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Killing off some FindBugs 'Realiability' issues

This commit is contained in:
Eric Banks 2012-08-16 14:00:48 -04:00
parent dac3958461
commit ded0e11b45
30 changed files with 48 additions and 72 deletions
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8
public/java/src/org/broadinstitute/sting/alignment/reference/bwt/Bases.java
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@ -12,10 +12,10 @@ import java.util.*;
*/ */
public class Bases implements Iterable<Byte> public class Bases implements Iterable<Byte>
{ {
public static byte A = 'A'; public static final byte A = 'A';
public static byte C = 'C'; public static final byte C = 'C';
public static byte G = 'G'; public static final byte G = 'G';
public static byte T = 'T'; public static final byte T = 'T';
public static final Bases instance = new Bases(); public static final Bases instance = new Bases();

2
public/java/src/org/broadinstitute/sting/commandline/ArgumentTypeDescriptor.java
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@ -53,7 +53,7 @@ public abstract class ArgumentTypeDescriptor {
/** /**
* our log, which we want to capture anything from org.broadinstitute.sting * 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. * Fetch the given descriptor from the descriptor repository.

4
public/java/src/org/broadinstitute/sting/commandline/ParsingMethod.java
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@ -120,8 +120,8 @@ public abstract class ParsingMethod {
*/ */
private static final String TAG_TEXT = "[\\w\\-\\.\\=]*"; 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) {}; 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) {}; ArgumentDefinitions.ShortNameDefinitionMatcher) {};
} }

2
public/java/src/org/broadinstitute/sting/gatk/datasources/providers/ReadBasedReferenceOrderedView.java
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@ -118,7 +118,7 @@ class WindowedData {
rec.getAlignmentStart(), rec.getAlignmentStart(),
stop); stop);
states = new ArrayList<RMDDataState>(); states = new ArrayList<RMDDataState>();
if (provider != null && provider.getReferenceOrderedData() != null) if (provider.getReferenceOrderedData() != null)
for (ReferenceOrderedDataSource dataSource : provider.getReferenceOrderedData()) for (ReferenceOrderedDataSource dataSource : provider.getReferenceOrderedData())
states.add(new RMDDataState(dataSource, dataSource.seek(range))); states.add(new RMDDataState(dataSource, dataSource.seek(range)));
} }

3
public/java/src/org/broadinstitute/sting/gatk/datasources/reference/ReferenceDataSource.java
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@ -45,7 +45,6 @@ import org.broadinstitute.sting.utils.file.FileSystemInabilityToLockException;
import java.io.File; import java.io.File;
import java.util.ArrayList; import java.util.ArrayList;
import java.util.Collections; import java.util.Collections;
import java.util.LinkedList;
import java.util.List; import java.util.List;
/** /**
@ -56,7 +55,7 @@ public class ReferenceDataSource {
private IndexedFastaSequenceFile reference; private IndexedFastaSequenceFile reference;
/** our log, which we want to capture anything from this class */ /** 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 * Create reference data source from fasta file

2
public/java/src/org/broadinstitute/sting/gatk/executive/MicroScheduler.java
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@ -58,7 +58,7 @@ import java.util.Collection;
/** Shards and schedules data in manageable chunks. */ /** Shards and schedules data in manageable chunks. */
public abstract class MicroScheduler implements MicroSchedulerMBean { 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. * Counts the number of instances of the class that are currently alive.

4
public/java/src/org/broadinstitute/sting/gatk/executive/TreeReducer.java
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@ -66,13 +66,13 @@ public class TreeReducer implements Callable {
* @return Result of the reduce. * @return Result of the reduce.
*/ */
public Object call() { public Object call() {
Object result = null; Object result;
final long startTime = System.currentTimeMillis(); final long startTime = System.currentTimeMillis();
try { try {
if( lhs == null ) if( lhs == null )
result = lhs.get(); result = null;
// todo -- what the hell is this above line? Shouldn't it be the two below? // todo -- what the hell is this above line? Shouldn't it be the two below?
// if( lhs == null ) // if( lhs == null )
// throw new IllegalStateException(String.format("Insufficient data on which to reduce; lhs = %s, rhs = %s", lhs, rhs) ); // throw new IllegalStateException(String.format("Insufficient data on which to reduce; lhs = %s, rhs = %s", lhs, rhs) );

