diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/PrintLocusContextWalker.java b/java/src/org/broadinstitute/sting/gatk/walkers/qc/PrintLocusContextWalker.java similarity index 94% rename from java/src/org/broadinstitute/sting/gatk/walkers/PrintLocusContextWalker.java rename to java/src/org/broadinstitute/sting/gatk/walkers/qc/PrintLocusContextWalker.java index f4dbca939..cd0165b1a 100755 --- a/java/src/org/broadinstitute/sting/gatk/walkers/PrintLocusContextWalker.java +++ b/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; diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/ValidatingPileupWalker.java b/java/src/org/broadinstitute/sting/gatk/walkers/qc/ValidatingPileupWalker.java similarity index 98% rename from java/src/org/broadinstitute/sting/gatk/walkers/ValidatingPileupWalker.java rename to java/src/org/broadinstitute/sting/gatk/walkers/qc/ValidatingPileupWalker.java index 98ea6ac90..e86a1f358 100755 --- a/java/src/org/broadinstitute/sting/gatk/walkers/ValidatingPileupWalker.java +++ b/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; diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/varianteval/VariantEvalWalker.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/varianteval/VariantEvalWalker.java index 8fc813085..db5c9235e 100755 --- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/varianteval/VariantEvalWalker.java +++ b/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 { //public class VariantEvalWalker extends RodWalker { - @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) diff --git a/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/NewHotnessGenotypeLikelihoodsTest.java b/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/NewHotnessGenotypeLikelihoodsTest.java deleted file mode 100755 index 90bcea6af..000000000 --- a/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/NewHotnessGenotypeLikelihoodsTest.java +++ /dev/null @@ -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)*/ -} \ No newline at end of file diff --git a/java/test/org/broadinstitute/sting/playground/gatk/walkers/varianteval/VariantEvalWalkerIntegrationTest.java b/java/test/org/broadinstitute/sting/playground/gatk/walkers/varianteval/VariantEvalWalkerIntegrationTest.java index a703e3245..82329c72c 100644 --- a/java/test/org/broadinstitute/sting/playground/gatk/walkers/varianteval/VariantEvalWalkerIntegrationTest.java +++ b/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 result = executeTest("testEvalVariantRODConfSixty", spec).getFirst();