Merge a371f9f into 78bb9e5

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

@@ -52,8 +52,8 @@ class FlagStat(protected val args: FlagStatArgs) extends BDGSparkCommand[FlagSta
       AlignmentRecordField.readMapped,
       AlignmentRecordField.mateMapped,
       AlignmentRecordField.readPaired,
-      AlignmentRecordField.contigName,
-      AlignmentRecordField.mateContigName,
+      AlignmentRecordField.referenceName,
+      AlignmentRecordField.mateReferenceName,
       AlignmentRecordField.primaryAlignment,
       AlignmentRecordField.duplicateRead,
       AlignmentRecordField.readMapped,

adam-cli/src/test/scala/org/bdgenomics/adam/cli/TransformFeaturesSuite.scala

@@ -45,6 +45,6 @@ class TransformFeaturesSuite extends ADAMFunSuite {
     val converted = sc.loadFeatures(outputPath).rdd.collect
 
     assert(converted.size === 10)
-    assert(converted.find(_.getContigName != "chr1").isEmpty)
+    assert(converted.find(_.getReferenceName != "chr1").isEmpty)
   }
 }

adam-core/pom.xml

@@ -102,14 +102,14 @@
               <arguments>
                 <argument>org.bdgenomics.adam.sql</argument>
                 <argument>org.bdgenomics.formats.avro.AlignmentRecord</argument>
-                <argument>org.bdgenomics.formats.avro.Contig</argument>
                 <argument>org.bdgenomics.formats.avro.Dbxref</argument>
                 <argument>org.bdgenomics.formats.avro.Feature</argument>
                 <argument>org.bdgenomics.formats.avro.Fragment</argument>
                 <argument>org.bdgenomics.formats.avro.Genotype</argument>
                 <argument>org.bdgenomics.formats.avro.NucleotideContigFragment</argument>
                 <argument>org.bdgenomics.formats.avro.OntologyTerm</argument>
                 <argument>org.bdgenomics.formats.avro.ProcessingStep</argument>
+                <argument>org.bdgenomics.formats.avro.Reference</argument>
                 <argument>org.bdgenomics.formats.avro.TranscriptEffect</argument>
                 <argument>org.bdgenomics.formats.avro.Variant</argument>
                 <argument>org.bdgenomics.formats.avro.VariantAnnotation</argument>
@@ -130,7 +130,6 @@
               <arguments>
                 <argument>org.bdgenomics.adam.projections</argument>
                 <argument>org.bdgenomics.formats.avro.AlignmentRecord</argument>
-                <argument>org.bdgenomics.formats.avro.Contig</argument>
                 <argument>org.bdgenomics.formats.avro.Dbxref</argument>
                 <argument>org.bdgenomics.formats.avro.Feature</argument>
                 <argument>org.bdgenomics.formats.avro.Fragment</argument>
@@ -139,6 +138,7 @@
                 <argument>org.bdgenomics.formats.avro.OntologyTerm</argument>
                 <argument>org.bdgenomics.formats.avro.Read</argument>
                 <argument>org.bdgenomics.formats.avro.RecordGroup</argument>
+                <argument>org.bdgenomics.formats.avro.Reference</argument>
                 <argument>org.bdgenomics.formats.avro.Sample</argument>
                 <argument>org.bdgenomics.formats.avro.Sequence</argument>
                 <argument>org.bdgenomics.formats.avro.Slice</argument>

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

@@ -87,7 +87,7 @@ private[adam] class ConsensusGeneratorFromKnowns(rdd: RDD[Variant],
       // get region
       val start = reads.map(_.record.getStart).min
       val end = reads.map(_.getEnd).max
-      val refId = reads.head.record.getContigName
+      val refId = reads.head.record.getReferenceName
 
       val region = ReferenceRegion(refId, start, end + 1)
 

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

@@ -91,7 +91,7 @@ private[adam] class ConsensusGeneratorFromReads extends ConsensusGenerator {
         Consensus.generateAlternateConsensus(
           r.getSequence,
           ReferencePosition(
-            r.getContigName,
+            r.getReferenceName,
             r.getStart
           ),
           r.samtoolsCigar

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

@@ -257,7 +257,7 @@ class AlignmentRecordConverter extends Serializable {
       })
 
