diff --git a/public/java/src/org/broadinstitute/sting/alignment/reference/bwt/Bases.java b/public/java/src/org/broadinstitute/sting/alignment/reference/bwt/Bases.java index bc0a5b63d..7cd85cfd8 100644 --- a/public/java/src/org/broadinstitute/sting/alignment/reference/bwt/Bases.java +++ b/public/java/src/org/broadinstitute/sting/alignment/reference/bwt/Bases.java @@ -12,10 +12,10 @@ import java.util.*; */ public class Bases implements Iterable { - public static byte A = 'A'; - public static byte C = 'C'; - public static byte G = 'G'; - public static byte T = 'T'; + public static final byte A = 'A'; + public static final byte C = 'C'; + public static final byte G = 'G'; + public static final byte T = 'T'; public static final Bases instance = new Bases(); diff --git a/public/java/src/org/broadinstitute/sting/commandline/ArgumentTypeDescriptor.java b/public/java/src/org/broadinstitute/sting/commandline/ArgumentTypeDescriptor.java index c201e95f0..dd4a151bf 100644 --- a/public/java/src/org/broadinstitute/sting/commandline/ArgumentTypeDescriptor.java +++ b/public/java/src/org/broadinstitute/sting/commandline/ArgumentTypeDescriptor.java @@ -53,7 +53,7 @@ public abstract class ArgumentTypeDescriptor { /** * our log, which we want to capture anything from org.broadinstitute.sting */ - protected static Logger logger = Logger.getLogger(ArgumentTypeDescriptor.class); + protected static final Logger logger = Logger.getLogger(ArgumentTypeDescriptor.class); /** * Fetch the given descriptor from the descriptor repository. diff --git a/public/java/src/org/broadinstitute/sting/commandline/ParsingMethod.java b/public/java/src/org/broadinstitute/sting/commandline/ParsingMethod.java index 26af49e12..376b6f210 100755 --- a/public/java/src/org/broadinstitute/sting/commandline/ParsingMethod.java +++ b/public/java/src/org/broadinstitute/sting/commandline/ParsingMethod.java @@ -120,8 +120,8 @@ public abstract class ParsingMethod { */ private static final String TAG_TEXT = "[\\w\\-\\.\\=]*"; - public static ParsingMethod FullNameParsingMethod = new ParsingMethod(Pattern.compile(String.format("\\s*--(%1$s)(?:\\:(%2$s(?:,%2$s)*))?\\s*",ARGUMENT_TEXT,TAG_TEXT)), + public static final ParsingMethod FullNameParsingMethod = new ParsingMethod(Pattern.compile(String.format("\\s*--(%1$s)(?:\\:(%2$s(?:,%2$s)*))?\\s*",ARGUMENT_TEXT,TAG_TEXT)), ArgumentDefinitions.FullNameDefinitionMatcher) {}; - public static ParsingMethod ShortNameParsingMethod = new ParsingMethod(Pattern.compile(String.format("\\s*-(%1$s)(?:\\:(%2$s(?:,%2$s)*))?\\s*",ARGUMENT_TEXT,TAG_TEXT)), + public static final ParsingMethod ShortNameParsingMethod = new ParsingMethod(Pattern.compile(String.format("\\s*-(%1$s)(?:\\:(%2$s(?:,%2$s)*))?\\s*",ARGUMENT_TEXT,TAG_TEXT)), ArgumentDefinitions.ShortNameDefinitionMatcher) {}; } diff --git a/public/java/src/org/broadinstitute/sting/gatk/datasources/providers/ReadBasedReferenceOrderedView.java b/public/java/src/org/broadinstitute/sting/gatk/datasources/providers/ReadBasedReferenceOrderedView.java index 142c8a178..01e24df67 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/datasources/providers/ReadBasedReferenceOrderedView.java +++ b/public/java/src/org/broadinstitute/sting/gatk/datasources/providers/ReadBasedReferenceOrderedView.java @@ -118,7 +118,7 @@ class WindowedData { rec.getAlignmentStart(), stop); states = new ArrayList(); - if (provider != null && provider.getReferenceOrderedData() != null) + if (provider.getReferenceOrderedData() != null) for (ReferenceOrderedDataSource dataSource : provider.getReferenceOrderedData()) states.add(new RMDDataState(dataSource, dataSource.seek(range))); } diff --git a/public/java/src/org/broadinstitute/sting/gatk/datasources/reference/ReferenceDataSource.java b/public/java/src/org/broadinstitute/sting/gatk/datasources/reference/ReferenceDataSource.java index 4ecfe472d..b131e36c1 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/datasources/reference/ReferenceDataSource.java +++ b/public/java/src/org/broadinstitute/sting/gatk/datasources/reference/ReferenceDataSource.java @@ -45,7 +45,6 @@ import org.broadinstitute.sting.utils.file.FileSystemInabilityToLockException; import java.io.File; import java.util.ArrayList; import java.util.Collections; -import java.util.LinkedList; import java.util.List; /** @@ -56,7 +55,7 @@ public class ReferenceDataSource { private IndexedFastaSequenceFile reference; /** our log, which we want to capture anything from this class */ - protected static org.apache.log4j.Logger logger = org.apache.log4j.Logger.getLogger(ReferenceDataSource.class); + protected static final org.apache.log4j.Logger logger = org.apache.log4j.Logger.getLogger(ReferenceDataSource.class); /** * Create reference data source from fasta file diff --git a/public/java/src/org/broadinstitute/sting/gatk/executive/MicroScheduler.java b/public/java/src/org/broadinstitute/sting/gatk/executive/MicroScheduler.java index 508099708..95e39b7c6 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/executive/MicroScheduler.java +++ b/public/java/src/org/broadinstitute/sting/gatk/executive/MicroScheduler.java @@ -58,7 +58,7 @@ import java.util.Collection; /** Shards and schedules data in manageable chunks. */ public abstract class MicroScheduler implements MicroSchedulerMBean { - protected static Logger logger = Logger.getLogger(MicroScheduler.class); + protected static final Logger logger = Logger.getLogger(MicroScheduler.class); /** * Counts the number of instances of the class that are currently alive. diff --git a/public/java/src/org/broadinstitute/sting/gatk/executive/TreeReducer.java b/public/java/src/org/broadinstitute/sting/gatk/executive/TreeReducer.java index 632638f64..390da0cce 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/executive/TreeReducer.java +++ b/public/java/src/org/broadinstitute/sting/gatk/executive/TreeReducer.java @@ -66,13 +66,13 @@ public class TreeReducer implements Callable { * @return Result of the reduce. */ public Object call() { - Object result = null; + Object result; final long startTime = System.currentTimeMillis(); try { if( lhs == null ) - result = lhs.get(); + result = null; // todo -- what the hell is this above line? Shouldn't it be the two below? // if( lhs == null ) // throw new IllegalStateException(String.format("Insufficient data on which to reduce; lhs = %s, rhs = %s", lhs, rhs) ); diff --git a/public/java/src/org/broadinstitute/sting/gatk/phonehome/GATKRunReport.java b/public/java/src/org/broadinstitute/sting/gatk/phonehome/GATKRunReport.java index 4cf5046a2..b60a7845a 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/phonehome/GATKRunReport.java +++ b/public/java/src/org/broadinstitute/sting/gatk/phonehome/GATKRunReport.java @@ -93,7 +93,7 @@ public class GATKRunReport { /** * our log */ - protected static Logger logger = Logger.getLogger(GATKRunReport.class); + protected static final Logger logger = Logger.getLogger(GATKRunReport.class); @Element(required = false, name = "id") diff --git a/public/java/src/org/broadinstitute/sting/gatk/traversals/TraversalEngine.java b/public/java/src/org/broadinstitute/sting/gatk/traversals/TraversalEngine.java index 2593fc72e..abc71e549 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/traversals/TraversalEngine.java +++ b/public/java/src/org/broadinstitute/sting/gatk/traversals/TraversalEngine.java @@ -92,7 +92,7 @@ public abstract class TraversalEngine,Provide GenomeLocSortedSet targetIntervals = null; /** our log, which we want to capture anything from this class */ - protected static Logger logger = Logger.getLogger(TraversalEngine.class); + protected static final Logger logger = Logger.getLogger(TraversalEngine.class); protected GenomeAnalysisEngine engine; @@ -354,7 +354,7 @@ public abstract class TraversalEngine,Provide synchronized(performanceLogLock) { // Ignore multiple calls to reset the same lock. - if(performanceLogFile != null && performanceLogFile.equals(fileName)) + if(performanceLogFile != null && performanceLogFile.equals(file)) return; // Close an existing log diff --git a/public/java/src/org/broadinstitute/sting/gatk/traversals/TraverseLoci.java b/public/java/src/org/broadinstitute/sting/gatk/traversals/TraverseLoci.java index 5c9b83312..a5a6919a2 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/traversals/TraverseLoci.java +++ b/public/java/src/org/broadinstitute/sting/gatk/traversals/TraverseLoci.java @@ -19,7 +19,7 @@ public class TraverseLoci extends TraversalEngine,Locu /** * our log, which we want to capture anything from this class */ - protected static Logger logger = Logger.getLogger(TraversalEngine.class); + protected static final Logger logger = Logger.getLogger(TraversalEngine.class); @Override protected String getTraversalType() { diff --git a/public/java/src/org/broadinstitute/sting/gatk/traversals/TraverseReadPairs.java b/public/java/src/org/broadinstitute/sting/gatk/traversals/TraverseReadPairs.java index dd4402d82..ebaac40af 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/traversals/TraverseReadPairs.java +++ b/public/java/src/org/broadinstitute/sting/gatk/traversals/TraverseReadPairs.java @@ -24,7 +24,7 @@ import java.util.List; public class TraverseReadPairs extends TraversalEngine,ReadShardDataProvider> { /** our log, which we want to capture anything from this class */ - protected static Logger logger = Logger.getLogger(TraverseReadPairs.class); + protected static final Logger logger = Logger.getLogger(TraverseReadPairs.class); @Override protected String getTraversalType() { diff --git a/public/java/src/org/broadinstitute/sting/gatk/traversals/TraverseReads.java b/public/java/src/org/broadinstitute/sting/gatk/traversals/TraverseReads.java index 24b8ac986..cb094d29b 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/traversals/TraverseReads.java +++ b/public/java/src/org/broadinstitute/sting/gatk/traversals/TraverseReads.java @@ -51,7 +51,7 @@ import org.broadinstitute.sting.utils.sam.GATKSAMRecord; */ public class TraverseReads extends TraversalEngine,ReadShardDataProvider> { /** our log, which we want to capture anything from this class */ - protected static Logger logger = Logger.getLogger(TraverseReads.class); + protected static final Logger logger = Logger.getLogger(TraverseReads.class); @Override protected String getTraversalType() { diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/ChromosomeCounts.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/ChromosomeCounts.java index 54837baad..6bdd779c0 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/ChromosomeCounts.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/ChromosomeCounts.java @@ -53,8 +53,8 @@ import java.util.*; */ public class ChromosomeCounts extends InfoFieldAnnotation implements StandardAnnotation, ActiveRegionBasedAnnotation { - public static final String[] keyNames = { VCFConstants.ALLELE_NUMBER_KEY, VCFConstants.ALLELE_COUNT_KEY, VCFConstants.ALLELE_FREQUENCY_KEY }; - public static final VCFInfoHeaderLine[] descriptions = { + protected static final String[] keyNames = { VCFConstants.ALLELE_NUMBER_KEY, VCFConstants.ALLELE_COUNT_KEY, VCFConstants.ALLELE_FREQUENCY_KEY }; + protected static final VCFInfoHeaderLine[] descriptions = { VCFStandardHeaderLines.getInfoLine(VCFConstants.ALLELE_FREQUENCY_KEY), VCFStandardHeaderLines.getInfoLine(VCFConstants.ALLELE_COUNT_KEY), VCFStandardHeaderLines.getInfoLine(VCFConstants.ALLELE_NUMBER_KEY) }; diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/TandemRepeatAnnotator.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/TandemRepeatAnnotator.java index eced387b3..f220ecbd2 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/TandemRepeatAnnotator.