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Putative fix for BAQ problem.

This commit is contained in:
Mark DePristo 2011-09-21 11:09:54 -04:00
parent 7d11f93b82
commit ecc7f34774
1 changed files with 4 additions and 4 deletions
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8
public/java/src/org/broadinstitute/sting/utils/baq/BAQ.java
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@ -5,6 +5,7 @@ import net.sf.picard.reference.ReferenceSequence;
import net.sf.samtools.CigarElement;
import net.sf.samtools.CigarOperator;
import net.sf.samtools.SAMRecord;
import net.sf.samtools.SAMUtils;
import org.broadinstitute.sting.utils.collections.Pair;
import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
import org.broadinstitute.sting.utils.exceptions.UserException;
@ -131,19 +132,18 @@ public class BAQ {
private final static double EM = 0.33333333333;
private final static double EI = 0.25;
private double[][][] EPSILONS = new double[256][256][64];
private double[][][] EPSILONS = new double[256][256][SAMUtils.MAX_PHRED_SCORE+1];
private void initializeCachedData() {
for ( int i = 0; i < 256; i++ )
for ( int j = 0; j < 256; j++ )
for ( int q = 0; q < 64; q++ ) {
double qual = qual2prob[q < minBaseQual ? minBaseQual : q];
for ( int q = 0; q <= SAMUtils.MAX_PHRED_SCORE; q++ ) {
EPSILONS[i][j][q] = 1.0;
}
for ( char b1 : "ACGTacgt".toCharArray() ) {
for ( char b2 : "ACGTacgt".toCharArray() ) {
for ( int q = 0; q < 64; q++ ) {
for ( int q = 0; q <= SAMUtils.MAX_PHRED_SCORE; q++ ) {
double qual = qual2prob[q < minBaseQual ? minBaseQual : q];
double e = Character.toLowerCase(b1) == Character.toLowerCase(b2) ? 1 - qual : qual * EM;
EPSILONS[(byte)b1][(byte)b2][q] = e;