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Check header type instead of rod type, since rod type will now be VC and not VCF 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3792 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
ebanks 2010-07-14 19:10:09 +00:00
parent 0226412b11
commit e4bfb06888
1 changed files with 1 additions and 2 deletions
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3
java/src/org/broadinstitute/sting/utils/genotype/vcf/VCFUtils.java
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@ -61,7 +61,7 @@ public class VCFUtils {
List<ReferenceOrderedDataSource> dataSources = toolkit.getRodDataSources(); List<ReferenceOrderedDataSource> dataSources = toolkit.getRodDataSources();
for ( ReferenceOrderedDataSource source : dataSources ) { for ( ReferenceOrderedDataSource source : dataSources ) {
RMDTrack rod = source.getReferenceOrderedData(); RMDTrack rod = source.getReferenceOrderedData();
if ( rod.getRecordType().equals(VCFRecord.class) ) { if ( rod.getHeader() instanceof VCFHeader ) {
fields.addAll(rod.getHeader(VCFHeader.class).getMetaData()); fields.addAll(rod.getHeader(VCFHeader.class).getMetaData());
} }
} }
@ -126,7 +126,6 @@ public class VCFUtils {
public static Set<VCFHeaderLine> smartMergeHeaders(Collection<VCFHeader> headers, Logger logger) throws IllegalStateException { public static Set<VCFHeaderLine> smartMergeHeaders(Collection<VCFHeader> headers, Logger logger) throws IllegalStateException {
HashMap<String, VCFHeaderLine> map = new HashMap<String, VCFHeaderLine>(); // from KEY.NAME -> line HashMap<String, VCFHeaderLine> map = new HashMap<String, VCFHeaderLine>(); // from KEY.NAME -> line
HashSet<VCFHeaderLine> lines = new HashSet<VCFHeaderLine>();
// todo -- needs to remove all version headers from sources and add its own VCF version line // todo -- needs to remove all version headers from sources and add its own VCF version line
for ( VCFHeader source : headers ) { for ( VCFHeader source : headers ) {