zzh
/
gatk-3.8
1
0
Fork 0
Code Issues Pull Requests Packages Projects Releases Wiki Activity

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
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

8
public/java/src/org/broadinstitute/sting/alignment/reference/bwt/Bases.java
View File

@ -12,10 +12,10 @@ import java.util.*;
*/
public class Bases implements Iterable<Byte>
{
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();

2
public/java/src/org/broadinstitute/sting/commandline/ArgumentTypeDescriptor.java
View File

@ -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.

4
public/java/src/org/broadinstitute/sting/commandline/ParsingMethod.java
View File

@ -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) {};
}

2
public/java/src/org/broadinstitute/sting/gatk/datasources/providers/ReadBasedReferenceOrderedView.java
View File

@ -118,7 +118,7 @@ class WindowedData {
rec.getAlignmentStart(),
stop);
states = new ArrayList<RMDDataState>();
if (provider != null && provider.getReferenceOrderedData() != null)
if (provider.getReferenceOrderedData() != null)
for (ReferenceOrderedDataSource dataSource : provider.getReferenceOrderedData())
states.add(new RMDDataState(dataSource, dataSource.seek(range)));
}

3
public/java/src/org/broadinstitute/sting/gatk/datasources/reference/ReferenceDataSource.java
View File

@ -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

2
public/java/src/org/broadinstitute/sting/gatk/executive/MicroScheduler.java
View File

@ -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.

4
public/java/src/org/broadinstitute/sting/gatk/executive/TreeReducer.java
View File

@ -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) );

2
public/java/src/org/broadinstitute/sting/gatk/phonehome/GATKRunReport.java
View File

@ -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")

4
public/java/src/org/broadinstitute/sting/gatk/traversals/TraversalEngine.java
View File

@ -92,7 +92,7 @@ public abstract class TraversalEngine<M,T,WalkerType extends Walker<M,T>,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<M,T,WalkerType extends Walker<M,T>,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

2
public/java/src/org/broadinstitute/sting/gatk/traversals/TraverseLoci.java
View File

@ -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
*/
protected static Logger logger = Logger.getLogger(TraversalEngine.class);
protected static final Logger logger = Logger.getLogger(TraversalEngine.class);
@Override
protected String getTraversalType() {

2
public/java/src/org/broadinstitute/sting/gatk/traversals/TraverseReadPairs.java
View File

@ -24,7 +24,7 @@ import java.util.List;
public class TraverseReadPairs<M,T> extends TraversalEngine<M,T, ReadPairWalker<M,T>,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() {

2
public/java/src/org/broadinstitute/sting/gatk/traversals/TraverseReads.java
View File

@ -51,7 +51,7 @@ import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
*/
public class TraverseReads<M,T> extends TraversalEngine<M,T,ReadWalker<M,T>,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() {

4
public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/ChromosomeCounts.java
View File

@ -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) };

4
public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/TandemRepeatAnnotator.java
View File

@ -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)") };

6
public/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/targets/FindCoveredIntervals.java
View File

@ -78,9 +78,9 @@ public class FindCoveredIntervals extends ActiveRegionWalker<GenomeLoc, Long> {
public Long reduce(final GenomeLoc value, Long reduce) {
if (value != null) {
out.println(value.toString());
return ++reduce;
} else
return reduce;
reduce++;
}
return reduce;
}
@Override

2
public/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/DiffNode.java
View File

@ -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];

6
public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/ThetaVariantEvaluator.java
View File

@ -41,7 +41,7 @@ public class ThetaVariantEvaluator extends VariantEvaluator {
ConcurrentMap<String, Integer> alleleCounts = new ConcurrentHashMap<String, Integer>();
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);

24
public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariants.java
View File

@ -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<Integer, Integer> 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<Integer, Integer> 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<Integer, Integer> 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<VariantContext> compVCs = tracker.getValues(discordanceTrack, context.getLocation());
if (!isDiscordant(vc, compVCs))

2
public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToTable.java
View File

@ -372,7 +372,7 @@ public class VariantsToTable extends RodWalker<Integer, Integer> {
// ----------------------------------------------------------------------------------------------------
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 {
// #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT

8
public/java/src/org/broadinstitute/sting/utils/BaseUtils.java
View File

@ -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).

2
public/java/src/org/broadinstitute/sting/utils/baq/BAQ.java
View File

@ -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.
*

4
public/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFHeaderLine.java
View File

@ -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;

3
public/java/src/org/broadinstitute/sting/utils/pileup/PileupElement.java
View File

@ -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<PileupElement> {
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;
}

4
public/java/src/org/broadinstitute/sting/utils/recalibration/RecalDatum.java
View File

@ -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;

2
public/java/src/org/broadinstitute/sting/utils/recalibration/RecalDatumNode.java
View File

@ -21,7 +21,7 @@ import java.util.Set;
*/
public class RecalDatumNode<T extends RecalDatum> {
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

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 static String LANE_TAG = "LN";
public static final String LANE_TAG = "LN";
// the SAMReadGroupRecord data we're caching
private String mSample = null;

4
public/java/src/org/broadinstitute/sting/utils/sam/ReadUtils.java
View File

@ -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())

2
public/java/src/org/broadinstitute/sting/utils/variantcontext/GenotypeBuilder.java
View File

@ -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<Allele> alleles = Collections.emptyList();

2
public/java/src/org/broadinstitute/sting/utils/variantcontext/GenotypeLikelihoods.java
View File

@ -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:

2
public/java/src/org/broadinstitute/sting/utils/variantcontext/VariantContextUtils.java
View File

@ -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<VariantContext>());
mappedVCs.get(vc.getType()).add(otherVC);