Remove StructuralVariant and StructuralVariantType, add names field to Variant

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

@@ -49,8 +49,8 @@ class AlleleCountArgs extends Args4jBase with ParquetArgs {
 object AlleleCountHelper extends Serializable {
   def chooseAllele(x: (String, java.lang.Long, String, String, GenotypeAllele)) =
     x match {
-      case (chr, position, refAllele, varAllele, GenotypeAllele.Ref) => Some(chr, position, refAllele)
-      case (chr, position, refAllele, varAllele, GenotypeAllele.Alt) => Some(chr, position, varAllele)
+      case (chr, position, refAllele, varAllele, GenotypeAllele.REF) => Some(chr, position, refAllele)
+      case (chr, position, refAllele, varAllele, GenotypeAllele.ALT) => Some(chr, position, varAllele)
       case _ => None
     }
 

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

@@ -17,13 +17,15 @@
  */
 package org.bdgenomics.adam.converters
 
+import com.google.common.collect.ImmutableList
 import htsjdk.variant.variantcontext.{
   Allele,
   GenotypesContext,
   GenotypeLikelihoods,
   VariantContext => HtsjdkVariantContext,
   VariantContextBuilder
 }
+import htsjdk.variant.vcf.VCFConstants
 import java.util.Collections
 import org.bdgenomics.utils.misc.Logging
 import org.bdgenomics.adam.models.{
@@ -72,10 +74,10 @@ private[adam] object VariantContextConverter {
    * @return The Avro representation for this allele.
    */
   private def convertAllele(vc: HtsjdkVariantContext, allele: Allele): GenotypeAllele = {
-    if (allele.isNoCall) GenotypeAllele.NoCall
-    else if (allele.isReference) GenotypeAllele.Ref
-    else if (allele == NON_REF_ALLELE || !vc.hasAlternateAllele(allele)) GenotypeAllele.OtherAlt
-    else GenotypeAllele.Alt
+    if (allele.isNoCall) GenotypeAllele.NO_CALL
+    else if (allele.isReference) GenotypeAllele.REF
+    else if (allele == NON_REF_ALLELE || !vc.hasAlternateAllele(allele)) GenotypeAllele.OTHER_ALT
+    else GenotypeAllele.ALT
   }
 
   /**
@@ -123,9 +125,9 @@ private[adam] object VariantContextConverter {
     var alleles = g.getAlleles
     if (alleles == null) return Collections.emptyList[Allele]
     else g.getAlleles.map {
-      case GenotypeAllele.NoCall                        => Allele.NO_CALL
-      case GenotypeAllele.Ref | GenotypeAllele.OtherAlt => Allele.create(g.getVariant.getReferenceAllele, true)
-      case GenotypeAllele.Alt                           => Allele.create(g.getVariant.getAlternateAllele)
+      case GenotypeAllele.NO_CALL                        => Allele.NO_CALL
+      case GenotypeAllele.REF | GenotypeAllele.OTHER_ALT => Allele.create(g.getVariant.getReferenceAllele, true)
+      case GenotypeAllele.ALT                            => Allele.create(g.getVariant.getAlternateAllele)
     }
   }
 }
@@ -312,6 +314,36 @@ private[adam] class VariantContextConverter(dict: Option[SequenceDictionary] = N
     contigToRefSeq.getOrElse(vc.getChr, vc.getChr)
   }
 
