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

public/java/src/org/broadinstitute/sting/gatk/executive/HierarchicalMicroScheduler.java

@@ -11,6 +11,7 @@ import org.broadinstitute.sting.gatk.io.ThreadLocalOutputTracker;
 import org.broadinstitute.sting.gatk.walkers.TreeReducible;
 import org.broadinstitute.sting.gatk.walkers.Walker;
 import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
+import org.broadinstitute.sting.utils.exceptions.StingException;
 import org.broadinstitute.sting.utils.threading.ThreadPoolMonitor;
 
 import java.util.Collection;
@@ -101,7 +102,7 @@ public class HierarchicalMicroScheduler extends MicroScheduler implements Hierar
         while (isShardTraversePending() || isTreeReducePending()) {
             // Check for errors during execution.
             if(hasTraversalErrorOccurred())
-                throw new ReviewedStingException("An error has occurred during the traversal.",getTraversalError());
+                throw getTraversalError();
 
             // Too many files sitting around taking up space?  Merge them.
             if (isMergeLimitExceeded())
@@ -344,10 +345,15 @@ public class HierarchicalMicroScheduler extends MicroScheduler implements Hierar
         return error != null;
     }
 
-    private synchronized Throwable getTraversalError() {
+    private synchronized StingException getTraversalError() {
         if(!hasTraversalErrorOccurred())
             throw new ReviewedStingException("User has attempted to retrieve a traversal error when none exists");
-        return error;
+
+        // If the error is already a StingException, pass it along as is.  Otherwise, wrap it.
+        if(error instanceof StingException)
+            return (StingException)error;
+        else
+            return new ReviewedStingException("An error occurred during the traversal.",error);
     }
 
     /**

public/java/src/org/broadinstitute/sting/gatk/iterators/LocusIteratorByState.java

@@ -82,7 +82,6 @@ public class LocusIteratorByState extends LocusIterator {
         CigarElement curElement = null;
         int nCigarElements = 0;
 
-
         int cigarElementCounter = -1;           // how far are we into a single cigarElement
 
         // The logical model for generating extended events is as follows: the "record state" implements the traversal
@@ -468,7 +467,7 @@ public class LocusIteratorByState extends LocusIterator {
 
                         if (op == CigarOperator.D) {
                             if (readInfo.includeReadsWithDeletionAtLoci()) {          // only add deletions to the pileup if we are authorized to do so
-                                pile.add(new PileupElement(read, readOffset, true, nextOp == CigarOperator.I, false));
+                                pile.add(new PileupElement(read, readOffset, true, nextOp == CigarOperator.I, nextOp == CigarOperator.S || (state.getGenomeOffset() == 0 && read.getSoftStart() != read.getAlignmentStart())));
                                 size++;
                                 nDeletions++;
                                 if (read.getMappingQuality() == 0)
@@ -477,7 +476,7 @@ public class LocusIteratorByState extends LocusIterator {
                         }
                         else {
                             if (!filterBaseInRead(read, location.getStart())) {
-                                pile.add(new PileupElement(read, readOffset, false, nextOp == CigarOperator.I, op == CigarOperator.S));
+                                pile.add(new PileupElement(read, readOffset, false, nextOp == CigarOperator.I, nextOp == CigarOperator.S || (state.getGenomeOffset() == 0 && read.getSoftStart() != read.getAlignmentStart())));
                                 size++;
                                 if (read.getMappingQuality() == 0)
                                     nMQ0Reads++;

public/java/src/org/broadinstitute/sting/gatk/traversals/TraverseActiveRegions.java

@@ -216,7 +216,7 @@ public class TraverseActiveRegions <M,T> extends TraversalEngine<M,T,ActiveRegio
     // band-pass filter the list of isActive probabilities and turn into active regions
     private ArrayList<ActiveRegion> integrateActiveList( final ArrayList<Double> activeList, final GenomeLoc firstIsActiveStart, final int activeRegionExtension ) {
 
-        final double ACTIVE_PROB_THRESHOLD = 0.2;
+        final double ACTIVE_PROB_THRESHOLD = 0.2; // BUGBUG: needs to be set-able by the walker author
         final ArrayList<ActiveRegion> returnList = new ArrayList<ActiveRegion>();
         if( activeList.size() == 0 ) {
             return returnList;
@@ -227,8 +227,8 @@ public class TraverseActiveRegions <M,T> extends TraversalEngine<M,T,ActiveRegio
         } else {
             final Double[] activeProbArray = activeList.toArray(new Double[activeList.size()]);
             final double[] filteredProbArray = new double[activeProbArray.length];
-            final int FILTER_SIZE = 10;
+            final int FILTER_SIZE = 50; // BUGBUG: needs to be set-able by the walker author
-            final int MAX_ACTIVE_REGION = 200;
+            final int MAX_ACTIVE_REGION = 425; // BUGBUG: needs to be set-able by the walker author
             for( int iii = 0; iii < activeProbArray.length; iii++ ) {
                 double maxVal = 0;
                 for( int jjj = Math.max(0, iii-FILTER_SIZE); jjj < Math.min(activeList.size(), iii+FILTER_SIZE); jjj++ ) {

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

@@ -335,7 +335,7 @@ public class IndelGenotypeLikelihoodsCalculationModel extends GenotypeLikelihood
         if (ref.getWindow().getStop() < loc.getStop() + HAPLOTYPE_SIZE)
             return null;
         if (!(priors instanceof DiploidIndelGenotypePriors))
-            throw new StingException("Only diploid-based Indel priors are supported in the DINDEL GL model");
+            throw new StingException("Only diploid-based Indel priors are supported in the INDEL GL model");
 
         if (alleleList.isEmpty())
             return null;

