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A few more char -> byte cleanups 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3398 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
depristo 2010-05-20 00:02:06 +00:00
parent 8a725b6c93
commit 5abac5c057
9 changed files with 47 additions and 36 deletions
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4
java/src/org/broadinstitute/sting/gatk/contexts/ReferenceContext.java
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@ -53,6 +53,9 @@ public class ReferenceContext {
*/
private byte[] bases;
/**
* A cache of the bases converted to characters for walkers not yet using byte[] interface
*/
private char[] basesAsCharCached = null;
/**
@ -64,6 +67,7 @@ public class ReferenceContext {
this( locus, locus, new byte[] { base } );
}
// todo -- this really should take the referenceview as an option and only grab the bases if necessary
public ReferenceContext( GenomeLoc locus, GenomeLoc window, byte[] bases ) {
// if( !window.containsP(locus) )
// throw new StingException("Invalid locus or window; window does not contain locus");

7
java/src/org/broadinstitute/sting/gatk/walkers/genotyper/BatchedCallsMerger.java
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@ -1,5 +1,5 @@
/*
* Copyright (c) 2010.
* Copyright (c) 2010, The Broad Institute
*
* Permission is hereby granted, free of charge, to any person
* obtaining a copy of this software and associated documentation
@ -12,15 +12,14 @@
*
* The above copyright notice and this permission notice shall be
* included in all copies or substantial portions of the Software.
*
* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
* EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
* OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
* NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
* HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
* WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
* FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR
* THE USE OR OTHER DEALINGS IN THE SOFTWARE.
* FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
* OTHER DEALINGS IN THE SOFTWARE.
*/
package org.broadinstitute.sting.gatk.walkers.genotyper;

7
java/src/org/broadinstitute/sting/gatk/walkers/genotyper/CreateTriggerTrack.java
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@ -1,5 +1,5 @@
/*
* Copyright (c) 2010.
* Copyright (c) 2010, The Broad Institute
*
* Permission is hereby granted, free of charge, to any person
* obtaining a copy of this software and associated documentation
@ -12,15 +12,14 @@
*
* The above copyright notice and this permission notice shall be
* included in all copies or substantial portions of the Software.
*
* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
* EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
* OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
* NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
* HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
* WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
* FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR
* THE USE OR OTHER DEALINGS IN THE SOFTWARE.
* FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
* OTHER DEALINGS IN THE SOFTWARE.
*/
package org.broadinstitute.sting.gatk.walkers.genotyper;

10
java/src/org/broadinstitute/sting/gatk/walkers/genotyper/DiploidGenotypePriors.java
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@ -73,7 +73,7 @@ public class DiploidGenotypePriors {
* @param ref
* @param heterozygosity
*/
public DiploidGenotypePriors(char ref, double heterozygosity, boolean dontPolarize) {
public DiploidGenotypePriors(byte ref, double heterozygosity, boolean dontPolarize) {
if ( dontPolarize ) {
double[] vals = heterozygosity2DiploidProbabilities(heterozygosity);
priors = getReferenceIndependentPriors(ref, vals[0], vals[1], vals[2]);
@ -90,7 +90,7 @@ public class DiploidGenotypePriors {
* @param heterozygosity
* @param probOfTriStateGenotype The prob of seeing a true B/C het when the reference is A
*/
public DiploidGenotypePriors(char ref, double heterozygosity, double probOfTriStateGenotype) {
public DiploidGenotypePriors(byte ref, double heterozygosity, double probOfTriStateGenotype) {
priors = getReferencePolarizedPriors(ref, heterozygosity, probOfTriStateGenotype);
}
@ -226,7 +226,7 @@ public class DiploidGenotypePriors {
* @param heterozyosity
* @param pRefError
*/
public static double[] getReferencePolarizedPriors(char ref, double heterozyosity, double pRefError ) {
public static double[] getReferencePolarizedPriors(byte ref, double heterozyosity, double pRefError ) {
if ( ! MathUtils.isBounded(pRefError, 0.0, 0.01) ) {
throw new RuntimeException(String.format("BUG: p Reference error is out of bounds (0.0 - 0.01) is allow range %f", pRefError));
}
@ -276,7 +276,7 @@ public class DiploidGenotypePriors {
* @param priorHomVar
*/
@Deprecated
public static double[] getReferenceIndependentPriors(char ref, double priorHomRef, double priorHet, double priorHomVar ) {
public static double[] getReferenceIndependentPriors(byte ref, double priorHomRef, double priorHet, double priorHomVar ) {
if ((priorHomRef + priorHet + priorHomVar) != 1) {
throw new RuntimeException(String.format("Prior probabilities don't sum to one => %f, %f, %f", priorHomRef, priorHet, priorHomVar));
}
@ -284,7 +284,7 @@ public class DiploidGenotypePriors {
double[] priors = new double[DiploidGenotype.values().length];
for ( DiploidGenotype g : DiploidGenotype.values() ) {
int nRefBases = MathUtils.countOccurrences(ref, g.toString());
int nRefBases = MathUtils.countOccurrences((char)ref, g.toString()); // todo -- fixme
double log10POfG = 0.0;
switch ( nRefBases ) {

