From 8645a79978990e2c7d598b6f24bc4c3e7fbab9c3 Mon Sep 17 00:00:00 2001 From: Chris Vittal Date: Wed, 10 May 2023 11:39:09 -0400 Subject: [PATCH] [query] Better message for LocalLDPrune only taking diploid calls resolves #12971 --- hail/src/main/scala/is/hail/methods/LocalLDPrune.scala | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/hail/src/main/scala/is/hail/methods/LocalLDPrune.scala b/hail/src/main/scala/is/hail/methods/LocalLDPrune.scala index 72561e02d55..a8ad1e29ac3 100644 --- a/hail/src/main/scala/is/hail/methods/LocalLDPrune.scala +++ b/hail/src/main/scala/is/hail/methods/LocalLDPrune.scala @@ -46,7 +46,9 @@ class BitPackedVectorBuilder(nSamples: Int) { def addGT(call: Int): Unit = { require(idx < nSamples) - require(Call.isDiploid(call)) + if (!Call.isDiploid(call)) { + fatal(s"hail LD prune does not support non-diploid calls, found ${Call.toString(call)}") + } val gt = Call.nNonRefAlleles(call) pack = pack | ((gt & 3).toLong << packOffset)