2
public/java/src/org/broadinstitute/sting/gatk/phonehome/GATKRunReport.java
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@ -93,7 +93,7 @@ public class GATKRunReport {
/** /**
* our log * our log
*/ */
protected static Logger logger = Logger.getLogger(GATKRunReport.class); protected static final Logger logger = Logger.getLogger(GATKRunReport.class);
@Element(required = false, name = "id") @Element(required = false, name = "id")

4
public/java/src/org/broadinstitute/sting/gatk/traversals/TraversalEngine.java
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@ -92,7 +92,7 @@ public abstract class TraversalEngine<M,T,WalkerType extends Walker<M,T>,Provide
GenomeLocSortedSet targetIntervals = null; GenomeLocSortedSet targetIntervals = null;
/** our log, which we want to capture anything from this class */ /** 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; protected GenomeAnalysisEngine engine;
@ -354,7 +354,7 @@ public abstract class TraversalEngine<M,T,WalkerType extends Walker<M,T>,Provide
synchronized(performanceLogLock) { synchronized(performanceLogLock) {
// Ignore multiple calls to reset the same lock. // Ignore multiple calls to reset the same lock.
if(performanceLogFile != null && performanceLogFile.equals(fileName)) if(performanceLogFile != null && performanceLogFile.equals(file))
return; return;
// Close an existing log // Close an existing log

2
public/java/src/org/broadinstitute/sting/gatk/traversals/TraverseLoci.java
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@ -19,7 +19,7 @@ public class TraverseLoci<M,T> extends TraversalEngine<M,T,LocusWalker<M,T>,Locu
/** /**
* our log, which we want to capture anything from this class * 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 @Override
protected String getTraversalType() { protected String getTraversalType() {

2
public/java/src/org/broadinstitute/sting/gatk/traversals/TraverseReadPairs.java
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@ -24,7 +24,7 @@ import java.util.List;
public class TraverseReadPairs<M,T> extends TraversalEngine<M,T, ReadPairWalker<M,T>,ReadShardDataProvider> { public class TraverseReadPairs<M,T> extends TraversalEngine<M,T, ReadPairWalker<M,T>,ReadShardDataProvider> {
/** our log, which we want to capture anything from this class */ /** 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 @Override
protected String getTraversalType() { protected String getTraversalType() {

2
public/java/src/org/broadinstitute/sting/gatk/traversals/TraverseReads.java
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@ -51,7 +51,7 @@ import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
*/ */
public class TraverseReads<M,T> extends TraversalEngine<M,T,ReadWalker<M,T>,ReadShardDataProvider> { public class TraverseReads<M,T> extends TraversalEngine<M,T,ReadWalker<M,T>,ReadShardDataProvider> {
/** our log, which we want to capture anything from this class */ /** 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 @Override
protected String getTraversalType() { protected String getTraversalType() {

4
public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/ChromosomeCounts.java
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@ -53,8 +53,8 @@ import java.util.*;
*/ */
public class ChromosomeCounts extends InfoFieldAnnotation implements StandardAnnotation, ActiveRegionBasedAnnotation { 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 }; protected static final String[] keyNames = { VCFConstants.ALLELE_NUMBER_KEY, VCFConstants.ALLELE_COUNT_KEY, VCFConstants.ALLELE_FREQUENCY_KEY };
public static final VCFInfoHeaderLine[] descriptions = { protected static final VCFInfoHeaderLine[] descriptions = {
VCFStandardHeaderLines.getInfoLine(VCFConstants.ALLELE_FREQUENCY_KEY), VCFStandardHeaderLines.getInfoLine(VCFConstants.ALLELE_FREQUENCY_KEY),
VCFStandardHeaderLines.getInfoLine(VCFConstants.ALLELE_COUNT_KEY), VCFStandardHeaderLines.getInfoLine(VCFConstants.ALLELE_COUNT_KEY),
VCFStandardHeaderLines.getInfoLine(VCFConstants.ALLELE_NUMBER_KEY) }; VCFStandardHeaderLines.getInfoLine(VCFConstants.ALLELE_NUMBER_KEY) };

