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

public/java/src/org/broadinstitute/sting/gatk/GenomeAnalysisEngine.java

@@ -356,10 +356,6 @@ public class GenomeAnalysisEngine {
     public BAQ.QualityMode getWalkerBAQQualityMode()         { return WalkerManager.getBAQQualityMode(walker); }
     public BAQ.ApplicationTime getWalkerBAQApplicationTime() { return WalkerManager.getBAQApplicationTime(walker); }    
 
-    protected boolean generateExtendedEvents() {
-        return walker.generateExtendedEvents();
-    }
-
     protected boolean includeReadsWithDeletionAtLoci() {
         return walker.includeReadsWithDeletionAtLoci();
     }
@@ -766,7 +762,6 @@ public class GenomeAnalysisEngine {
                 new ValidationExclusion(Arrays.asList(argCollection.unsafe)),
                 filters,
                 includeReadsWithDeletionAtLoci(),
-                generateExtendedEvents(),
                 getWalkerBAQApplicationTime() == BAQ.ApplicationTime.ON_INPUT ? argCollection.BAQMode : BAQ.CalculationMode.OFF,
                 getWalkerBAQQualityMode(),
                 refReader,

public/java/src/org/broadinstitute/sting/gatk/ReadProperties.java

@@ -36,7 +36,6 @@ public class ReadProperties {
     private final Collection<ReadFilter> supplementalFilters;
     private final boolean includeReadsWithDeletionAtLoci;
     private final boolean useOriginalBaseQualities;
-    private final boolean generateExtendedEvents;
     private final BAQ.CalculationMode cmode;
     private final BAQ.QualityMode qmode;
     private final IndexedFastaSequenceFile refReader; // read for BAQ, if desired
@@ -52,16 +51,9 @@ public class ReadProperties {
         return includeReadsWithDeletionAtLoci;
     }
 
-    /**
+    @Deprecated
-     * Return true if the walker wants to see additional piles of "extended" events (indels). An indel is associated,
-     * by convention, with the reference base immediately preceding the insertion/deletion, and if this flag is set
-     * to 'true', any locus with an indel associated with it will cause exactly two subsequent calls to walker's map(): first call
-     * will be made with a "conventional" base pileup, the next call will be made with a pileup of extended (indel/noevent)
-     * events.
-     * @return
-     */
     public boolean generateExtendedEvents() {
-        return generateExtendedEvents;
+        return false;
     }
 
     /**
@@ -144,9 +136,6 @@ public class ReadProperties {
      * @param downsamplingMethod Method for downsampling reads at a given locus.
      * @param exclusionList what safety checks we're willing to let slide
      * @param supplementalFilters additional filters to dynamically apply.
-     * @param generateExtendedEvents if true, the engine will issue an extra call to walker's map() with
-     *        a pile of indel/noevent extended events at every locus with at least one indel associated with it
-     *        (in addition to a "regular" call to map() at this locus performed with base pileup)
      * @param includeReadsWithDeletionAtLoci if 'true', the base pileups sent to the walker's map() method
      *         will explicitly list reads with deletion over the current reference base; otherwise, only observed
      *        bases will be seen in the pileups, and the deletions will be skipped silently.
@@ -163,7 +152,6 @@ public class ReadProperties {
            ValidationExclusion exclusionList,
            Collection<ReadFilter> supplementalFilters,
            boolean includeReadsWithDeletionAtLoci,
-           boolean generateExtendedEvents,
            BAQ.CalculationMode cmode,
            BAQ.QualityMode qmode,           
            IndexedFastaSequenceFile refReader,
@@ -176,7 +164,6 @@ public class ReadProperties {
         this.exclusionList = exclusionList == null ? new ValidationExclusion() : exclusionList;
         this.supplementalFilters = supplementalFilters;
         this.includeReadsWithDeletionAtLoci = includeReadsWithDeletionAtLoci;
-        this.generateExtendedEvents = generateExtendedEvents;
         this.useOriginalBaseQualities = useOriginalBaseQualities;
         this.cmode = cmode;
         this.qmode = qmode;

public/java/src/org/broadinstitute/sting/gatk/datasources/reads/SAMDataSource.java

