From abc13d0a90a3e1986262ff28b3a46eb72a247343 Mon Sep 17 00:00:00 2001 From: hanna Date: Mon, 29 Nov 2010 23:37:30 +0000 Subject: [PATCH] Temporary hack: force abort with an intelligent message suggesting that users specify -B:dbsnp,vcf if the filename passed if the --DBSNP argument value contains 'vcf'. We'll replace this functionality once dbSNP 132 starts playing nicely with the tagging system. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4749 348d0f76-0448-11de-a6fe-93d51630548a --- .../sting/gatk/refdata/tracks/builders/RMDTrackBuilder.java | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/java/src/org/broadinstitute/sting/gatk/refdata/tracks/builders/RMDTrackBuilder.java b/java/src/org/broadinstitute/sting/gatk/refdata/tracks/builders/RMDTrackBuilder.java index cca74eb25..f2bc8af4b 100644 --- a/java/src/org/broadinstitute/sting/gatk/refdata/tracks/builders/RMDTrackBuilder.java +++ b/java/src/org/broadinstitute/sting/gatk/refdata/tracks/builders/RMDTrackBuilder.java @@ -399,8 +399,11 @@ public class RMDTrackBuilder extends PluginManager { } private void initializeConvenienceBindings(AbstractGenomeAnalysisEngine engine, GATKArgumentCollection argCollection) { - if (argCollection.DBSNPFile != null) + if (argCollection.DBSNPFile != null) { + if(argCollection.DBSNPFile.toLowerCase().contains("vcf")) + throw new UserException("--DBSNP (-D) argument currently does not support VCF. To use dbSNP in VCF format, please use -B:dbsnp,vcf ."); inputs.add(new RMDTriplet(DbSNPHelper.STANDARD_DBSNP_TRACK_NAME, "dbsnp", argCollection.DBSNPFile)); + } } /**