Merge branch 'master' of ssh://gsa4.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable

protected/java/src/org/broadinstitute/sting/gatk/walkers/compression/reducereads/ReduceReads.java

@@ -25,9 +25,6 @@
 
 package org.broadinstitute.sting.gatk.walkers.compression.reducereads;
 
-import net.sf.samtools.Cigar;
-import net.sf.samtools.CigarElement;
-import net.sf.samtools.CigarOperator;
 import net.sf.samtools.util.SequenceUtil;
 import org.broadinstitute.sting.commandline.Argument;
 import org.broadinstitute.sting.commandline.Hidden;
@@ -183,7 +180,7 @@ public class ReduceReads extends ReadWalker<LinkedList<GATKSAMRecord>, ReduceRea
      * A value of 0 turns downsampling off.
      */
     @Argument(fullName = "downsample_coverage", shortName = "ds", doc = "", required = false)
-    protected int downsampleCoverage = 0;
+    protected int downsampleCoverage = 250;
 
     @Hidden
     @Argument(fullName = "", shortName = "dl", doc = "", required = false)
@@ -535,81 +532,12 @@ public class ReduceReads extends ReadWalker<LinkedList<GATKSAMRecord>, ReduceRea
         if (debugLevel == 1)
             System.out.println("BAM: " + read.getCigar() + " " + read.getAlignmentStart() + " " + read.getAlignmentEnd());
 
-//        if (!DONT_USE_SOFTCLIPPED_BASES)
-//            reSoftClipBases(read);
-
         if (!DONT_COMPRESS_READ_NAMES)
             compressReadName(read);
 
         out.addAlignment(read);
     }
 
-    private void reSoftClipBases(GATKSAMRecord read) {
-        Integer left = (Integer) read.getTemporaryAttribute("SL");
-        Integer right = (Integer) read.getTemporaryAttribute("SR");
-        if (left != null || right != null) {
-            Cigar newCigar = new Cigar();
-            for (CigarElement element : read.getCigar().getCigarElements()) {
-                newCigar.add(new CigarElement(element.getLength(), element.getOperator()));
-            }
-
-            if (left != null) {
-                newCigar = updateFirstSoftClipCigarElement(left, newCigar);
-                read.setAlignmentStart(read.getAlignmentStart() + left);
-            }
-
-            if (right != null) {
-                Cigar invertedCigar = invertCigar(newCigar);
-                newCigar = invertCigar(updateFirstSoftClipCigarElement(right, invertedCigar));
-            }
-            read.setCigar(newCigar);
-        }
-    }
-
-    /**
-     * Facility routine to revert the first element of a Cigar string (skipping hard clips) into a soft-clip.
-     * To be used on both ends if provided a flipped Cigar
-     *
-     * @param softClipSize  the length of the soft clipped element to add
-     * @param originalCigar the original Cigar string
-     * @return a new Cigar object with the soft clips added
-     */
-    private Cigar updateFirstSoftClipCigarElement (int softClipSize, Cigar originalCigar) {
-        Cigar result = new Cigar();
-        CigarElement leftElement = new CigarElement(softClipSize, CigarOperator.S);
-        boolean updated = false;
-        for (CigarElement element : originalCigar.getCigarElements()) {
-            if (!updated && element.getOperator() == CigarOperator.M) {
-                result.add(leftElement);
-                int newLength = element.getLength() - softClipSize;
-                if (newLength > 0)
-                    result.add(new CigarElement(newLength, CigarOperator.M));
-                updated = true;
-            }
-            else
-                result.add(element);
-        }
-        return result;
-    }
-
-    /**
-     * Given a cigar string, returns the inverted cigar string.
-     *
-     * @param cigar the original cigar
-     * @return the inverted cigar
-     */
-    private Cigar invertCigar(Cigar cigar) {
-        Stack<CigarElement> stack = new Stack<CigarElement>();
-        for (CigarElement e : cigar.getCigarElements())
-            stack.push(e);
-        Cigar inverted = new Cigar();
-        while (!stack.empty()) {
-            inverted.add(stack.pop());
-        }
-        return inverted;
-    }
-
-
     /**
      * Quality control procedure that checks if the consensus reads contains too many
      * mismatches with the reference. This should never happen and is a good trigger for

protected/java/src/org/broadinstitute/sting/gatk/walkers/compression/reducereads/SlidingWindow.java

