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Improvements to error messages about @Requires and @Allows 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4334 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
depristo 2010-09-23 12:08:27 +00:00
parent 7841b301c4
commit d081b9b352
1 changed files with 6 additions and 6 deletions
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12
java/src/org/broadinstitute/sting/gatk/GenomeAnalysisEngine.java
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@ -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()));
}
}