- Rename minConfidenceScore in VariantEval to minPhredConfidenceScore

- Moved validation walkers to new qc dir
- Killed unused test



git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2218 348d0f76-0448-11de-a6fe-93d51630548a

java/src/org/broadinstitute/sting/gatk/walkers/qc/PrintLocusContextWalker.java

@@ -1,8 +1,9 @@
-package org.broadinstitute.sting.gatk.walkers;
+package org.broadinstitute.sting.gatk.walkers.qc;
 
 import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
+import org.broadinstitute.sting.gatk.walkers.*;
 
 import java.util.List;
 import java.util.Arrays;

java/src/org/broadinstitute/sting/gatk/walkers/qc/ValidatingPileupWalker.java

@@ -1,10 +1,11 @@
-package org.broadinstitute.sting.gatk.walkers;
+package org.broadinstitute.sting.gatk.walkers.qc;
 
 import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
 import org.broadinstitute.sting.gatk.refdata.rodSAMPileup;
 import org.broadinstitute.sting.gatk.refdata.SAMPileupRecord;
+import org.broadinstitute.sting.gatk.walkers.*;
 import org.broadinstitute.sting.utils.cmdLine.Argument;
 import org.broadinstitute.sting.utils.Utils;
 import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;

java/src/org/broadinstitute/sting/playground/gatk/walkers/varianteval/VariantEvalWalker.java

@@ -29,7 +29,7 @@ import java.util.*;
 //@Allows(value={DataSource.REFERENCE},referenceMetaData = {@RMD(name="eval",type=ReferenceOrderedDatum.class), @RMD(name="dbsnp",type=rodDbSNP.class),@RMD(name="hapmap-chip",type=ReferenceOrderedDatum.class), @RMD(name="interval",type=IntervalRod.class), @RMD(name="validation",type=RodGenotypeChipAsGFF.class)})
 public class VariantEvalWalker extends RefWalker<Integer, Integer> {
 //public class VariantEvalWalker extends RodWalker<Integer, Integer> {
-    @Argument(shortName="minConfidenceScore", doc="Minimum confidence score to consider an evaluation SNP a variant", required=false)
+    @Argument(shortName="minPhredConfidenceScore", doc="Minimum confidence score to consider an evaluation SNP a variant", required=false)
     public int minConfidenceScore = -1;
 
     @Argument(shortName="printVariants", doc="If true, prints the variants in all of the variant tracks that are examined", required=false)

java/test/org/broadinstitute/sting/gatk/walkers/genotyper/NewHotnessGenotypeLikelihoodsTest.java

@@ -1,66 +0,0 @@
-package org.broadinstitute.sting.gatk.walkers.genotyper;
-
-import org.broadinstitute.sting.BaseTest;
-import org.junit.Ignore;
-
-/**
- * Stable, error checking version of the Bayesian genotyper.  Useful for calculating the likelihoods, priors,
- * and posteriors given a pile of bases and quality scores
- *
- * Suppose we have bases b1, b2, ..., bN with qualities scores q1, q2, ..., qN.  This object
- * calculates:
- *
- * P(G | D) = P(G) * P(D | G)
- *
- * where
- *
- * P(D | G) = sum_i log10 P(bi | G)
- *
- * and
- *
- * P(bi | G) = 1 - P(error | q1) if bi is in G
- *           = P(error | q1) / 3 if bi is not in G
- *
- * for homozygous genotypes and
- *
- * P(bi | G) = 1 - P(error | q1) / 2 + P(error | q1) / 6 if bi is in G
- *           = P(error | q1) / 3 if bi is not in G
- *
- * for the 10 unique diploid genotypes AA, AC, AG, .., TT
- *
- * Everything is stored as arrays indexed by DiploidGenotype.ordinal() values in log10 space.
- *
- * The priors contain the relative probabilities of each genotype, and must be provided at object creation.
- * From then on, you can call any of the add() routines to update the likelihoods and posteriors in the above
- * model.
- */
-@Ignore
-public class NewHotnessGenotypeLikelihoodsTest extends BaseTest {
-    int x;
-/*    private int coverage = 0;
-    private double[] likelihoods = null;
-    private double[] priors = null;
-    private double[] posteriors = null;
-
-    GenotypeLikelihoods();
-    GenotypeLikelihoods(char ref, double heterozygosity)
-    GenotypeLikelihoods(char ref, double priorHomRef, double priorHet, double priorHomVar);
-    GenotypeLikelihoods(double[] log10Priors)
-    double[] getLikelihoods()
-    double getLikelihood(DiploidGenotype g);
-    double[] getPosteriors();
-    double getPosterior(DiploidGenotype g);
-
-    double[] getPriors()
-    double getPrior(DiploidGenotype g)
-    int getCoverage()
-    boolean isFilteringQ0Bases()
-    void filterQ0Bases(boolean filterQ0Bases)
-    int add(char ref, char read, byte qual)
-    int add(char observedBase, byte qualityScore)
-    private boolean badBase(char observedBase)
-    int add(ReadBackedPileup pileup, boolean ignoreBadBases)
-    private double calculateBaseLikelihood(char read, String genotype, byte qual)
-    String toString()
-    boolean validate(boolean throwException)*/
-}

java/test/org/broadinstitute/sting/playground/gatk/walkers/varianteval/VariantEvalWalkerIntegrationTest.java

@@ -75,7 +75,7 @@ public class VariantEvalWalkerIntegrationTest extends WalkerTest {
                         " -L 1:10,000,000-11,000,000" +
                         " --outerr %s" +
                         " --supressDateInformation" +
-                        " -minConfidenceScore 60",
+                        " -minPhredConfidenceScore 60",
                 1, // just one output file
                 md5);
         List<File> result = executeTest("testEvalVariantRODConfSixty", spec).getFirst();