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Better error message for malformed input recal file.

This commit is contained in:
Ryan Poplin 2012-03-23 10:47:01 -04:00
parent b8cd959461
commit ab288354e9
1 changed files with 2 additions and 0 deletions
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public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/ApplyRecalibration.java
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@ -184,6 +184,8 @@ public class ApplyRecalibration extends RodWalker<Integer, Integer> {
} }
} catch ( FileNotFoundException e ) { } catch ( FileNotFoundException e ) {
throw new UserException.CouldNotReadInputFile(RECAL_FILE, e); throw new UserException.CouldNotReadInputFile(RECAL_FILE, e);
} catch ( Exception e ) {
throw new UserException.MalformedFile(RECAL_FILE, "Could not parse LOD and annotation information in input recal file. File is somehow malformed.");
} }
} }