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Fixed issue with RODWalker parallelization. 

Turns out that someone previously upped the declared size of a ROD shard to 100M bases, making
each ROD shard larger than the size of chr20.  Why didn't we see this in Stable?  Because the
ShardStrategy/ShardStrategyFactory mechanism was dutifully ignoring the shard size specification.
When I rolled the ShardStrategy/ShardStrategyFactory mechanics back into the DataSources as part
of the async I/O project, I inadvertently reenabled this specifier.
This commit is contained in:
Matt Hanna 2011-12-07 11:55:42 -05:00
parent 5869a87e48
commit 15533e08df
1 changed files with 1 additions and 1 deletions
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public/java/src/org/broadinstitute/sting/gatk/GenomeAnalysisEngine.java
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@ -469,7 +469,7 @@ public class GenomeAnalysisEngine {
throw new ReviewedStingException("Unable to determine walker type for walker " + walker.getClass().getName());
}
else {
final int SHARD_SIZE = walker instanceof RodWalker ? 100000000 : 100000;
final int SHARD_SIZE = walker instanceof RodWalker ? 1000000 : 100000;
if(intervals == null)
return referenceDataSource.createShardsOverEntireReference(readsDataSource,genomeLocParser,SHARD_SIZE);
else