4
public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/TandemRepeatAnnotator.java
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@ -66,8 +66,8 @@ public class TandemRepeatAnnotator extends InfoFieldAnnotation implements Standa
return map; return map;
} }
public static final String[] keyNames = {STR_PRESENT, REPEAT_UNIT_KEY,REPEATS_PER_ALLELE_KEY }; protected static final String[] keyNames = {STR_PRESENT, REPEAT_UNIT_KEY,REPEATS_PER_ALLELE_KEY };
public static final VCFInfoHeaderLine[] descriptions = { protected static final VCFInfoHeaderLine[] descriptions = {
new VCFInfoHeaderLine(STR_PRESENT, 0, VCFHeaderLineType.Flag, "Variant is a short tandem repeat"), 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(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)") }; new VCFInfoHeaderLine(REPEATS_PER_ALLELE_KEY, VCFHeaderLineCount.UNBOUNDED, VCFHeaderLineType.Integer, "Number of times tandem repeat unit is repeated, for each allele (including reference)") };

6
public/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/targets/FindCoveredIntervals.java
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@ -78,9 +78,9 @@ public class FindCoveredIntervals extends ActiveRegionWalker<GenomeLoc, Long> {
public Long reduce(final GenomeLoc value, Long reduce) { public Long reduce(final GenomeLoc value, Long reduce) {
if (value != null) { if (value != null) {
out.println(value.toString()); out.println(value.toString());
return ++reduce; reduce++;
} else }
return reduce; return reduce;
} }
@Override @Override

2
public/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/DiffNode.java
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@ -224,7 +224,7 @@ public class DiffNode extends DiffValue {
// X=(A=A B=B C=(D=D)) // X=(A=A B=B C=(D=D))
String[] parts = tree.split("=", 2); String[] parts = tree.split("=", 2);
if ( parts.length != 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 name = parts[0];
String value = parts[1]; String value = parts[1];

6
public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/ThetaVariantEvaluator.java
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@ -41,7 +41,7 @@ public class ThetaVariantEvaluator extends VariantEvaluator {
ConcurrentMap<String, Integer> alleleCounts = new ConcurrentHashMap<String, Integer>(); ConcurrentMap<String, Integer> alleleCounts = new ConcurrentHashMap<String, Integer>();
int numHetsHere = 0; int numHetsHere = 0;
float numGenosHere = 0; int numGenosHere = 0;
int numIndsHere = 0; int numIndsHere = 0;
for (final Genotype genotype : vc.getGenotypes()) { for (final Genotype genotype : vc.getGenotypes()) {
@ -68,7 +68,7 @@ public class ThetaVariantEvaluator extends VariantEvaluator {
//only if have one called genotype at least //only if have one called genotype at least
this.numSites++; this.numSites++;
this.totalHet += numHetsHere / numGenosHere; this.totalHet += numHetsHere / (double)numGenosHere;
//compute based on num sites //compute based on num sites
float harmonicFactor = 0; float harmonicFactor = 0;
@ -79,7 +79,7 @@ public class ThetaVariantEvaluator extends VariantEvaluator {
//now compute pairwise mismatches //now compute pairwise mismatches
float numPairwise = 0; float numPairwise = 0;
float numDiffs = 0; int numDiffs = 0;
for (String allele1 : alleleCounts.keySet()) { for (String allele1 : alleleCounts.keySet()) {
int allele1Count = alleleCounts.get(allele1); int allele1Count = alleleCounts.get(allele1);

24
public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariants.java
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@ -31,7 +31,6 @@ import org.broadinstitute.sting.gatk.arguments.StandardVariantContextInputArgume
import org.broadinstitute.sting.gatk.contexts.AlignmentContext; import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext; import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; 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.RodWalker;
import org.broadinstitute.sting.gatk.walkers.TreeReducible; import org.broadinstitute.sting.gatk.walkers.TreeReducible;
import org.broadinstitute.sting.gatk.walkers.annotator.ChromosomeCounts; import org.broadinstitute.sting.gatk.walkers.annotator.ChromosomeCounts;
@ -311,10 +310,6 @@ public class SelectVariants extends RodWalker<Integer, Integer> implements TreeR
private File rsIDFile = null; private File rsIDFile = null;
@Hidden
@Argument(fullName="outMVFile", shortName="outMVFile", doc="", required=false)
private String outMVFile = null;
@Hidden @Hidden
@Argument(fullName="fullyDecode", doc="If true, the incoming VariantContext will be fully decoded", required=false) @Argument(fullName="fullyDecode", doc="If true, the incoming VariantContext will be fully decoded", required=false)
private boolean fullyDecode = false; private boolean fullyDecode = false;
@ -369,8 +364,6 @@ public class SelectVariants extends RodWalker<Integer, Integer> implements TreeR
private int positionToAdd = 0; private int positionToAdd = 0;
private RandomVariantStructure [] variantArray; private RandomVariantStructure [] variantArray;
private PrintStream outMVFileStream = null;
//Random number generator for the genotypes to remove //Random number generator for the genotypes to remove
private Random randomGenotypes = new Random(); private Random randomGenotypes = new Random();
@ -528,23 +521,6 @@ public class SelectVariants extends RodWalker<Integer, Integer> implements TreeR
if (MENDELIAN_VIOLATIONS && mv.countViolations(this.getSampleDB().getFamilies(samples),vc) < 1) if (MENDELIAN_VIOLATIONS && mv.countViolations(this.getSampleDB().getFamilies(samples),vc) < 1)
break; 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) { if (DISCORDANCE_ONLY) {
Collection<VariantContext> compVCs = tracker.getValues(discordanceTrack, context.getLocation()); Collection<VariantContext> compVCs = tracker.getValues(discordanceTrack, context.getLocation());
if (!isDiscordant(vc, compVCs)) if (!isDiscordant(vc, compVCs))

