ReferenceSequenceFile drivingDataSource,
GenomeLocSortedSet intervals,
Integer maxIterations,
ValidationExclusion exclusions) {
if(readsDataSource != null && !readsDataSource.hasIndex() ) {
<BUG>if(!exclusions.contains(ValidationExclusion.TYPE.ALLOW_UNINDEXED_BAM) || intervals != null)
throw new StingException("The GATK cannot currently process unindexed BAM files without the -U ALLOW_UNINDEXED_BAM, or with unindexed BAM files with the -L option");
Shard.ShardType shardType;</BUG>
if(walker instanceof LocusWalker) {
if(readsDataSource != null && readsDataSource.getSortOrder() != SAMFileHeader.SortOrder.coordinate)

ReferenceSequenceFile drivingDataSource,
GenomeLocSortedSet intervals,
Integer maxIterations,
ValidationExclusion exclusions) {
if(readsDataSource != null && !readsDataSource.hasIndex() ) {
if(!exclusions.contains(ValidationExclusion.TYPE.ALLOW_UNINDEXED_BAM))
throw new StingException("The GATK cannot currently process unindexed BAM files without the -U ALLOW_UNINDEXED_BAM");
if(intervals != null && WalkerManager.getWalkerDataSource(walker) != DataSource.REFERENCE)
throw new StingException("Cannot shard input by interval when walker is not driven by reference.");
Shard.ShardType shardType;
if(walker instanceof LocusWalker) {
if(readsDataSource != null && readsDataSource.getSortOrder() != SAMFileHeader.SortOrder.coordinate)
