120f90da5b400826e99005ed9b3bc8d6afb0cab0,java/src/org/broadinstitute/sting/gatk/GenomeAnalysisEngine.java,GenomeAnalysisEngine,getShardStrategy,#Walker#ReferenceSequenceFile#GenomeLocSortedSet#number#ValidationExclusion#,728
Before Change
else
throw new StingException("The GATK cannot currently process unindexed BAM files");
return new MonolithicShardStrategy(shardType,drivingDataSource.getSequenceDictionary());
}
ShardStrategy shardStrategy = null;
After Change
region = intervals.toList();
else {
region = new ArrayList<GenomeLoc>();
for(SAMSequenceRecord sequenceRecord: drivingDataSource.getSequenceDictionary().getSequences())
region.add(GenomeLocParser.createGenomeLoc(sequenceRecord.getSequenceName(),1,sequenceRecord.getSequenceLength()));
}