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Meaningful error message when an IntervalArg file fails to parse correctly

This commit is contained in:
Mark DePristo 2011-11-10 17:10:26 -05:00
parent bb7bf74aa8
commit dc9b351b5e
1 changed files with 4 additions and 1 deletions
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5
public/java/src/org/broadinstitute/sting/commandline/IntervalBinding.java
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@ -92,7 +92,10 @@ public final class IntervalBinding<T extends Feature> {
codec.readHeader(lineReader);
String line = lineReader.readLine();
while ( line != null ) {
intervals.add(toolkit.getGenomeLocParser().createGenomeLoc(codec.decodeLoc(line)));
final Feature feature = codec.decodeLoc(line);
if ( feature == null )
throw new UserException.MalformedFile(featureIntervals.getSource(), "Couldn't parse line '" + line + "'");
intervals.add(toolkit.getGenomeLocParser().createGenomeLoc(feature));
line = lineReader.readLine();
}
} catch (IOException e) {