@@ -499,7 +499,7 @@ public class SlidingWindow {
         result.addAll(addToSyntheticReads(0, start));
         result.addAll(finalizeAndAdd(ConsensusType.BOTH));
 
-        for (GATKSAMRecord read : result) {
+        for (GATKSAMRecord read : allReads) {
             readsInWindow.remove(read);                                                                                 // todo -- not optimal, but needs to be done so the next region doesn't try to remove the same reads from the header counts.
         }
 
@@ -627,7 +627,7 @@ public class SlidingWindow {
         int locationIndex = startLocation < 0 ? 0 : readStart - startLocation;
 
         if (removeRead && locationIndex < 0)
-            throw new ReviewedStingException("read is behind the Sliding Window. read: " + read + " cigar: " + read.getCigarString() + " window: " + startLocation + "," + stopLocation);
+            throw new ReviewedStingException("read is behind the Sliding Window. read: " + read + " start " + read.getUnclippedStart() + "," + read.getUnclippedEnd() + " cigar: " + read.getCigarString() + " window: " + startLocation + "," + stopLocation);
 
         if (!removeRead) {                                                                                              // we only need to create new header elements if we are adding the read, not when we're removing it
             if (locationIndex < 0) {                                                                                    // Do we need to add extra elements before the start of the header? -- this may happen if the previous read was clipped and this alignment starts before the beginning of the window

protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeCaller.java

@@ -332,11 +332,11 @@ public class HaplotypeCaller extends ActiveRegionWalker<Integer, Integer> implem
         final Map<String, AlignmentContext> splitContexts = AlignmentContextUtils.splitContextBySampleName(context);
         final GenotypesContext genotypes = GenotypesContext.create(splitContexts.keySet().size());
         final MathUtils.RunningAverage averageHQSoftClips = new MathUtils.RunningAverage();
-        for( final String sample : splitContexts.keySet() ) {
+        for( Map.Entry<String, AlignmentContext> sample : splitContexts.entrySet() ) {
             final double[] genotypeLikelihoods = new double[3]; // ref versus non-ref (any event)
             Arrays.fill(genotypeLikelihoods, 0.0);
 
-            for( final PileupElement p : splitContexts.get(sample).getBasePileup() ) {
+            for( final PileupElement p : sample.getValue().getBasePileup() ) {
                 final byte qual = ( USE_EXPANDED_TRIGGER_SET ?
                                         ( p.isNextToSoftClip() || p.isBeforeInsertion() || p.isAfterInsertion() ? ( p.getQual() > QualityUtils.MIN_USABLE_Q_SCORE ? p.getQual() : (byte) 20 ) : p.getQual() )
                                         : p.getQual() );
@@ -362,7 +362,7 @@ public class HaplotypeCaller extends ActiveRegionWalker<Integer, Integer> implem
                     genotypeLikelihoods[BB] += p.getRepresentativeCount() * QualityUtils.qualToErrorProbLog10(qual) + LOG_ONE_THIRD;
                 }
             }
-            genotypes.add( new GenotypeBuilder(sample).alleles(noCall).PL(genotypeLikelihoods).make() );
+            genotypes.add( new GenotypeBuilder(sample.getKey()).alleles(noCall).PL(genotypeLikelihoods).make() );
         }
 
         final ArrayList<Allele> alleles = new ArrayList<Allele>();

protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/LikelihoodCalculationEngine.java

@@ -53,8 +53,8 @@ public class LikelihoodCalculationEngine {
     public void computeReadLikelihoods( final ArrayList<Haplotype> haplotypes, final HashMap<String, ArrayList<GATKSAMRecord>> perSampleReadList ) {
 
