From 579e0d59fac34c076309ed434a9f9279ae91cb4e Mon Sep 17 00:00:00 2001 From: hanna Date: Fri, 14 Jan 2011 21:32:53 +0000 Subject: [PATCH] Rewrote warning message to discourage use of unsafe mode. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5003 348d0f76-0448-11de-a6fe-93d51630548a --- .../src/org/broadinstitute/sting/gatk/GenomeAnalysisEngine.java | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/java/src/org/broadinstitute/sting/gatk/GenomeAnalysisEngine.java b/java/src/org/broadinstitute/sting/gatk/GenomeAnalysisEngine.java index fb8b91d8f..eec54118c 100755 --- a/java/src/org/broadinstitute/sting/gatk/GenomeAnalysisEngine.java +++ b/java/src/org/broadinstitute/sting/gatk/GenomeAnalysisEngine.java @@ -377,7 +377,7 @@ public class GenomeAnalysisEngine { // sharding system; it's required with the new sharding system only for locus walkers. if(readsDataSource != null && !readsDataSource.hasIndex() ) { if(!exclusions.contains(ValidationExclusion.TYPE.ALLOW_UNINDEXED_BAM)) - throw new UserException.CommandLineException("The GATK cannot currently process unindexed BAM files without the -U ALLOW_UNINDEXED_BAM"); + throw new UserException.CommandLineException("Cannot process the provided BAM file(s) because they were not indexed. The GATK does offer limited processing of unindexed BAMs in --unsafe mode, but this GATK feature is currently unsupported."); if(intervals != null) throw new UserException.CommandLineException("Cannot perform interval processing when reads are present but no index is available.");