Misc. fixes upon pull request review

-- DeBruijnAssemblerUnitTest and AlignmentUtilsUnitTest were both in DEBUG = true mode (bad!)
-- Remove the maxHaplotypesToConsider feature of HC as it's not useful

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

@@ -92,7 +92,6 @@ public class DeBruijnAssembler extends LocalAssemblyEngine {
     private final boolean debugGraphTransformations;
     private final PrintStream graphWriter;
     private final int minKmer;
-    private final int maxHaplotypesToConsider;
     private final byte minBaseQualityToUseInAssembly;
 
     private final int onlyBuildKmersOfThisSizeWhenDebuggingGraphAlgorithms;
@@ -100,14 +99,13 @@ public class DeBruijnAssembler extends LocalAssemblyEngine {
     private int PRUNE_FACTOR = 2;
 
     protected DeBruijnAssembler() {
-        this(false, -1, null, 11, 1000, DEFAULT_MIN_BASE_QUALITY_TO_USE);
+        this(false, -1, null, 11, DEFAULT_MIN_BASE_QUALITY_TO_USE);
     }
 
     public DeBruijnAssembler(final boolean debug,
                              final int debugGraphTransformations,
                              final PrintStream graphWriter,
                              final int minKmer,
-                             final int maxHaplotypesToConsider,
                              final byte minBaseQualityToUseInAssembly) {
         super();
         this.debug = debug;
@@ -115,7 +113,6 @@ public class DeBruijnAssembler extends LocalAssemblyEngine {
         this.onlyBuildKmersOfThisSizeWhenDebuggingGraphAlgorithms = debugGraphTransformations;
         this.graphWriter = graphWriter;
         this.minKmer = minKmer;
-        this.maxHaplotypesToConsider = maxHaplotypesToConsider;
         this.minBaseQualityToUseInAssembly = minBaseQualityToUseInAssembly;
     }
 
@@ -371,39 +368,22 @@ public class DeBruijnAssembler extends LocalAssemblyEngine {
             }
         }
 
-        final List<Haplotype> finalHaplotypes = selectHighestScoringHaplotypes(returnHaplotypes);
-        if ( finalHaplotypes.size() < returnHaplotypes.size() )
-            logger.info("Found " + finalHaplotypes.size() + " candidate haplotypes of " + returnHaplotypes.size() + " possible combinations to evaluate every read against at " + refLoc);
+        if ( returnHaplotypes.size() < returnHaplotypes.size() )
+            logger.info("Found " + returnHaplotypes.size() + " candidate haplotypes of " + returnHaplotypes.size() + " possible combinations to evaluate every read against at " + refLoc);
 
         if( debug ) {
-            if( finalHaplotypes.size() > 1 ) {
-                System.out.println("Found " + finalHaplotypes.size() + " candidate haplotypes of " + returnHaplotypes.size() + " possible combinations to evaluate every read against.");
+            if( returnHaplotypes.size() > 1 ) {
+                System.out.println("Found " + returnHaplotypes.size() + " candidate haplotypes of " + returnHaplotypes.size() + " possible combinations to evaluate every read against.");
             } else {
                 System.out.println("Found only the reference haplotype in the assembly graph.");
             }
-            for( final Haplotype h : finalHaplotypes ) {
+            for( final Haplotype h : returnHaplotypes ) {
                 System.out.println( h.toString() );
                 System.out.println( "> Cigar = " + h.getCigar() + " : " + h.getCigar().getReferenceLength() + " score " + h.getScore() );
             }
         }
 
-        return finalHaplotypes;
-    }
-
-    /**
-     * Select the best scoring haplotypes among all present, returning no more than maxHaplotypesToConsider
-     *
-     * @param haplotypes a list of haplotypes to consider
-     * @return a sublist of the best haplotypes, with size() <= maxHaplotypesToConsider
-     */
-    private List<Haplotype> selectHighestScoringHaplotypes(final List<Haplotype> haplotypes) {
-        if ( haplotypes.size() <= maxHaplotypesToConsider )
-            return haplotypes;
-        else {
-            final List<Haplotype> sorted = new ArrayList<Haplotype>(haplotypes);
-            Collections.sort(sorted, new Haplotype.ScoreComparator());
-            return sorted.subList(0, maxHaplotypesToConsider);
-        }
+        return returnHaplotypes;
     }
 
     /**

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

@@ -206,10 +206,6 @@ public class HaplotypeCaller extends ActiveRegionWalker<Integer, Integer> implem
     @Argument(fullName="minKmer", shortName="minKmer", doc="Minimum kmer length to use in the assembly graph", required = false)
     protected int minKmer = 11;
 
-    @Advanced
-    @Argument(fullName="maxHaplotypesToConsider", shortName="maxHaplotypesToConsider", doc="Maximum number of haplotypes to consider in the likelihood calculation.  Setting this number too high can have dramatic performance implications", required = false)
-    protected int maxHaplotypesToConsider = 100000;
-
     /**
      * If this flag is provided, the haplotype caller will include unmapped reads in the assembly and calling
      * when these reads occur in the region being analyzed.  Typically, for paired end analyses, one pair of the
@@ -393,7 +389,7 @@ public class HaplotypeCaller extends ActiveRegionWalker<Integer, Integer> implem
         }
 
         final byte minBaseQualityToUseInAssembly = useLowQualityBasesForAssembly ? (byte)1 : DeBruijnAssembler.DEFAULT_MIN_BASE_QUALITY_TO_USE;
-        assemblyEngine = new DeBruijnAssembler( DEBUG, debugGraphTransformations, graphWriter, minKmer, maxHaplotypesToConsider, minBaseQualityToUseInAssembly );
+        assemblyEngine = new DeBruijnAssembler( DEBUG, debugGraphTransformations, graphWriter, minKmer, minBaseQualityToUseInAssembly );
         likelihoodCalculationEngine = new LikelihoodCalculationEngine( (byte)gcpHMM, DEBUG, pairHMM );
         genotypingEngine = new GenotypingEngine( DEBUG, annotationEngine, USE_FILTERED_READ_MAP_FOR_ANNOTATIONS );
 

protected/java/test/org/broadinstitute/sting/gatk/walkers/haplotypecaller/DeBruijnAssemblerUnitTest.java

@@ -61,13 +61,12 @@ import org.broadinstitute.sting.utils.Utils;
 import org.broadinstitute.sting.utils.sam.AlignmentUtils;
 import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
 import org.testng.Assert;
-import org.testng.annotations.DataProvider;
 import org.testng.annotations.Test;
 
 import java.util.*;
 
 public class DeBruijnAssemblerUnitTest extends BaseTest {
-    private final static boolean DEBUG = true;
+    private final static boolean DEBUG = false;
 
     @Test(enabled = !DEBUG)
     public void testReferenceCycleGraph() {

public/java/test/org/broadinstitute/sting/utils/sam/AlignmentUtilsUnitTest.java

@@ -37,7 +37,7 @@ import org.testng.annotations.Test;
 import java.util.*;
 
 public class AlignmentUtilsUnitTest {
-    private final static boolean DEBUG = true;
+    private final static boolean DEBUG = false;
     private SAMFileHeader header;
 
     /** Basic aligned and mapped read. */