         int X_METRIC_LENGTH = 0;
-        for( final String sample : perSampleReadList.keySet() ) {
+        for( final Map.Entry<String, ArrayList<GATKSAMRecord>> sample : perSampleReadList.entrySet() ) {
-            for( final GATKSAMRecord read : perSampleReadList.get(sample) ) {
+            for( final GATKSAMRecord read : sample.getValue() ) {
                 final int readLength = read.getReadLength();
                 if( readLength > X_METRIC_LENGTH ) { X_METRIC_LENGTH = readLength; }
             }
@@ -326,9 +326,9 @@ public class LikelihoodCalculationEngine {
     public static Map<String, Map<Allele, List<GATKSAMRecord>>> partitionReadsBasedOnLikelihoods( final GenomeLocParser parser, final HashMap<String, ArrayList<GATKSAMRecord>> perSampleReadList, final HashMap<String, ArrayList<GATKSAMRecord>> perSampleFilteredReadList, final Pair<VariantContext, HashMap<Allele,ArrayList<Haplotype>>> call) {
         final Map<String, Map<Allele, List<GATKSAMRecord>>> returnMap = new HashMap<String, Map<Allele, List<GATKSAMRecord>>>();
         final GenomeLoc callLoc = parser.createGenomeLoc(call.getFirst());
-        for( final String sample : perSampleReadList.keySet() ) {
+        for( final Map.Entry<String, ArrayList<GATKSAMRecord>> sample : perSampleReadList.entrySet() ) {
             final Map<Allele, List<GATKSAMRecord>> alleleReadMap = new HashMap<Allele, List<GATKSAMRecord>>();
-            final ArrayList<GATKSAMRecord> readsForThisSample = perSampleReadList.get(sample);
+            final ArrayList<GATKSAMRecord> readsForThisSample = sample.getValue();
             for( int iii = 0; iii < readsForThisSample.size(); iii++ ) {
                 final GATKSAMRecord read = readsForThisSample.get(iii); // BUGBUG: assumes read order in this list and haplotype likelihood list are the same!
                 // only count the read if it overlaps the event, otherwise it is not added to the output read list at all
@@ -338,7 +338,7 @@ public class LikelihoodCalculationEngine {
                     for( final Allele a : call.getFirst().getAlleles() ) { // find the allele with the highest haplotype likelihood
                         double maxLikelihood = Double.NEGATIVE_INFINITY;
                         for( final Haplotype h : call.getSecond().get(a) ) { // use the max likelihood from all the haplotypes which mapped to this allele (achieved via the haplotype mapper object)
-                            final double likelihood = h.getReadLikelihoods(sample)[iii];
+                            final double likelihood = h.getReadLikelihoods(sample.getKey())[iii];
                             if( likelihood > maxLikelihood ) {
                                 maxLikelihood = likelihood;
                             }
@@ -373,13 +373,13 @@ public class LikelihoodCalculationEngine {
                 readList = new ArrayList<GATKSAMRecord>();
                 alleleReadMap.put(Allele.NO_CALL, readList);
             }
-            for( final GATKSAMRecord read : perSampleFilteredReadList.get(sample) ) {
+            for( final GATKSAMRecord read : perSampleFilteredReadList.get(sample.getKey()) ) {
                 // only count the read if it overlaps the event, otherwise it is not added to the output read list at all
                 if( callLoc.overlapsP(parser.createGenomeLoc(read)) ) {
                     readList.add(read);
                 }
             }
-            returnMap.put(sample, alleleReadMap);
+            returnMap.put(sample.getKey(), alleleReadMap);
         }
         return returnMap;
     }

protected/java/test/org/broadinstitute/sting/gatk/walkers/compression/reducereads/ReduceReadsIntegrationTest.java

@@ -21,28 +21,28 @@ public class ReduceReadsIntegrationTest extends WalkerTest {
 
     @Test(enabled = true)
     public void testDefaultCompression() {
-        RRTest("testDefaultCompression ", L, "323dd4deabd7767efa0f2c6e7fa4189f");
+        RRTest("testDefaultCompression ", L, "72eb6db9d7a09a0cc25eaac1aafa97b7");
     }
 
     @Test(enabled = true)
     public void testMultipleIntervals() {
         String intervals = "-L 20:10,100,000-10,100,500 -L 20:10,200,000-10,200,500 -L 20:10,300,000-10,300,500 -L 20:10,400,000-10,500,000 -L 20:10,500,050-10,500,060 -L 20:10,600,000-10,600,015 -L 20:10,700,000-10,700,110";
-        RRTest("testMultipleIntervals ", intervals, "c437fb160547ff271f8eba30e5f3ff76");
+        RRTest("testMultipleIntervals ", intervals, "104b1a1d9fa5394c6fea95cd32967b78");
     }
 
