From 286b658fab8bd062e70bfa3158694dc212fb602b Mon Sep 17 00:00:00 2001 From: Eric Banks Date: Mon, 20 Aug 2012 21:25:14 -0400 Subject: [PATCH] Re-enabling parallelism in the BaseRecalibrator now that the release is out. --- .../sting/gatk/walkers/bqsr/BQSRIntegrationTest.java | 9 ++++----- .../sting/gatk/walkers/bqsr/BaseRecalibrator.java | 4 ---- 2 files changed, 4 insertions(+), 9 deletions(-) diff --git a/protected/java/test/org/broadinstitute/sting/gatk/walkers/bqsr/BQSRIntegrationTest.java b/protected/java/test/org/broadinstitute/sting/gatk/walkers/bqsr/BQSRIntegrationTest.java index 580667ee2..bd75806dd 100644 --- a/protected/java/test/org/broadinstitute/sting/gatk/walkers/bqsr/BQSRIntegrationTest.java +++ b/protected/java/test/org/broadinstitute/sting/gatk/walkers/bqsr/BQSRIntegrationTest.java @@ -75,11 +75,10 @@ public class BQSRIntegrationTest extends WalkerTest { Arrays.asList(params.md5)); executeTest("testBQSR-"+params.args, spec).getFirst(); - // TODO -- re-enable once parallelization is fixed in BaseRecalibrator - //WalkerTestSpec specNT2 = new WalkerTestSpec( - // params.getCommandLine() + " -nt 2", - // Arrays.asList(params.md5)); - //executeTest("testBQSR-nt2-"+params.args, specNT2).getFirst(); + WalkerTestSpec specNT2 = new WalkerTestSpec( + params.getCommandLine() + " -nt 2", + Arrays.asList(params.md5)); + executeTest("testBQSR-nt2-"+params.args, specNT2).getFirst(); } @Test diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/BaseRecalibrator.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/BaseRecalibrator.java index 91d982f20..e45cad971 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/BaseRecalibrator.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/BaseRecalibrator.java @@ -136,10 +136,6 @@ public class BaseRecalibrator extends LocusWalker implements TreeRed */ public void initialize() { - // TODO -- remove me after the 2.1 release - if ( getToolkit().getArguments().numberOfThreads > 1 ) - throw new UserException("We have temporarily disabled the ability to run BaseRecalibrator multi-threaded for performance reasons. We hope to have this fixed for the next GATK release (2.2) and apologize for the inconvenience."); - // check for unsupported access if (getToolkit().isGATKLite() && !getToolkit().getArguments().disableIndelQuals) throw new UserException.NotSupportedInGATKLite("base insertion/deletion recalibration is not supported, please use the --disable_indel_quals argument");