Active Region Traversal should use GATKSAMRecords everywhere instead of SAMRecords. misc cleanup.

public/java/src/org/broadinstitute/sting/analyzecovariates/AnalyzeCovariates.java

@@ -139,11 +139,11 @@ public class AnalyzeCovariates extends CommandLineProgram {
      */
     @Argument(fullName="max_histogram_value", shortName="maxHist", required = false, doc="If supplied, this value will be the max value of the histogram plots")
     private int MAX_HISTOGRAM_VALUE = 0;
+
     @Hidden
     @Argument(fullName="do_indel_quality", shortName="indels", required = false, doc="If supplied, do indel quality plotting")
     private boolean DO_INDEL_QUALITY = false;
 
-
     /////////////////////////////
     // Private Member Variables
     /////////////////////////////
@@ -274,7 +274,6 @@ public class AnalyzeCovariates extends CommandLineProgram {
         RecalDatum datum = new RecalDatum( Long.parseLong( vals[iii] ), Long.parseLong( vals[iii + 1] ), Double.parseDouble( vals[1] ), 0.0 );
         // Add that datum to all the collapsed tables which will be used in the sequential calculation
         dataManager.addToAllTables( key, datum, IGNORE_QSCORES_LESS_THAN );
-
     }
 
     private void writeDataTables() {
@@ -341,7 +340,7 @@ public class AnalyzeCovariates extends CommandLineProgram {
 
                 // for each covariate
                 for( int iii = 1; iii < requestedCovariates.size(); iii++ ) {
-                    Covariate cov = requestedCovariates.get(iii);
+                    final Covariate cov = requestedCovariates.get(iii);
                     final File outputFile = new File(OUTPUT_DIR, readGroup + "." + cov.getClass().getSimpleName()+ ".dat");
                     if (DO_INDEL_QUALITY) {
                         RScriptExecutor executor = new RScriptExecutor();

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

@@ -1,6 +1,5 @@
 package org.broadinstitute.sting.gatk.traversals;
 
-import net.sf.samtools.SAMRecord;
 import org.apache.log4j.Logger;
 import org.broadinstitute.sting.gatk.WalkerManager;
 import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
@@ -29,7 +28,7 @@ public class TraverseActiveRegions <M,T> extends TraversalEngine<M,T,ActiveRegio
     protected static Logger logger = Logger.getLogger(TraversalEngine.class);
 
     private final Queue<ActiveRegion> workQueue = new LinkedList<ActiveRegion>();
-    private final LinkedHashSet<SAMRecord> myReads = new LinkedHashSet<SAMRecord>();
+    private final LinkedHashSet<GATKSAMRecord> myReads = new LinkedHashSet<GATKSAMRecord>();
 
     @Override
     protected String getTraversalType() {
@@ -101,7 +100,7 @@ public class TraverseActiveRegions <M,T> extends TraversalEngine<M,T,ActiveRegio
 
                 // Grab all the previously unseen reads from this pileup and add them to the massive read list
                 for( final PileupElement p : locus.getBasePileup() ) {
-                    final SAMRecord read = p.getRead();
+                    final GATKSAMRecord read = p.getRead();
                     if( !myReads.contains(read) ) {
                         myReads.add(read);
                     }
@@ -111,7 +110,7 @@ public class TraverseActiveRegions <M,T> extends TraversalEngine<M,T,ActiveRegio
                 //   which active regions in the work queue are now safe to process
                 if( !locusView.hasNext() ) {
                     for( final PileupElement p : locus.getBasePileup() ) {
-                        final SAMRecord read = p.getRead();
+                        final GATKSAMRecord read = p.getRead();
                         if( !myReads.contains(read) ) {
                             myReads.add(read);
                         }
@@ -156,9 +155,9 @@ public class TraverseActiveRegions <M,T> extends TraversalEngine<M,T,ActiveRegio
         return sum;
     }
 
