContig(rec))
- }
+ builder.setContigName(samRecord.getReferenceName)
 
  // set read alignment flag
  val start: Int = samRecord.getAlignmentStart
@@ -127,9 +125,7 @@ class SAMRecordConverter extends Serializable with Logging {
  val mateReference: Int = samRecord.getMateReferenceIndex
 
  if (mateReference != SAMRecord.NO_ALIGNMENT_REFERENCE_INDEX) {
- dict(samRecord.getMateReferenceName).foreach { (rec) =>
- builder.setMateContig(SequenceRecord.toADAMContig(rec))
- }
+ builder.setMateContigName(samRecord.getMateReferenceName)
 
  val mateStart = samRecord.getMateAlignmentStart
  if (mateStart > 0) {

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

@@ -49,7 +49,7 @@ object ReferencePosition extends Serializable {
  * @see fivePrime
  */
  def apply(record: AlignmentRecord): ReferencePosition = {
- new ReferencePosition(record.getContig.getContigName, record.getStart)
+ new ReferencePosition(record.getContigName, record.getStart)
  }
 
  /**

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

@@ -82,7 +82,7 @@ object ReferenceRegion {
  if (record.getReadMapped) {
  Some(
  ReferenceRegion(
- record.getContig.getContigName,
+ record.getContigName,
  record.getStart,
  record.getEnd
  )
@@ -92,7 +92,7 @@ object ReferenceRegion {
  }
 
  def apply(record: AlignmentRecord): ReferenceRegion = {
- ReferenceRegion(record.getContig.getContigName, record.getStart, record.getEnd)
+ ReferenceRegion(record.getContigName, record.getStart, record.getEnd)
  }
 
  /**

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

@@ -345,27 +345,6 @@ object SequenceRecord {
  fromADAMContig(fragment.getContig)
  }
 
- /**
- * Convert an Read into one or more SequenceRecords.
- * The reason that we can't simply use the "fromSpecificRecord" method, below, is that each Read
- * can (through the fact that it could be a pair of reads) contain 1 or 2 possible SequenceRecord entries
- * for the SequenceDictionary itself. Both have to be extracted, separately.
- *
- * @param rec The Read from which to extract the SequenceRecord entries
- * @return a list of all SequenceRecord entries derivable from this record.
- */
- def fromADAMRecord(rec: AlignmentRecord): Set[SequenceRecord] = {
- assert(rec != null, "Read was null")
- if (rec.getContig != null || rec.getMateContig != null) {
- // The contig should be null for unmapped read
- List(Option(rec.getContig), Option(rec.getMateContig))
- .flatten
- .map(fromADAMContig)
- .toSet
- } else
- Set()
- }
-
  def fromSpecificRecord(rec: IndexedRecord): SequenceRecord = {
  val schema = rec.getSchema
  if (schema.getField("referenceId") != null) {
@@ -381,4 +360,6 @@ object SequenceRecord {
  throw new AssertionError("Missing information to generate SequenceRecord")
  }
  }
+
 }
+

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

@@ -229,9 +229,7 @@ class ADAMContext(@transient val sc: SparkContext) extends Serializable with Log
  val projected: RDD[T] = loadParquet[T](filePath, None, projection = Some(projection))
 
  val recs: RDD[SequenceRecord] =
- if (isADAMRecord) {
- projected.asInstanceOf[RDD[AlignmentRecord]].distinct().flatMap(rec => SequenceRecord.fromADAMRecord(rec))
- } else if (isADAMContig) {
+ if (isADAMContig) {
  projected.asInstanceOf[RDD[NucleotideContigFragment]].distinct().map(ctg => SequenceRecord.fromADAMContigFragment(ctg))
  } else {
  projected.distinct().map(SequenceRecord.fromSpecificRecord(_))

adam-core/src/main/scala/org/bdgenomics/adam/rdd/fragment/FragmentRDDFunctions.scala

