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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
This commit is contained in:
hanna 2009-12-10 19:15:48 +00:00
parent 5eac510b2f
commit adb2fdbee7
1 changed files with 2 additions and 1 deletions
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3
java/src/org/broadinstitute/sting/gatk/GenomeAnalysisEngine.java
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@ -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.