@@ -168,7 +168,6 @@ public class SAMDataSource {
                 null,
                 new ValidationExclusion(),
                 new ArrayList<ReadFilter>(),
-                false,
                 false);
     }
 
@@ -186,8 +185,7 @@ public class SAMDataSource {
             DownsamplingMethod downsamplingMethod,
             ValidationExclusion exclusionList,
             Collection<ReadFilter> supplementalFilters,
-            boolean includeReadsWithDeletionAtLoci,
+            boolean includeReadsWithDeletionAtLoci) {
-            boolean generateExtendedEvents) {
         this(   samFiles,
                 threadAllocation,
                 numFileHandles,
@@ -199,7 +197,6 @@ public class SAMDataSource {
                 exclusionList,
                 supplementalFilters,
                 includeReadsWithDeletionAtLoci,
-                generateExtendedEvents,
                 BAQ.CalculationMode.OFF,
                 BAQ.QualityMode.DONT_MODIFY,
                 null, // no BAQ
@@ -216,9 +213,6 @@ public class SAMDataSource {
      * @param downsamplingMethod Method for downsampling reads at a given locus.
      * @param exclusionList what safety checks we're willing to let slide
      * @param supplementalFilters additional filters to dynamically apply.
-     * @param generateExtendedEvents if true, the engine will issue an extra call to walker's map() with
-     *        a pile of indel/noevent extended events at every locus with at least one indel associated with it
-     *        (in addition to a "regular" call to map() at this locus performed with base pileup)
      * @param includeReadsWithDeletionAtLoci if 'true', the base pileups sent to the walker's map() method
      *         will explicitly list reads with deletion over the current reference base; otherwise, only observed
      *        bases will be seen in the pileups, and the deletions will be skipped silently.
@@ -236,7 +230,6 @@ public class SAMDataSource {
             ValidationExclusion exclusionList,
             Collection<ReadFilter> supplementalFilters,
             boolean includeReadsWithDeletionAtLoci,
-            boolean generateExtendedEvents,
             BAQ.CalculationMode cmode,
             BAQ.QualityMode qmode,
             IndexedFastaSequenceFile refReader,
@@ -309,7 +302,6 @@ public class SAMDataSource {
                 exclusionList,
                 supplementalFilters,
                 includeReadsWithDeletionAtLoci,
-                generateExtendedEvents,
                 cmode,
                 qmode,
                 refReader,

public/java/src/org/broadinstitute/sting/gatk/walkers/PileupWalker.java

@@ -66,9 +66,6 @@ public class PileupWalker extends LocusWalker<Integer, Integer> implements TreeR
     @Output
     PrintStream out;
 
-    @Argument(fullName="showIndelPileups",shortName="show_indels",doc="In addition to base pileups, generate pileups of extended indel events")
-    public boolean SHOW_INDEL_PILEUPS = false;
-
     @Argument(fullName="showVerbose",shortName="verbose",doc="Add an extra verbose section to the pileup output")
     public boolean SHOW_VERBOSE = false;
 
@@ -78,8 +75,6 @@ public class PileupWalker extends LocusWalker<Integer, Integer> implements TreeR
     public void initialize() {
     }
 
-    public boolean generateExtendedEvents() { return SHOW_INDEL_PILEUPS; }
-
     public Integer map(RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) {
 
         String rods = getReferenceOrderedData( tracker );
@@ -92,17 +87,6 @@ public class PileupWalker extends LocusWalker<Integer, Integer> implements TreeR
             out.println();
         }
 
