Add downsampling arguments to Mutect

	- maxReadsInRegionPErSample, minReadsPerAlignment start are now M2 args
	- maxReadsInMemoryPerSample is an activeRegionWalker arg

public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/traversals/TraverseActiveRegions.java

@@ -162,8 +162,8 @@ public void initialize(GenomeAnalysisEngine engine, Walker walker, ProgressMeter
         activityProfile = new BandPassActivityProfile(engine.getGenomeLocParser(), engine.getIntervals(), this.walker.maxProbPropagationDistance, this.walker.activeProbThreshold,
                 BandPassActivityProfile.MAX_FILTER_SIZE, bandPassSigma);
 
-        final int maxReadsAcrossSamples = annotation.maxReadsToHoldInMemoryPerSample() * ReadUtils.getSAMFileSamples(engine.getSAMFileHeader()).size();
-        final int maxReadsToHoldInMemory = Math.min(maxReadsAcrossSamples, annotation.maxReadsToHoldTotal());
+        final int maxReadsAcrossSamples = this.walker.maxReadsInMemoryPerSample * ReadUtils.getSAMFileSamples(engine.getSAMFileHeader()).size();
+        final int maxReadsToHoldInMemory = Math.min(maxReadsAcrossSamples, this.walker.maxTotalReadsInMemory);
         myReads = new TAROrderedReadCache(maxReadsToHoldInMemory);
     }
 

public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/walkers/ActiveRegionTraversalParameters.java

@@ -78,20 +78,4 @@
      * @return the breadth of the band pass gaussian kernel we want for our traversal
      */
     public double bandPassSigma() default BandPassActivityProfile.DEFAULT_SIGMA;
-
-    /**
-     * What is the maximum number of reads we're willing to hold in memory per sample
-     * during the traversal?  This limits our exposure to unusually large amounts
-     * of coverage in the engine.
-     * @return the maximum number of reads we're willing to hold in memory
-     */
-    public int maxReadsToHoldInMemoryPerSample() default 30000;
-
-    /**
-     * No matter what the per sample value says, we will never hold more than this
-     * number of reads in memory at any time.  Provides an upper bound on the total number
-     * of reads in the case where we have a lot of samples.
-     * @return the maximum number of reads to hold in memory
-     */
-    public int maxReadsToHoldTotal() default 10000000;
 }

public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/walkers/ActiveRegionWalker.java

@@ -108,6 +108,24 @@ public abstract class ActiveRegionWalker<MapType, ReduceType> extends Walker<Map
     @Argument(fullName="bandPassSigma", shortName="bandPassSigma", doc="The sigma of the band pass filter Gaussian kernel; if not provided defaults to Walker annotated default", required = false)
     public Double bandPassSigma = null;
 
+    /**
+     * What is the maximum number of reads we're willing to hold in memory per sample
+     * during the traversal?  This limits our exposure to unusually large amounts
+     * of coverage in the engine.
+     */
+    @Advanced
+    @Argument(fullName="maxReadsInMemoryPerSample", shortName="maxReadsInMemoryPerSample", doc="Maximum reads per sample given to traversal map() function", required = false)
+    public int maxReadsInMemoryPerSample = 30000;
+
+    /**
+     * What is the maximum number of reads we're willing to hold in memory per sample
+     * during the traversal?  This limits our exposure to unusually large amounts
+     * of coverage in the engine.
+     */
+    @Advanced
+    @Argument(fullName="maxTotalReadsInMemory", shortName="maxTotalReadsInMemory", doc="Maximum total reads given to traversal map() function", required = false)
+    public int maxTotalReadsInMemory = 10000000;
+
     /*
      * For active region limits in ActivityProfile
 *   */