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Merge branch 'master' of ssh://gsa3.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable

This commit is contained in:
Menachem Fromer 2012-10-26 00:14:58 -04:00
parent 0fe36b1c72 d879c77aca
commit e0fa7d1497
2 changed files with 2 additions and 22 deletions
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2
public/java/src/org/broadinstitute/sting/queue/extensions/gatk/ArgumentDefinitionField.java
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@ -346,7 +346,7 @@ public abstract class ArgumentDefinitionField extends ArgumentField {
@Override
protected String getFreezeFields() {
return String.format("if (num_threads.isDefined) nCoresRequest = num_threads%n");
return String.format("if (num_threads.isDefined) nCoresRequest = num_threads%nif (num_cpu_threads_per_data_thread.isDefined) nCoresRequest = Some(nCoresRequest.getOrElse(1) * num_cpu_threads_per_data_thread.getOrElse(1))%n");
}
}

22
public/java/src/org/broadinstitute/sting/utils/recalibration/BaseRecalibration.java
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@ -61,17 +61,6 @@ public class BaseRecalibration {
// qualityScoreByFullCovariateKey[i] = new NestedHashMap();
// }
/**
* Thread local cache to allow multi-threaded use of this class
*/
private ThreadLocal<ReadCovariates> readCovariatesCache;
{
readCovariatesCache = new ThreadLocal<ReadCovariates> () {
@Override protected ReadCovariates initialValue() {
return new ReadCovariates(MAXIMUM_RECALIBRATED_READ_LENGTH, requestedCovariates.length);
}
};
}
/**
* Constructor using a GATK Report file
@ -113,16 +102,7 @@ public class BaseRecalibration {
}
}
// Compute all covariates for the read
// TODO -- the need to clear here suggests there's an error in the indexing / assumption code
// TODO -- for BI and DI. Perhaps due to the indel buffer size on the ends of the reads?
// TODO -- the output varies depending on whether we clear or not
//final ReadCovariates readCovariates = readCovariatesCache.get().clear();
// the original code -- doesn't do any clearing
final ReadCovariates readCovariates = readCovariatesCache.get();
RecalUtils.computeCovariates(read, requestedCovariates, readCovariates);
final ReadCovariates readCovariates = RecalUtils.computeCovariates(read, requestedCovariates);
for (final EventType errorModel : EventType.values()) { // recalibrate all three quality strings
if (disableIndelQuals && errorModel != EventType.BASE_SUBSTITUTION) {