diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/GeneralPloidyIndelGenotypeLikelihoods.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/GeneralPloidyIndelGenotypeLikelihoods.java index 4f42f820e..34267b9a8 100644 --- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/GeneralPloidyIndelGenotypeLikelihoods.java +++ b/protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/GeneralPloidyIndelGenotypeLikelihoods.java @@ -142,8 +142,6 @@ public class GeneralPloidyIndelGenotypeLikelihoods extends GeneralPloidyGenotype List numSeenBases = new ArrayList(this.alleles.size()); if (!hasReferenceSampleData) { - final int numHaplotypes = haplotypeMap.size(); - final int readCounts[] = new int[pileup.getNumberOfElements()]; readHaplotypeLikelihoods = pairModel.computeGeneralReadHaplotypeLikelihoods(pileup, haplotypeMap, refContext, eventLength, IndelGenotypeLikelihoodsCalculationModel.getIndelLikelihoodMap(), readCounts); n = readHaplotypeLikelihoods.length; diff --git a/public/java/src/org/broadinstitute/sting/commandline/ArgumentDefinitionGroup.java b/public/java/src/org/broadinstitute/sting/commandline/ArgumentDefinitionGroup.java index b47677b08..474225e2a 100644 --- a/public/java/src/org/broadinstitute/sting/commandline/ArgumentDefinitionGroup.java +++ b/public/java/src/org/broadinstitute/sting/commandline/ArgumentDefinitionGroup.java @@ -55,10 +55,8 @@ public class ArgumentDefinitionGroup implements Iterable { * Does the name of this argument group match the name of another? */ public boolean groupNameMatches( ArgumentDefinitionGroup other ) { - if( this.groupName == null && other.groupName == null ) - return true; - if( this.groupName == null && other.groupName != null ) - return false; + if( this.groupName == null ) + return other.groupName == null; return this.groupName.equals(other.groupName); } diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/beagle/BeagleOutputToVCF.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/beagle/BeagleOutputToVCF.java index 9eb0e4dda..83b10dd91 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/beagle/BeagleOutputToVCF.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/beagle/BeagleOutputToVCF.java @@ -30,7 +30,6 @@ import org.broadinstitute.sting.gatk.CommandLineGATK; import org.broadinstitute.sting.gatk.arguments.StandardVariantContextInputArgumentCollection; import org.broadinstitute.sting.gatk.contexts.AlignmentContext; import org.broadinstitute.sting.gatk.contexts.ReferenceContext; -import org.broadinstitute.sting.gatk.datasources.rmd.ReferenceOrderedDataSource; import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; import org.broadinstitute.sting.gatk.walkers.RodWalker; import org.broadinstitute.sting.utils.GenomeLoc; @@ -142,9 +141,6 @@ public class BeagleOutputToVCF extends RodWalker { hInfo.add(new VCFFilterHeaderLine("BGL_RM_WAS_G", "This 'G' site was set to monomorphic by Beagle")); hInfo.add(new VCFFilterHeaderLine("BGL_RM_WAS_T", "This 'T' site was set to monomorphic by Beagle")); - // Open output file specified by output VCF ROD - final List dataSources = this.getToolkit().getRodDataSources(); - if ( comp.isBound() ) { hInfo.add(new VCFInfoHeaderLine("ACH", 1, VCFHeaderLineType.Integer, "Allele Count from Comparison ROD at this site")); hInfo.add(new VCFInfoHeaderLine("ANH", 1, VCFHeaderLineType.Integer, "Allele Frequency from Comparison ROD at this site")); diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperEngine.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperEngine.java index c9656dd00..05e12b43d 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperEngine.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperEngine.java @@ -183,7 +183,7 @@ public class UnifiedGenotyperEngine { for ( final GenotypeLikelihoodsCalculationModel.Model model : models ) { final Map stratifiedContexts = getFilteredAndStratifiedContexts(UAC, refContext, rawContext, model); if ( stratifiedContexts == null ) { - results.add(UAC.OutputMode == OUTPUT_MODE.EMIT_ALL_SITES && UAC.GenotypingMode == GenotypeLikelihoodsCalculationModel.GENOTYPING_MODE.GENOTYPE_GIVEN_ALLELES ? generateEmptyContext(tracker, refContext, stratifiedContexts, rawContext) : null); + results.add(UAC.OutputMode == OUTPUT_MODE.EMIT_ALL_SITES && UAC.GenotypingMode == GenotypeLikelihoodsCalculationModel.GENOTYPING_MODE.GENOTYPE_GIVEN_ALLELES ? generateEmptyContext(tracker, refContext, null, rawContext) : null); } else { final VariantContext vc = calculateLikelihoods(tracker, refContext, stratifiedContexts, AlignmentContextUtils.ReadOrientation.COMPLETE, null, true, model); @@ -202,7 +202,7 @@ public class UnifiedGenotyperEngine { final List withAllSamples = new ArrayList(calls.size()); for ( final VariantCallContext call : calls ) { if ( call == null ) - withAllSamples.add(call); + withAllSamples.add(null); else { final VariantContext withoutMissing = VariantContextUtils.addMissingSamples(call, allSamples); withAllSamples.add(new VariantCallContext(withoutMissing, call.confidentlyCalled, call.shouldEmit)); diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/PhaseByTransmission.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/PhaseByTransmission.java index bbd4bf92f..0dcafb30a 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/PhaseByTransmission.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/PhaseByTransmission.java @@ -645,7 +645,7 @@ public class PhaseByTransmission extends RodWalker, HashMa bestChildGenotype.clear(); bestChildGenotype.add(childGenotype.getKey()); } - else if(configurationLikelihood == bestConfigurationLikelihood) { + else if(MathUtils.compareDoubles(configurationLikelihood, bestConfigurationLikelihood) == 0) { bestFirstParentGenotype.add(firstParentGenotype.getKey()); bestSecondParentGenotype.add(secondParentGenotype.getKey()); bestChildGenotype.add(childGenotype.getKey()); diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToBinaryPed.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToBinaryPed.java index 7e82fc454..14c811b03 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToBinaryPed.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToBinaryPed.java @@ -8,8 +8,6 @@ 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.RodWalker; -import org.broadinstitute.sting.utils.R.RScriptExecutorException; -import org.broadinstitute.sting.utils.codecs.vcf.VCFConstants; import org.broadinstitute.sting.utils.codecs.vcf.VCFHeader; import org.broadinstitute.sting.utils.codecs.vcf.VCFUtils; import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; @@ -18,7 +16,6 @@ import org.broadinstitute.sting.utils.help.DocumentedGATKFeature; import org.broadinstitute.sting.utils.text.XReadLines; import org.broadinstitute.sting.utils.variantcontext.Genotype; import org.broadinstitute.sting.utils.variantcontext.VariantContext; -import org.broadinstitute.sting.utils.variantcontext.VariantContextBuilder; import org.broadinstitute.sting.utils.variantcontext.VariantContextUtils; import java.io.*; @@ -95,7 +92,6 @@ public class VariantsToBinaryPed extends RodWalker { // write to the fam file, the first six columns of the standard ped file // first, load data from the input meta data file Map> metaValues = new HashMap>(); - Set samplesToUse = new HashSet(); logger.debug("Reading in metadata..."); try { if ( metaDataFile.getAbsolutePath().endsWith(".fam") ) { diff --git a/public/java/src/org/broadinstitute/sting/utils/MannWhitneyU.java b/public/java/src/org/broadinstitute/sting/utils/MannWhitneyU.java index ecb381e3f..d1bc75583 100755 --- a/public/java/src/org/broadinstitute/sting/utils/MannWhitneyU.java +++ b/public/java/src/org/broadinstitute/sting/utils/MannWhitneyU.java @@ -199,9 +199,9 @@ public class MannWhitneyU { else if ( z > n ) { return 0.0; } else { if ( z > ((double) n) /2 ) { - return 1.0-1/((double)Arithmetic.factorial(n))*uniformSumHelper(z, (int) Math.floor(z), n, 0); + return 1.0-1/(Arithmetic.factorial(n))*uniformSumHelper(z, (int) Math.floor(z), n, 0); } else { - return 1/((double)Arithmetic.factorial(n))*uniformSumHelper(z, (int) Math.floor(z), n, 