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Temporarily disabling multi-threaded usage of BaseRecalibrator for performance reasons.

This commit is contained in:
Eric Banks 2012-08-20 12:43:17 -04:00
parent 97b191f578
commit 154f65e0de
2 changed files with 9 additions and 4 deletions
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9
protected/java/test/org/broadinstitute/sting/gatk/walkers/bqsr/BQSRIntegrationTest.java
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@ -75,10 +75,11 @@ public class BQSRIntegrationTest extends WalkerTest {
Arrays.asList(params.md5)); Arrays.asList(params.md5));
executeTest("testBQSR-"+params.args, spec).getFirst(); executeTest("testBQSR-"+params.args, spec).getFirst();
WalkerTestSpec specNT2 = new WalkerTestSpec( // TODO -- re-enable once parallelization is fixed in BaseRecalibrator
params.getCommandLine() + " -nt 2", //WalkerTestSpec specNT2 = new WalkerTestSpec(
Arrays.asList(params.md5)); // params.getCommandLine() + " -nt 2",
executeTest("testBQSR-nt2-"+params.args, specNT2).getFirst(); // Arrays.asList(params.md5));
//executeTest("testBQSR-nt2-"+params.args, specNT2).getFirst();
} }
@Test @Test

4
public/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/BaseRecalibrator.java
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@ -136,6 +136,10 @@ public class BaseRecalibrator extends LocusWalker<Long, Long> implements TreeRed
*/ */
public void initialize() { 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 // check for unsupported access
if (getToolkit().isGATKLite() && !getToolkit().getArguments().disableIndelQuals) if (getToolkit().isGATKLite() && !getToolkit().getArguments().disableIndelQuals)
throw new UserException.NotSupportedInGATKLite("base insertion/deletion recalibration is not supported, please use the --disable_indel_quals argument"); throw new UserException.NotSupportedInGATKLite("base insertion/deletion recalibration is not supported, please use the --disable_indel_quals argument");