@@ -21,18 +21,14 @@ import org.apache.spark.rdd.RDD
 import org.bdgenomics.adam.converters.AlignmentRecordConverter
 import org.bdgenomics.adam.models.SequenceRecord
 import org.bdgenomics.adam.rdd.ADAMSequenceDictionaryRDDAggregator
+import org.apache.spark.Logging
 import org.bdgenomics.formats.avro._
 import scala.collection.JavaConversions._
 
-class FragmentRDDFunctions(rdd: RDD[Fragment]) extends ADAMSequenceDictionaryRDDAggregator[Fragment](rdd) {
+class FragmentRDDFunctions(rdd: RDD[Fragment]) extends Serializable with Logging {
 
  def toReads: RDD[AlignmentRecord] = {
  val converter = new AlignmentRecordConverter
  rdd.flatMap(converter.convertFragment)
  }
-
- def getSequenceRecordsFromElement(elem: Fragment): Set[SequenceRecord] = {
- val alignments = asScalaBuffer(elem.getAlignments)
- alignments.flatMap(SequenceRecord.fromADAMRecord).toSet
- }
 }

adam-core/src/main/scala/org/bdgenomics/adam/rdd/read/AlignmentRecordRDDFunctions.scala

@@ -32,7 +32,7 @@ import org.apache.avro.specific.{ SpecificDatumWriter, SpecificRecordBase }
 import org.apache.hadoop.conf.Configuration
 import org.apache.hadoop.fs.{ FileSystem, FileUtil, Path }
 import org.apache.hadoop.io.LongWritable
-import org.apache.spark.SparkContext
+import org.apache.spark.{ Logging, SparkContext }
 import org.apache.spark.broadcast.Broadcast
 import org.apache.spark.rdd.MetricsContext._
 import org.apache.spark.rdd.RDD
@@ -53,9 +53,7 @@ import scala.annotation.tailrec
 import scala.language.implicitConversions
 import scala.reflect.ClassTag
 
-class AlignmentRecordRDDFunctions(rdd: RDD[AlignmentRecord])
- extends ADAMSequenceDictionaryRDDAggregator[AlignmentRecord](rdd) {
-
+class AlignmentRecordRDDFunctions(rdd: RDD[AlignmentRecord]) extends Serializable with Logging {
  /**
  * Calculates the subset of the RDD whose AlignmentRecords overlap the corresponding
  * query ReferenceRegion. Equality of the reference sequence (to which these are aligned)
@@ -72,7 +70,7 @@ class AlignmentRecordRDDFunctions(rdd: RDD[AlignmentRecord])
  def filterByOverlappingRegion(query: ReferenceRegion): RDD[AlignmentRecord] = {
  def overlapsQuery(rec: AlignmentRecord): Boolean =
  rec.getReadMapped &&
- rec.getContig.getContigName == query.referenceName &&
+ rec.getContigName == query.referenceName &&
  rec.getStart < query.end &&
  rec.getEnd > query.start
  rdd.filter(overlapsQuery)
@@ -126,7 +124,6 @@ class AlignmentRecordRDDFunctions(rdd: RDD[AlignmentRecord])
  * As such, we must force the user to pass in the schema.
  *
  * @tparam T The type of the specific record we are saving.
- *
  * @param filename Path to save records to.
  * @param sc SparkContext used for identifying underlying file system.
  * @param schema Schema of records we are saving.
@@ -171,7 +168,6 @@ class AlignmentRecordRDDFunctions(rdd: RDD[AlignmentRecord])
  * aligned to.
  * @param rgd Record group dictionary describing the record groups these
  * reads are from.
- *
  * @see adamSave
  * @see adamAlignedRecordSave
  */
@@ -212,7 +208,6 @@ class AlignmentRecordRDDFunctions(rdd: RDD[AlignmentRecord])
  * aligned to.
  * @param rgd Record group dictionary describing the record groups these
  * reads are from.
- *
  * @see adamSave
  * @see adamSAMSave
  * @see saveAsParquet
@@ -235,7 +230,6 @@ class AlignmentRecordRDDFunctions(rdd: RDD[AlignmentRecord])
  * aligned to.
  * @param rgd Record group dictionary describing the record groups these
  * reads are from.
- *
  * @see adamAlignedRecordSave
  * @see adamSAMSave
  * @see saveAsParquet
@@ -263,9 +257,7 @@ class AlignmentRecordRDDFunctions(rdd: RDD[AlignmentRecord])
  * aligned to.
  * @param rgd Record group dictionary describing the record groups these
  * reads are from.
- *
  * @return A string on the driver representing this RDD of reads in SAM format.
- *
  * @see adamConvertToSAM
  */
  def adamSAMString(sd: SequenceDictionary,
@@ -593,10 +585,6 @@ class AlignmentRecordRDDFunctions(rdd: RDD[AlignmentRecord])
  }
  }
 