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/TandemRepeatAnnotator.java @@ -66,8 +66,8 @@ public class TandemRepeatAnnotator extends InfoFieldAnnotation implements Standa return map; } - public static final String[] keyNames = {STR_PRESENT, REPEAT_UNIT_KEY,REPEATS_PER_ALLELE_KEY }; - public static final VCFInfoHeaderLine[] descriptions = { + protected static final String[] keyNames = {STR_PRESENT, REPEAT_UNIT_KEY,REPEATS_PER_ALLELE_KEY }; + protected static final VCFInfoHeaderLine[] descriptions = { new VCFInfoHeaderLine(STR_PRESENT, 0, VCFHeaderLineType.Flag, "Variant is a short tandem repeat"), new VCFInfoHeaderLine(REPEAT_UNIT_KEY, 1, VCFHeaderLineType.String, "Tandem repeat unit (bases)"), new VCFInfoHeaderLine(REPEATS_PER_ALLELE_KEY, VCFHeaderLineCount.UNBOUNDED, VCFHeaderLineType.Integer, "Number of times tandem repeat unit is repeated, for each allele (including reference)") }; diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/targets/FindCoveredIntervals.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/targets/FindCoveredIntervals.java index 373c8232e..e17c6cdb7 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/targets/FindCoveredIntervals.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/targets/FindCoveredIntervals.java @@ -78,9 +78,9 @@ public class FindCoveredIntervals extends ActiveRegionWalker { public Long reduce(final GenomeLoc value, Long reduce) { if (value != null) { out.println(value.toString()); - return ++reduce; - } else - return reduce; + reduce++; + } + return reduce; } @Override diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/DiffNode.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/DiffNode.java index 2f48de2d3..7315fe503 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/DiffNode.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/DiffNode.java @@ -224,7 +224,7 @@ public class DiffNode extends DiffValue { // X=(A=A B=B C=(D=D)) String[] parts = tree.split("=", 2); if ( parts.length != 2 ) - throw new ReviewedStingException("Unexpected tree structure: " + tree + " parts=" + parts); + throw new ReviewedStingException("Unexpected tree structure: " + tree); String name = parts[0]; String value = parts[1]; diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/ThetaVariantEvaluator.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/ThetaVariantEvaluator.java index a509294ff..b87a8ee85 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/ThetaVariantEvaluator.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/ThetaVariantEvaluator.java @@ -41,7 +41,7 @@ public class ThetaVariantEvaluator extends VariantEvaluator { ConcurrentMap alleleCounts = new ConcurrentHashMap(); int numHetsHere = 0; - float numGenosHere = 0; + int numGenosHere = 0; int numIndsHere = 0; for (final Genotype genotype : vc.getGenotypes()) { @@ -68,7 +68,7 @@ public class ThetaVariantEvaluator extends VariantEvaluator { //only if have one called genotype at least this.numSites++; - this.totalHet += numHetsHere / numGenosHere; + this.totalHet += numHetsHere / (double)numGenosHere; //compute based on num sites float harmonicFactor = 0; @@ -79,7 +79,7 @@ public class ThetaVariantEvaluator extends VariantEvaluator { //now compute pairwise mismatches float numPairwise = 0; - float numDiffs = 0; + int numDiffs = 0; for (String allele1 : alleleCounts.keySet()) { int allele1Count = alleleCounts.get(allele1); diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariants.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariants.java index f775c8dd6..bfd9aa52f 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariants.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariants.java @@ -31,7 +31,6 @@ import org.broadinstitute.sting.gatk.arguments.StandardVariantContextInputArgume 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.samples.Sample; import org.broadinstitute.sting.gatk.walkers.RodWalker; import org.broadinstitute.sting.gatk.walkers.TreeReducible; import org.broadinstitute.sting.gatk.walkers.annotator.ChromosomeCounts; @@ -311,10 +310,6 @@ public class SelectVariants extends RodWalker implements TreeR private File rsIDFile = null; - @Hidden - @Argument(fullName="outMVFile", shortName="outMVFile", doc="", required=false) - private String outMVFile = null; - @Hidden @Argument(fullName="fullyDecode", doc="If true, the incoming VariantContext will be fully decoded", required=false) private boolean fullyDecode = false; @@ -369,8 +364,6 @@ public class SelectVariants extends RodWalker implements TreeR private int positionToAdd = 0; private RandomVariantStructure [] variantArray; - private PrintStream outMVFileStream = null; - //Random number generator for the genotypes to remove private Random randomGenotypes = new Random(); @@ -528,23 +521,6 @@ public class SelectVariants extends RodWalker implements TreeR if (MENDELIAN_VIOLATIONS && mv.countViolations(this.getSampleDB().getFamilies(samples),vc) < 1) break; - if (outMVFile != null){ - for( String familyId : mv.getViolationFamilies()){ - for(Sample sample : this.getSampleDB().getFamily(familyId)){ - if(sample.getParents().size() > 0){ - outMVFileStream.format("MV@%s:%d. REF=%s, ALT=%s, AC=%d, momID=%s, dadID=%s, childID=%s, momG=%s, momGL=%s, dadG=%s, dadGL=%s, " + - "childG=%s childGL=%s\n",vc.getChr(), vc.getStart(), - vc.getReference().getDisplayString(), vc.getAlternateAllele(0).getDisplayString(), vc.getCalledChrCount(vc.getAlternateAllele(0)), - sample.getMaternalID(), sample.getPaternalID(), sample.getID(), - vc.getGenotype(sample.getMaternalID()).toBriefString(), vc.getGenotype(sample.getMaternalID()).getLikelihoods().getAsString(), - vc.getGenotype(sample.getPaternalID()).toBriefString(), vc.getGenotype(sample.getPaternalID()).getLikelihoods().getAsString(), - vc.getGenotype(sample.getID()).toBriefString(),vc.getGenotype(sample.getID()).getLikelihoods().getAsString() ); - - } - } - } - } - if (DISCORDANCE_ONLY) { Collection compVCs = tracker.getValues(discordanceTrack, context.getLocation()); if (!isDiscordant(vc, compVCs)) diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToTable.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToTable.java index b73a498bc..b9577ca9b 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToTable.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToTable.java @@ -372,7 +372,7 @@ public class VariantsToTable extends RodWalker { // ---------------------------------------------------------------------------------------------------- public static abstract class Getter { public abstract String get(VariantContext vc); } - public static Map getters = new HashMap(); + public static final Map getters = new HashMap(); static { // #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT diff --git a/public/java/src/org/broadinstitute/sting/utils/BaseUtils.java b/public/java/src/org/broadinstitute/sting/utils/BaseUtils.java index 0065f9258..13571df78 100644 --- a/public/java/src/org/broadinstitute/sting/utils/BaseUtils.java +++ b/public/java/src/org/broadinstitute/sting/utils/BaseUtils.java @@ -67,10 +67,10 @@ public class BaseUtils { public static final byte DELETION_INDEX = 4; public static final byte NO_CALL_INDEX = 5; // (this is 'N') - public static int gIndex = BaseUtils.simpleBaseToBaseIndex((byte) 'G'); - public static int cIndex = BaseUtils.simpleBaseToBaseIndex((byte) 'C'); - public static int aIndex = BaseUtils.simpleBaseToBaseIndex((byte) 'A'); - public static int tIndex = BaseUtils.simpleBaseToBaseIndex((byte) 'T'); + public static final int aIndex = BaseUtils.simpleBaseToBaseIndex((byte) 'A'); + public static final int cIndex = BaseUtils.simpleBaseToBaseIndex((byte) 'C'); + public static final int gIndex = BaseUtils.simpleBaseToBaseIndex((byte) 'G'); + public static final int tIndex = BaseUtils.simpleBaseToBaseIndex((byte) 'T'); /// In genetics, a transition is a mutation changing a purine to another purine nucleotide (A <-> G) or // a pyrimidine to another pyrimidine nucleotide (C <-> T). diff --git a/public/java/src/org/broadinstitute/sting/utils/baq/BAQ.java b/public/java/src/org/broadinstitute/sting/utils/baq/BAQ.java