-        if ( context.hasExtendedEventPileup() ) {
-            ReadBackedExtendedEventPileup indelPileup = context.getExtendedEventPileup();
-            List<Pair<String,Integer>> eventCounts = indelPileup.getEventStringsWithCounts(ref.getBases());
-
-            out.printf("%s %s ", indelPileup.getShortPileupString(), rods);
-            int i = 0;
-            for ( ; i < eventCounts.size() - 1 ; i++ ) {
-                out.printf("%s:%d,",eventCounts.get(i).first,eventCounts.get(i).second);
-            }
-            out.printf("%s:%d%n",eventCounts.get(i).first,eventCounts.get(i).second);
-        }
         return 1;
     }
 

public/java/src/org/broadinstitute/sting/gatk/walkers/Walker.java

@@ -114,35 +114,6 @@ public abstract class Walker<MapType, ReduceType> {
         return false;
     }
 
-    /**
-     * This method states whether you want to see pileups of "extended events" (currently, indels only)
-     * at every locus that has at least one indel associated with it. Consider the following situation:
-     *
-     * ref:    AT--CTGA  (note that we expanded the ref here with -- to accomodate insertion in read3)
-     * read1:  AT--CTGA  (perfectly matches the ref)
-     * read2:  AT----GA  (deletion -CT w.r.t. the ref)
-     * read3:  ATGGCTGA  (insertion +GG w.r.t the ref)
-     *
-     * Normally, the locus iterator only returns read base pileups over reference bases, optionally with deleted bases
-     * included (see #includeReadsWithDeletionAtLoci()). In other words, the pileup over the second reference base (T)
-     * will be [T,T,T] (all reads count), for the next reference base (C) the pileup will be [C,C] (or [C,-,C] if
-     * #includeReadsWithDeletionAtLoci() is true), next pileup generated over the next reference
-     * base (T) will be either [T,T], or [T,'-',T], etc. In this default mode, a) insertions are not seen by a walker at all, and
-     * b) deletions are (optionally) seen only on a base-by-base basis (as the step-by-step traversal over the reference
-     * bases is performed). In the extended event mode, however, if there is at least one indel associated with a reference
-     * locus, the engine will generate an <i>additional</i> call to the walker's map() method, with a pileup of
-     * full-length extended indel/noevent calls. This call will be made <i>after</i> the conventional base pileup call
-     * at that locus. Thus, in the example above, a conventional call will be first made at the second reference base (T),
-     * with the [T,T,T] pileup of read bases, then an extended event call will be made at the <i>same</i> locus with
-     * pileup [no_event, -CT, +GG] (i.e. extended events associated with that reference base). After that, the traversal
-     * engine will move to the next reference base.
-     *
-     * @return false if you do not want to receive extra pileups with extended events, or true if you do.
-     */
-    public boolean generateExtendedEvents() {
-        return false;
-    }
-
     public void initialize() { }
 
     /**

public/java/src/org/broadinstitute/sting/gatk/walkers/coverage/GCContentByIntervalWalker.java

@@ -74,10 +74,6 @@ public class GCContentByIntervalWalker extends LocusWalker<Long, Long> {
     public void initialize() {
     }
 
-    public boolean generateExtendedEvents() {
-        return false;
-    }
-
     public Long reduceInit() {
         return 0L;
     }

public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/ReadBackedPhasingWalker.java

@@ -227,10 +227,6 @@ public class ReadBackedPhasingWalker extends RodWalker<PhasingStatsAndOutput, Ph
         }
     }
 
-    public boolean generateExtendedEvents() {
-        return false;
-    }
-
     public PhasingStats reduceInit() {
         return new PhasingStats();
     }

public/java/src/org/broadinstitute/sting/gatk/walkers/qc/PrintLocusContextWalker.java

