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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
This commit is contained in:
ebanks 2010-03-19 03:56:27 +00:00
parent 0311980668
commit e757f6f078
2 changed files with 2 additions and 6 deletions
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4
java/src/org/broadinstitute/sting/gatk/refdata/VariantContextAdaptors.java
View File

@ -352,9 +352,7 @@ public class VariantContextAdaptors {
Set<String> keys = new HashSet<String>();
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);

4
java/src/org/broadinstitute/sting/utils/genotype/vcf/VCFGenotypeRecord.java
View File

@ -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;
}