2
public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToTable.java
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@ -372,7 +372,7 @@ public class VariantsToTable extends RodWalker<Integer, Integer> {
// ---------------------------------------------------------------------------------------------------- // ----------------------------------------------------------------------------------------------------
public static abstract class Getter { public abstract String get(VariantContext vc); } public static abstract class Getter { public abstract String get(VariantContext vc); }
public static Map<String, Getter> getters = new HashMap<String, Getter>(); public static final Map<String, Getter> getters = new HashMap<String, Getter>();
static { static {
// #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT // #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT

8
public/java/src/org/broadinstitute/sting/utils/BaseUtils.java
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@ -67,10 +67,10 @@ public class BaseUtils {
public static final byte DELETION_INDEX = 4; public static final byte DELETION_INDEX = 4;
public static final byte NO_CALL_INDEX = 5; // (this is 'N') public static final byte NO_CALL_INDEX = 5; // (this is 'N')
public static int gIndex = BaseUtils.simpleBaseToBaseIndex((byte) 'G'); public static final int aIndex = BaseUtils.simpleBaseToBaseIndex((byte) 'A');
public static int cIndex = BaseUtils.simpleBaseToBaseIndex((byte) 'C'); public static final int cIndex = BaseUtils.simpleBaseToBaseIndex((byte) 'C');
public static int aIndex = BaseUtils.simpleBaseToBaseIndex((byte) 'A'); public static final int gIndex = BaseUtils.simpleBaseToBaseIndex((byte) 'G');
public static int tIndex = BaseUtils.simpleBaseToBaseIndex((byte) 'T'); 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 /// 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). // a pyrimidine to another pyrimidine nucleotide (C <-> T).

2
public/java/src/org/broadinstitute/sting/utils/baq/BAQ.java
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@ -68,7 +68,7 @@ public class BAQ {
} }
// Phred scaled now (changed 1/10/2011) // 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. /* Takes a Phred Scale quality score and returns the error probability.
* *

4
public/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFHeaderLine.java
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@ -38,8 +38,8 @@ import java.util.Map;
* A class representing a key=value entry in the VCF header * A class representing a key=value entry in the VCF header
*/ */
public class VCFHeaderLine implements Comparable { public class VCFHeaderLine implements Comparable {
protected static boolean ALLOW_UNBOUND_DESCRIPTIONS = true; protected static final boolean ALLOW_UNBOUND_DESCRIPTIONS = true;
protected static String UNBOUND_DESCRIPTION = "Not provided in original VCF header"; protected static final String UNBOUND_DESCRIPTION = "Not provided in original VCF header";
private String mKey = null; private String mKey = null;
private String mValue = null; private String mValue = null;

3
public/java/src/org/broadinstitute/sting/utils/pileup/PileupElement.java
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@ -3,6 +3,7 @@ package org.broadinstitute.sting.utils.pileup;
import com.google.java.contract.Ensures; import com.google.java.contract.Ensures;
import com.google.java.contract.Requires; import com.google.java.contract.Requires;
import org.broadinstitute.sting.utils.BaseUtils; 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.ReviewedStingException;
import org.broadinstitute.sting.utils.exceptions.UserException; import org.broadinstitute.sting.utils.exceptions.UserException;
import org.broadinstitute.sting.utils.sam.GATKSAMRecord; import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
@ -220,7 +221,7 @@ public class PileupElement implements Comparable<PileupElement> {
if (isDeletion() && (offset + 1 >= read.getReadLength()) ) // deletion in the end of the read 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())); 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; return representativeCount;
} }