2
java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperEngine.java
View File

@ -215,7 +215,7 @@ public class UnifiedGenotyperEngine {
if ( stratifiedContexts == null )
return null;
DiploidGenotypePriors priors = new DiploidGenotypePriors(ref, UAC.heterozygosity, DiploidGenotypePriors.PROB_OF_REFERENCE_ERROR);
DiploidGenotypePriors priors = new DiploidGenotypePriors((byte)ref, UAC.heterozygosity, DiploidGenotypePriors.PROB_OF_REFERENCE_ERROR);
call = gcm.get().callLocus(tracker, ref, rawContext.getLocation(), stratifiedContexts, priors);
// annotate the call, if possible

26
java/src/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalWalker.java
View File

@ -638,19 +638,19 @@ public class VariantEvalWalker extends RodWalker<Integer, Integer> {
}
}
private String formatKeyword(String keyWord) {
//System.out.printf("keyword %s%n", keyWord);
StringBuilder s = new StringBuilder();
int i = 0;
for ( String part : keyWord.split("\\.") ) {
//System.out.printf("part %s %d%n", part, nameSizes[i]);
s.append(String.format("%" + nameSizes[i] + "s ", part));
i++;
}
return s.toString();
}
// private String formatKeyword(String keyWord) {
// //System.out.printf("keyword %s%n", keyWord);
//
// StringBuilder s = new StringBuilder();
// int i = 0;
// for ( String part : keyWord.split("\\.") ) {
// //System.out.printf("part %s %d%n", part, nameSizes[i]);
// s.append(String.format("%" + nameSizes[i] + "s ", part));
// i++;
// }
//
// return s.toString();
// }
public void onTraversalDone(Integer result) {
// our report mashaller

2
java/src/org/broadinstitute/sting/playground/gatk/walkers/papergenotyper/GATKPaperGenotyper.java
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@ -68,7 +68,7 @@ public class GATKPaperGenotyper extends LocusWalker<SimpleCall, Integer> impleme
if (ref.getBase() == 'N' || ref.getBase() == 'n') return null; // we don't deal with the N ref base case
ReadBackedPileup pileup = context.getPileup();
double likelihoods[] = DiploidGenotypePriors.getReferencePolarizedPriors(ref.getBaseAsChar(),
double likelihoods[] = DiploidGenotypePriors.getReferencePolarizedPriors(ref.getBase(),
DiploidGenotypePriors.HUMAN_HETEROZYGOSITY,
0.01);
// get the bases and qualities from the pileup

19
java/src/org/broadinstitute/sting/utils/genotype/DiploidGenotype.java
View File

@ -47,22 +47,31 @@ public enum DiploidGenotype {
GT ('G', 'T'),
TT ('T', 'T');
public char base1, base2;
public byte base1, base2;
private DiploidGenotype(char base1, char base2) {
this((byte)base1, (byte)base2);
}
private DiploidGenotype(byte base1, byte base2) {
this.base1 = base1;
this.base2 = base2;
}
public boolean isHomRef(char r) {
public boolean isHomRef(byte r) {
return isHom() && r == base1;
}
public boolean isHomVar(char r) {
public boolean isHomVar(byte r) {
return isHom() && r != base1;
}
public boolean isHetRef(char r) {
return MathUtils.countOccurrences(r, this.toString()) == 1;
public boolean isHetRef(byte r) {
if ( base1 == r )
return r != base2;
else
return base2 == r;
//return MathUtils.countOccurrences(r, this.toString()) == 1;
}
public boolean isHom() {

6
java/test/org/broadinstitute/sting/gatk/walkers/genotyper/GenotypeLikelihoodsUnitTest.java
View File

@ -70,9 +70,9 @@ public class GenotypeLikelihoodsUnitTest extends BaseTest {
private void testGenotypePriors(char ref, double h, double[] array) {
for ( DiploidGenotype g : DiploidGenotype.values() ) {
double val = 0.0;
if ( g.isHomRef(ref) ) val = DiploidGenotypePriors.heterozygosity2HomRefProbability(h);
if ( g.isHomRef((byte)ref) ) val = DiploidGenotypePriors.heterozygosity2HomRefProbability(h);
if ( g.isHet() ) val = DiploidGenotypePriors.heterozygosity2HetProbability(h);
if ( g.isHomVar(ref) ) val = DiploidGenotypePriors.heterozygosity2HomVarProbability(h);
if ( g.isHomVar((byte)ref) ) val = DiploidGenotypePriors.heterozygosity2HomVarProbability(h);
val = log10(val);
double e = array[g.ordinal()];
@ -99,7 +99,7 @@ public class GenotypeLikelihoodsUnitTest extends BaseTest {
}
private void testPolarizedGenotypePriors(char ref, double h, double pRefError, double[] array) {
DiploidGenotypePriors priors = new DiploidGenotypePriors(ref, h, pRefError);
DiploidGenotypePriors priors = new DiploidGenotypePriors((byte)ref, h, pRefError);
for ( DiploidGenotype g : DiploidGenotype.values() ) {
double val = Math.pow(10, priors.getPrior(g));
double e = array[g.ordinal()];