diff --git a/java/src/org/broadinstitute/sting/gatk/GenomeAnalysisEngine.java b/java/src/org/broadinstitute/sting/gatk/GenomeAnalysisEngine.java index e537aadb1..5ce8c6ae4 100755 --- a/java/src/org/broadinstitute/sting/gatk/GenomeAnalysisEngine.java +++ b/java/src/org/broadinstitute/sting/gatk/GenomeAnalysisEngine.java @@ -599,16 +599,16 @@ public class GenomeAnalysisEngine { private void validateSuppliedReadsAgainstWalker(Walker walker, GATKArgumentCollection arguments) { // Check what the walker says is required against what was provided on the command line. if (WalkerManager.isRequired(walker, DataSource.READS) && (arguments.samFiles == null || arguments.samFiles.size() == 0)) - throw new ArgumentException("Walker requires reads but none were provided. If this is incorrect, alter the walker's @Requires annotation."); + throw new ArgumentException("Walker requires reads but none were provided."); // Check what the walker says is allowed against what was provided on the command line. if ((arguments.samFiles != null && arguments.samFiles.size() > 0) && !WalkerManager.isAllowed(walker, DataSource.READS)) - throw new ArgumentException("Walker does not allow reads but reads were provided. If this is incorrect, alter the walker's @Allows annotation"); + throw new ArgumentException("Walker does not allow reads but reads were provided."); } /** * Verifies that the supplied reference file mesh with what the walker says it requires. - * + * 611 * @param walker Walker to test. * @param arguments Supplied reads files. */ @@ -616,11 +616,11 @@ public class GenomeAnalysisEngine { // Check what the walker says is required against what was provided on the command line. // 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."); + throw new ArgumentException("Walker requires a reference but none was provided."); // Check what the walker says is allowed against what was provided on the command line. if (arguments.referenceFile != null && !WalkerManager.isAllowed(walker, DataSource.REFERENCE)) - throw new ArgumentException("Walker does not allow a reference but one was provided. If this is incorrect, alter the walker's @Allows annotation"); + throw new ArgumentException("Walker does not allow a reference but one was provided."); } /** @@ -646,7 +646,7 @@ public class GenomeAnalysisEngine { // Check to see that no forbidden rods are present. for (RMDTrack rod : rods) { if (!WalkerManager.isAllowed(walker, rod)) - throw new ArgumentException(String.format("Walker of type %s does not allow access to metadata: %s. If this is incorrect, change the @Allows metadata", walker.getClass(), rod.getName())); + throw new ArgumentException(String.format("Walker of type %s does not allow access to metadata: %s", walker.getClass(), rod.getName())); } }