From ac5e58a265e7563a866ad8b5f4fd756af8fa9579 Mon Sep 17 00:00:00 2001 From: Mark DePristo Date: Fri, 26 Oct 2012 16:34:07 -0400 Subject: [PATCH] Bugfix for GSA-540 / Update metadata maps when adding lines to VCFHeader -- https://jira.broadinstitute.org/browse/GSA-540 -- http://gatkforums.broadinstitute.org/discussion/1433/possible-bug-and-fix-in-java-code-of-vcfheader-org-broadinstitute-sting-utils-codecs-vcf-vcfheader --- .../org/broadinstitute/sting/utils/codecs/vcf/VCFHeader.java | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFHeader.java b/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFHeader.java index 2663e848f..44a3e9af3 100755 --- a/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFHeader.java +++ b/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFHeader.java @@ -159,6 +159,7 @@ public class VCFHeader { */ public void addMetaDataLine(VCFHeaderLine headerLine) { mMetaData.add(headerLine); + loadMetaDataMaps(); } /** @@ -236,7 +237,6 @@ public class VCFHeader { + VCFConstants.GENOTYPE_PL_KEY + " field. As the GATK now only manages PL fields internally" + " automatically adding a corresponding PL field to your VCF header"); addMetaDataLine(new VCFFormatHeaderLine(VCFConstants.GENOTYPE_PL_KEY, VCFHeaderLineCount.G, VCFHeaderLineType.Integer, "Normalized, Phred-scaled likelihoods for genotypes as defined in the VCF specification")); - loadMetaDataMaps(); } }