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Improvements and bug fixes galore. (1) Now properly handles Q0 bases, filtering them out, you can disable this if you need to (2) support for three-state base probabilities (see email), which is disabled by default (still experimental) but appears to be more emppowered to detect variants (see email too) 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1326 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
depristo 2009-07-28 13:21:27 +00:00
parent d665d9714f
commit 46643d3724
1 changed files with 68 additions and 26 deletions
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94
java/src/org/broadinstitute/sting/playground/utils/GenotypeLikelihoods.java
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@ -10,12 +10,23 @@ import java.util.HashMap;
public class GenotypeLikelihoods {
// precalculate these for performance (pow/log10 is expensive!)
/**
* SOLID data uses Q0 bases to represent reference-fixed bases -- they shouldn't be counted
* during GL calculations. If this field is true, Q0 bases will be removed in add().
*/
private boolean filterQ0Bases = true;
private static final double[] oneMinusData = new double[Byte.MAX_VALUE];
private static final double[] oneHalfMinusDataArachne = new double[Byte.MAX_VALUE];
private static final double[] oneHalfMinusData3Base = new double[Byte.MAX_VALUE];
private static final double log10Of1_3 = log10(1.0 / 3);
private static final double log10Of2_3 = log10(2.0 / 3);
static {
for (int qual = 0; qual < Byte.MAX_VALUE; qual++) {
oneMinusData[qual] = log10(1.0 - pow(10, (qual / -10.0)));
//oneMinusData[qual] = log10(1.0 - QualityUtils.qualToProb(qual));
}
}
@ -23,16 +34,17 @@ public class GenotypeLikelihoods {
return oneMinusData[qual];
}
private static final double[] oneHalfMinusData = new double[Byte.MAX_VALUE];
static {
for (int qual = 0; qual < Byte.MAX_VALUE; qual++) {
oneHalfMinusData[qual] = log10(0.5 - pow(10, (qual / -10.0)) / 2.0);
//oneHalfMinusData[qual] = log10(0.5 - QualityUtils.qualToProb(qual) / 2.0);
double e = pow(10, (qual / -10.0));
oneHalfMinusDataArachne[qual] = log10(0.5 - e / 2.0);
oneHalfMinusData3Base[qual] = log10(0.5 - e / 2.0 + e / 6.0);
//System.out.printf("qual=%d, e=%f, oneHalfMinusDataArachne=%f, oneHalfMinusData3Base=%f%n", qual, e, oneHalfMinusDataArachne[qual], oneHalfMinusData3Base[qual]);
}
}
private static double getOneHalfMinusQual(final byte qual) {
private double getOneHalfMinusQual(final byte qual) {
return oneHalfMinusData[qual];
}
@ -56,6 +68,8 @@ public class GenotypeLikelihoods {
private double priorHomRef;
private double priorHet;
private double priorHomVar;
private double[] oneHalfMinusData;
private boolean threeBaseErrors = false;
// Store the 2nd-best base priors for on-genotype primary bases
private HashMap<String, Double> onNextBestBasePriors = new HashMap<String, Double>();
@ -67,21 +81,41 @@ public class GenotypeLikelihoods {
double[] p2ndon = {0.000, 0.302, 0.366, 0.142, 0.000, 0.548, 0.370, 0.000, 0.319, 0.000};
double[] p2ndoff = {0.480, 0.769, 0.744, 0.538, 0.575, 0.727, 0.768, 0.589, 0.762, 0.505};
initialize(1.0 - 1e-3, 1e-3, 1e-5, p2ndon, p2ndoff);
initialize(false, 1.0 - 1e-3, 1e-3, 1e-5, p2ndon, p2ndoff);
}
public GenotypeLikelihoods(double priorHomRef, double priorHet, double priorHomVar) {
public GenotypeLikelihoods(boolean threeBaseErrors , double priorHomRef, double priorHet, double priorHomVar) {
double[] p2ndon = {0.000, 0.302, 0.366, 0.142, 0.000, 0.548, 0.370, 0.000, 0.319, 0.000};
double[] p2ndoff = {0.480, 0.769, 0.744, 0.538, 0.575, 0.727, 0.768, 0.589, 0.762, 0.505};
initialize(priorHomRef, priorHet, priorHomVar, p2ndon, p2ndoff);
initialize(threeBaseErrors, priorHomRef, priorHet, priorHomVar, p2ndon, p2ndoff);
}
public GenotypeLikelihoods(double priorHomRef, double priorHet, double priorHomVar, double[] p2ndon, double[] p2ndoff) {
initialize(priorHomRef, priorHet, priorHomVar, p2ndon, p2ndoff);
public GenotypeLikelihoods(boolean threeBaseErrors , double priorHomRef, double priorHet, double priorHomVar, double[] p2ndon, double[] p2ndoff) {
initialize(threeBaseErrors, priorHomRef, priorHet, priorHomVar, p2ndon, p2ndoff);
}
private void initialize(double priorHomRef, double priorHet, double priorHomVar, double[] p2ndon, double[] p2ndoff) {
/**
* Are we ignoring Q0 bases during calculations?
