From 8762313a0dffa7f04c8fd40e3c0edf06a3209657 Mon Sep 17 00:00:00 2001 From: Eric Banks Date: Thu, 22 Dec 2011 20:54:35 -0500 Subject: [PATCH] Better TODO message --- .../org/broadinstitute/sting/gatk/GenomeAnalysisEngine.java | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/public/java/src/org/broadinstitute/sting/gatk/GenomeAnalysisEngine.java b/public/java/src/org/broadinstitute/sting/gatk/GenomeAnalysisEngine.java index f6956f530..f954d7650 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/GenomeAnalysisEngine.java +++ b/public/java/src/org/broadinstitute/sting/gatk/GenomeAnalysisEngine.java @@ -469,7 +469,10 @@ public class GenomeAnalysisEngine { throw new ReviewedStingException("Unable to determine walker type for walker " + walker.getClass().getName()); } 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) return referenceDataSource.createShardsOverEntireReference(readsDataSource,genomeLocParser,SHARD_SIZE); else