From 3a15ba21022b61c3b9521de16a21ad1304bbebbe Mon Sep 17 00:00:00 2001 From: Eric Banks Date: Thu, 31 May 2012 16:05:53 -0400 Subject: [PATCH] Malformed VCF headers should be User Errors --- .../sting/utils/codecs/vcf/VCFHeaderLineTranslator.java | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFHeaderLineTranslator.java b/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFHeaderLineTranslator.java index 88fed75d7..dcc38a6f9 100755 --- a/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFHeaderLineTranslator.java +++ b/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFHeaderLineTranslator.java @@ -1,5 +1,7 @@ package org.broadinstitute.sting.utils.codecs.vcf; +import org.broadinstitute.sting.utils.exceptions.UserException; + import java.util.*; /** @@ -75,10 +77,10 @@ class VCF4Parser implements VCFLineParser { index = 0; if ( expectedTagOrder != null ) { if ( ret.size() > expectedTagOrder.size() ) - throw new IllegalArgumentException("Unexpected tag count " + ret.size() + " in string " + expectedTagOrder.size()); + throw new UserException.MalformedVCFHeader("unexpected tag count " + ret.size() + " in line " + valueLine); for ( String str : ret.keySet() ) { if ( !expectedTagOrder.get(index).equals(str) ) - throw new IllegalArgumentException("Unexpected tag " + str + " in string " + valueLine); + throw new UserException.MalformedVCFHeader("Unexpected tag " + str + " in line " + valueLine); index++; } }