From 5a9610d87591fb9327e6fac552bdf26cba28a6b3 Mon Sep 17 00:00:00 2001 From: Mark DePristo Date: Thu, 30 Aug 2012 10:39:16 -0400 Subject: [PATCH] ReadShards now default to 10K (up from 1K) reads per samFile up to 250K -- This should help make the inputs for parallel read walkers a little meater, and avoid spinning the shard creation infrastructure so often --- .../sting/gatk/datasources/reads/SAMDataSource.java | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/SAMDataSource.java b/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/SAMDataSource.java index c8b654f81..2b88775b1 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/SAMDataSource.java +++ b/public/java/src/org/broadinstitute/sting/gatk/datasources/reads/SAMDataSource.java @@ -262,7 +262,7 @@ public class SAMDataSource { else { // Choose a sensible default for the read buffer size. For the moment, we're picking 1000 reads per BAM per shard (which effectively // will mean per-thread once ReadWalkers are parallelized) with a max cap of 250K reads in memory at once. - ReadShard.setReadBufferSize(Math.min(1000*samFiles.size(),250000)); + ReadShard.setReadBufferSize(Math.min(10000*samFiles.size(),250000)); } resourcePool = new SAMResourcePool(Integer.MAX_VALUE);