     // set the reference name, and alignment position, for mate
-    Option(adamRecord.getMateContigName)
+    Option(adamRecord.getMateReferenceName)
       .foreach(builder.setMateReferenceName)
     Option(adamRecord.getMateAlignmentStart)
       .foreach(s => builder.setMateAlignmentStart(s.toInt + 1))
@@ -293,8 +293,8 @@ class AlignmentRecordConverter extends Serializable {
         // only set alignment flags if read is aligned
         if (m) {
           // if we are aligned, we must have a reference
-          require(adamRecord.getContigName != null, "Cannot have null contig if aligned.")
-          builder.setReferenceName(adamRecord.getContigName)
+          require(adamRecord.getReferenceName != null, "Cannot have null reference if aligned.")
+          builder.setReferenceName(adamRecord.getReferenceName)
 
           // set the cigar, if provided
           Option(adamRecord.getCigar).foreach(builder.setCigarString)

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

@@ -18,7 +18,7 @@
 package org.bdgenomics.adam.converters
 
 import org.apache.spark.rdd.RDD
-import org.bdgenomics.formats.avro.{ Contig, NucleotideContigFragment }
+import org.bdgenomics.formats.avro.{ NucleotideContigFragment, Reference }
 import scala.collection.mutable
 
 /**
@@ -45,25 +45,25 @@ private[adam] object FastaConverter {
                                   seqId: Int = 0,
                                   descriptionLine: Option[String] = None) {
     /**
-     * The contig name and description that was parsed out of this description line.
+     * The reference name and description that was parsed out of this description line.
      */
-    val (contigName, contigDescription) = parseDescriptionLine(descriptionLine, fileIndex)
+    val (referenceName, referenceDescription) = parseDescriptionLine(descriptionLine, fileIndex)
 
     /**
      * Parses the text of a given line.
      *
-     * Assumes that the line contains the contig name followed by an optional
-     * description of the contig, with the two separated by a space.
+     * Assumes that the line contains the reference name followed by an optional
+     * description of the reference, with the two separated by a space.
      *
      * @throws IllegalArgumentException if there is no name in the line and the
      *   line is not the only record in a file (i.e., the file contains multiple
-     *   contigs).
+     *   reference sequences).
      *
-     * @param descriptionLine The optional string describing the contig. If this
+     * @param descriptionLine The optional string describing the reference. If this
      *   is not set and this isn't the only line in the file, we throw.
-     * @param id The index of this contig in the file.
-     * @return Returns a tuple containing (the optional contig name, and the
-     *   optional contig description).
+     * @param id The index of this reference in the file.
+     * @return Returns a tuple containing (the optional reference name, and the
+     *   optional reference description).
      */
     private def parseDescriptionLine(descriptionLine: Option[String],
                                      id: Long): (Option[String], Option[String]) = {
@@ -80,10 +80,10 @@ private[adam] object FastaConverter {
           if (split._1.contains('|')) {
             (None, Some(dL.stripPrefix(">").trim))
           } else {
-            val contigName: String = split._1.stripPrefix(">").trim
-            val contigDescription: String = split._2.trim
+            val referenceName: String = split._1.stripPrefix(">").trim
+            val referenceDescription: String = split._2.trim
 
-            (Some(contigName), Some(contigDescription))
+            (Some(referenceName), Some(referenceDescription))
           }
         } else {
           (Some(dL.stripPrefix(">").trim), None)
@@ -121,33 +121,33 @@ private[adam] object FastaConverter {
       .filter((kv: (Long, String)) => isFasta(kv._2))
 
     val descriptionLines: Map[Long, FastaDescriptionLine] = getDescriptionLines(filtered)
-    val indexToContigDescription = rdd.context.broadcast(descriptionLines)
+    val indexToReferenceDescription = rdd.context.broadcast(descriptionLines)
 
     val sequenceLines = filtered.filter(kv => !isDescriptionLine(kv._2))
 
     val keyedSequences =
-      if (indexToContigDescription.value.isEmpty) {
+      if (indexToReferenceDescription.value.isEmpty) {
         sequenceLines.keyBy(kv => -1L)
       } else {
-        sequenceLines.keyBy(row => findContigIndex(row._1, indexToContigDescription.value.keys.toList))
+        sequenceLines.keyBy(row => findReferenceIndex(row._1, indexToReferenceDescription.value.keys.toList))
       }
 
-    val groupedContigs = keyedSequences.groupByKey()
+    val groupedReferences = keyedSequences.groupByKey()
 
     val converter = new FastaConverter(maximumLength)
 
