From eb07c7f7f80c9545c0fc4883cdf761c3e54850ee Mon Sep 17 00:00:00 2001 From: rpoplin Date: Mon, 16 Nov 2009 18:44:54 +0000 Subject: [PATCH] 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 --- .../gatk/walkers/Recalibration/CovariateCounterWalker.java | 5 +++++ 1 file changed, 5 insertions(+) diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/Recalibration/CovariateCounterWalker.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/Recalibration/CovariateCounterWalker.java index f24136cd3..f39d136cb 100755 --- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/Recalibration/CovariateCounterWalker.java +++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/Recalibration/CovariateCounterWalker.java @@ -114,6 +114,11 @@ public class CovariateCounterWalker extends LocusWalker { 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 requestedCovariates = new ArrayList(); if( validateOldRecalibrator ) {