     @Test(enabled = true)
     public void testHighCompression() {
-        RRTest("testHighCompression ", " -cs 10 -minvar 0.3 -mindel 0.3 " + L, "3a607bc3ebaf84e9dc44e005c5f8a047");
+        RRTest("testHighCompression ", " -cs 10 -minvar 0.3 -mindel 0.3 " + L, "c55140cec60fa8c35161680289d74d47");
     }
 
     @Test(enabled = true)
     public void testLowCompression() {
-        RRTest("testLowCompression ", " -cs 30 -minvar 0.01 -mindel 0.01 -minmap 5 -minqual 5 " + L, "afd39459c841b68a442abdd5ef5f8f27");
+        RRTest("testLowCompression ", " -cs 30 -minvar 0.01 -mindel 0.01 -minmap 5 -minqual 5 " + L, "0f2e57b7f6de03cc4da1ffcc8cf8f1a7");
     }
 
     @Test(enabled = true)
     public void testIndelCompression() {
-        RRTest("testIndelCompression ", " -cs 50 -L 20:10,100,500-10,100,600 ", "f7b9fa44c10bc4b2247813d2b8dc1973");
+        RRTest("testIndelCompression ", " -cs 50 -L 20:10,100,500-10,100,600 ", "dda0c95f56f90e5f633c2437c2b21031");
     }
 
     @Test(enabled = true)

public/java/src/org/broadinstitute/sting/gatk/refdata/VariantContextAdaptors.java

@@ -309,7 +309,6 @@ public class VariantContextAdaptors {
             int index = hapmap.getStart() - ref.getWindow().getStart();
             if ( index < 0 )
                 return null; // we weren't given enough reference context to create the VariantContext
-            Byte refBaseForIndel = new Byte(ref.getBases()[index]);
 
             HashSet<Allele> alleles = new HashSet<Allele>();
             Allele refSNPAllele = Allele.create(ref.getBase(), true);

public/java/src/org/broadinstitute/sting/gatk/walkers/ClipReads.java

@@ -574,7 +574,7 @@ public class ClipReads extends ReadWalker<ClipReads.ReadClipperWithData, ClipRea
         }
     }
 
-    public class ReadClipperWithData extends ReadClipper {
+    public static class ReadClipperWithData extends ReadClipper {
         private ClippingData data;
 
         public ReadClipperWithData(GATKSAMRecord read, List<SeqToClip> clipSeqs) {

public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/BaseQualityRankSumTest.java

@@ -65,12 +65,12 @@ public class BaseQualityRankSumTest extends RankSumTest implements StandardAnnot
                 // by design, first element in LinkedHashMap was ref allele
                 double refLikelihood=0.0, altLikelihood=Double.NEGATIVE_INFINITY;
 
-                for (Allele a : el.keySet()) {
+                for (Map.Entry<Allele, Double> entry : el.entrySet()) {
 
-                    if (a.isReference())
+                    if (entry.getKey().isReference())
-                        refLikelihood =el.get(a);
+                        refLikelihood = entry.getValue();
                     else {
-                        double like = el.get(a);
+                        double like = entry.getValue();
                         if (like >= altLikelihood)
                             altLikelihood = like;
                     }

public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/FisherStrand.java

@@ -291,8 +291,8 @@ public class FisherStrand extends InfoFieldAnnotation implements StandardAnnotat
         
         int[][] table = new int[2][2];
 
-        for ( String sample : stratifiedContexts.keySet() ) {
+        for ( Map.Entry<String, AlignmentContext> sample : stratifiedContexts.entrySet() ) {
-            final AlignmentContext context = stratifiedContexts.get(sample);
+            final AlignmentContext context = sample.getValue();
             if ( context == null )
                 continue;
 
@@ -313,12 +313,12 @@ public class FisherStrand extends InfoFieldAnnotation implements StandardAnnotat
 
                     double refLikelihood=0.0, altLikelihood=Double.NEGATIVE_INFINITY;
 
-                    for (Allele a : el.keySet()) {
+                    for (Map.Entry<Allele,Double> entry : el.entrySet()) {
 
