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

java/src/org/broadinstitute/sting/gatk/walkers/genotyper/DiploidGenotypeCalculationModel.java

@@ -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);

java/src/org/broadinstitute/sting/gatk/walkers/genotyper/DiploidGenotypePriors.java

@@ -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;
 

java/src/org/broadinstitute/sting/gatk/walkers/genotyper/GenotypeCalculationModel.java

@@ -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;
+        this.logger = logger;
-        GENOTYPE_MODE = UAC.GENOTYPE;
-        POOL_SIZE = UAC.POOLSIZE;
-        CONFIDENCE_THRESHOLD = UAC.CONFIDENCE_THRESHOLD;
-        REPORT_SLOD = ! UAC.NO_SLOD;
         this.verboseWriter = verboseWriter;
         this.beagleWriter = beagleWriter;
     }

java/src/org/broadinstitute/sting/gatk/walkers/genotyper/JointEstimateGenotypeCalculationModel.java

@@ -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) )
+        if ( !triggerTrack && !UAC.ALL_BASES_MODE && ((!UAC.GENOTYPE_MODE && bestAFguess == 0) || phredScaledConfidence < UAC.CONFIDENCE_THRESHOLD) )
-            return new VariantCallContext(phredScaledConfidence >= 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);
     }
 }

java/src/org/broadinstitute/sting/gatk/walkers/genotyper/SimpleIndelCalculationModel.java

@@ -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.*;
 

java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedArgumentCollection.java

@@ -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;
+    }
+
+
 }

java/src/org/broadinstitute/sting/oneoffprojects/walkers/BaseTransitionTableCalculatorJavaWalker.java

@@ -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>();

java/src/org/broadinstitute/sting/playground/gatk/walkers/LocusMismatchWalker.java

@@ -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

java/src/org/broadinstitute/sting/playground/gatk/walkers/SnpCallRateByCoverageWalker.java

@@ -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");

java/src/org/broadinstitute/sting/playground/gatk/walkers/secondaryBases/SecondaryBaseTransitionTableWalker.java

@@ -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();