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Very annoying: we have been emitting an extra TAB in the header of the VCF (which breaks some parsers) for sites-only file. Hopefully not too many integration tests will need to be fixed...

This commit is contained in:
Eric Banks 2012-05-07 12:20:11 -04:00
parent a90482c772
commit 66838a073e
1 changed files with 5 additions and 1 deletions
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6
public/java/src/org/broadinstitute/sting/utils/codecs/vcf/StandardVCFWriter.java
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@ -108,9 +108,13 @@ public class StandardVCFWriter extends IndexingVCFWriter {
// write out the column line // write out the column line
mWriter.write(VCFHeader.HEADER_INDICATOR); mWriter.write(VCFHeader.HEADER_INDICATOR);
boolean isFirst = true;
for ( VCFHeader.HEADER_FIELDS field : mHeader.getHeaderFields() ) { for ( VCFHeader.HEADER_FIELDS field : mHeader.getHeaderFields() ) {
mWriter.write(field.toString()); if ( isFirst )
isFirst = false; // don't write out a field separator
else
mWriter.write(VCFConstants.FIELD_SEPARATOR); mWriter.write(VCFConstants.FIELD_SEPARATOR);
mWriter.write(field.toString());
} }
if ( mHeader.hasGenotypingData() ) { if ( mHeader.hasGenotypingData() ) {