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fix old squiggly lines
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ehigham committed Sep 19, 2024

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bastianallgeier Bastian Allgeier
1 parent 39413f7 commit 4576acf
Showing 1 changed file with 7 additions and 8 deletions.
Original file line number Diff line number Diff line change
@@ -13,7 +13,7 @@ import is.hail.expr.ir.functions.IRFunctionRegistry
import is.hail.io.reference.{IndexedFastaSequenceFile, LiftOver}
import is.hail.linalg.RowMatrix
import is.hail.types.physical.PStruct
import is.hail.types.virtual.{TArray, TInterval, TStruct}
import is.hail.types.virtual.{TArray, TInterval}
import is.hail.utils.{defaultJSONFormats, fatal, log, toRichIterable, HailException, Interval}
import is.hail.variant.ReferenceGenome

@@ -151,7 +151,7 @@ trait Py4JBackendExtensions {
val tir = TableLiteral(
TableValue(
ctx,
signature.virtualType.asInstanceOf[TStruct],
signature.virtualType,
key,
df.rdd,
Some(signature),
@@ -176,17 +176,16 @@ trait Py4JBackendExtensions {
case json4s.JObject(values) => values.toMap
}

val paths =
kvs("paths").asInstanceOf[json4s.JArray].arr.toArray.map { case json4s.JString(s) =>
s
}
val paths = kvs("paths").asInstanceOf[json4s.JArray].arr.toArray.map {
case json4s.JString(s) => s
}

val intervalPointType = parseType(kvs("intervalPointType").asInstanceOf[json4s.JString].s)
val intervalObjects =
JSONAnnotationImpex.importAnnotation(kvs("intervals"), TArray(TInterval(intervalPointType)))
.asInstanceOf[IndexedSeq[Interval]]

val opts = NativeReaderOptions(intervalObjects, intervalPointType, filterIntervals = false)
val opts = NativeReaderOptions(intervalObjects, intervalPointType)
val matrixReaders: IndexedSeq[MatrixIR] = paths.map { p =>
log.info(s"creating MatrixRead node for $p")
val mnr = MatrixNativeReader(ctx.fs, p, Some(opts))
@@ -207,7 +206,7 @@ trait Py4JBackendExtensions {
references(name).addLiftover(references(destRGName), LiftOver(ctx.fs, chainFile))
}

def pyRemoveLiftover(name: String, destRGName: String) =
def pyRemoveLiftover(name: String, destRGName: String): Unit =
references(name).removeLiftover(destRGName)

private[this] def addReference(rg: ReferenceGenome): Unit = {

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