-    groupedContigs.flatMap {
+    groupedReferences.flatMap {
       case (id, lines) =>
 
-        val descriptionLine = indexToContigDescription.value.getOrElse(id, FastaDescriptionLine())
+        val descriptionLine = indexToReferenceDescription.value.getOrElse(id, FastaDescriptionLine())
         assert(lines.nonEmpty, s"Sequence ${descriptionLine.seqId} has no sequence data.")
 
         val sequence: Seq[String] = lines.toSeq.sortBy(_._1).map(kv => cleanSequence(kv._2))
         converter.convert(
-          descriptionLine.contigName,
+          descriptionLine.referenceName,
           descriptionLine.seqId,
           sequence,
-          descriptionLine.contigDescription
+          descriptionLine.referenceDescription
         )
     }
   }
@@ -194,18 +194,18 @@ private[adam] object FastaConverter {
   }
 
   /**
-   * Finds the index of a contig.
+   * Finds the index of a reference sequence.
    *
-   * The index of a contig is the highest index below the index of our row.
+   * The index of a reference is the highest index below the index of our row.
    * Here, we define the index as the row number of the description line that
-   * describes this contig.
+   * describes this reference sequence.
    *
-   * @param rowIdx The row number of the contig row to check.
+   * @param rowIdx The row number of the reference sequence row to check.
    * @param indices A list containing the row numbers of all description lines.
    * @return Returns the row index of the description line that describes this
    *   sequence line.
    */
-  private[converters] def findContigIndex(rowIdx: Long, indices: List[Long]): Long = {
+  private[converters] def findReferenceIndex(rowIdx: Long, indices: List[Long]): Long = {
     val idx = indices.filter(_ <= rowIdx)
     idx.max
   }

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

@@ -114,26 +114,26 @@ private[adam] object FragmentConverter extends Serializable {
   }
 
   /**
-   * Converts a contig assembly into one or more reads.
+   * Converts a reference assembly into one or more reads.
    *
    * Takes in a reduced key value pair containing merged FragmentCollectors.
    * The strings that are in this FragmentCollector are used to create reads.
-   * The Contig key is used to populate the metadata for the contig.
+   * The reference key is used to populate the metadata for the reference.
    *
-   * @param kv (Contig metadata, FragmentCollector) key value pair.
+   * @param kv (Reference metadata, FragmentCollector) key value pair.
    * @return Returns one alignment record per sequence in the collector.
    */
   private[converters] def convertFragment(kv: (String, FragmentCollector)): Seq[AlignmentRecord] = {
     // extract kv pair
-    val (contigName, fragment) = kv
+    val (referenceName, fragment) = kv
 
     // extract the fragment string and region
     fragment.fragments.map(p => {
       val (fragmentRegion, fragmentString) = p
 
       // build record
       AlignmentRecord.newBuilder()
-        .setContigName(contigName)
+        .setReferenceName(referenceName)
         .setStart(fragmentRegion.start)
         .setEnd(fragmentRegion.end)
         .setSequence(fragmentString)

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

@@ -101,11 +101,11 @@ private[adam] 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) {
-        builder.setContigName(samRecord.getReferenceName)
+        builder.setReferenceName(samRecord.getReferenceName)
 
         // set read alignment flag
         val start: Int = samRecord.getAlignmentStart
-        assert(start != 0, "Start cannot equal 0 if contig is set.")
+        assert(start != 0, "Start cannot equal 0 if reference is set.")
         builder.setStart(start - 1L)
 
         // set OP and OC flags, if applicable
@@ -146,7 +146,7 @@ private[adam] class SAMRecordConverter extends Serializable with Logging {
       val mateReference: Int = samRecord.getMateReferenceIndex
 
       if (mateReference != SAMRecord.NO_ALIGNMENT_REFERENCE_INDEX) {
-        builder.setMateContigName(samRecord.getMateReferenceName)
+        builder.setMateReferenceName(samRecord.getMateReferenceName)
 