-                        if (a.isReference())
+                        if (entry.getKey().isReference())
-                            refLikelihood =el.get(a);
+                            refLikelihood = entry.getValue();
                         else {
-                            double like = el.get(a);
+                            double like = entry.getValue();
                             if (like >= altLikelihood)
                                 altLikelihood = like;
                         }

public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/HaplotypeScore.java

@@ -103,7 +103,7 @@ public class HaplotypeScore extends InfoFieldAnnotation implements StandardAnnot
         return map;
     }
 
-    private class HaplotypeComparator implements Comparator<Haplotype> {
+    private static class HaplotypeComparator implements Comparator<Haplotype> {
 
         public int compare(Haplotype a, Haplotype b) {
             if (a.getQualitySum() < b.getQualitySum())
@@ -362,8 +362,8 @@ public class HaplotypeScore extends InfoFieldAnnotation implements StandardAnnot
                 // Score all the reads in the pileup, even the filtered ones
                 final double[] scores = new double[el.size()];
                 int i = 0;
-                for (Allele a : el.keySet()) {
+                for (Map.Entry<Allele, Double> a : el.entrySet()) {
-                    scores[i++] = -el.get(a);
+                    scores[i++] = -a.getValue();
                     if (DEBUG) {
                         System.out.printf("  vs. haplotype %d = %f%n", i - 1, scores[i - 1]);
                     }

public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/MappingQualityRankSumTest.java

@@ -61,12 +61,12 @@ public class MappingQualityRankSumTest extends RankSumTest implements StandardAn
                 // by design, first element in LinkedHashMap was ref allele
                 double refLikelihood=0.0, altLikelihood=Double.NEGATIVE_INFINITY;
 
-                for (Allele a : el.keySet()) {
+                for (Map.Entry<Allele,Double> a : el.entrySet()) {
 
-                    if (a.isReference())
+                    if (a.getKey().isReference())
-                        refLikelihood =el.get(a);
+                        refLikelihood = a.getValue();
                     else {
-                        double like = el.get(a);
+                        double like = a.getValue();
                         if (like >= altLikelihood)
                             altLikelihood = like;
                     }

public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/ReadPosRankSumTest.java

@@ -87,11 +87,11 @@ public class ReadPosRankSumTest extends RankSumTest implements StandardAnnotatio
                 LinkedHashMap<Allele, Double> el = indelLikelihoodMap.get(p);           // retrieve likelihood information corresponding to this read
                 double refLikelihood = 0.0, altLikelihood = Double.NEGATIVE_INFINITY;   // by design, first element in LinkedHashMap was ref allele
 
-                for (Allele a : el.keySet()) {
+                for (Map.Entry<Allele,Double> a : el.entrySet()) {
-                    if (a.isReference())
+                    if (a.getKey().isReference())
-                        refLikelihood = el.get(a);
+                        refLikelihood = a.getValue();
                     else {
-                        double like = el.get(a);
+                        double like = a.getValue();
                         if (like >= altLikelihood)
                             altLikelihood = like;
                     }
@@ -100,7 +100,6 @@ public class ReadPosRankSumTest extends RankSumTest implements StandardAnnotatio
                 int readPos = getOffsetFromClippedReadStart(p.getRead(), p.getOffset());
                 final int numAlignedBases = getNumAlignedBases(p.getRead());
 
-                int rp = readPos;
                 if (readPos > numAlignedBases / 2) {
                     readPos = numAlignedBases - (readPos + 1);
                 }

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

@@ -24,6 +24,7 @@
 
 package org.broadinstitute.sting.gatk.walkers.diagnostics.targets;
 
+import org.broadinstitute.sting.commandline.Argument;
 import org.broadinstitute.sting.commandline.Output;
 import org.broadinstitute.sting.gatk.CommandLineGATK;
 import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
@@ -46,6 +47,9 @@ public class FindCoveredIntervals extends ActiveRegionWalker<GenomeLoc, Long> {
     @Output(required = true)
     private PrintStream out;
 
+    @Argument(fullName = "coverage_threshold", shortName = "cov", doc = "The minimum allowable coverage to be considered covered", required = false)
+    private int coverageThreshold = 20;
+
     @Override
     // Look to see if the region has sufficient coverage
     public ActivityProfileResult isActive(final RefMetaDataTracker tracker, final ReferenceContext ref, final AlignmentContext context) {
@@ -53,8 +57,7 @@ public class FindCoveredIntervals extends ActiveRegionWalker<GenomeLoc, Long> {
         int depth = ThresHolder.DEFAULTS.getFilteredCoverage(context.getBasePileup());
 