+  /**
+   * Split the htsjdk variant context ID field into an array of names.
+   *
+   * @param vc htsjdk variant context
+   * @return Returns an Option wrapping an array of names split from the htsjdk
+   *    variant context ID field
+   */
+  private def splitIds(vc: HtsjdkVariantContext): Option[java.util.List[String]] = {
+    if (vc.hasID()) {
+      Some(ImmutableList.copyOf(vc.getID().split(VCFConstants.ID_FIELD_SEPARATOR)))
+    } else {
+      None
+    }
+  }
+
+  /**
+   * Join the array of variant names into a string for the htsjdk variant context ID field.
+   *
+   * @param variant variant
+   * @return Returns an Option wrapping a string for the htsjdk variant context ID field joined
+   *    from the array of variant names
+   */
+  private def joinNames(variant: Variant): Option[String] = {
+    if (variant.getNames != null && variant.getNames.length > 0) {
+      Some(variant.getNames.mkString(VCFConstants.ID_FIELD_SEPARATOR))
+    } else {
+      None
+    }
+  }
+
   /**
    * Builds an avro Variant for a site with a defined alt allele.
    *
@@ -321,16 +353,14 @@ private[adam] class VariantContextConverter(dict: Option[SequenceDictionary] = N
    * @return Returns an Avro description of the genotyped site.
    */
   private def createADAMVariant(vc: HtsjdkVariantContext, alt: Option[String]): Variant = {
-    // VCF CHROM, POS, REF and ALT
+    // VCF CHROM, POS, ID, REF and ALT
     val builder = Variant.newBuilder
       .setContigName(createContig(vc))
       .setStart(vc.getStart - 1 /* ADAM is 0-indexed */ )
       .setEnd(vc.getEnd /* ADAM is 0-indexed, so the 1-indexed inclusive end becomes exclusive */ )
       .setReferenceAllele(vc.getReference.getBaseString)
-    if (vc.hasLog10PError) {
-      builder.setVariantErrorProbability(vc.getPhredScaledQual.intValue())
-    }
     alt.foreach(builder.setAlternateAllele(_))
+    splitIds(vc).foreach(builder.setNames(_))
     builder.build
   }
 
@@ -392,7 +422,7 @@ private[adam] class VariantContextConverter(dict: Option[SequenceDictionary] = N
           .setVariantCallingAnnotations(annotations)
           .setSampleId(g.getSampleName)
           .setAlleles(g.getAlleles.map(VariantContextConverter.convertAllele(vc, _)))
-          .setIsPhased(g.isPhased)
+          .setPhased(g.isPhased)
 
         if (g.hasGQ) genotype.setGenotypeQuality(g.getGQ)
         if (g.hasDP) genotype.setReadDepth(g.getDP)
@@ -538,7 +568,10 @@ private[adam] class VariantContextConverter(dict: Option[SequenceDictionary] = N
       .stop(variant.getStart + variant.getReferenceAllele.length)
       .alleles(VariantContextConverter.convertAlleles(variant))
 
-    vc.databases.flatMap(d => Option(d.getDbSnpId)).foreach(d => vcb.id("rs" + d))
+    joinNames(variant) match {
+      case None    => vcb.noID()
+      case Some(s) => vcb.id(s)
+    }
 
     // TODO: Extract provenance INFO fields
     try {
@@ -547,7 +580,7 @@ private[adam] class VariantContextConverter(dict: Option[SequenceDictionary] = N
           g.getSampleId, VariantContextConverter.convertAlleles(g)
         )
 
-        Option(g.getIsPhased).foreach(gb.phased(_))
+        Option(g.getPhased).foreach(gb.phased(_))
         Option(g.getGenotypeQuality).foreach(gb.GQ(_))
         Option(g.getReadDepth).foreach(gb.DP(_))
 

adam-core/src/main/scala/org/bdgenomics/adam/projections/FeatureField.scala

@@ -24,5 +24,5 @@ import org.bdgenomics.formats.avro.Feature
  */
 object FeatureField extends FieldEnumeration(Feature.SCHEMA$) {
 
-  val featureId, name, source, featureType, contigName, start, end, strand, phase, frame, score, geneId, transcriptId, exonId, aliases, parentIds, target, gap, derivesFrom, notes, dbxrefs, ontologyTerms, isCircular, attributes = SchemaValue
+  val featureId, name, source, featureType, contigName, start, end, strand, phase, frame, score, geneId, transcriptId, exonId, aliases, parentIds, target, gap, derivesFrom, notes, dbxrefs, ontologyTerms, circular, attributes = SchemaValue
 }

adam-core/src/main/scala/org/bdgenomics/adam/projections/GenotypeField.scala

@@ -24,5 +24,5 @@ import org.bdgenomics.formats.avro.Genotype
  */
 object GenotypeField extends FieldEnumeration(Genotype.SCHEMA$) {
 
