From e077347cc21ec10584fafeb0f475822f4876dcad Mon Sep 17 00:00:00 2001 From: David Roazen Date: Fri, 21 Sep 2012 22:27:45 -0400 Subject: [PATCH] Re-allow running the GATK with experimental downsampling It's now possible to run with experimental downsampling enabled using the --enable_experimental_downsampling engine argument. This is scheduled to become the GATK-wide default next week after diff engine output for failing tests has been examined. --- .../org/broadinstitute/sting/gatk/GenomeAnalysisEngine.java | 5 ----- 1 file changed, 5 deletions(-) diff --git a/public/java/src/org/broadinstitute/sting/gatk/GenomeAnalysisEngine.java b/public/java/src/org/broadinstitute/sting/gatk/GenomeAnalysisEngine.java index 077d208d5..67e5ad95b 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/GenomeAnalysisEngine.java +++ b/public/java/src/org/broadinstitute/sting/gatk/GenomeAnalysisEngine.java @@ -445,11 +445,6 @@ public class GenomeAnalysisEngine { GATKArgumentCollection argCollection = this.getArguments(); boolean useExperimentalDownsampling = argCollection.enableExperimentalDownsampling; - // until the file pointer bug with the experimental downsamplers is fixed, disallow running with experimental downsampling - if ( useExperimentalDownsampling ) { - throw new UserException("The experimental downsampling implementation is currently crippled by a file-pointer-related bug. Until this bug is fixed, it's not safe (or possible) for anyone to use the experimental implementation!"); - } - DownsamplingMethod commandLineMethod = argCollection.getDownsamplingMethod(); DownsamplingMethod walkerMethod = WalkerManager.getDownsamplingMethod(walker, useExperimentalDownsampling); DownsamplingMethod defaultMethod = DownsamplingMethod.getDefaultDownsamplingMethod(walker, useExperimentalDownsampling);