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Better TODO message

This commit is contained in:
Eric Banks 2011-12-22 20:54:35 -05:00
parent a815e875a8
commit 8762313a0d
1 changed files with 4 additions and 1 deletions
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public/java/src/org/broadinstitute/sting/gatk/GenomeAnalysisEngine.java
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@ -469,7 +469,10 @@ public class GenomeAnalysisEngine {
throw new ReviewedStingException("Unable to determine walker type for walker " + walker.getClass().getName()); throw new ReviewedStingException("Unable to determine walker type for walker " + walker.getClass().getName());
} }
else { else {
final int SHARD_SIZE = walker instanceof RodWalker ? 1000000 : 100000; // TODO -- make it a multiple of 16K // TODO -- Determine what the ideal shard size should be here. Matt suggested that a multiple of 16K might work well
// TODO -- (because of how VCF indexes work), but my empirical experience has been simply that the larger the shard
// TODO -- size the more efficient the traversal (at least for RODWalkers). Keeping the previous values for now. [EB]
final int SHARD_SIZE = walker instanceof RodWalker ? 1000000 : 100000;
if(intervals == null) if(intervals == null)
return referenceDataSource.createShardsOverEntireReference(readsDataSource,genomeLocParser,SHARD_SIZE); return referenceDataSource.createShardsOverEntireReference(readsDataSource,genomeLocParser,SHARD_SIZE);
else else