From 9a54478e3693489c7aa764726d8b7ee80750baf8 Mon Sep 17 00:00:00 2001 From: Michael L Heuer Date: Fri, 31 Mar 2017 15:53:43 -0500 Subject: [PATCH] Rename recalibateBaseQualities method as recalibrateBaseQualities --- adam-cli/src/main/scala/org/bdgenomics/adam/cli/Transform.scala | 2 +- .../scala/org/bdgenomics/adam/rdd/read/AlignmentRecordRDD.scala | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/adam-cli/src/main/scala/org/bdgenomics/adam/cli/Transform.scala b/adam-cli/src/main/scala/org/bdgenomics/adam/cli/Transform.scala index 4ec875b362..6e2f21fff1 100644 --- a/adam-cli/src/main/scala/org/bdgenomics/adam/cli/Transform.scala +++ b/adam-cli/src/main/scala/org/bdgenomics/adam/cli/Transform.scala @@ -247,7 +247,7 @@ class Transform(protected val args: TransformArgs) extends BDGSparkCommand[Trans } // run bqsr - val bqsredRdd = rdd.recalibateBaseQualities( + val bqsredRdd = rdd.recalibrateBaseQualities( broadcastedSnps, args.minAcceptableQuality, optSl diff --git a/adam-core/src/main/scala/org/bdgenomics/adam/rdd/read/AlignmentRecordRDD.scala b/adam-core/src/main/scala/org/bdgenomics/adam/rdd/read/AlignmentRecordRDD.scala index b043bde6a5..9ad6ad665c 100644 --- a/adam-core/src/main/scala/org/bdgenomics/adam/rdd/read/AlignmentRecordRDD.scala +++ b/adam-core/src/main/scala/org/bdgenomics/adam/rdd/read/AlignmentRecordRDD.scala @@ -638,7 +638,7 @@ case class AlignmentRecordRDD( * of the first stage of BQSR. Defaults to StorageLevel.MEMORY_ONLY. * @return Returns an RDD of recalibrated reads. */ - def recalibateBaseQualities( + def recalibrateBaseQualities( knownSnps: Broadcast[SnpTable], minAcceptableQuality: Int = 5, optStorageLevel: Option[StorageLevel] = Some(StorageLevel.MEMORY_ONLY)): AlignmentRecordRDD = BQSRInDriver.time {