         // note the linear probability scale
-        int coverageThreshold = 20;
+        return new ActivityProfileResult(Math.min(depth / coverageThreshold, 1));
-        return new ActivityProfileResult(Math.min((double) depth / coverageThreshold, 1));
 
     }
 

public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/ConsensusAlleleCounter.java

@@ -148,8 +148,8 @@ public class ConsensusAlleleCounter {
                     boolean foundKey = false;
                     // copy of hashmap into temp arrayList
                     ArrayList<Pair<String,Integer>> cList = new ArrayList<Pair<String,Integer>>();
-                    for (String s : consensusIndelStrings.keySet()) {
+                    for (Map.Entry<String, Integer> s : consensusIndelStrings.entrySet()) {
-                        cList.add(new Pair<String, Integer>(s,consensusIndelStrings.get(s)));
+                        cList.add(new Pair<String, Integer>(s.getKey(), s.getValue()));
                     }
 
                     if (read.getAlignmentEnd() == loc.getStart()) {

public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/SNPGenotypeLikelihoodsCalculationModel.java

@@ -208,7 +208,7 @@ public class SNPGenotypeLikelihoodsCalculationModel extends GenotypeLikelihoodsC
         return new ReadBackedPileupImpl( pileup.getLocation(), BAQedElements );
     }
 
-    public class BAQedPileupElement extends PileupElement {
+    public static class BAQedPileupElement extends PileupElement {
         public BAQedPileupElement( final PileupElement PE ) {
             super(PE.getRead(), PE.getOffset(), PE.isDeletion(), PE.isBeforeDeletedBase(), PE.isAfterDeletedBase(), PE.isBeforeInsertion(), PE.isAfterInsertion(), PE.isNextToSoftClip());
         }

public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedArgumentCollection.java

@@ -263,7 +263,6 @@ public class UnifiedArgumentCollection {
         uac.referenceSampleName = referenceSampleName;
         uac.samplePloidy = samplePloidy;
         uac.maxQualityScore = minQualityScore;
-        uac.maxQualityScore = maxQualityScore;
         uac.phredScaledPrior = phredScaledPrior;
         uac.minPower = minPower;
         uac.minReferenceDepth = minReferenceDepth;

public/java/src/org/broadinstitute/sting/gatk/walkers/indels/ConstrainedMateFixingManager.java

@@ -124,7 +124,7 @@ public class ConstrainedMateFixingManager {
         return first;
     }
 
-    private class SAMRecordHashObject {
+    private static class SAMRecordHashObject {
         public SAMRecord record;
         public boolean wasModified;
 

public/java/src/org/broadinstitute/sting/gatk/walkers/indels/HaplotypeIndelErrorModel.java

@@ -35,6 +35,7 @@ import org.broadinstitute.sting.utils.variantcontext.Allele;
 
 import java.util.Arrays;
 import java.util.HashMap;
+import java.util.Map;
 
 public class HaplotypeIndelErrorModel {
 
@@ -427,8 +428,8 @@ public class HaplotypeIndelErrorModel {
             // for each read/haplotype combination, compute likelihoods, ie -10*log10(Pr(R | Hi))
             // = sum_j(-10*log10(Pr(R_j | Hi) since reads are assumed to be independent
             int j=0;
-            for (Allele a: haplotypesInVC.keySet()) {
+            for (Map.Entry<Allele,Haplotype> a: haplotypesInVC.entrySet()) {
-                readLikelihoods[i][j]= computeReadLikelihoodGivenHaplotype(haplotypesInVC.get(a), read);
+                readLikelihoods[i][j]= computeReadLikelihoodGivenHaplotype(a.getValue(), read);
                 if (DEBUG) {
                     System.out.print(read.getReadName()+" ");
 

public/java/src/org/broadinstitute/sting/gatk/walkers/indels/RealignerTargetCreator.java