-  val variant, contigName, start, end, variantCallingAnnotations, sampleId, sampleDescription, processingDescription, alleles, referenceReadDepth, alternateReadDepth, readDepth, genotypeQuality, genotypeLikelihoods, splitFromMultiAllelic, isPhased, phaseSetId, phaseQuality = SchemaValue
+  val variant, contigName, start, end, variantCallingAnnotations, sampleId, sampleDescription, processingDescription, alleles, expectedAlleleDosage, referenceReadDepth, alternateReadDepth, readDepth, minReadDepth, genotypeQuality, genotypeLikelihoods, nonReferenceLikelihoods, strandBiasComponents, splitFromMultiAllelic, phased, phaseSetId, phaseQuality = SchemaValue
 }

adam-core/src/main/scala/org/bdgenomics/adam/projections/VariantField.scala

@@ -24,5 +24,5 @@ import org.bdgenomics.formats.avro.Variant
  */
 object VariantField extends FieldEnumeration(Variant.SCHEMA$) {
 
-  val contig, start, end, referenceAllele, variantAllele = SchemaValue
+  val contigName, start, end, names, referenceAllele, alternateAllele, somatic = SchemaValue
 }

adam-core/src/main/scala/org/bdgenomics/adam/rdd/features/Features.scala

@@ -138,7 +138,7 @@ private[features] object Features {
         case "Target"        => f.setTarget(entry._2)
         case "Gap"           => f.setGap(entry._2)
         case "Derives_from"  => f.setDerivesFrom(entry._2)
-        case "Is_circular"   => f.setIsCircular(entry._2.toBoolean)
+        case "Is_circular"   => f.setCircular(entry._2.toBoolean)
         case "Alias"         => aliases += entry._2
         case "Note"          => notes += entry._2
         case "Parent"        => parentIds += entry._2
@@ -185,7 +185,7 @@ private[features] object Features {
     Option(feature.getTarget).foreach(attrs += Tuple2("Target", _))
     Option(feature.getGap).foreach(attrs += Tuple2("Gap", _))
     Option(feature.getDerivesFrom).foreach(attrs += Tuple2("Derives_from", _))
-    Option(feature.getIsCircular).foreach(addBooleanTuple)
+    Option(feature.getCircular).foreach(addBooleanTuple)
     Option(feature.getGeneId).foreach(attrs += Tuple2("gene_id", _))
     Option(feature.getTranscriptId).foreach(attrs += Tuple2("transcript_id", _))
     Option(feature.getExonId).foreach(attrs += Tuple2("exon_id", _))

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

@@ -40,26 +40,26 @@ class RichGenotype(val genotype: Genotype) {
       distinctListOfAlleles match {
 
         // If all alleles are the reference allele, the genotype is Homozygous Reference (HOM_REF)
-        case List(GenotypeAllele.Ref)      => GenotypeType.HOM_REF
+        case List(GenotypeAllele.REF)       => GenotypeType.HOM_REF
 
         // If all alleles are the primary alternative allele, the genotype is Homozygous Alternative (HOM_ALT)
-        case List(GenotypeAllele.Alt)      => GenotypeType.HOM_ALT
+        case List(GenotypeAllele.ALT)       => GenotypeType.HOM_ALT
 
         // If all alleles are not called, the genotype is not called  (NO_CALL)
-        case List(GenotypeAllele.NoCall)   => GenotypeType.NO_CALL
+        case List(GenotypeAllele.NO_CALL)   => GenotypeType.NO_CALL
 
