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Legacy BaseRecalibrator walker is neither TreeReducible nor NanoSchedulable 

The old BaseRecalibrator walker is and never will be thread-safe, since it's a
LocusWalker that uses read attributes to track state.

ONLY the newer DelocalizedBaseRecalibrator is believed likely to be thread-safe
at this point. It is safe to run the DelocalizedBaseRecalibrator with -nct > 1
for testing purposes, but wait for further testing to be done before using it
for production purposes in multithreaded mode.
This commit is contained in:
David Roazen 2012-10-24 15:06:13 -04:00
parent 32a6d7000a
commit 02018ca764
2 changed files with 1 additions and 11 deletions
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5
protected/java/test/org/broadinstitute/sting/gatk/walkers/bqsr/BQSRIntegrationTest.java
View File

@ -73,11 +73,6 @@ public class BQSRIntegrationTest extends WalkerTest {
params.getCommandLine(),
Arrays.asList(params.md5));
executeTest("testBQSR-"+params.args, spec).getFirst();
WalkerTestSpec specNT2 = new WalkerTestSpec(
params.getCommandLine() + " -nt 2",
Arrays.asList(params.md5));
executeTest("testBQSR-nt2-"+params.args, specNT2).getFirst();
}
@Test

7
public/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/BaseRecalibrator.java
View File

@ -109,7 +109,7 @@ import java.util.ArrayList;
@ReadFilters({MappingQualityZeroFilter.class, MappingQualityUnavailableFilter.class}) // only look at covered loci, not every loci of the reference file
@Requires({DataSource.READS, DataSource.REFERENCE}) // filter out all reads with zero or unavailable mapping quality
@PartitionBy(PartitionType.LOCUS) // this walker requires both -I input.bam and -R reference.fasta
public class BaseRecalibrator extends LocusWalker<Long, Long> implements TreeReducible<Long>, NanoSchedulable {
public class BaseRecalibrator extends LocusWalker<Long, Long> {
@ArgumentCollection
private final RecalibrationArgumentCollection RAC = new RecalibrationArgumentCollection(); // all the command line arguments for BQSR and it's covariates
@ -277,11 +277,6 @@ public class BaseRecalibrator extends LocusWalker<Long, Long> implements TreeRed
return sum;
}
public Long treeReduce(Long sum1, Long sum2) {
sum1 += sum2;
return sum1;
}
@Override
public void onTraversalDone(Long result) {
logger.info("Calculating quantized quality scores...");