From 9b61d95d9c3f1f9590f8464d3f859fe88212a620 Mon Sep 17 00:00:00 2001 From: hanna Date: Fri, 19 Mar 2010 02:43:46 +0000 Subject: [PATCH] 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 --- .../org/broadinstitute/sting/gatk/GenomeAnalysisEngine.java | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/java/src/org/broadinstitute/sting/gatk/GenomeAnalysisEngine.java b/java/src/org/broadinstitute/sting/gatk/GenomeAnalysisEngine.java index 0ccfeb40b..d77ed666a 100755 --- a/java/src/org/broadinstitute/sting/gatk/GenomeAnalysisEngine.java +++ b/java/src/org/broadinstitute/sting/gatk/GenomeAnalysisEngine.java @@ -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);