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Small runtime improvement in TableRecalibration. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2519 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
rpoplin 2010-01-06 15:51:12 +00:00
parent b745c2f8d7
commit 370a365147
1 changed files with 11 additions and 13 deletions
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24
java/src/org/broadinstitute/sting/gatk/walkers/recalibration/TableRecalibrationWalker.java
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@ -351,16 +351,14 @@ public class TableRecalibrationWalker extends ReadWalker<SAMRecord, SAMFileWrite
*/ */
private byte performSequentialQualityCalculation(Object... key ) { private byte performSequentialQualityCalculation(Object... key ) {
final String readGroupKeyElement = key[0].toString(); final byte qualFromRead = (byte)Integer.parseInt(key[1].toString());
final int qualityScoreKeyElement = Integer.parseInt(key[1].toString());
final byte qualFromRead = (byte)qualityScoreKeyElement;
final Object[] readGroupCollapsedKey = new Object[1]; final Object[] readGroupCollapsedKey = new Object[1];
final Object[] qualityScoreCollapsedKey = new Object[2]; final Object[] qualityScoreCollapsedKey = new Object[2];
final Object[] covariateCollapsedKey = new Object[3]; final Object[] covariateCollapsedKey = new Object[3];
// The global quality shift (over the read group only) // The global quality shift (over the read group only)
readGroupCollapsedKey[0] = readGroupKeyElement; readGroupCollapsedKey[0] = key[0];
RecalDatum globalRecalDatum = ((RecalDatum)dataManager.getCollapsedTable(0).get( readGroupCollapsedKey )); final RecalDatum globalRecalDatum = ((RecalDatum)dataManager.getCollapsedTable(0).get( readGroupCollapsedKey ));
double globalDeltaQ = 0.0; double globalDeltaQ = 0.0;
if( globalRecalDatum != null ) { if( globalRecalDatum != null ) {
double globalDeltaQEmpirical = globalRecalDatum.getEmpiricalQuality(); double globalDeltaQEmpirical = globalRecalDatum.getEmpiricalQuality();
@ -369,9 +367,9 @@ public class TableRecalibrationWalker extends ReadWalker<SAMRecord, SAMFileWrite
} }
// The shift in quality between reported and empirical // The shift in quality between reported and empirical
qualityScoreCollapsedKey[0] = readGroupKeyElement; qualityScoreCollapsedKey[0] = key[0];
qualityScoreCollapsedKey[1] = qualityScoreKeyElement; qualityScoreCollapsedKey[1] = key[1];
RecalDatum qReportedRecalDatum = ((RecalDatum)dataManager.getCollapsedTable(1).get( qualityScoreCollapsedKey )); final RecalDatum qReportedRecalDatum = ((RecalDatum)dataManager.getCollapsedTable(1).get( qualityScoreCollapsedKey ));
double deltaQReported = 0.0; double deltaQReported = 0.0;
if( qReportedRecalDatum != null ) { if( qReportedRecalDatum != null ) {
double deltaQReportedEmpirical = qReportedRecalDatum.getEmpiricalQuality(); double deltaQReportedEmpirical = qReportedRecalDatum.getEmpiricalQuality();
@ -381,11 +379,11 @@ public class TableRecalibrationWalker extends ReadWalker<SAMRecord, SAMFileWrite
// The shift in quality due to each covariate by itself in turn // The shift in quality due to each covariate by itself in turn
double deltaQCovariates = 0.0; double deltaQCovariates = 0.0;
double deltaQCovariateEmpirical; double deltaQCovariateEmpirical;
covariateCollapsedKey[0] = readGroupKeyElement; covariateCollapsedKey[0] = key[0];
covariateCollapsedKey[1] = qualityScoreKeyElement; covariateCollapsedKey[1] = key[1];
for( int iii = 2; iii < key.length; iii++ ) { for( int iii = 2; iii < key.length; iii++ ) {
covariateCollapsedKey[2] = key[iii]; // The given covariate covariateCollapsedKey[2] = key[iii]; // The given covariate
RecalDatum covariateRecalDatum = ((RecalDatum)dataManager.getCollapsedTable(iii).get( covariateCollapsedKey )); final RecalDatum covariateRecalDatum = ((RecalDatum)dataManager.getCollapsedTable(iii).get( covariateCollapsedKey ));
if( covariateRecalDatum != null ) { if( covariateRecalDatum != null ) {
deltaQCovariateEmpirical = covariateRecalDatum.getEmpiricalQuality(); deltaQCovariateEmpirical = covariateRecalDatum.getEmpiricalQuality();
deltaQCovariates += ( deltaQCovariateEmpirical - qualFromRead - (globalDeltaQ + deltaQReported) ); deltaQCovariates += ( deltaQCovariateEmpirical - qualFromRead - (globalDeltaQ + deltaQReported) );
@ -393,7 +391,7 @@ public class TableRecalibrationWalker extends ReadWalker<SAMRecord, SAMFileWrite
} }
final double newQuality = qualFromRead + globalDeltaQ + deltaQReported + deltaQCovariates; final double newQuality = qualFromRead + globalDeltaQ + deltaQReported + deltaQCovariates;
final byte newQualityByte = QualityUtils.boundQual( (int)Math.round(newQuality), QualityUtils.MAX_REASONABLE_Q_SCORE ); return QualityUtils.boundQual( (int)Math.round(newQuality), QualityUtils.MAX_REASONABLE_Q_SCORE );
// Verbose printouts used to validate with old recalibrator // Verbose printouts used to validate with old recalibrator
@ -406,7 +404,7 @@ public class TableRecalibrationWalker extends ReadWalker<SAMRecord, SAMFileWrite
// key.get(0).toString(), key.get(3).toString(), key.get(2).toString(), key.get(1).toString(), qualFromRead, globalDeltaQ, deltaQReported, deltaQPos, deltaQDinuc, newQualityByte) ); // key.get(0).toString(), key.get(3).toString(), key.get(2).toString(), key.get(1).toString(), qualFromRead, globalDeltaQ, deltaQReported, deltaQPos, deltaQDinuc, newQualityByte) );
//} //}
return newQualityByte; //return newQualityByte;
} }
/** /**