- def getSequenceRecordsFromElement(elem: AlignmentRecord): Set[SequenceRecord] = {
- SequenceRecord.fromADAMRecord(elem).toSet
- }
-
  /**
  * Converts an RDD of ADAM read records into SAM records.
  *
@@ -635,7 +623,6 @@ class AlignmentRecordRDDFunctions(rdd: RDD[AlignmentRecord])
  *
  * @param kmerLength The value of _k_ to use for cutting _k_-mers.
  * @return Returns an RDD containing k-mer/count pairs.
- *
  * @see adamCountQmers
  */
  def adamCountKmers(kmerLength: Int): RDD[(String, Long)] = {
@@ -696,15 +683,13 @@ class AlignmentRecordRDDFunctions(rdd: RDD[AlignmentRecord])
  * Realigns indels using a concensus-based heuristic.
  *
  * @see RealignIndels
- *
  * @param isSorted If the input data is sorted, setting this parameter to true avoids a second sort.
  * @param maxIndelSize The size of the largest indel to use for realignment.
  * @param maxConsensusNumber The maximum number of consensus sequences to realign against per
  * target region.
  * @param lodThreshold Log-odds threhold to use when realigning; realignments are only finalized
  * if the log-odds threshold is exceeded.
  * @param maxTargetSize The maximum width of a single target region for realignment.
- *
  * @return Returns an RDD of mapped reads which have been realigned.
  */
  def adamRealignIndels(
@@ -724,6 +709,7 @@ class AlignmentRecordRDDFunctions(rdd: RDD[AlignmentRecord])
 
  /**
  * Groups all reads by record group and read name
+ *
  * @return SingleReadBuckets with primary, secondary and unmapped reads
  */
  def adamSingleReadBuckets(): RDD[SingleReadBucket] = {
@@ -759,6 +745,7 @@ class AlignmentRecordRDDFunctions(rdd: RDD[AlignmentRecord])
 
  /**
  * Returns the subset of the ADAMRecords which have an attribute with the given name.
+ *
  * @param tagName The name of the attribute to filter on (should be length 2)
  * @return An RDD[Read] containing the subset of records with a tag that matches the given name.
  */
@@ -928,7 +915,6 @@ class AlignmentRecordRDDFunctions(rdd: RDD[AlignmentRecord])
  * were _originally_ paired together.
  *
  * @note The RDD that this is called on should be the RDD with the first read from the pair.
- *
  * @param secondPairRdd The rdd containing the second read from the pairs.
  * @param validationStringency How stringently to validate the reads.
  * @return Returns an RDD with the pair information recomputed.