@@ -332,7 +332,7 @@ public class RealignerTargetCreator extends RodWalker<RealignerTargetCreator.Eve
 
     private enum EVENT_TYPE { POINT_EVENT, INDEL_EVENT, BOTH }
 
-    class EventPair {
+    static class EventPair {
         public Event left, right;
         public TreeSet<GenomeLoc> intervals = new TreeSet<GenomeLoc>();
 

public/java/src/org/broadinstitute/sting/gatk/walkers/indels/SomaticIndelDetector.java

@@ -1304,7 +1304,7 @@ public class SomaticIndelDetector extends ReadWalker<Integer,Integer> {
 
     @Override
     public Integer reduceInit() {
-        return new Integer(0);
+        return 0;
     }
 
 

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

@@ -426,10 +426,10 @@ public class PhaseByTransmission extends RodWalker<HashMap<Byte,Integer>, HashMa
         Map<String,Set<Sample>> families = this.getSampleDB().getFamilies();
         Set<Sample> family;
         ArrayList<Sample> parents;
-        for(String familyID : families.keySet()){
+        for(Map.Entry<String,Set<Sample>> familyEntry : families.entrySet()){
-            family = families.get(familyID);
+            family = familyEntry.getValue();
             if(family.size()<2 || family.size()>3){
-                logger.info(String.format("Caution: Family %s has %d members; At the moment Phase By Transmission only supports trios and parent/child pairs. Family skipped.",familyID,family.size()));
+                logger.info(String.format("Caution: Family %s has %d members; At the moment Phase By Transmission only supports trios and parent/child pairs. Family skipped.",familyEntry.getKey(),family.size()));
             }
             else{
                 for(Sample familyMember : family){
@@ -438,7 +438,7 @@ public class PhaseByTransmission extends RodWalker<HashMap<Byte,Integer>, HashMa
                         if(family.containsAll(parents))
                             this.trios.add(familyMember);
                         else
-                            logger.info(String.format("Caution: Family %s skipped as it is not a trio nor a parent/child pair; At the moment Phase By Transmission only supports trios and parent/child pairs. Family skipped.",familyID));
+                            logger.info(String.format("Caution: Family %s skipped as it is not a trio nor a parent/child pair; At the moment Phase By Transmission only supports trios and parent/child pairs. Family skipped.",familyEntry.getKey()));
                         break;
                     }
                 }

public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalReportWriter.java

@@ -183,13 +183,13 @@ public class VariantEvalReportWriter {
                     throw new ReviewedStingException("Datamap is empty for analysis " + scanner.getAnalysis());
                 
                 // add DataPoint's for each field marked as such
-                for (final Field field : datamap.keySet()) {
+                for (final Map.Entry<Field, DataPoint> field : datamap.entrySet()) {
                     try {
-                        field.setAccessible(true);
+                        field.getKey().setAccessible(true);
 
                         // this is an atomic value, add a column for it
-                        final String format = datamap.get(field).format();
+                        final String format = field.getValue().format();
-                        table.addColumn(field.getName(), format);
+                        table.addColumn(field.getKey().getName(), format);
                     } catch (SecurityException e) {
                         throw new StingException("SecurityException: " + e);
                     }

public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/FilterLiftedVariants.java

@@ -34,15 +34,13 @@ import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
 import org.broadinstitute.sting.gatk.walkers.*;
 import org.broadinstitute.sting.utils.SampleUtils;
 import org.broadinstitute.sting.utils.codecs.vcf.VCFHeader;
+import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLine;
 import org.broadinstitute.sting.utils.codecs.vcf.VCFUtils;
 import org.broadinstitute.sting.utils.help.DocumentedGATKFeature;
 import org.broadinstitute.sting.utils.variantcontext.writer.VariantContextWriter;
 import org.broadinstitute.sting.utils.variantcontext.VariantContext;
 
-import java.util.Arrays;
+import java.util.*;
-import java.util.Collection;
-import java.util.Map;
-import java.util.Set;
 
 /**
  * Filters a lifted-over VCF file for ref bases that have been changed.
@@ -66,7 +64,7 @@ public class FilterLiftedVariants extends RodWalker<Integer, Integer> {
         Set<String> samples = SampleUtils.getSampleListWithVCFHeader(getToolkit(), Arrays.asList(trackName));
         Map<String, VCFHeader> vcfHeaders = VCFUtils.getVCFHeadersFromRods(getToolkit(), Arrays.asList(trackName));
 
