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Point MAX_QUAL_SCORE to SAMUtils.MAX_PHRED_SCORE. 

Also, array size for caches should be max score + 1.



git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2444 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
ebanks 2009-12-24 20:47:32 +00:00
parent 438d21842a
commit 0571d9dcb9
3 changed files with 5 additions and 3 deletions
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2
java/src/org/broadinstitute/sting/gatk/walkers/genotyper/GenotypeLikelihoods.java
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@ -328,7 +328,7 @@ public class GenotypeLikelihoods implements Cloneable {
return 1;
}
static GenotypeLikelihoods[][][][][][] CACHE = new GenotypeLikelihoods[BaseMismatchModel.values().length][EmpiricalSubstitutionProbabilities.SequencerPlatform.values().length][BaseUtils.BASES.length][QualityUtils.MAX_QUAL_SCORE][MAX_PLOIDY][2];
static GenotypeLikelihoods[][][][][][] CACHE = new GenotypeLikelihoods[BaseMismatchModel.values().length][EmpiricalSubstitutionProbabilities.SequencerPlatform.values().length][BaseUtils.BASES.length][QualityUtils.MAX_QUAL_SCORE+1][MAX_PLOIDY][2];
private boolean inCache( char observedBase, byte qualityScore, int ploidy, SAMRecord read) {
return getCache(CACHE, observedBase, qualityScore, ploidy, read) != null;

2
java/src/org/broadinstitute/sting/gatk/walkers/genotyper/PooledCalculationModel.java
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@ -77,7 +77,7 @@ public class PooledCalculationModel extends JointEstimateGenotypeCalculationMode
static double[][][][][][][][] CACHE = null;
static int N_CACHED = 0;
private static void makeCache(int pool_size) {
CACHE = new double[BaseMismatchModel.values().length][EmpiricalSubstitutionProbabilities.SequencerPlatform.values().length][BaseUtils.BASES.length][BaseUtils.BASES.length][BaseUtils.BASES.length][QualityUtils.MAX_QUAL_SCORE][2][2 * pool_size+1];
CACHE = new double[BaseMismatchModel.values().length][EmpiricalSubstitutionProbabilities.SequencerPlatform.values().length][BaseUtils.BASES.length][BaseUtils.BASES.length][BaseUtils.BASES.length][QualityUtils.MAX_QUAL_SCORE+1][2][2 * pool_size+1];
}
protected void setCache( int refIndex, int altIndex, int nAltAlleles, char base, byte qual, SAMRecord read, double val ) {

4
java/src/org/broadinstitute/sting/utils/QualityUtils.java
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@ -1,5 +1,7 @@
package org.broadinstitute.sting.utils;
import net.sf.samtools.SAMUtils;
/**
* QualityUtils is a static class (no instantiation allowed!) with some utility methods for manipulating
* quality scores.
@ -7,7 +9,7 @@ package org.broadinstitute.sting.utils;
* @author Kiran Garimella
*/
public class QualityUtils {
public final static byte MAX_QUAL_SCORE = 63;
public final static byte MAX_QUAL_SCORE = SAMUtils.MAX_PHRED_SCORE;
public final static double MIN_REASONABLE_ERROR = 0.0001;
public final static byte MAX_REASONABLE_Q_SCORE = 40;