@@ -1,56 +0,0 @@
-package org.broadinstitute.sting.gatk.walkers.qc;
-
-import org.broadinstitute.sting.commandline.Output;
-import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
-import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
-import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
-import org.broadinstitute.sting.gatk.walkers.LocusWalker;
-import org.broadinstitute.sting.gatk.walkers.TreeReducible;
-import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
-
-import java.io.PrintStream;
-import java.util.Arrays;
-import java.util.List;
-
-/**
- * At each locus in the input data set, prints the reference base, genomic location, and
- * all aligning reads in a compact but human-readable form. 
- */
-public class PrintLocusContextWalker extends LocusWalker<AlignmentContext, Integer> implements TreeReducible<Integer> {
-    @Output
-    private PrintStream out;
-
-    public AlignmentContext map(RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) {
-        out.printf( "In map: ref = %s, loc = %s %s, reads = %s%n", ref.getBaseAsChar(),
-                                                                   context.getLocation(),
-                                                                   context.hasExtendedEventPileup() ? "[extended]" : "",
-                                                                   Arrays.deepToString( getReadNames(context.getReads()) ) );
-        return context;
-    }
-
-
-
-    public Integer reduceInit() { return 0; }
-
-    public Integer reduce(AlignmentContext context, Integer sum) {
-        return sum + 1;
-    }
-
-    public Integer treeReduce(Integer lhs, Integer rhs) {
-        return lhs + rhs;
-    }
-
-    private String[] getReadNames( List<GATKSAMRecord> reads ) {
-        String[] readNames = new String[ reads.size() ];
-        for( int i = 0; i < reads.size(); i++ ) {
-            readNames[i] = String.format("%nname = %s, start = %d, end = %d", reads.get(i).getReadName(), reads.get(i).getAlignmentStart(), reads.get(i).getAlignmentEnd());
-        }
-        //Arrays.sort(readNames);
-        return readNames;
-    }
-
-    @Override
-    public boolean generateExtendedEvents() {
-        return true;
-    }    
-}

public/java/test/org/broadinstitute/sting/gatk/datasources/reads/DownsamplerBenchmark.java

@@ -76,7 +76,6 @@ public class DownsamplerBenchmark extends ReadProcessingBenchmark {
                                                                new ValidationExclusion(Collections.singletonList(ValidationExclusion.TYPE.ALL)),
                                                                Collections.<ReadFilter>emptyList(),
                                                                false,
-                                                               false,
                                                                BAQ.CalculationMode.OFF,
                                                                BAQ.QualityMode.DONT_MODIFY,
                                                                null, // no BAQ

public/java/test/org/broadinstitute/sting/gatk/datasources/reads/SAMDataSourceUnitTest.java

@@ -109,7 +109,6 @@ public class SAMDataSourceUnitTest extends BaseTest {
                 null,
                 new ValidationExclusion(),
                 new ArrayList<ReadFilter>(),
-                false,
                 false);
 
         Iterable<Shard> strat = data.createShardIteratorOverMappedReads(seq.getSequenceDictionary(),new LocusShardBalancer());

public/java/test/org/broadinstitute/sting/gatk/iterators/LocusIteratorByStateUnitTest.java

@@ -43,49 +43,6 @@ public class LocusIteratorByStateUnitTest extends BaseTest {
         return new LocusIteratorByState(new FakeCloseableIterator<SAMRecord>(reads.iterator()), readAttributes, genomeLocParser, LocusIteratorByState.sampleListForSAMWithoutReadGroups());
     }
 
