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

@@ -116,7 +116,6 @@ 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])

adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala

@@ -121,7 +121,7 @@ class VariantContextConverterSuite extends ADAMFunSuite {
  val adamGTs = adamVCs.flatMap(_.genotypes)
  assert(adamGTs.length === 1)
  val adamGT = adamGTs.head
- assert(adamGT.getAlleles.sameElements(List(GenotypeAllele.Ref, GenotypeAllele.Alt)))
+ assert(adamGT.getAlleles.sameElements(List(GenotypeAllele.REF, GenotypeAllele.ALT)))
  assert(adamGT.getPhaseSetId === 1)
  assert(adamGT.getPhaseQuality === 50)
  }
@@ -182,7 +182,7 @@ class VariantContextConverterSuite extends ADAMFunSuite {
  val genotype = Genotype.newBuilder
  .setVariant(variant)
  .setSampleId("NA12878")
- .setAlleles(List(GenotypeAllele.Ref, GenotypeAllele.Alt))
+ .setAlleles(List(GenotypeAllele.REF, GenotypeAllele.ALT))
  .setVariantCallingAnnotations(VariantCallingAnnotations.newBuilder()
  .setFisherStrandBiasPValue(3.0f)
  .setRmsMapQ(0.0f)
@@ -233,19 +233,19 @@ class VariantContextConverterSuite extends ADAMFunSuite {
  val adamGT = adamVC.genotypes.head
  assert(adamGT.getSplitFromMultiAllelic)
  assert(adamGT.getReferenceReadDepth === 4)
- assert(adamGT.getIsPhased)
+ assert(adamGT.getPhased)
  }
 
  val adamGT1 = adamVCs(0).genotypes.head
  val adamGT2 = adamVCs(1).genotypes.head
- assert(adamGT1.getAlleles.sameElements(List(GenotypeAllele.Alt, GenotypeAllele.OtherAlt)))
+ assert(adamGT1.getAlleles.sameElements(List(GenotypeAllele.ALT, GenotypeAllele.OTHER_ALT)))
  assert(adamGT1.getAlternateReadDepth === 2)
  assert(adamGT1.getGenotypeLikelihoods
  .map(f => f: scala.Float)
  .map(PhredUtils.logProbabilityToPhred)
  .sameElements(List(59, 0, 256)))
 
- assert(adamGT2.getAlleles.sameElements(List(GenotypeAllele.OtherAlt, GenotypeAllele.Alt)))
+ assert(adamGT2.getAlleles.sameElements(List(GenotypeAllele.OTHER_ALT, GenotypeAllele.ALT)))
  assert(adamGT2.getAlternateReadDepth === 3)
  assert(adamGT2.getGenotypeLikelihoods
  .map(f => f: scala.Float)
@@ -269,7 +269,7 @@ class VariantContextConverterSuite extends ADAMFunSuite {
  assert(adamGTs.length === 1)
  val adamGT = adamGTs.head
  assert(adamGT.getVariant.getAlternateAllele === null)
- assert(adamGT.getAlleles.sameElements(List(GenotypeAllele.Ref, GenotypeAllele.Ref)))
+ assert(adamGT.getAlleles.sameElements(List(GenotypeAllele.REF, GenotypeAllele.REF)))
  assert(adamGT.getMinReadDepth === 38)
  assert(adamGT.getGenotypeLikelihoods.isEmpty)
  assert(adamGT.getNonReferenceLikelihoods

adam-core/src/test/scala/org/bdgenomics/adam/rdd/features/FeatureRDDSuite.scala

@@ -44,7 +44,7 @@ class FeatureRDDSuite extends ADAMFunSuite with TypeCheckedTripleEquals {
  a.getTarget === b.getTarget &&
  a.getGap === b.getGap &&
  a.getDerivesFrom === b.getDerivesFrom &&
- a.getIsCircular === b.getIsCircular &&
+ a.getCircular === b.getCircular &&
  a.getAliases === b.getAliases &&
  a.getNotes === b.getNotes &&
  a.getParentIds === b.getParentIds &&

adam-core/src/test/scala/org/bdgenomics/adam/rdd/variation/VariantContextRDDSuite.scala

