Minor reformating for pooled calling

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2063 348d0f76-0448-11de-a6fe-93d51630548a

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

@@ -18,6 +18,10 @@ public class DiploidGenotypeCalculationModel extends JointEstimateGenotypeCalcul
         return splitContextBySample(context);
     }
 
+    protected int getNSamples(HashMap<String, AlignmentContextBySample> contexts) {
+        return contexts.size();
+    }
+
     protected void initializeLikelihoods(char ref, HashMap<String, AlignmentContextBySample> contexts, StratifiedContext contextType) {
         GLs.clear();
 

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

@@ -36,7 +36,7 @@ public abstract class JointEstimateGenotypeCalculationModel extends GenotypeCalc
     protected abstract void initializeLikelihoods(char ref, HashMap<String, AlignmentContextBySample> contexts, StratifiedContext contextType);
     protected abstract double computeLog10PofDgivenAFi(DiploidGenotype refGenotype, DiploidGenotype hetGenotype, DiploidGenotype homGenotype, double f);
     protected abstract List<Genotype> makeGenotypeCalls(char ref, HashMap<String, AlignmentContextBySample> contexts, GenomeLoc loc);
-
+    protected abstract int getNSamples(HashMap<String, AlignmentContextBySample> contexts);
 
     public Pair<List<Genotype>, GenotypeLocusData> calculateGenotype(RefMetaDataTracker tracker, char ref, AlignmentContext context, DiploidGenotypePriors priors) {
 
@@ -45,7 +45,7 @@ public abstract class JointEstimateGenotypeCalculationModel extends GenotypeCalc
         if ( contexts == null )
             return null;
 
-        int numSamples = contexts.size();
+        int numSamples = getNSamples(contexts);
         int frequencyEstimationPoints = (2 * numSamples) + 1;  // (add 1 for allele frequency of zero)
 
         initializeAlleleFrequencies(frequencyEstimationPoints);

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

@@ -10,9 +10,13 @@ import net.sf.samtools.SAMRecord;
 
 public class PooledCalculationModel extends JointEstimateGenotypeCalculationModel {
 
-    protected PooledCalculationModel() {}
+    protected PooledCalculationModel() {
-
+    }
 
+    protected int getNSamples(HashMap<String, AlignmentContextBySample> contexts) {
+        return POOL_SIZE;
+    }
+    
     protected HashMap<String, AlignmentContextBySample> createContexts(AlignmentContext context) {
         // for testing purposes, we may want to throw multi-samples at pooled mode,
         // so we can't use the standard splitContextBySample() method here
@@ -48,10 +52,10 @@ public class PooledCalculationModel extends JointEstimateGenotypeCalculationMode
     }
     
     protected double computeLog10PofDgivenAFi(DiploidGenotype refGenotype, DiploidGenotype hetGenotype, DiploidGenotype homGenotype, double f) {
-
+        System.out.printf("%s %.2f%n", hetGenotype, f);
         // TODO -- IMPLEMENT ME
 
-        return 0.0;
+        return -100.0;
     }
 
     protected List<Genotype> makeGenotypeCalls(char ref, HashMap<String, AlignmentContextBySample> contexts, GenomeLoc loc) {

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

@@ -77,7 +77,7 @@ public class UnifiedArgumentCollection {
     @Argument(fullName = "max_deletions", shortName = "deletions", doc = "Maximum reads with deletions spanning this locus for it to be callable [to disable, set to < 0; default:1]", required = false)
     public Integer MAX_DELETIONS = 1;
 
-    @Argument(fullName = "max_coverage", shortName = "coverage", doc = "Maximum reads at this locus for it to be callable; to disable, provide value < 1 [default:10,000]", required = false)
+    @Argument(fullName = "max_coverage", shortName = "mc", doc = "Maximum reads at this locus for it to be callable; to disable, provide value < 1 [default:10,000]", required = false)
     public Integer MAX_READS_IN_PILEUP = 10000;
 
     @Argument(fullName = "min_allele_frequency", shortName = "min_freq", doc = "The minimum possible allele frequency in a population (advanced)", required = false)