-    @Test
-    public void testIndelBaseQualityFiltering() {
-        final byte[] bases = new byte[] {'A','A','A','A','A','A','A','A','A','A'};
-
-        // create a test version of the Reads object
-        ReadProperties readAttributes = createTestReadProperties();
-        JVMUtils.setFieldValue(JVMUtils.findField(ReadProperties.class,"generateExtendedEvents"),readAttributes,true);
-
-        SAMRecord before = ArtificialSAMUtils.createArtificialRead(header,"before",0,1,10);
-        before.setReadBases(bases);
-        before.setBaseQualities(new byte[] {20,20,20,20,0,20,20,20,20,20});
-        before.setCigarString("10M");
-
-        SAMRecord during = ArtificialSAMUtils.createArtificialRead(header,"during",0,2,10);
-        during.setReadBases(bases);
-        during.setBaseQualities(new byte[] {20,20,20,20,20,20,20,20,20,20,20});
-        during.setCigarString("4M1I6M");
-
-        SAMRecord after  = ArtificialSAMUtils.createArtificialRead(header,"after",0,3,10);
-        after.setReadBases(bases);
-        after.setBaseQualities(new byte[] {20,20,0,20,20,20,20,20,20,20});
-        after.setCigarString("10M");
-
-        List<SAMRecord> reads = Arrays.asList(before,during,after);
-
-        // create the iterator by state with the fake reads and fake records
-        li = makeLTBS(reads,readAttributes);
-
-        boolean foundExtendedEventPileup = false;
-        while (li.hasNext()) {
-            AlignmentContext context = li.next();
-            if(!context.hasExtendedEventPileup())
-                continue;
-
-            ReadBackedExtendedEventPileup pileup = context.getExtendedEventPileup().getBaseFilteredPileup(10);
-            Assert.assertEquals(pileup.getLocation().getStart(), 5, "Extended event pileup at wrong location");
-            Assert.assertEquals(pileup.getNumberOfElements(), 3, "Pileup size is incorrect");
-
-            foundExtendedEventPileup = true;
-        }
-
-        Assert.assertTrue(foundExtendedEventPileup,"Extended event pileup not found");
-    }
     @Test
     public void testIndelsInRegularPileup() {
         final byte[] bases = new byte[] {'A','A','A','A','A','A','A','A','A','A'};
@@ -93,7 +50,6 @@ public class LocusIteratorByStateUnitTest extends BaseTest {
 
         // create a test version of the Reads object
         ReadProperties readAttributes = createTestReadProperties();
-        JVMUtils.setFieldValue(JVMUtils.findField(ReadProperties.class,"generateExtendedEvents"),readAttributes,true);
 
         SAMRecord before = ArtificialSAMUtils.createArtificialRead(header,"before",0,1,10);
         before.setReadBases(bases);
@@ -136,59 +92,6 @@ public class LocusIteratorByStateUnitTest extends BaseTest {
          Assert.assertTrue(foundIndel,"Indel in pileup not found");
     }
 