* @return
*/
public boolean isFilteringQ0Bases() {
return filterQ0Bases;
}
/**
* Enable / disable filtering of Q0 bases. Enabled by default
*
* @param filterQ0Bases
*/
public void filterQ0Bases(boolean filterQ0Bases) {
this.filterQ0Bases = filterQ0Bases;
}
private void initialize(boolean threeBaseErrors , double priorHomRef, double priorHet, double priorHomVar, double[] p2ndon, double[] p2ndoff) {
this.threeBaseErrors = threeBaseErrors ;
this.oneHalfMinusData = threeBaseErrors ? oneHalfMinusData3Base : oneHalfMinusDataArachne;
this.priorHomRef = priorHomRef;
this.priorHet = priorHet;
this.priorHomVar = priorHomVar;
@ -92,8 +126,6 @@ public class GenotypeLikelihoods {
for (int i = 0; i < likelihoods.length; i++) { likelihoods[i] = Math.log10(0.1); }
for (int genotypeIndex = 0; genotypeIndex < 10; genotypeIndex++) {
onNextBestBasePriors.put(genotypes[genotypeIndex], p2ndon[genotypeIndex]);
offNextBestBasePriors.put(genotypes[genotypeIndex], p2ndoff[genotypeIndex]);
@ -156,9 +188,15 @@ public class GenotypeLikelihoods {
}
}
public void add(char ref, char read, byte qual)
{
if (qual <= 0) { qual = 1; }
public int add(char ref, char read, byte qual)
{
if (qual <= 0) {
if ( isFilteringQ0Bases() ) {
return 0;
} else {
qual = 1;
}
}
if (coverage == 0)
{
@ -167,23 +205,23 @@ public class GenotypeLikelihoods {
likelihoods[i] = 0;
}
}
double sum = 0.0;
for (int i = 0; i < genotypes.length; i++)
for (int i = 0; i < genotypes.length; i++)
{
double likelihood = calculateAlleleLikelihood(ref, read, genotypes[i], qual);
double likelihood = calculateAlleleLikelihood(ref, read, genotypes[i], qual);
//if ( originalQual == 0 ) System.out.printf("Likelihood is %f for %c %c %d %s%n", likelihood, ref, read, qual, genotypes[i]);
likelihoods[i] += likelihood;
coverage += 1;
// if (i == 8) {
// System.out.println(genotypes[8] + " " + likelihood + " " + likelihoods[8] + " " + coverage);
// }
}
return 1;
}
private double calculateAlleleLikelihood(char ref, char read, String genotype, byte qual) {
if (qual == 0) {
qual = 1;
} // zero quals are wrong.
// zero quals are wrong
throw new RuntimeException(String.format("Unexpected Q0 base discovered in calculateAlleleLikelihood: %c %c %d", ref, read, qual));
}
char h1 = genotype.charAt(0);
char h2 = genotype.charAt(1);
@ -193,9 +231,13 @@ public class GenotypeLikelihoods {
if ((h1 == h2) && (h1 == read)) {
// hom
p_base = getOneMinusQual(qual);
} else if ((h1 != h2) && ((h1 == read) || (h2 == read))) {
} else if ( (h1 != h2) && ((h1 == read) || (h2 == read)) ) {
// het
p_base = getOneHalfMinusQual(qual);
} else if ( this.threeBaseErrors ) {
// error
//System.out.printf("%s %b %f %f%n", genotype, h1 != h2, log10Of2_3, log10Of1_3 );
p_base = qual / -10.0 + ( h1 != h2 ? log10Of1_3 : log10Of1_3 );
} else {
// error
p_base = qual / -10.0;