4
public/java/src/org/broadinstitute/sting/utils/recalibration/RecalDatum.java
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@ -94,8 +94,8 @@ public class RecalDatum {
* @param reportedQuality * @param reportedQuality
*/ */
public RecalDatum(final long _numObservations, final long _numMismatches, final byte reportedQuality) { public RecalDatum(final long _numObservations, final long _numMismatches, final byte reportedQuality) {
if ( numObservations < 0 ) throw new IllegalArgumentException("numObservations < 0"); if ( _numObservations < 0 ) throw new IllegalArgumentException("numObservations < 0");
if ( numMismatches < 0 ) throw new IllegalArgumentException("numMismatches < 0"); if ( _numMismatches < 0 ) throw new IllegalArgumentException("numMismatches < 0");
if ( reportedQuality < 0 ) throw new IllegalArgumentException("reportedQuality < 0"); if ( reportedQuality < 0 ) throw new IllegalArgumentException("reportedQuality < 0");
numObservations = _numObservations; numObservations = _numObservations;

2
public/java/src/org/broadinstitute/sting/utils/recalibration/RecalDatumNode.java
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@ -21,7 +21,7 @@ import java.util.Set;
*/ */
public class RecalDatumNode<T extends RecalDatum> { public class RecalDatumNode<T extends RecalDatum> {
private final static double SMALLEST_CHI2_PVALUE = 1e-300; 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 * fixedPenalty is this value if it's considered fixed

2
public/java/src/org/broadinstitute/sting/utils/sam/GATKSAMReadGroupRecord.java
View File

@ -13,7 +13,7 @@ import org.broadinstitute.sting.utils.NGSPlatform;
*/ */
public class GATKSAMReadGroupRecord extends SAMReadGroupRecord { public class GATKSAMReadGroupRecord extends SAMReadGroupRecord {
public static String LANE_TAG = "LN"; public static final String LANE_TAG = "LN";
// the SAMReadGroupRecord data we're caching // the SAMReadGroupRecord data we're caching
private String mSample = null; private String mSample = null;

4
public/java/src/org/broadinstitute/sting/utils/sam/ReadUtils.java
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@ -53,8 +53,8 @@ public class ReadUtils {
private ReadUtils() { private ReadUtils() {
} }
private static int DEFAULT_ADAPTOR_SIZE = 100; private static final int DEFAULT_ADAPTOR_SIZE = 100;
public static int CLIPPING_GOAL_NOT_REACHED = -1; public static final int CLIPPING_GOAL_NOT_REACHED = -1;
public static int getMeanRepresentativeReadCount(GATKSAMRecord read) { public static int getMeanRepresentativeReadCount(GATKSAMRecord read) {
if (!read.isReducedRead()) if (!read.isReducedRead())

2
public/java/src/org/broadinstitute/sting/utils/variantcontext/GenotypeBuilder.java
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@ -53,7 +53,7 @@ import java.util.*;
*/ */
@Invariant({"alleles != null"}) @Invariant({"alleles != null"})
public final class GenotypeBuilder { 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 String sampleName = null;
private List<Allele> alleles = Collections.emptyList(); private List<Allele> alleles = Collections.emptyList();

2
public/java/src/org/broadinstitute/sting/utils/variantcontext/GenotypeLikelihoods.java
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@ -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 // 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: * get the allele index pair for the given PL using the deprecated PL ordering:

2
public/java/src/org/broadinstitute/sting/utils/variantcontext/VariantContextUtils.java
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@ -730,7 +730,7 @@ public class VariantContextUtils {
vcList.remove(k); vcList.remove(k);
// avoid having empty lists // avoid having empty lists
if (vcList.size() == 0) if (vcList.size() == 0)
mappedVCs.remove(vcList); mappedVCs.remove(type);
if ( !mappedVCs.containsKey(vc.getType()) ) if ( !mappedVCs.containsKey(vc.getType()) )
mappedVCs.put(vc.getType(), new ArrayList<VariantContext>()); mappedVCs.put(vc.getType(), new ArrayList<VariantContext>());
mappedVCs.get(vc.getType()).add(otherVC); mappedVCs.get(vc.getType()).add(otherVC);