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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@2054 348d0f76-0448-11de-a6fe-93d51630548a
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rpoplin 2009-11-16 18:44:54 +00:00
parent 4558375575
commit eb07c7f7f8
1 changed files with 5 additions and 0 deletions
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5
java/src/org/broadinstitute/sting/playground/gatk/walkers/Recalibration/CovariateCounterWalker.java
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@ -114,6 +114,11 @@ public class CovariateCounterWalker extends LocusWalker<Integer, PrintStream> {
System.exit( 0 ); // early exit here because user requested it System.exit( 0 ); // early exit here because user requested it
} }
// 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?");
}
// Initialize the requested covariates by parsing the -cov argument // Initialize the requested covariates by parsing the -cov argument
requestedCovariates = new ArrayList<Covariate>(); requestedCovariates = new ArrayList<Covariate>();
if( validateOldRecalibrator ) { if( validateOldRecalibrator ) {