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

@@ -212,7 +212,7 @@ public class SNPGenotypeLikelihoodsCalculationModel extends GenotypeLikelihoodsC
 
     public class BAQedPileupElement extends PileupElement {
         public BAQedPileupElement( final PileupElement PE ) {
-            super(PE.getRead(), PE.getOffset(), PE.isDeletion(), PE.isBeforeInsertion(), PE.isSoftClipped());
+            super(PE.getRead(), PE.getOffset(), PE.isDeletion(), PE.isBeforeInsertion(), PE.isNextToSoftClip());
         }
 
         @Override

public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/IndelLengthHistogram.java

@@ -15,7 +15,7 @@ import org.broadinstitute.sting.utils.variantcontext.VariantContext;
  * @Author chartl
  * @Date May 26, 2010
  */
-@Analysis(name = "Indel length histograms", description = "Shows the distrbution of insertion/deletion event lengths (negative for deletion, positive for insertion)")
+@Analysis(name = "Indel length histograms", description = "Shows the distribution of insertion/deletion event lengths (negative for deletion, positive for insertion)")
 public class IndelLengthHistogram extends VariantEvaluator {
     private static final int SIZE_LIMIT = 100;
     @DataPoint(description="Histogram of indel lengths")

public/java/src/org/broadinstitute/sting/utils/pileup/AbstractReadBackedPileup.java

@@ -204,7 +204,7 @@ public abstract class AbstractReadBackedPileup<RBP extends AbstractReadBackedPil
 
     protected abstract AbstractReadBackedPileup<RBP, PE> createNewPileup(GenomeLoc loc, PileupElementTracker<PE> pileupElementTracker);
 
-    protected abstract PE createNewPileupElement(GATKSAMRecord read, int offset, boolean isDeletion, boolean isBeforeInsertion, boolean isSoftClipped);
+    protected abstract PE createNewPileupElement(GATKSAMRecord read, int offset, boolean isDeletion, boolean isBeforeInsertion, boolean isNextToSoftClip);
 
     // --------------------------------------------------------
     //

public/java/src/org/broadinstitute/sting/utils/pileup/PileupElement.java

@@ -24,7 +24,7 @@ public class PileupElement implements Comparable<PileupElement> {
     protected final int offset;
     protected final boolean isDeletion;
     protected final boolean isBeforeInsertion;
-    protected final boolean isSoftClipped;
+    protected final boolean isNextToSoftClip;
 
 
     /**
@@ -34,13 +34,13 @@ public class PileupElement implements Comparable<PileupElement> {
      * @param offset            the position in the read for this base. All deletions must be left aligned! (-1 is only allowed for reads starting with insertions)
      * @param isDeletion        whether or not this base is a deletion
      * @param isBeforeInsertion whether or not this base is before an insertion
-     * @param isSoftClipped     whether or not this base was softclipped
+     * @param isNextToSoftClip  whether or not this base is next to a soft clipped base
      */
     @Requires({
             "read != null",
             "offset >= -1",
             "offset <= read.getReadLength()"})
-    public PileupElement(final GATKSAMRecord read, final int offset, final boolean isDeletion, final boolean isBeforeInsertion, final boolean isSoftClipped) {
+    public PileupElement(final GATKSAMRecord read, final int offset, final boolean isDeletion, final boolean isBeforeInsertion, final boolean isNextToSoftClip) {
         if (offset < 0 && isDeletion)
             throw new ReviewedStingException("Pileup Element cannot create a deletion with a negative offset");
 
@@ -48,7 +48,7 @@ public class PileupElement implements Comparable<PileupElement> {
         this.offset = offset;
         this.isDeletion = isDeletion;
         this.isBeforeInsertion = isBeforeInsertion;
-        this.isSoftClipped = isSoftClipped;
+        this.isNextToSoftClip = isNextToSoftClip;
     }
 
     public boolean isDeletion() {
@@ -59,8 +59,8 @@ public class PileupElement implements Comparable<PileupElement> {
         return isBeforeInsertion;
     }
 
-    public boolean isSoftClipped() {
+    public boolean isNextToSoftClip() {
-        return isSoftClipped;
+        return isNextToSoftClip;
     }
 
     public boolean isInsertionAtBeginningOfRead() {

public/java/src/org/broadinstitute/sting/utils/pileup/ReadBackedExtendedEventPileupImpl.java

@@ -96,7 +96,7 @@ public class ReadBackedExtendedEventPileupImpl extends AbstractReadBackedPileup<
     }
 
     @Override
-    protected ExtendedEventPileupElement createNewPileupElement(GATKSAMRecord read, int offset, boolean isDeletion, boolean isBeforeInsertion, boolean isSoftClipped) {
+    protected ExtendedEventPileupElement createNewPileupElement(GATKSAMRecord read, int offset, boolean isDeletion, boolean isBeforeInsertion, boolean isNextToSoftClip) {
         throw new UnsupportedOperationException("Not enough information provided to create a new pileup element");
     }
 

public/java/src/org/broadinstitute/sting/utils/pileup/ReadBackedPileupImpl.java

@@ -71,7 +71,7 @@ public class ReadBackedPileupImpl extends AbstractReadBackedPileup<ReadBackedPil
     }
 
     @Override
-    protected PileupElement createNewPileupElement(GATKSAMRecord read, int offset, boolean isDeletion, boolean isBeforeInsertion, boolean isSoftClipped) {
+    protected PileupElement createNewPileupElement(GATKSAMRecord read, int offset, boolean isDeletion, boolean isBeforeInsertion, boolean isNextToSoftClip) {
-        return new PileupElement(read, offset, isDeletion, isBeforeInsertion, isSoftClipped);
+        return new PileupElement(read, offset, isDeletion, isBeforeInsertion, isNextToSoftClip);
     }
 }