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Throw a UserException in the BQSR when there is no data instead of creating an empty csv file

This commit is contained in:
Ryan Poplin 2011-10-26 15:56:41 -04:00
parent 585a45b7a3
commit 86871bd1e3
1 changed files with 3 additions and 0 deletions
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3
public/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/CountCovariatesWalker.java
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@ -526,6 +526,9 @@ public class CountCovariatesWalker extends LocusWalker<CountCovariatesWalker.Cou
*/ */
public void onTraversalDone( CountedData sum ) { public void onTraversalDone( CountedData sum ) {
logger.info( "Writing raw recalibration data..." ); logger.info( "Writing raw recalibration data..." );
if( sum.countedBases == 0L ) {
throw new UserException.BadInput("Could not find any usable data in the input BAM file(s).");
}
outputToCSV( sum, RECAL_FILE ); outputToCSV( sum, RECAL_FILE );
logger.info( "...done!" ); logger.info( "...done!" );
} }