index 439a0d8ed..f37451cba 100644 --- a/public/java/src/org/broadinstitute/sting/utils/baq/BAQ.java +++ b/public/java/src/org/broadinstitute/sting/utils/baq/BAQ.java @@ -68,7 +68,7 @@ public class BAQ { } // Phred scaled now (changed 1/10/2011) - public static double DEFAULT_GOP = 40; + public static final double DEFAULT_GOP = 40; /* Takes a Phred Scale quality score and returns the error probability. * 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 83e55cb12..9b5886c65 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 @@ -38,8 +38,8 @@ import java.util.Map; * A class representing a key=value entry in the VCF header */ public class VCFHeaderLine implements Comparable { - protected static boolean ALLOW_UNBOUND_DESCRIPTIONS = true; - protected static String UNBOUND_DESCRIPTION = "Not provided in original VCF header"; + protected static final boolean ALLOW_UNBOUND_DESCRIPTIONS = true; + protected static final String UNBOUND_DESCRIPTION = "Not provided in original VCF header"; private String mKey = null; private String mValue = null; diff --git a/public/java/src/org/broadinstitute/sting/utils/pileup/PileupElement.java b/public/java/src/org/broadinstitute/sting/utils/pileup/PileupElement.java index e5cd9f4d5..8cba5ec23 100755 --- a/public/java/src/org/broadinstitute/sting/utils/pileup/PileupElement.java +++ b/public/java/src/org/broadinstitute/sting/utils/pileup/PileupElement.java @@ -3,6 +3,7 @@ package org.broadinstitute.sting.utils.pileup; import com.google.java.contract.Ensures; import com.google.java.contract.Requires; import org.broadinstitute.sting.utils.BaseUtils; +import org.broadinstitute.sting.utils.MathUtils; import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; import org.broadinstitute.sting.utils.exceptions.UserException; import org.broadinstitute.sting.utils.sam.GATKSAMRecord; @@ -220,7 +221,7 @@ public class PileupElement implements Comparable { if (isDeletion() && (offset + 1 >= read.getReadLength()) ) // deletion in the end of the read throw new UserException.MalformedBAM(read, String.format("Adjacent I/D events in read %s -- cigar: %s", read.getReadName(), read.getCigarString())); - representativeCount = (isDeletion()) ? Math.round((read.getReducedCount(offset) + read.getReducedCount(offset + 1)) / 2) : read.getReducedCount(offset); + representativeCount = (isDeletion()) ? MathUtils.fastRound((read.getReducedCount(offset) + read.getReducedCount(offset + 1)) / 2.0) : read.getReducedCount(offset); } return representativeCount; } diff --git a/public/java/src/org/broadinstitute/sting/utils/recalibration/RecalDatum.java b/public/java/src/org/broadinstitute/sting/utils/recalibration/RecalDatum.java index 249422c17..8c8815b54 100755 --- a/public/java/src/org/broadinstitute/sting/utils/recalibration/RecalDatum.java +++ b/public/java/src/org/broadinstitute/sting/utils/recalibration/RecalDatum.java @@ -94,8 +94,8 @@ public class RecalDatum { * @param reportedQuality */ public RecalDatum(final long _numObservations, final long _numMismatches, final byte reportedQuality) { - if ( numObservations < 0 ) throw new IllegalArgumentException("numObservations < 0"); - if ( numMismatches < 0 ) throw new IllegalArgumentException("numMismatches < 0"); + if ( _numObservations < 0 ) throw new IllegalArgumentException("numObservations < 0"); + if ( _numMismatches < 0 ) throw new IllegalArgumentException("numMismatches < 0"); if ( reportedQuality < 0 ) throw new IllegalArgumentException("reportedQuality < 0"); numObservations = _numObservations; diff --git a/public/java/src/org/broadinstitute/sting/utils/recalibration/RecalDatumNode.java b/public/java/src/org/broadinstitute/sting/utils/recalibration/RecalDatumNode.java index 102aa4433..41e96222c 100644 --- a/public/java/src/org/broadinstitute/sting/utils/recalibration/RecalDatumNode.java +++ b/public/java/src/org/broadinstitute/sting/utils/recalibration/RecalDatumNode.java @@ -21,7 +21,7 @@ import