-        // If all alleles are OtherAlt.
-        // If genotype.getAlleles returns a single OtherAlt, the genotype is Homozygous Alternative (HOM_ALT)
-        // If genotype.getAlleles returns a multiple OtherAlt, the genotype is
-        // A) The OtherAlt alleles are the same OtherAlt alleles: Homozygous Alternative (HOM_ALT)
-        // B) The OtherAlt allales are different OtherAlt alleles: Heterozygous
+        // If all alleles are OTHER_ALT.
+        // If genotype.getAlleles returns a single OTHER_ALT, the genotype is Homozygous Alternative (HOM_ALT)
+        // If genotype.getAlleles returns a multiple OTHER_ALT, the genotype is
+        // A) The OTHER_ALT alleles are the same OTHER_ALT alleles: Homozygous Alternative (HOM_ALT)
+        // B) The OTHER_ALT alleles are different OTHER_ALT alleles: Heterozygous
         // For now return NO_CALL as the genotypes, as was done in the previous getType function
         // See also issue https://github.com/bigdatagenomics/adam/issues/897
-        case List(GenotypeAllele.OtherAlt) => GenotypeType.NO_CALL
+        case List(GenotypeAllele.OTHER_ALT) => GenotypeType.NO_CALL
 
         // only the four above alleles are possible
         // https://github.com/bigdatagenomics/bdg-formats/blob/master/src/main/resources/avro/bdg.avdl#L464
-        case _                             => throw new IllegalStateException("Found single distinct allele other than the four possible alleles: Ref, Alt, NoCall and OtherAlt")
+        case _                              => throw new IllegalStateException("Found single distinct allele other than the four possible alleles: REF, ALT, NO_CALL and OTHER_ALT")
       }
     } // In the case that there are multiple distinct alleles
     // This should be applicable to any genome ploidy.
@@ -69,9 +69,9 @@ class RichGenotype(val genotype: Genotype) {
       // IN HTS-JDK this would be GenotypeType.MIXED , this type is not available in BDG / ADAM
       // https://github.com/bigdatagenomics/bdg-formats/blob/master/src/main/resources/avro/bdg.avdl#L483
       // https://github.com/samtools/htsjdk/blob/master/src/java/htsjdk/variant/variantcontext/Genotype.java#L218
-      if (distinctListOfAlleles contains GenotypeAllele.NoCall) {
+      if (distinctListOfAlleles contains GenotypeAllele.NO_CALL) {
         GenotypeType.NO_CALL
-      } // Otherwise the distinct alleles are a combination of 2 or 3 alleles from the list  (GenotypeAllele.Ref, GenotypeAllele.Alt, GenotypeAllele.OtherAlt)
+      } // Otherwise the distinct alleles are a combination of 2 or 3 alleles from the list (GenotypeAllele.REF, GenotypeAllele.ALT, GenotypeAllele.OTHER_ALT)
       // Therefore the genotype is Heterozygous HET
       else {
         GenotypeType.HET

adam-core/src/main/scala/org/bdgenomics/adam/serialization/ADAMKryoRegistrator.scala

@@ -57,6 +57,7 @@ import org.bdgenomics.formats.avro._
 import org.codehaus.jackson.node.{ BooleanNode, NullNode, TextNode }
 import org.seqdoop.hadoop_bam.{ VariantContextWithHeader, VariantContextWritable }
 import scala.collection.immutable
+import scala.collection.mutable.ArrayBuffer
 import scala.reflect.ClassTag
 
 case class InputStreamWithDecoder(size: Int) {
@@ -104,6 +105,7 @@ class ADAMKryoRegistrator extends KryoRegistrator {
 
     kryo.register(classOf[Genotype], new AvroSerializer[Genotype])
     kryo.register(classOf[Array[Genotype]])
+    kryo.register(classOf[ArrayBuffer[Genotype]])
 
     kryo.register(classOf[Variant], new AvroSerializer[Variant])
     kryo.register(classOf[Array[Variant]])
@@ -116,7 +118,6 @@ class ADAMKryoRegistrator extends KryoRegistrator {
 
     kryo.register(classOf[Contig], new AvroSerializer[Contig])
     kryo.register(classOf[RecordGroupMetadata], new AvroSerializer[RecordGroupMetadata])
-    kryo.register(classOf[StructuralVariant], new AvroSerializer[StructuralVariant])
     kryo.register(classOf[VariantCallingAnnotations], new AvroSerializer[VariantCallingAnnotations])
     kryo.register(classOf[TranscriptEffect], new AvroSerializer[TranscriptEffect])
     kryo.register(classOf[VariantAnnotation], new AvroSerializer[VariantAnnotation])