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Make BaseRecalibration thread-safe 

-- In the process uncovered two strange things
    1 -- qualityScoreByFullCovariateKey was created but never used.  Seems like a cache?
    2 -- Discovered nasty bug in BaseRecalibrator: https://jira.broadinstitute.org/browse/GSA-534
This commit is contained in:
Mark DePristo 2012-08-31 13:42:29 -04:00
parent 27ddebee53
commit c9ea213c9b
2 changed files with 38 additions and 9 deletions
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34
public/java/src/org/broadinstitute/sting/utils/recalibration/BaseRecalibration.java
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@ -27,12 +27,11 @@ package org.broadinstitute.sting.utils.recalibration;
import net.sf.samtools.SAMTag;
import net.sf.samtools.SAMUtils;
import org.broadinstitute.sting.utils.recalibration.covariates.Covariate;
import org.broadinstitute.sting.utils.MathUtils;
import org.broadinstitute.sting.utils.QualityUtils;
import org.broadinstitute.sting.utils.collections.NestedIntegerArray;
import org.broadinstitute.sting.utils.collections.NestedHashMap;
import org.broadinstitute.sting.utils.exceptions.UserException;
import org.broadinstitute.sting.utils.recalibration.covariates.Covariate;
import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
import java.io.File;
@ -46,7 +45,6 @@ import java.io.File;
public class BaseRecalibration {
private final static int MAXIMUM_RECALIBRATED_READ_LENGTH = 5000;
private final ReadCovariates readCovariates;
private final QuantizationInfo quantizationInfo; // histogram containing the map for qual quantization (calculated after recalibration is done)
private final RecalibrationTables recalibrationTables;
@ -56,10 +54,23 @@ public class BaseRecalibration {
private final int preserveQLessThan;
private final boolean emitOriginalQuals;
private static final NestedHashMap[] qualityScoreByFullCovariateKey = new NestedHashMap[EventType.values().length]; // Caches the result of performSequentialQualityCalculation(..) for all sets of covariate values.
static {
for (int i = 0; i < EventType.values().length; i++)
qualityScoreByFullCovariateKey[i] = new NestedHashMap();
// TODO -- was this supposed to be used somewhere?
// private static final NestedHashMap[] qualityScoreByFullCovariateKey = new NestedHashMap[EventType.values().length]; // Caches the result of performSequentialQualityCalculation(..) for all sets of covariate values.
// static {
// for (int i = 0; i < EventType.values().length; i++)
// 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);
}
};
}
/**
@ -81,7 +92,6 @@ public class BaseRecalibration {
else if (quantizationLevels > 0 && quantizationLevels != quantizationInfo.getQuantizationLevels()) // any other positive value means, we want a different quantization than the one pre-calculated in the recalibration report. Negative values mean the user did not provide a quantization argument, and just wnats to use what's in the report.
quantizationInfo.quantizeQualityScores(quantizationLevels);
readCovariates = new ReadCovariates(MAXIMUM_RECALIBRATED_READ_LENGTH, requestedCovariates.length);
this.disableIndelQuals = disableIndelQuals;
this.preserveQLessThan = preserveQLessThan;
this.emitOriginalQuals = emitOriginalQuals;
@ -104,6 +114,11 @@ 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 with -nt 1 and -nt 2 if you don't call clear here
// TODO -- needs to be fixed.
final ReadCovariates readCovariates = readCovariatesCache.get().clear();
RecalUtils.computeCovariates(read, requestedCovariates, readCovariates);
for (final EventType errorModel : EventType.values()) { // recalibrate all three quality strings
@ -130,6 +145,7 @@ public class BaseRecalibration {
}
}
/**
* Implements a serial recalibration of the reads using the combinational table.
* First, we perform a positional recalibration, and then a subsequent dinuc correction.
@ -147,7 +163,7 @@ public class BaseRecalibration {
* @param errorModel the event type
* @return A recalibrated quality score as a byte
*/
protected byte performSequentialQualityCalculation(final int[] key, final EventType errorModel) {
private byte performSequentialQualityCalculation(final int[] key, final EventType errorModel) {
final byte qualFromRead = (byte)(long)key[1];
final double globalDeltaQ = calculateGlobalDeltaQ(recalibrationTables.getTable(RecalibrationTables.TableType.READ_GROUP_TABLE), key, errorModel);

13
public/java/src/org/broadinstitute/sting/utils/recalibration/ReadCovariates.java
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@ -1,5 +1,7 @@
package org.broadinstitute.sting.utils.recalibration;
import java.util.Arrays;
/**
* The object temporarily held by a read that describes all of it's covariates.
*
@ -21,6 +23,17 @@ public class ReadCovariates {
currentCovariateIndex = index;
}
/**
* Necessary due to bug in BaseRecalibration recalibrateRead function. It is clearly seeing space it's not supposed to
* @return
*/
public ReadCovariates clear() {
for ( int i = 0; i < keys.length; i++ )
for ( int j = 0; j < keys[i].length; j++)
Arrays.fill(keys[i][j], 0);
return this;
}
public void addCovariate(final int mismatch, final int insertion, final int deletion, final int readOffset) {
keys[EventType.BASE_SUBSTITUTION.index][readOffset][currentCovariateIndex] = mismatch;
keys[EventType.BASE_INSERTION.index][readOffset][currentCovariateIndex] = insertion;