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Khalid found an out-of-memory condition with the new sharding system when 

merging lots of BAMs, and the fix is taking longer than I thought.  Disable
experimental sharding when merging until the fix is ready.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3036 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
hanna 2010-03-19 02:43:46 +00:00
parent b8e8852b4f
commit 9b61d95d9c
1 changed files with 4 additions and 0 deletions
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4
java/src/org/broadinstitute/sting/gatk/GenomeAnalysisEngine.java
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@ -753,6 +753,10 @@ public class GenomeAnalysisEngine {
if (reads.getReadsFiles().size() == 0)
return null;
// Force dynamic merging to use original sharding method until memory usage is under control.
if (reads.getReadsFiles().size() > 1)
argCollection.disableExperimentalSharding = true;
SAMDataSource dataSource = null;
if(!argCollection.disableExperimentalSharding)
dataSource = new BlockDrivenSAMDataSource(reads);