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

@@ -44,7 +44,7 @@ object DuplicateMetrics {
  b2i(f(record)),
  b2i(f(record) && record.getReadMapped && record.getMateMapped),
  b2i(f(record) && record.getReadMapped && !record.getMateMapped),
- b2i(f(record) && (!isSameContig(record.getContig, record.getMateContig)))
+ b2i(f(record) && (!isSameContig(record.getContigName, record.getMateContigName)))
  )
  }
  (duplicateMetrics(isPrimary), duplicateMetrics(isSecondary))
@@ -97,7 +97,7 @@ object FlagStat {
  rdd.map {
  p =>
  val mateMappedToDiffChromosome =
- p.getReadPaired && p.getReadMapped && p.getMateMapped && !isSameContig(p.getContig, p.getMateContig)
+ p.getReadPaired && p.getReadMapped && p.getMateMapped && !isSameContig(p.getContigName, p.getMateContigName)
  val (primaryDuplicates, secondaryDuplicates) = DuplicateMetrics(p)
  new FlagStatMetrics(
  1,

adam-core/src/main/scala/org/bdgenomics/adam/rdd/read/MDTagging.scala

@@ -72,8 +72,7 @@ case class MDTagging(
  val referenceFileB = sc.broadcast(referenceFile)
  reads.map(read => {
  (for {
- contig <- Option(read.getContig)
- contigName <- Option(contig.getContigName)
+ contig <- Option(read.getContigName)
  if read.getReadMapped
  } yield {
  maybeMDTagRead(read, referenceFileB.value.extract(ReferenceRegion(read)))
@@ -105,5 +104,5 @@ object MDTagging {
 
 case class IncorrectMDTagException(read: AlignmentRecord, mdTag: String) extends Exception {
  override def getMessage: String =
- s"Read: ${read.getReadName}, pos: ${read.getContig.getContigName}:${read.getStart}, cigar: ${read.getCigar}, existing MD tag: ${read.getMismatchingPositions}, correct MD tag: $mdTag"
+ s"Read: ${read.getReadName}, pos: ${read.getContigName}:${read.getStart}, cigar: ${read.getCigar}, existing MD tag: ${read.getMismatchingPositions}, correct MD tag: $mdTag"
 }

adam-core/src/main/scala/org/bdgenomics/adam/rdd/read/realignment/IndelRealignmentTarget.scala

@@ -102,7 +102,7 @@ object IndelRealignmentTarget {
  maxIndelSize: Int): Seq[IndelRealignmentTarget] = CreateIndelRealignmentTargets.time {
 
  val region = ReferenceRegion(read.record)
- val refId = read.record.getContig.getContigName
+ val refId = read.record.getContigName
  var pos = List[ReferenceRegion]()
  var referencePos = read.record.getStart
  val cigar = read.samtoolsCigar

adam-core/src/main/scala/org/bdgenomics/adam/rdd/read/realignment/RealignIndels.scala

@@ -251,7 +251,7 @@ private[rdd] class RealignIndels(
 
  // get reference from reads
  val (reference, refStart, refEnd) = getReferenceFromReads(reads.map(r => new RichAlignmentRecord(r)))
- val refRegion = ReferenceRegion(reads.head.record.getContig.getContigName, refStart, refEnd)
+ val refRegion = ReferenceRegion(reads.head.record.getContigName, refStart, refEnd)
 
  // preprocess reads and get consensus
  val readsToClean = consensusModel.preprocessReadsForRealignment(

adam-core/src/main/scala/org/bdgenomics/adam/rich/RichAlignmentRecord.scala

@@ -132,7 +132,7 @@ class RichAlignmentRecord(val record: AlignmentRecord) {
  } else {
  Strand.Forward
  }
- ReferencePosition(record.getContig.getContigName, fivePrimePosition, strand)
+ ReferencePosition(record.getContigName, fivePrimePosition, strand)
  } catch {
  case e: Throwable => {
  println("caught " + e + " when trying to get position for " + record)
@@ -167,7 +167,7 @@ class RichAlignmentRecord(val record: AlignmentRecord) {
 
  def getReferenceContext(readOffset: Int, referencePosition: Long, cigarElem: CigarElement, elemOffset: Int): ReferenceSequenceContext = {
  val position = if (record.getReadMapped) {
- Some(ReferencePosition(record.getContig.getContigName, referencePosition))
+ Some(ReferencePosition(record.getContigName, referencePosition))
  } else {
  None
  }