From fa9b2a91d05c1e5a5ecfb4db8028835e6881e264 Mon Sep 17 00:00:00 2001 From: Mark DePristo Date: Fri, 26 Oct 2012 16:25:22 -0400 Subject: [PATCH] Bugfix for GSA-552 -- https://jira.broadinstitute.org/browse/GSA-552 -- User reports a null exception while using VariantsToVCF: http://gatkforums.broadinstitute.org/discussion/1461/nullpointerexception-converting-vcf3-to-vcf-using-variantstovcf The problem is that he left out an input VCF file for the --variant argument and the command-line argument parsing code didn't catch this, so we NPE out later on. --- .../sting/commandline/ArgumentTypeDescriptor.java | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/public/java/src/org/broadinstitute/sting/commandline/ArgumentTypeDescriptor.java b/public/java/src/org/broadinstitute/sting/commandline/ArgumentTypeDescriptor.java index 54ade61f6..5d7eba16c 100644 --- a/public/java/src/org/broadinstitute/sting/commandline/ArgumentTypeDescriptor.java +++ b/public/java/src/org/broadinstitute/sting/commandline/ArgumentTypeDescriptor.java @@ -406,7 +406,7 @@ public abstract class ArgumentTypeDescriptor { else throw new UserException.CommandLineException( String.format("Failed to parse value %s for argument %s. Message: %s", - value.asString(), fieldName, e.getMessage())); + value, fieldName, e.getMessage())); } } }