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first pass of well-formatted tribble exceptions 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4352 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
aaron 2010-09-25 03:29:33 +00:00
parent edaa278edd
commit 70f03a7113
1 changed files with 6 additions and 6 deletions
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12
java/src/org/broadinstitute/sting/gatk/refdata/tracks/builders/RMDTrackBuilder.java
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@ -50,7 +50,7 @@ import java.util.*;
/** /**
* *
* @author aaron * @author aaron
* * `
* Class RMDTrackBuilder * Class RMDTrackBuilder
* *
* This class keeps track of the available codecs, and knows how to put together a track of * This class keeps track of the available codecs, and knows how to put together a track of
@ -168,8 +168,8 @@ public class RMDTrackBuilder extends PluginManager<FeatureCodec> {
logger.info("Attempting to blindly load " + inputFile + " as a tabix indexed file"); logger.info("Attempting to blindly load " + inputFile + " as a tabix indexed file");
try { try {
return new Pair<BasicFeatureSource, SAMSequenceDictionary>(BasicFeatureSource.getFeatureSource(inputFile.getAbsolutePath(), createCodec(targetClass, name)),null); return new Pair<BasicFeatureSource, SAMSequenceDictionary>(BasicFeatureSource.getFeatureSource(inputFile.getAbsolutePath(), createCodec(targetClass, name)),null);
} catch (IOException e) { } catch (TribbleException e) {
throw new UserException.CouldNotReadInputFile(inputFile, "Unable to create feature reader from file", e); throw new UserException(e.getTribbleExceptionMessage(), e);
} }
} }
@ -210,10 +210,10 @@ public class RMDTrackBuilder extends PluginManager<FeatureCodec> {
index, index,
createCodec(targetClass, name)), createCodec(targetClass, name)),
dictFromIndex); dictFromIndex);
} catch (FileNotFoundException e) { } catch (TribbleException e) {
throw new UserException.CouldNotReadInputFile(inputFile, "Unable to create reader with file", e); throw new UserException(e.getTribbleExceptionMessage());
} catch (IOException e) { } catch (IOException e) {
throw new UserException("Unable to make the index file for " + inputFile, e); throw new UserException("Unable to create the index file for " + inputFile, e);
} }
return reader; return reader;
} }