We're unable to make the naive deduper more worldly, so we're killing it instead.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3587 348d0f76-0448-11de-a6fe-93d51630548a

java/src/org/broadinstitute/sting/gatk/DownsampleType.java

@@ -10,6 +10,5 @@ package org.broadinstitute.sting.gatk;
 public enum DownsampleType {
     NONE,
     ALL_READS,
-    EXPERIMENTAL_BY_SAMPLE,
+    EXPERIMENTAL_BY_SAMPLE
-    EXPERIMENTAL_NAIVE_DUPLICATE_ELIMINATOR
 }

java/src/org/broadinstitute/sting/gatk/DownsamplingMethod.java

@@ -29,7 +29,7 @@ public class DownsamplingMethod {
         // Do some basic sanity checks on the downsampling parameters passed in.
 
         // Can't leave toFraction and toCoverage null unless type is experimental naive duplicate eliminator.
-        if(type != DownsampleType.NONE && type != DownsampleType.EXPERIMENTAL_NAIVE_DUPLICATE_ELIMINATOR && toFraction == null && toCoverage == null)
+        if(type != DownsampleType.NONE && toFraction == null && toCoverage == null)
             throw new StingException("Must specify either toFraction or toCoverage when downsampling.");
 
         // Fraction and coverage cannot both be specified.

java/src/org/broadinstitute/sting/gatk/executive/WindowMaker.java

@@ -69,7 +69,7 @@ public class WindowMaker implements Iterable<WindowMaker.WindowMakerIterator>, I
         LocusIterator locusIterator;
         Iterator<SAMRecord> wrappedIterator = TraversalEngine.addMandatoryFilteringIterators(iterator, filters);
         if(sourceInfo.getDownsamplingMethod() != null &&
-          (sourceInfo.getDownsamplingMethod().type == DownsampleType.EXPERIMENTAL_BY_SAMPLE || sourceInfo.getDownsamplingMethod().type == DownsampleType.EXPERIMENTAL_NAIVE_DUPLICATE_ELIMINATOR)) {
+          (sourceInfo.getDownsamplingMethod().type == DownsampleType.EXPERIMENTAL_BY_SAMPLE)) {
             if ( discards.size() > 0 )
                 throw new StingException("Experimental downsampling iterator doesn't support base discarding at this point; complain to Matt Hanna");
             locusIterator = new DownsamplingLocusIteratorByState(wrappedIterator,sourceInfo);

java/src/org/broadinstitute/sting/gatk/iterators/DownsamplingLocusIteratorByState.java

@@ -552,20 +552,10 @@ public class DownsamplingLocusIteratorByState extends LocusIterator {
 
         private int totalReadStates = 0;
 
-        /**
-         * Store a random number generator with a consistent seed for consistent downsampling from run to run.
-         * Note that each shard will be initialized with the same random seed; this will ensure consistent results
-         * across parallelized runs, at the expense of decreasing our level of randomness.
-         */
-        private Random downsampleRandomizer = new Random(38148309L);
-
         public ReadStateManager(Iterator<SAMRecord> source, DownsamplingMethod downsamplingMethod, int maxReadsAtLocus, Collection<String> sampleNames) {
             this.iterator = new PeekableIterator<SAMRecord>(source);
             this.downsamplingMethod = downsamplingMethod;
             switch(downsamplingMethod.type) {
-                case EXPERIMENTAL_NAIVE_DUPLICATE_ELIMINATOR:
-                    this.targetCoverage = downsamplingMethod.toCoverage != null ? downsamplingMethod.toCoverage : 1;
-                    break;
                 case EXPERIMENTAL_BY_SAMPLE:
                     if(downsamplingMethod.toCoverage == null)
                         throw new StingException("Downsampling coverage (-dcov) must be specified when downsampling by sample");
@@ -580,12 +570,7 @@ public class DownsamplingLocusIteratorByState extends LocusIterator {
             for(String sampleName: sampleNames)
                 readStatesBySample.put(sampleName,new PerSampleReadStateManager());
 
-            ReadSelector primaryReadSelector;
+            ReadSelector primaryReadSelector= samplePartitioner;
-            if(downsamplingMethod.type == DownsampleType.EXPERIMENTAL_NAIVE_DUPLICATE_ELIMINATOR) {
-                primaryReadSelector = new NRandomReadSelector(samplePartitioner,targetCoverage);
-            }
-            else
-                primaryReadSelector = samplePartitioner;
 
             chainedReadSelector = maxReadsAtLocus!=Integer.MAX_VALUE ? new FirstNReadSelector(primaryReadSelector,maxReadsAtLocus) : primaryReadSelector;
         }
@@ -660,7 +645,7 @@ public class DownsamplingLocusIteratorByState extends LocusIterator {
                 PerSampleReadStateManager statesBySample = readStatesBySample.get(sampleName);
                 int numReads = statesBySample.size();
 
-                if(numReads+newReads.size()<=targetCoverage || downsamplingMethod.type==DownsampleType.NONE || downsamplingMethod.type==DownsampleType.EXPERIMENTAL_NAIVE_DUPLICATE_ELIMINATOR) {
+                if(numReads+newReads.size()<=targetCoverage || downsamplingMethod.type==DownsampleType.NONE) {
                     long readLimit = aggregator.getNumReadsSeen();
                     boolean mrlViolation = false;
                     if(readLimit > maxReadsAtLocus-totalReadStates) {