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()));
            }