zzh
/
gatk-3.8
1
0
Fork 0
Code Issues Pull Requests Packages Projects Releases Wiki Activity

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
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

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>(); Set<String> keys = new HashSet<String>();
for ( Genotype g : vc.getGenotypes().values() ) { for ( Genotype g : vc.getGenotypes().values() ) {
for ( String key : g.getAttributes().keySet() ) { keys.addAll(g.getAttributes().keySet());
keys.add(key);
}
} }
keys.add(VCFGenotypeRecord.GENOTYPE_QUALITY_KEY); 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) { public static String getMissingFieldValue(String field) {
String result; String result = "";
if ( field.equals(GENOTYPE_QUALITY_KEY) ) if ( field.equals(GENOTYPE_QUALITY_KEY) )
result = String.valueOf(MISSING_GENOTYPE_QUALITY); result = String.valueOf(MISSING_GENOTYPE_QUALITY);
else if ( field.equals(DEPTH_KEY) || field.equals(OLD_DEPTH_KEY) ) else if ( field.equals(DEPTH_KEY) || field.equals(OLD_DEPTH_KEY) )
@ -328,8 +328,6 @@ public class VCFGenotypeRecord {
// TODO -- support haplotype quality // TODO -- support haplotype quality
//else if ( field.equals(HAPLOTYPE_QUALITY_KEY) ) //else if ( field.equals(HAPLOTYPE_QUALITY_KEY) )
// result = String.valueOf(MISSING_HAPLOTYPE_QUALITY); // result = String.valueOf(MISSING_HAPLOTYPE_QUALITY);
else
result = "-1";
return result; return result;
} }