Skip to content

ArrayList cannot be cast to class String in VariantContextConverter #2419

@heuermh

Description

@heuermh
$ adam-submit transformVariants NA12878.hg38.g.vcf.gz NA12878.hg38.variants.parquet
...
Caused by: java.lang.ClassCastException: class java.util.ArrayList cannot be cast to class java.lang.String (java.util.ArrayList and java.lang.String are in module java.base of loader 'bootstrap')
	at org.bdgenomics.adam.converters.VariantContextConverter.asString(VariantContextConverter.scala:1350)
	at org.bdgenomics.adam.converters.VariantContextConverter.$anonfun$lineToVariantContextExtractor$17(VariantContextConverter.scala:1512)
	at scala.Option.map(Option.scala:230)
	at org.bdgenomics.adam.converters.VariantContextConverter.variantContextFieldExtractor(VariantContextConverter.scala:1469)
	at org.bdgenomics.adam.converters.VariantContextConverter.$anonfun$lineToVariantContextExtractor$16(VariantContextConverter.scala:1512)
	at org.bdgenomics.adam.converters.VariantContextConverter.$anonfun$lineToVariantContextExtractor$16$adapted(VariantContextConverter.scala:1510)
	at org.bdgenomics.adam.converters.VariantContextConverter.$anonfun$makeVariantFormatFn$13(VariantContextConverter.scala:1774)
	at scala.collection.TraversableLike.$anonfun$flatMap$1(TraversableLike.scala:293)
	at scala.collection.mutable.ResizableArray.foreach(ResizableArray.scala:62)
	at scala.collection.mutable.ResizableArray.foreach$(ResizableArray.scala:55)
	at scala.collection.mutable.ArrayBuffer.foreach(ArrayBuffer.scala:49)
	at scala.collection.TraversableLike.flatMap(TraversableLike.scala:293)
	at scala.collection.TraversableLike.flatMap$(TraversableLike.scala:290)
	at scala.collection.AbstractTraversable.flatMap(Traversable.scala:108)
	at org.bdgenomics.adam.converters.VariantContextConverter.convert$1(VariantContextConverter.scala:1774)

Metadata

Metadata

Assignees

No one assigned

    Labels

    No labels
    No labels

    Type

    No type

    Projects

    No projects

    Milestone

    No milestone

    Relationships

    None yet

    Development

    No branches or pull requests

    Issue actions