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[query] Liftover NoSuchElementException

See original GitHub issue

Topics: https://hail.zulipchat.com/#narrow/stream/123010-Hail-0.2E2.20support/topic/key.20not.20found.3A.20GRCh38/near/247317975 https://discuss.hail.is/t/potential-liftover-issue-error-summary-nosuchelementexception-key-not-found-grch37/2154

Stack trace:

java.util.NoSuchElementException: key not found: GRCh37
	at scala.collection.MapLike.default(MapLike.scala:235)
	at scala.collection.MapLike.default$(MapLike.scala:234)
	at scala.collection.AbstractMap.default(Map.scala:65)
	at scala.collection.mutable.HashMap.apply(HashMap.scala:69)
	at is.hail.variant.ReferenceGenome.getLiftover(ReferenceGenome.scala:412)
	at is.hail.variant.ReferenceGenome.liftoverLocus(ReferenceGenome.scala:423)
	at __C700Compiled.applyregion0_8(Emit.scala)
	at __C700Compiled.apply(Emit.scala)
	at is.hail.expr.ir.TableMapRows.$anonfun$execute$43(TableIR.scala:1936)

See Lindo’s comment in the Zulip thread to replicate (hopefully)

Issue Analytics

State:
Created 2 years ago
Comments:5

Top GitHub Comments

1reaction

tpoterbacommented, Aug 23, 2021

I’m intending to debug/fix this today. I’ll update this evening about progress.

0reactions

DSuvegescommented, Dec 6, 2021

Oh sorry @tpoterba , this issue got completely slipped off my radar.

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