-    private T processActiveRegion( final ActiveRegion activeRegion, final LinkedHashSet<SAMRecord> reads, final Queue<ActiveRegion> workQueue, final T sum, final ActiveRegionWalker<M,T> walker ) {
+    private T processActiveRegion( final ActiveRegion activeRegion, final LinkedHashSet<GATKSAMRecord> reads, final Queue<ActiveRegion> workQueue, final T sum, final ActiveRegionWalker<M,T> walker ) {
-        final ArrayList<SAMRecord> placedReads = new ArrayList<SAMRecord>();
+        final ArrayList<GATKSAMRecord> placedReads = new ArrayList<GATKSAMRecord>();
-        for( final SAMRecord read : reads ) {
+        for( final GATKSAMRecord read : reads ) {
             final GenomeLoc readLoc = this.engine.getGenomeLocParser().createGenomeLoc( read );
             if( activeRegion.getLocation().overlapsP( readLoc ) ) {
                 // The region which the highest amount of overlap is chosen as the primary region for the read (tie breaking is done as right most region)
@@ -170,22 +169,22 @@ public class TraverseActiveRegions <M,T> extends TraversalEngine<M,T,ActiveRegio
                         bestRegion = otherRegionToTest;
                     }
                 }
-                bestRegion.add( (GATKSAMRecord) read );
+                bestRegion.add( read );
 
                 // The read is also added to all other regions in which it overlaps but marked as non-primary
                 if( walker.wantsNonPrimaryReads() ) {
                     if( !bestRegion.equals(activeRegion) ) {
-                        activeRegion.add( (GATKSAMRecord) read );
+                        activeRegion.add( read );
                     }
                     for( final ActiveRegion otherRegionToTest : workQueue ) {
                         if( !bestRegion.equals(otherRegionToTest) && otherRegionToTest.getExtendedLoc().overlapsP( readLoc ) ) {
-                            otherRegionToTest.add( (GATKSAMRecord) read );
+                            otherRegionToTest.add( read );
                         }
                     }
                 }
                 placedReads.add( read );
             } else if( activeRegion.getExtendedLoc().overlapsP( readLoc ) && walker.wantsNonPrimaryReads() ) {
-                activeRegion.add( (GATKSAMRecord) read );
+                activeRegion.add( read );
             }
         }
         reads.removeAll( placedReads ); // remove all the reads which have been placed into their active region

public/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/CountCovariatesWalker.java

@@ -354,7 +354,7 @@ public class CountCovariatesWalker extends LocusWalker<CountCovariatesWalker.Cou
         if( tracker.getValues(knownSites).size() == 0 ) { // If something here is in one of the knownSites tracks then skip over it, otherwise proceed
             // For each read at this locus
             for( final PileupElement p : context.getBasePileup() ) {
-                final GATKSAMRecord gatkRead = (GATKSAMRecord) p.getRead();
+                final GATKSAMRecord gatkRead = p.getRead();
                 int offset = p.getOffset();
 
                 if( gatkRead.containsTemporaryAttribute( SKIP_RECORD_ATTRIBUTE ) ) {

public/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/TableRecalibrationWalker.java

@@ -399,7 +399,7 @@ public class TableRecalibrationWalker extends ReadWalker<SAMRecord, SAMFileWrite
 
         //compute all covariate values for this read
         final Comparable[][] covariateValues_offset_x_covar =
-            RecalDataManager.computeCovariates((GATKSAMRecord) read, requestedCovariates);
+            RecalDataManager.computeCovariates(read, requestedCovariates);
 
         // For each base in the read
         for( int offset = 0; offset < read.getReadLength(); offset++ ) {

public/java/src/org/broadinstitute/sting/utils/baq/BAQ.java

@@ -673,7 +673,7 @@ public class BAQ {
     }
 
     /**
-     * Returns true if we don't think this read is eligable for the BAQ calculation.  Examples include non-PF reads,
+     * Returns true if we don't think this read is eligible for the BAQ calculation.  Examples include non-PF reads,
      * duplicates, or unmapped reads.  Used by baqRead to determine if a read should fall through the calculation.
      *
      * @param read