From 967215066d53c15c2f68eccab6ac4926f4a4b690 Mon Sep 17 00:00:00 2001 From: rpoplin Date: Mon, 16 Nov 2009 19:16:46 +0000 Subject: [PATCH] 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 --- .../gatk/walkers/recalibration/CovariateCounterWalker.java | 5 +++++ 1 file changed, 5 insertions(+) diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/CovariateCounterWalker.java b/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/CovariateCounterWalker.java index 31cd4fd4e..c860993f2 100644 --- a/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/CovariateCounterWalker.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/CovariateCounterWalker.java @@ -76,6 +76,11 @@ public class CovariateCounterWalker extends LocusWalker { 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())); }