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The old CountCovariates now warns the user if they didn't supply a dbSNP rod file. Thanks Kiran for the use case. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2055 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
rpoplin 2009-11-16 19:16:46 +00:00
parent eb07c7f7f8
commit 967215066d
1 changed files with 5 additions and 0 deletions
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5
java/src/org/broadinstitute/sting/gatk/walkers/recalibration/CovariateCounterWalker.java
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@ -76,6 +76,11 @@ public class CovariateCounterWalker extends LocusWalker<Integer, PrintStream> {
readGroups.add(readGroup.getReadGroupId());
}
// Warn the user if no dbSNP file was specified
if( this.getToolkit().getArguments().DBSNPFile == null ) {
Utils.warnUser("This calculation is critically dependent on being able to skip over known variant sites. Are you sure you want to be running without a dbSNP rod specified?");
}
covariateCounter = new CovariateCounter(readGroups, collapsePos, collapseDinuc, assumeFaultyHeader);
logger.info(String.format("Created recalibration data collectors for %d read group(s)", covariateCounter.getNReadGroups()));
}