Killing off some FindBugs 'Usability' issues

protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/GeneralPloidyIndelGenotypeLikelihoods.java

@@ -142,8 +142,6 @@ public class GeneralPloidyIndelGenotypeLikelihoods extends GeneralPloidyGenotype
         List<Integer> numSeenBases = new ArrayList<Integer>(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;

public/java/src/org/broadinstitute/sting/commandline/ArgumentDefinitionGroup.java

@@ -55,10 +55,8 @@ public class ArgumentDefinitionGroup implements Iterable<ArgumentDefinition> {
      * Does the name of this argument group match the name of another?
      */
     public boolean groupNameMatches( ArgumentDefinitionGroup other ) {
-        if( this.groupName == null && other.groupName == null )
+        if( this.groupName == null )
-            return true;
+            return other.groupName == null;
-        if( this.groupName == null && other.groupName != null )
-            return false;
         return this.groupName.equals(other.groupName);
     }
 

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<Integer, Integer> {
         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<ReferenceOrderedDataSource> 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"));

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<String, AlignmentContext> 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<VariantCallContext> withAllSamples = new ArrayList<VariantCallContext>(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));

public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/PhaseByTransmission.java

@@ -645,7 +645,7 @@ public class PhaseByTransmission extends RodWalker<HashMap<Byte,Integer>, 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());

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<Integer,Integer> {
         // write to the fam file, the first six columns of the standard ped file
         // first, load data from the input meta data file
         Map<String,Map<String,String>> metaValues = new HashMap<String,Map<String,String>>();
-        Set<String> samplesToUse = new HashSet<String>();
         logger.debug("Reading in metadata...");
         try {
             if ( metaDataFile.getAbsolutePath().endsWith(".fam") ) {

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);
             }
         }
     }

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<Double> 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();

public/java/src/org/broadinstitute/sting/utils/Utils.java

@@ -563,7 +563,6 @@ public class Utils {
         List<T> t = new ArrayList<T>(c.keySet());
         Collections.sort(t);
 
-        List<V> l = new ArrayList<V>();
         List<String> pairs = new ArrayList<String>();
         for ( T k : t ) {
             pairs.add(k + "=" + c.get(k));

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;
     }

public/java/src/org/broadinstitute/sting/utils/help/GenericDocumentationHandler.java

@@ -587,7 +587,7 @@ public class GenericDocumentationHandler extends DocumentedGATKFeatureHandler {
     private List<Map<String, Object>> 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<Map<String, Object>> bindings = new ArrayList<Map<String, Object>>();
         for (final FieldDoc field : doc.fields(false)) {

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<NGSPlatform> DISCRETE_CYCLE_PLATFORMS = EnumSet.of(NGSPlatform.ILLUMINA, NGSPlatform.SOLID, NGSPlatform.PACBIO, NGSPlatform.COMPLETE_GENOMICS);
     private static final EnumSet<NGSPlatform> FLOW_CYCLE_PLATFORMS = EnumSet.of(NGSPlatform.LS454, NGSPlatform.ION_TORRENT);