From e757f6f07822b96bae57a2491bb6e5b2bb7cadb5 Mon Sep 17 00:00:00 2001 From: ebanks Date: Fri, 19 Mar 2010 03:56:27 +0000 Subject: [PATCH] Missing value for arbitrary format entries is empty string (need to revisit at some point, but it will require updating the VCF spec). git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3038 348d0f76-0448-11de-a6fe-93d51630548a --- .../sting/gatk/refdata/VariantContextAdaptors.java | 4 +--- .../sting/utils/genotype/vcf/VCFGenotypeRecord.java | 4 +--- 2 files changed, 2 insertions(+), 6 deletions(-) diff --git a/java/src/org/broadinstitute/sting/gatk/refdata/VariantContextAdaptors.java b/java/src/org/broadinstitute/sting/gatk/refdata/VariantContextAdaptors.java index a417a6b62..bc644a72a 100755 --- a/java/src/org/broadinstitute/sting/gatk/refdata/VariantContextAdaptors.java +++ b/java/src/org/broadinstitute/sting/gatk/refdata/VariantContextAdaptors.java @@ -352,9 +352,7 @@ public class VariantContextAdaptors { Set keys = new HashSet(); for ( Genotype g : vc.getGenotypes().values() ) { - for ( String key : g.getAttributes().keySet() ) { - keys.add(key); - } + keys.addAll(g.getAttributes().keySet()); } keys.add(VCFGenotypeRecord.GENOTYPE_QUALITY_KEY); diff --git a/java/src/org/broadinstitute/sting/utils/genotype/vcf/VCFGenotypeRecord.java b/java/src/org/broadinstitute/sting/utils/genotype/vcf/VCFGenotypeRecord.java index 2ab618586..606866436 100644 --- a/java/src/org/broadinstitute/sting/utils/genotype/vcf/VCFGenotypeRecord.java +++ b/java/src/org/broadinstitute/sting/utils/genotype/vcf/VCFGenotypeRecord.java @@ -316,7 +316,7 @@ public class VCFGenotypeRecord { } public static String getMissingFieldValue(String field) { - String result; + String result = ""; if ( field.equals(GENOTYPE_QUALITY_KEY) ) result = String.valueOf(MISSING_GENOTYPE_QUALITY); else if ( field.equals(DEPTH_KEY) || field.equals(OLD_DEPTH_KEY) ) @@ -328,8 +328,6 @@ public class VCFGenotypeRecord { // TODO -- support haplotype quality //else if ( field.equals(HAPLOTYPE_QUALITY_KEY) ) // result = String.valueOf(MISSING_HAPLOTYPE_QUALITY); - else - result = "-1"; return result; }