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Reorg of UG args; checking in first before upcoming changes that will break integration tests. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3274 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
ebanks 2010-04-30 14:48:46 +00:00
parent ba78d146ec
commit 1714c322c2
10 changed files with 41 additions and 35 deletions
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2
java/src/org/broadinstitute/sting/gatk/walkers/genotyper/DiploidGenotypeCalculationModel.java
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@ -74,7 +74,7 @@ public class DiploidGenotypeCalculationModel extends JointEstimateGenotypeCalcul
ReadBackedPileup pileup = context.getContext(contextType).getBasePileup();
// create the GenotypeLikelihoods object
GenotypeLikelihoods GL = new GenotypeLikelihoods(baseModel, priors, defaultPlatform);
GenotypeLikelihoods GL = new GenotypeLikelihoods(UAC.baseModel, priors, UAC.defaultPlatform);
GL.add(pileup, true);
GLs.put(sample, GL);

1
java/src/org/broadinstitute/sting/gatk/walkers/genotyper/DiploidGenotypePriors.java
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@ -25,7 +25,6 @@
package org.broadinstitute.sting.gatk.walkers.genotyper;
import org.broadinstitute.sting.utils.Utils;
import org.broadinstitute.sting.utils.MathUtils;
import org.broadinstitute.sting.utils.genotype.DiploidGenotype;

21
java/src/org/broadinstitute/sting/gatk/walkers/genotyper/GenotypeCalculationModel.java
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@ -25,18 +25,10 @@ public abstract class GenotypeCalculationModel implements Cloneable {
INDELS
}
protected BaseMismatchModel baseModel;
protected UnifiedArgumentCollection UAC;
protected Set<String> samples;
protected Logger logger;
protected double heterozygosity;
protected EmpiricalSubstitutionProbabilities.SequencerPlatform defaultPlatform;
protected GenotypeWriterFactory.GENOTYPE_FORMAT OUTPUT_FORMAT;
protected boolean ALL_BASE_MODE;
protected boolean GENOTYPE_MODE;
protected int POOL_SIZE;
protected double CONFIDENCE_THRESHOLD;
protected double MINIMUM_ALLELE_FREQUENCY;
protected boolean REPORT_SLOD;
protected PrintStream verboseWriter;
protected PrintStream beagleWriter;
@ -62,17 +54,10 @@ public abstract class GenotypeCalculationModel implements Cloneable {
GenotypeWriterFactory.GENOTYPE_FORMAT outputFormat,
PrintStream verboseWriter,
PrintStream beagleWriter) {
this.UAC = UAC.clone();
this.samples = new TreeSet<String>(samples);
this.logger = logger;
baseModel = UAC.baseModel;
heterozygosity = UAC.heterozygosity;
defaultPlatform = UAC.defaultPlatform;
OUTPUT_FORMAT = outputFormat;
ALL_BASE_MODE = UAC.ALL_BASES;
GENOTYPE_MODE = UAC.GENOTYPE;
POOL_SIZE = UAC.POOLSIZE;
CONFIDENCE_THRESHOLD = UAC.CONFIDENCE_THRESHOLD;
REPORT_SLOD = ! UAC.NO_SLOD;
this.logger = logger;
this.verboseWriter = verboseWriter;
this.beagleWriter = beagleWriter;
}

