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Fixed null pointer exception in Integration Tests 

When running Utils.setupWriter with NO_PG_TAG set, the writer was attempting to create a program record with the null pointer. Fixed.
This commit is contained in:
Mauricio Carneiro 2012-11-26 11:12:27 -05:00
parent 8b749673bc
commit a3f5932501
1 changed files with 5 additions and 3 deletions
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8
public/java/src/org/broadinstitute/sting/utils/Utils.java
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@ -701,11 +701,13 @@ public class Utils {
List<SAMProgramRecord> oldRecords = header.getProgramRecords();
List<SAMProgramRecord> newRecords = new ArrayList<SAMProgramRecord>(oldRecords.size()+1);
for ( SAMProgramRecord record : oldRecords )
if ( !record.getId().startsWith(programRecord.getId()) || KEEP_ALL_PG_RECORDS )
if ( (programRecord != null && !record.getId().startsWith(programRecord.getId())) || KEEP_ALL_PG_RECORDS )
newRecords.add(record);
newRecords.add(programRecord);
header.setProgramRecords(newRecords);
if (programRecord != null) {
newRecords.add(programRecord);
header.setProgramRecords(newRecords);
}
return header;
}