0); + return 1/(Arithmetic.factorial(n))*uniformSumHelper(z, (int) Math.floor(z), n, 0); } } } diff --git a/public/java/src/org/broadinstitute/sting/utils/MathUtils.java b/public/java/src/org/broadinstitute/sting/utils/MathUtils.java index 96704f0b8..7d1561fc5 100644 --- a/public/java/src/org/broadinstitute/sting/utils/MathUtils.java +++ b/public/java/src/org/broadinstitute/sting/utils/MathUtils.java @@ -767,7 +767,7 @@ public class MathUtils { for (byte v : vals) { sum += v; } - return (byte) Math.floor(sum / vals.length); + return (byte) (sum / vals.length); } public static double averageDouble(List vals) { @@ -1044,7 +1044,6 @@ public class MathUtils { // the list is assumed *not* to be sorted final Comparable x = list.get(orderStat); - ListIterator iterator = list.listIterator(); ArrayList lessThanX = new ArrayList(); ArrayList equalToX = new ArrayList(); ArrayList greaterThanX = new ArrayList(); diff --git a/public/java/src/org/broadinstitute/sting/utils/Utils.java b/public/java/src/org/broadinstitute/sting/utils/Utils.java index 476098ae6..a5b5eca6a 100755 --- a/public/java/src/org/broadinstitute/sting/utils/Utils.java +++ b/public/java/src/org/broadinstitute/sting/utils/Utils.java @@ -563,7 +563,6 @@ public class Utils { List t = new ArrayList(c.keySet()); Collections.sort(t); - List l = new ArrayList(); List pairs = new ArrayList(); for ( T k : t ) { pairs.add(k + "=" + c.get(k)); diff --git a/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFHeaderLine.java b/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFHeaderLine.java index 162c34d80..83e55cb12 100755 --- a/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFHeaderLine.java +++ b/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFHeaderLine.java @@ -53,7 +53,7 @@ public class VCFHeaderLine implements Comparable { */ public VCFHeaderLine(String key, String value) { if ( key == null ) - throw new IllegalArgumentException("VCFHeaderLine: key cannot be null: key = " + key); + throw new IllegalArgumentException("VCFHeaderLine: key cannot be null"); mKey = key; mValue = value; } diff --git a/public/java/src/org/broadinstitute/sting/utils/help/GenericDocumentationHandler.java b/public/java/src/org/broadinstitute/sting/utils/help/GenericDocumentationHandler.java index 69d2e7c9e..dc0668cea 100644 --- a/public/java/src/org/broadinstitute/sting/utils/help/GenericDocumentationHandler.java +++ b/public/java/src/org/broadinstitute/sting/utils/help/GenericDocumentationHandler.java @@ -587,7 +587,7 @@ public class GenericDocumentationHandler extends DocumentedGATKFeatureHandler { private List> docForEnumArgument(Class enumClass) { ClassDoc doc = this.getDoclet().getClassDocForClass(enumClass); if (doc == null) // || ! doc.isEnum() ) - throw new RuntimeException("Tried to get docs for enum " + enumClass + " but got instead: " + doc); + throw new RuntimeException("Tried to get docs for enum " + enumClass + " but got null instead"); List> bindings = new ArrayList>(); for (final FieldDoc field : doc.fields(false)) { diff --git a/public/java/src/org/broadinstitute/sting/utils/recalibration/covariates/CycleCovariate.java b/public/java/src/org/broadinstitute/sting/utils/recalibration/covariates/CycleCovariate.java index 4f15419c7..cdf12d284 100755 --- a/public/java/src/org/broadinstitute/sting/utils/recalibration/covariates/CycleCovariate.java +++ b/public/java/src/org/broadinstitute/sting/utils/recalibration/covariates/CycleCovariate.java @@ -51,7 +51,7 @@ public class CycleCovariate implements StandardCovariate { private static final int MAXIMUM_CYCLE_VALUE = 1000; private static final int CUSHION_FOR_INDELS = 4; - private static String default_platform = null; + private String default_platform = null; private static final EnumSet DISCRETE_CYCLE_PLATFORMS = EnumSet.of(NGSPlatform.ILLUMINA, NGSPlatform.SOLID, NGSPlatform.PACBIO, NGSPlatform.COMPLETE_GENOMICS); private static final EnumSet FLOW_CYCLE_PLATFORMS = EnumSet.of(NGSPlatform.LS454, NGSPlatform.ION_TORRENT);