14
java/src/org/broadinstitute/sting/gatk/walkers/genotyper/JointEstimateGenotypeCalculationModel.java
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@ -60,7 +60,7 @@ public abstract class JointEstimateGenotypeCalculationModel extends GenotypeCalc
// if there are no non-ref bases...
if ( bestAlternateAllele == null ) {
// if we don't want all bases, then we don't need to calculate genotype likelihoods
if ( !triggerTrack && !ALL_BASE_MODE && !GENOTYPE_MODE ) {
if ( !triggerTrack && !UAC.ALL_BASES_MODE && !UAC.GENOTYPE_MODE ) {
VariantCallContext vcc = new VariantCallContext(false);
estimateReferenceConfidence(vcc, contexts, DiploidGenotypePriors.HUMAN_HETEROZYGOSITY, false);
return vcc;
@ -152,7 +152,7 @@ public abstract class JointEstimateGenotypeCalculationModel extends GenotypeCalc
sigma_1_over_I += 1.0 / (double)i;
// delta = theta / sum(1/i)
double delta = heterozygosity / sigma_1_over_I;
double delta = UAC.heterozygosity / sigma_1_over_I;
// calculate the null allele frequencies for 1-N
AFs = new double[N];
@ -190,7 +190,7 @@ public abstract class JointEstimateGenotypeCalculationModel extends GenotypeCalc
P_of_ref *= 1.0 - (theta / 2.0) * MathUtils.binomialProbability(0, depth, 0.5);
}
vcc.confidentlyCalled = QualityUtils.phredScaleErrorRate(1.0 - P_of_ref) >= CONFIDENCE_THRESHOLD;
vcc.confidentlyCalled = QualityUtils.phredScaleErrorRate(1.0 - P_of_ref) >= UAC.CONFIDENCE_THRESHOLD;
}
protected void calculateAlleleFrequencyPosteriors(char ref, int frequencyEstimationPoints, Map<String, StratifiedAlignmentContext> contexts, StratifiedAlignmentContext.StratifiedContextType contextType) {
@ -350,8 +350,8 @@ public abstract class JointEstimateGenotypeCalculationModel extends GenotypeCalc
}
// return a null call if we don't pass the confidence cutoff or the most likely allele frequency is zero
if ( !triggerTrack && !ALL_BASE_MODE && ((!GENOTYPE_MODE && bestAFguess == 0) || phredScaledConfidence < CONFIDENCE_THRESHOLD) )
return new VariantCallContext(phredScaledConfidence >= CONFIDENCE_THRESHOLD);
if ( !triggerTrack && !UAC.ALL_BASES_MODE && ((!UAC.GENOTYPE_MODE && bestAFguess == 0) || phredScaledConfidence < UAC.CONFIDENCE_THRESHOLD) )
return new VariantCallContext(phredScaledConfidence >= UAC.CONFIDENCE_THRESHOLD);
// output to beagle file if requested
if ( beagleWriter != null ) {
@ -384,7 +384,7 @@ public abstract class JointEstimateGenotypeCalculationModel extends GenotypeCalc
if ( dbsnp != null )
attributes.put("ID", dbsnp.getRS_ID());
if ( REPORT_SLOD ) {
if ( !UAC.NO_SLOD ) {
// the overall lod
double overallLog10PofNull = log10AlleleFrequencyPriors[0] + log10PofDgivenAFi[indexOfMax][0];
double overallLog10PofF = log10AlleleFrequencyPriors[bestAFguess] + log10PofDgivenAFi[indexOfMax][bestAFguess];
@ -422,6 +422,6 @@ public abstract class JointEstimateGenotypeCalculationModel extends GenotypeCalc
VariantContext vc = new VariantContext("UG_SNP_call", loc, alleles, genotypes, phredScaledConfidence/10.0, null, attributes);
return new VariantCallContext(vc, phredScaledConfidence >= CONFIDENCE_THRESHOLD);
return new VariantCallContext(vc, phredScaledConfidence >= UAC.CONFIDENCE_THRESHOLD);
}
}

2
java/src/org/broadinstitute/sting/gatk/walkers/genotyper/SimpleIndelCalculationModel.java
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@ -1,11 +1,9 @@
package org.broadinstitute.sting.gatk.walkers.genotyper;
import org.broadinstitute.sting.utils.*;
import org.broadinstitute.sting.utils.genotype.vcf.VCFRecord;
import org.broadinstitute.sting.utils.collections.Pair;
import org.broadinstitute.sting.utils.pileup.*;
import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
import org.broadinstitute.sting.gatk.refdata.rodDbSNP;
import org.broadinstitute.sting.gatk.contexts.*;
import org.broadinstitute.sting.gatk.contexts.variantcontext.*;

