From adb2fdbee7ebbd49de1795d9b1b7c8f6035f0d93 Mon Sep 17 00:00:00 2001 From: hanna Date: Thu, 10 Dec 2009 19:15:48 +0000 Subject: [PATCH] Before, we were only checking that the reference was present if @Requires required that a reference was present. Now we always check that a reference is present, so that we get an intelligent error message. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2311 348d0f76-0448-11de-a6fe-93d51630548a --- .../org/broadinstitute/sting/gatk/GenomeAnalysisEngine.java | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/java/src/org/broadinstitute/sting/gatk/GenomeAnalysisEngine.java b/java/src/org/broadinstitute/sting/gatk/GenomeAnalysisEngine.java index 3243985a7..80c7c6ec8 100755 --- a/java/src/org/broadinstitute/sting/gatk/GenomeAnalysisEngine.java +++ b/java/src/org/broadinstitute/sting/gatk/GenomeAnalysisEngine.java @@ -440,7 +440,8 @@ public class GenomeAnalysisEngine { */ private void validateSuppliedReferenceAgainstWalker(Walker walker, GATKArgumentCollection arguments) { // Check what the walker says is required against what was provided on the command line. - if (WalkerManager.isRequired(walker, DataSource.REFERENCE) && arguments.referenceFile == null) + // TODO: Temporarily disabling WalkerManager.isRequired check on the reference because the reference is always required. + if (/*WalkerManager.isRequired(walker, DataSource.REFERENCE) &&*/ arguments.referenceFile == null) throw new ArgumentException("Walker requires a reference but none was provided. If this is incorrect, alter the walker's @Requires annotation."); // Check what the walker says is allowed against what was provided on the command line.