-        final VCFHeader vcfHeader = new VCFHeader(vcfHeaders.containsKey(trackName) ? vcfHeaders.get(trackName).getMetaDataInSortedOrder() : null, samples);
+        final VCFHeader vcfHeader = new VCFHeader(vcfHeaders.containsKey(trackName) ? vcfHeaders.get(trackName).getMetaDataInSortedOrder() : Collections.<VCFHeaderLine>emptySet(), samples);
         writer.writeHeader(vcfHeader);
     }
 

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

@@ -329,7 +329,7 @@ public class SelectVariants extends RodWalker<Integer, Integer> implements TreeR
 
 
     /* Private class used to store the intermediate variants in the integer random selection process */
-    private class RandomVariantStructure {
+    private static class RandomVariantStructure {
         private VariantContext vc;
 
         RandomVariantStructure(VariantContext vcP) {

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

@@ -329,7 +329,7 @@ public class SequenceDictionaryUtils {
      */
     private static class CompareSequenceRecordsByIndex implements Comparator<SAMSequenceRecord> {
         public int compare(SAMSequenceRecord x, SAMSequenceRecord y) {
-            return new Integer(x.getSequenceIndex()).compareTo(y.getSequenceIndex());
+            return Integer.valueOf(x.getSequenceIndex()).compareTo(y.getSequenceIndex());
         }
     }
 

public/java/src/org/broadinstitute/sting/utils/clipping/ClippingOp.java

@@ -538,7 +538,7 @@ public class ClippingOp {
         return 0;
     }
 
-    private class CigarShift {
+    private static class CigarShift {
         private Cigar cigar;
         private int shiftFromStart;
         private int shiftFromEnd;

public/java/src/org/broadinstitute/sting/utils/codecs/bcf2/BCF2Codec.java

@@ -492,6 +492,6 @@ public final class BCF2Codec implements FeatureCodec<VariantContext> {
     }
 
     private final void error(final String message) throws RuntimeException {
-        throw new UserException.MalformedBCF2(String.format("At record %d with position %d:", recordNo, pos, message));
+        throw new UserException.MalformedBCF2(String.format("%s, at record %d with position %d:", message, recordNo, pos));
     }
 }

public/java/src/org/broadinstitute/sting/utils/interval/IntervalUtils.java

@@ -681,8 +681,8 @@ public class IntervalUtils {
 
         LinkedHashMap<String, List<GenomeLoc>> locsByContig = splitByContig(sorted);
         List<GenomeLoc> expanded = new ArrayList<GenomeLoc>();
-        for (String contig: locsByContig.keySet()) {
+        for (Map.Entry<String, List<GenomeLoc>> contig: locsByContig.entrySet()) {
-            List<GenomeLoc> contigLocs = locsByContig.get(contig);
+            List<GenomeLoc> contigLocs = contig.getValue();
             int contigLocsSize = contigLocs.size();
 
             GenomeLoc startLoc, stopLoc;

public/java/src/org/broadinstitute/sting/utils/recalibration/QualQuantizer.java

@@ -223,7 +223,7 @@ public class QualQuantizer {
 
         @Override
         public int compareTo(final QualInterval qualInterval) {
-            return new Integer(this.qStart).compareTo(qualInterval.qStart);
+            return Integer.valueOf(this.qStart).compareTo(qualInterval.qStart);
         }
 
         /**

public/java/src/org/broadinstitute/sting/utils/recalibration/RecalDatumNode.java

@@ -401,10 +401,11 @@ public class RecalDatumNode<T extends RecalDatum> {
 
             if ( minPenaltyNode == null || minPenaltyNode.getSecond() > maxPenalty ) {
                 // nothing to merge, or the best candidate is above our max allowed
-                if ( minPenaltyNode == null )
+                if ( minPenaltyNode == null ) {
                     if ( logger.isDebugEnabled() ) logger.debug("Stopping because no candidates could be found");
-                else
+                } else {
                     if ( logger.isDebugEnabled() ) logger.debug("Stopping because node " + minPenaltyNode.getFirst() + " has penalty " + minPenaltyNode.getSecond() + " > max " + maxPenalty);
+                }
                 break;
             } else {
                 // remove the lowest penalty element, and continue