@@ -46,7 +46,7 @@ class VariantContextRDDSuite extends ADAMFunSuite {
 
  val g0 = Genotype.newBuilder().setVariant(v0)
  .setSampleId("NA12878")
- .setAlleles(List(GenotypeAllele.Ref, GenotypeAllele.Alt))
+ .setAlleles(List(GenotypeAllele.REF, GenotypeAllele.ALT))
  .build
 
  VariantContextRDD(sc.parallelize(List(

adam-core/src/test/scala/org/bdgenomics/adam/rich/RichGenotypeSuite.scala

@@ -32,31 +32,30 @@ class RichGenotypeSuite extends FunSuite {
  test("different ploidy") {
  val gb = Genotype.newBuilder.setVariant(v0).setSampleId("NA12878")
  for (ploidy <- 0 until 3) {
- val g = gb.setAlleles(List.fill(ploidy)(GenotypeAllele.Ref)).build
+ val g = gb.setAlleles(List.fill(ploidy)(GenotypeAllele.REF)).build
  assert(g.ploidy === ploidy)
  }
  }
 
  test("all types for diploid genotype") {
  val gb = Genotype.newBuilder.setVariant(v0).setSampleId("NA12878")
 
- val hom_ref = gb.setAlleles(List(GenotypeAllele.Ref, GenotypeAllele.Ref)).build
+ val hom_ref = gb.setAlleles(List(GenotypeAllele.REF, GenotypeAllele.REF)).build
  assert(hom_ref.getType === GenotypeType.HOM_REF)
 
- val het1 = gb.setAlleles(List(GenotypeAllele.Ref, GenotypeAllele.Alt)).build
+ val het1 = gb.setAlleles(List(GenotypeAllele.REF, GenotypeAllele.ALT)).build
  assert(het1.getType === GenotypeType.HET)
- val het2 = gb.setAlleles(List(GenotypeAllele.Alt, GenotypeAllele.Ref)).build
+ val het2 = gb.setAlleles(List(GenotypeAllele.ALT, GenotypeAllele.REF)).build
  assert(het2.getType === GenotypeType.HET)
 
- val hom_alt = gb.setAlleles(List(GenotypeAllele.Alt, GenotypeAllele.Alt)).build
+ val hom_alt = gb.setAlleles(List(GenotypeAllele.ALT, GenotypeAllele.ALT)).build
  assert(hom_alt.getType === GenotypeType.HOM_ALT)
 
  for (a <- GenotypeAllele.values) {
- val no_call1 = gb.setAlleles(List(GenotypeAllele.NoCall, a)).build
+ val no_call1 = gb.setAlleles(List(GenotypeAllele.NO_CALL, a)).build
  assert(no_call1.getType === GenotypeType.NO_CALL)
- val no_call2 = gb.setAlleles(List(a, GenotypeAllele.NoCall)).build
+ val no_call2 = gb.setAlleles(List(a, GenotypeAllele.NO_CALL)).build
  assert(no_call2.getType === GenotypeType.NO_CALL)
  }
  }
-
 }

pom.xml

@@ -27,7 +27,7 @@
  <hadoop.version>2.6.0</hadoop.version>
  <hadoop-bam.version>7.6.0</hadoop-bam.version>
  <slf4j.version>1.7.21</slf4j.version>
- <bdg-formats.version>0.9.0</bdg-formats.version>
+ <bdg-formats.version>0.9.1-SNAPSHOT</bdg-formats.version>
  <bdg-utils.version>0.2.7</bdg-utils.version>
  <htsjdk.version>2.5.0</htsjdk.version>
  </properties>