diff --git a/adam-cli/src/main/scala/org/bdgenomics/adam/cli/AlleleCount.scala b/adam-cli/src/main/scala/org/bdgenomics/adam/cli/AlleleCount.scala
index 0e347869d7..39206d6a80 100644
--- a/adam-cli/src/main/scala/org/bdgenomics/adam/cli/AlleleCount.scala
+++ b/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
}
diff --git a/adam-core/src/main/scala/org/bdgenomics/adam/converters/VariantContextConverter.scala b/adam-core/src/main/scala/org/bdgenomics/adam/converters/VariantContextConverter.scala
index 3b304d7a22..d8f754676c 100644
--- a/adam-core/src/main/scala/org/bdgenomics/adam/converters/VariantContextConverter.scala
+++ b/adam-core/src/main/scala/org/bdgenomics/adam/converters/VariantContextConverter.scala
@@ -17,6 +17,7 @@
*/
package org.bdgenomics.adam.converters
+import com.google.common.collect.ImmutableList
import htsjdk.variant.variantcontext.{
Allele,
GenotypesContext,
@@ -24,6 +25,7 @@ import htsjdk.variant.variantcontext.{
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(_))
diff --git a/adam-core/src/main/scala/org/bdgenomics/adam/projections/FeatureField.scala b/adam-core/src/main/scala/org/bdgenomics/adam/projections/FeatureField.scala
index a421f7d0b1..297a2e51e7 100644
--- a/adam-core/src/main/scala/org/bdgenomics/adam/projections/FeatureField.scala
+++ b/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$) {
- val featureId, name, source, featureType, contigName, start, end, strand, phase, frame, score, geneId, transcriptId, exonId, aliases, parentIds, target, gap, derivesFrom, notes, dbxrefs, ontologyTerms, isCircular, attributes = SchemaValue
+ val featureId, name, source, featureType, contigName, start, end, strand, phase, frame, score, geneId, transcriptId, exonId, aliases, parentIds, target, gap, derivesFrom, notes, dbxrefs, ontologyTerms, circular, attributes = SchemaValue
}
diff --git a/adam-core/src/main/scala/org/bdgenomics/adam/projections/GenotypeField.scala b/adam-core/src/main/scala/org/bdgenomics/adam/projections/GenotypeField.scala
index f1bf083c5c..ee58581998 100644
--- a/adam-core/src/main/scala/org/bdgenomics/adam/projections/GenotypeField.scala
+++ b/adam-core/src/main/scala/org/bdgenomics/adam/projections/GenotypeField.scala
@@ -24,5 +24,5 @@ import org.bdgenomics.formats.avro.Genotype
*/
object GenotypeField extends FieldEnumeration(Genotype.SCHEMA$) {
- 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
}
diff --git a/adam-core/src/main/scala/org/bdgenomics/adam/projections/VariantField.scala b/adam-core/src/main/scala/org/bdgenomics/adam/projections/VariantField.scala
index f3464162e9..9080bcecc7 100644
--- a/adam-core/src/main/scala/org/bdgenomics/adam/projections/VariantField.scala
+++ b/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
}
diff --git a/adam-core/src/main/scala/org/bdgenomics/adam/rdd/features/Features.scala b/adam-core/src/main/scala/org/bdgenomics/adam/rdd/features/Features.scala
index ee6968c8c7..448cdfd949 100644
--- a/adam-core/src/main/scala/org/bdgenomics/adam/rdd/features/Features.scala
+++ b/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", _))
diff --git a/adam-core/src/main/scala/org/bdgenomics/adam/rich/RichGenotype.scala b/adam-core/src/main/scala/org/bdgenomics/adam/rich/RichGenotype.scala
index ec20b6a324..fca64e30f3 100644
--- a/adam-core/src/main/scala/org/bdgenomics/adam/rich/RichGenotype.scala
+++ b/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
diff --git a/adam-core/src/main/scala/org/bdgenomics/adam/serialization/ADAMKryoRegistrator.scala b/adam-core/src/main/scala/org/bdgenomics/adam/serialization/ADAMKryoRegistrator.scala
index fee76f1e9c..3ba0cf5ea2 100644
--- a/adam-core/src/main/scala/org/bdgenomics/adam/serialization/ADAMKryoRegistrator.scala
+++ b/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])
diff --git a/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala b/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala
index 8eab9cae45..f0d82c0dbb 100644
--- a/adam-core/src/test/scala/org/bdgenomics/adam/converters/VariantContextConverterSuite.scala
+++ b/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
diff --git a/adam-core/src/test/scala/org/bdgenomics/adam/rdd/features/FeatureRDDSuite.scala b/adam-core/src/test/scala/org/bdgenomics/adam/rdd/features/FeatureRDDSuite.scala
index f958fb888f..2d467d30e2 100644
--- a/adam-core/src/test/scala/org/bdgenomics/adam/rdd/features/FeatureRDDSuite.scala
+++ b/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 &&
diff --git a/adam-core/src/test/scala/org/bdgenomics/adam/rdd/variation/VariantContextRDDSuite.scala b/adam-core/src/test/scala/org/bdgenomics/adam/rdd/variation/VariantContextRDDSuite.scala
index 10e04845f7..cf974e7ef3 100644
--- a/adam-core/src/test/scala/org/bdgenomics/adam/rdd/variation/VariantContextRDDSuite.scala
+++ b/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(
diff --git a/adam-core/src/test/scala/org/bdgenomics/adam/rich/RichGenotypeSuite.scala b/adam-core/src/test/scala/org/bdgenomics/adam/rich/RichGenotypeSuite.scala
index da2f6eb5d0..fb1a344f5c 100644
--- a/adam-core/src/test/scala/org/bdgenomics/adam/rich/RichGenotypeSuite.scala
+++ b/adam-core/src/test/scala/org/bdgenomics/adam/rich/RichGenotypeSuite.scala
@@ -32,7 +32,7 @@ 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)
}
}
@@ -40,23 +40,22 @@ class RichGenotypeSuite extends FunSuite {
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)
}
}
-
}
diff --git a/pom.xml b/pom.xml
index fa0531ca9f..fa0d58e200 100644
--- a/pom.xml
+++ b/pom.xml
@@ -27,7 +27,7 @@
2.6.0
7.6.0
1.7.21
- 0.10.0-SNAPSHOT
+ 0.9.1-SNAPSHOT
0.2.7
2.5.0