java.util.Set; */ public class RecalDatumNode { private final static double SMALLEST_CHI2_PVALUE = 1e-300; - protected static Logger logger = Logger.getLogger(RecalDatumNode.class); + protected static final Logger logger = Logger.getLogger(RecalDatumNode.class); /** * fixedPenalty is this value if it's considered fixed diff --git a/public/java/src/org/broadinstitute/sting/utils/sam/GATKSAMReadGroupRecord.java b/public/java/src/org/broadinstitute/sting/utils/sam/GATKSAMReadGroupRecord.java index df1ff2a0e..849a7ddee 100755 --- a/public/java/src/org/broadinstitute/sting/utils/sam/GATKSAMReadGroupRecord.java +++ b/public/java/src/org/broadinstitute/sting/utils/sam/GATKSAMReadGroupRecord.java @@ -13,7 +13,7 @@ import org.broadinstitute.sting.utils.NGSPlatform; */ public class GATKSAMReadGroupRecord extends SAMReadGroupRecord { - public static String LANE_TAG = "LN"; + public static final String LANE_TAG = "LN"; // the SAMReadGroupRecord data we're caching private String mSample = null; diff --git a/public/java/src/org/broadinstitute/sting/utils/sam/ReadUtils.java b/public/java/src/org/broadinstitute/sting/utils/sam/ReadUtils.java index c16470c48..bd908727f 100755 --- a/public/java/src/org/broadinstitute/sting/utils/sam/ReadUtils.java +++ b/public/java/src/org/broadinstitute/sting/utils/sam/ReadUtils.java @@ -53,8 +53,8 @@ public class ReadUtils { private ReadUtils() { } - private static int DEFAULT_ADAPTOR_SIZE = 100; - public static int CLIPPING_GOAL_NOT_REACHED = -1; + private static final int DEFAULT_ADAPTOR_SIZE = 100; + public static final int CLIPPING_GOAL_NOT_REACHED = -1; public static int getMeanRepresentativeReadCount(GATKSAMRecord read) { if (!read.isReducedRead()) diff --git a/public/java/src/org/broadinstitute/sting/utils/variantcontext/GenotypeBuilder.java b/public/java/src/org/broadinstitute/sting/utils/variantcontext/GenotypeBuilder.java index e3bef6bc5..c18f954a2 100755 --- a/public/java/src/org/broadinstitute/sting/utils/variantcontext/GenotypeBuilder.java +++ b/public/java/src/org/broadinstitute/sting/utils/variantcontext/GenotypeBuilder.java @@ -53,7 +53,7 @@ import java.util.*; */ @Invariant({"alleles != null"}) public final class GenotypeBuilder { - public static boolean MAKE_FAST_BY_DEFAULT = true; + public static final boolean MAKE_FAST_BY_DEFAULT = true; private String sampleName = null; private List alleles = Collections.emptyList(); diff --git a/public/java/src/org/broadinstitute/sting/utils/variantcontext/GenotypeLikelihoods.java b/public/java/src/org/broadinstitute/sting/utils/variantcontext/GenotypeLikelihoods.java index d644eda7d..7b4256b70 100755 --- a/public/java/src/org/broadinstitute/sting/utils/variantcontext/GenotypeLikelihoods.java +++ b/public/java/src/org/broadinstitute/sting/utils/variantcontext/GenotypeLikelihoods.java @@ -401,7 +401,7 @@ public class GenotypeLikelihoods { } // An index conversion from the deprecated PL ordering to the new VCF-based ordering for up to 3 alternate alleles - protected static int[] PLindexConversion = new int[]{0, 1, 3, 6, 2, 4, 7, 5, 8, 9}; + protected static final int[] PLindexConversion = new int[]{0, 1, 3, 6, 2, 4, 7, 5, 8, 9}; /** * get the allele index pair for the given PL using the deprecated PL ordering: diff --git a/public/java/src/org/broadinstitute/sting/utils/variantcontext/VariantContextUtils.java b/public/java/src/org/broadinstitute/sting/utils/variantcontext/VariantContextUtils.java index 5421960b2..ff6b0be70 100755 --- a/public/java/src/org/broadinstitute/sting/utils/variantcontext/VariantContextUtils.java +++ b/public/java/src/org/broadinstitute/sting/utils/variantcontext/VariantContextUtils.java @@ -730,7 +730,7 @@ public class VariantContextUtils { vcList.remove(k); // avoid having empty lists if (vcList.size() == 0) - mappedVCs.remove(vcList); + mappedVCs.remove(type); if ( !mappedVCs.containsKey(vc.getType()) ) mappedVCs.put(vc.getType(), new ArrayList()); mappedVCs.get(vc.getType()).add(otherVC);