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BQSR optimization: don't clone the original quals for each read, we can just overwrite the original array

This commit is contained in:
Eric Banks 2012-06-07 19:41:03 -04:00
parent 32e4fe5c87
commit 0fb9179f76
1 changed files with 6 additions and 7 deletions
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13
public/java/src/org/broadinstitute/sting/utils/recalibration/BaseRecalibration.java
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@ -88,19 +88,18 @@ public class BaseRecalibration {
public void recalibrateRead(final GATKSAMRecord read) {
final ReadCovariates readCovariates = RecalDataManager.computeCovariates(read, requestedCovariates); // compute all covariates for the read
for (final EventType errorModel : EventType.values()) { // recalibrate all three quality strings
final byte[] originalQuals = read.getBaseQualities(errorModel);
final byte[] recalQuals = originalQuals.clone();
final byte[] quals = read.getBaseQualities(errorModel);
for (int offset = 0; offset < read.getReadLength(); offset++) { // recalibrate all bases in the read
byte qualityScore = originalQuals[offset];
final byte originalQualityScore = quals[offset];
if (qualityScore >= QualityUtils.MIN_USABLE_Q_SCORE) { // only recalibrate usable qualities (the original quality will come from the instrument -- reported quality)
if (originalQualityScore >= QualityUtils.MIN_USABLE_Q_SCORE) { // only recalibrate usable qualities (the original quality will come from the instrument -- reported quality)
final BitSet[] keySet = readCovariates.getKeySet(offset, errorModel); // get the keyset for this base using the error model
qualityScore = performSequentialQualityCalculation(keySet, errorModel); // recalibrate the base
final byte recalibratedQualityScore = performSequentialQualityCalculation(keySet, errorModel); // recalibrate the base
quals[offset] = recalibratedQualityScore;
}
recalQuals[offset] = qualityScore;
}
read.setBaseQualities(recalQuals, errorModel);
read.setBaseQualities(quals, errorModel);
}
}