28
java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedArgumentCollection.java
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@ -45,10 +45,10 @@ public class UnifiedArgumentCollection {
// control the output
@Argument(fullName = "genotype", shortName = "genotype", doc = "Should we output confident genotypes (i.e. including ref calls) or just the variants?", required = false)
public boolean GENOTYPE = false;
public boolean GENOTYPE_MODE = false;
@Argument(fullName = "output_all_callable_bases", shortName = "all_bases", doc = "Should we output all callable bases?", required = false)
public boolean ALL_BASES = false;
public boolean ALL_BASES_MODE = false;
@Argument(fullName = "noSLOD", shortName = "nsl", doc = "If provided, we will not calculate the SLOD", required = false)
public boolean NO_SLOD = false;
@ -80,4 +80,28 @@ public class UnifiedArgumentCollection {
@Argument(fullName = "max_deletion_fraction", shortName = "deletions", doc = "Maximum fraction of reads with deletions spanning this locus for it to be callable [to disable, set to < 0 or > 1; default:0.05]", required = false)
public Double MAX_DELETION_FRACTION = 0.05;
public UnifiedArgumentCollection clone() {
UnifiedArgumentCollection uac = new UnifiedArgumentCollection();
uac.genotypeModel = genotypeModel;
uac.baseModel = baseModel;
uac.heterozygosity = heterozygosity;
uac.GENOTYPE_MODE = GENOTYPE_MODE;
uac.ALL_BASES_MODE = ALL_BASES_MODE;
uac.NO_SLOD = NO_SLOD;
uac.ASSUME_SINGLE_SAMPLE = ASSUME_SINGLE_SAMPLE;
uac.defaultPlatform = defaultPlatform;
uac.CONFIDENCE_THRESHOLD = CONFIDENCE_THRESHOLD;
uac.MIN_BASE_QUALTY_SCORE = MIN_BASE_QUALTY_SCORE;
uac.MIN_MAPPING_QUALTY_SCORE = MIN_MAPPING_QUALTY_SCORE;
uac.MAX_MISMATCHES = MAX_MISMATCHES;
uac.USE_BADLY_MATED_READS = USE_BADLY_MATED_READS;
uac.MAX_DELETION_FRACTION = MAX_DELETION_FRACTION;
return uac;
}
}

2
java/src/org/broadinstitute/sting/oneoffprojects/walkers/BaseTransitionTableCalculatorJavaWalker.java
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@ -85,7 +85,7 @@ public class BaseTransitionTableCalculatorJavaWalker extends LocusWalker<Set<Bas
}
UnifiedArgumentCollection uac = new UnifiedArgumentCollection();
uac.baseModel = BaseMismatchModel.THREE_STATE;
uac.ALL_BASES = true;
uac.ALL_BASES_MODE = true;
ug = new UnifiedGenotyperEngine(getToolkit(), uac);
// refWindow = new ReferenceContextWindow(nPreviousBases);
usePreviousBases = new ArrayList<Boolean>();

2
java/src/org/broadinstitute/sting/playground/gatk/walkers/LocusMismatchWalker.java
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@ -77,7 +77,7 @@ public class LocusMismatchWalker extends LocusWalker<String,Integer> implements
public void initialize() {
UnifiedArgumentCollection uac = new UnifiedArgumentCollection();
uac.baseModel = BaseMismatchModel.THREE_STATE;
uac.ALL_BASES = true;
uac.ALL_BASES_MODE = true;
ug = new UnifiedGenotyperEngine(getToolkit(), uac);
// print the header

2
java/src/org/broadinstitute/sting/playground/gatk/walkers/SnpCallRateByCoverageWalker.java
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@ -61,7 +61,7 @@ public class SnpCallRateByCoverageWalker extends LocusWalker<List<String>, Strin
public void initialize() {
UnifiedArgumentCollection uac = new UnifiedArgumentCollection();
uac.CONFIDENCE_THRESHOLD = confidence;
uac.ALL_BASES = true;
uac.ALL_BASES_MODE = true;
UG = new UnifiedGenotyperEngine(getToolkit(), uac);
out.println("#locus\tid\tdownsampled_coverage\tpct_coverage\titeration\tref\teval_call\tcomp_call\tvariant_concordance\tgenotype_concordance");

2
java/src/org/broadinstitute/sting/playground/gatk/walkers/secondaryBases/SecondaryBaseTransitionTableWalker.java
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@ -32,7 +32,7 @@ public class SecondaryBaseTransitionTableWalker extends LocusWalker<Integer, Int
public void initialize() {
UnifiedArgumentCollection uac = new UnifiedArgumentCollection();
uac.CONFIDENCE_THRESHOLD = 50;
uac.ALL_BASES = true;
uac.ALL_BASES_MODE = true;
ug = new UnifiedGenotyperEngine(getToolkit(), uac);
altTable = new NamedTable();