         val mateStart = samRecord.getMateAlignmentStart
         if (mateStart > 0) {

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

@@ -1679,7 +1679,7 @@ class VariantContextConverter(
 
       // create the builder
       val variantBuilder = Variant.newBuilder
-        .setContigName(vc.getChr)
+        .setReferenceName(vc.getChr)
         .setStart(vc.getStart - 1)
         .setEnd(vc.getEnd)
         .setReferenceAllele(vc.getReference.getBaseString)
@@ -1791,7 +1791,7 @@ class VariantContextConverter(
       // create the builder
       val builder = Genotype.newBuilder()
         .setVariant(variant)
-        .setContigName(variant.getContigName)
+        .setReferenceName(variant.getReferenceName)
         .setStart(variant.getStart)
         .setEnd(variant.getEnd)
         .setSampleId(g.getSampleName)
@@ -2182,7 +2182,7 @@ class VariantContextConverter(
       val hasNonRefAlleles = vc.genotypes
         .exists(_.getNonReferenceLikelihoods.length != 0)
       val builder = new VariantContextBuilder()
-        .chr(v.getContigName)
+        .chr(v.getReferenceName)
         .start(v.getStart + 1)
         .stop(v.getEnd)
         .alleles(VariantContextConverter.convertAlleles(v, hasNonRefAlleles))

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

@@ -45,14 +45,14 @@ private[adam] object Coverage {
    * @return Coverage spanning the specified feature
    */
   def apply(feature: Feature): Coverage = {
-    require(feature.getContigName != null && feature.getContigName.length > 0,
-      "Features must have Contig name to convert to Coverage")
+    require(feature.getReferenceName != null && feature.getReferenceName.length > 0,
+      "Features must have reference name to convert to Coverage")
     require(feature.getStart != null && feature.getEnd != null,
       "Features must have valid position data to convert to Coverage")
     require(feature.getScore != null,
       "Features must have valid score to convert to Coverage")
 
-    Coverage(feature.getContigName,
+    Coverage(feature.getReferenceName,
       feature.getStart,
       feature.getEnd,
       feature.getScore,
@@ -73,18 +73,18 @@ private[adam] object Coverage {
 /**
  * Coverage record for CoverageDataset.
  *
- * Contains Region indexed by contig name, start and end, as well as the average
+ * Contains Region indexed by reference name, start and end, as well as the average
  * coverage at each base pair in that region.
  *
- * @param contigName The chromosome that this coverage was observed on.
+ * @param referenceName The chromosome that this coverage was observed on.
  * @param start The start coordinate of the region where this coverage value was
  *   observed.
  * @param end The end coordinate of the region where this coverage value was
  *   observed.
  * @param optSampleId Option of sampleId for this Coverage record
  * @param count The average coverage across this region.
  */
-case class Coverage(contigName: String, start: Long, end: Long, count: Double, optSampleId: Option[String] = None) {
+case class Coverage(referenceName: String, start: Long, end: Long, count: Double, optSampleId: Option[String] = None) {
 
   /**
    * Converts Coverage to Feature, setting Coverage count in the score attribute.
@@ -93,7 +93,7 @@ case class Coverage(contigName: String, start: Long, end: Long, count: Double, o
    */
   def toFeature: Feature = {
     val featureBuilder = Feature.newBuilder()
-      .setContigName(contigName)
+      .setReferenceName(referenceName)
       .setStart(start)
       .setEnd(end)
       .setScore(count)
@@ -114,7 +114,7 @@ case class Coverage(contigName: String, start: Long, end: Long, count: Double, o
       name = None,
       source = None,
       featureType = None,
-      contigName = Some(contigName),
+      referenceName = Some(referenceName),
       start = Some(start),
       end = Some(end),
       strand = None,

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

@@ -25,7 +25,7 @@ import org.bdgenomics.formats.avro.Variant
 import org.bdgenomics.utils.misc.Logging
 
 private[adam] class IndelTable(private val table: Map[String, Iterable[Consensus]]) extends Serializable with Logging {
-  log.info("Indel table has %s contigs and %s entries".format(
+  log.info("Indel table has %s reference sequences and %s entries".format(
     table.size,
     table.values.map(_.size).sum
   ))
@@ -58,7 +58,7 @@ private[adam] object IndelTable {
   def apply(variants: RDD[Variant]): IndelTable = {
     val consensus: Map[String, Iterable[Consensus]] = variants.filter(v => v.getReferenceAllele.length != v.getAlternateAllele.length)
       .map(v => {
-        val referenceName = v.getContigName
+        val referenceName = v.getReferenceName
         val consensus = if (v.getReferenceAllele.length > v.getAlternateAllele.length) {
           // deletion
           val deletionLength = v.getReferenceAllele.length - v.getAlternateAllele.length