-    /**
-     * Right now, the GATK's extended event pileup DOES NOT include reads which stop immediately before an insertion
-     * but DOES include reads which stop immediately after an insertion.  This is almost certainly WRONG.  Eric is
-     * figuring out the right way to handle this; in the meantime, adding this test to monitor that:
-     *   A) the behavior is consistent
-     *   B) so that we do end up with an automated test for this case when the model is fixed.
-     */
-    @Test
-    public void testIndelPileupContainsAbuttingReads() {
-        final byte[] bases = new byte[] {'A','A','A','A','A','A','A','A','A','A'};
-        final byte[] quals = new byte[] { 20, 20, 20, 20, 20, 20, 20, 20, 20, 20};
-
-        // create a test version of the Reads object
-        ReadProperties readAttributes = createTestReadProperties();
-        JVMUtils.setFieldValue(JVMUtils.findField(ReadProperties.class,"generateExtendedEvents"),readAttributes,true);
-
-        SAMRecord before = ArtificialSAMUtils.createArtificialRead(header,"before",0,1,10);
-        before.setReadBases(bases);
-        before.setBaseQualities(quals);
-        before.setCigarString("10M");
-
-        SAMRecord during = ArtificialSAMUtils.createArtificialRead(header,"during",0,6,10);
-        during.setReadBases(bases);
-        during.setBaseQualities(quals);
-        during.setCigarString("5M1I5M");
-
-        SAMRecord after  = ArtificialSAMUtils.createArtificialRead(header,"after",0,11,10);
-        after.setReadBases(bases);
-        after.setBaseQualities(quals);
-        after.setCigarString("10M");
-
-        List<SAMRecord> reads = Arrays.asList(before,during,after);
-
-        // create the iterator by state with the fake reads and fake records
-        li = makeLTBS(reads,readAttributes);
-
-        boolean foundExtendedEventPileup = false;
-        while (li.hasNext()) {
-            AlignmentContext context = li.next();
-            if(!context.hasExtendedEventPileup())
-                continue;
-
-            Assert.assertEquals(context.getLocation().getStart(), 10, "Extended event pileup at wrong location");
-            Assert.assertEquals(context.size(), 2, "Pileup size is incorrect");
-            Assert.assertEquals(context.getExtendedEventPileup().getReads().get(0), during, "Read in pileup is incorrect");
-            Assert.assertEquals(context.getExtendedEventPileup().getReads().get(1), after, "Read in pileup is incorrect");
-
-            foundExtendedEventPileup = true;
-        }
-
-        Assert.assertTrue(foundExtendedEventPileup,"Extended event pileup not found");
-    }
-
     @Test
     public void testWholeIndelReadInIsolation() {
         final int firstLocus = 44367789;
@@ -214,17 +117,6 @@ public class LocusIteratorByStateUnitTest extends BaseTest {
         ReadBackedPileup basePileup = alignmentContext.getBasePileup();
         Assert.assertEquals(basePileup.getReads().size(),1,"Pileup is of incorrect size");
         Assert.assertSame(basePileup.getReads().get(0),indelOnlyRead,"Read in pileup is incorrect");
-
-        // Turn on extended events, and make sure the event is found.
-        JVMUtils.setFieldValue(JVMUtils.findField(ReadProperties.class,"generateExtendedEvents"),readAttributes,true);
-        li = makeLTBS(reads, readAttributes);
-
-        Assert.assertTrue(li.hasNext(),"LocusIteratorByState with extended events should contain exactly one pileup");
-        alignmentContext = li.next();
-        Assert.assertEquals(alignmentContext.getLocation().getStart(),firstLocus-1,"Extended event pileup is at incorrect location.");
-        ReadBackedExtendedEventPileup extendedEventPileup = alignmentContext.getExtendedEventPileup();
-        Assert.assertEquals(extendedEventPileup.getReads().size(),1,"Pileup is of incorrect size");
-        Assert.assertSame(extendedEventPileup.getReads().get(0),indelOnlyRead,"Read in pileup is incorrect");
     }
 
     /**
@@ -232,7 +124,7 @@ public class LocusIteratorByStateUnitTest extends BaseTest {
      * not negatively influence the ordering of the pileup.
      */
     @Test
-    public void testWholeIndelReadWithoutExtendedEvents() {
+    public void testWholeIndelRead() {
         final int firstLocus = 44367788, secondLocus = firstLocus + 1;
 
         SAMRecord leadingRead = ArtificialSAMUtils.createArtificialRead(header,"leading",0,firstLocus,76);
@@ -280,70 +172,6 @@ public class LocusIteratorByStateUnitTest extends BaseTest {
         Assert.assertEquals(numAlignmentContextsFound,2,"Found incorrect number of alignment contexts");
     }
 
-    /**
-     * Test to make sure that reads supporting only an indel (example cigar string: 76I) do
-     * not negatively influence the ordering of the pileup.
-     */
-    @Test
-    public void testWholeIndelReadWithExtendedEvents() {
-        final int firstLocus = 44367788, secondLocus = firstLocus + 1;
-
-        // create a test version of the Reads object
-        ReadProperties readAttributes = createTestReadProperties();
-        JVMUtils.setFieldValue(JVMUtils.findField(ReadProperties.class,"generateExtendedEvents"),readAttributes,true);
-
-        SAMRecord leadingRead = ArtificialSAMUtils.createArtificialRead(header,"leading",0,firstLocus,76);
-        leadingRead.setReadBases(Utils.dupBytes((byte)'A',76));
-        leadingRead.setBaseQualities(Utils.dupBytes((byte)'@',76));
-        leadingRead.setCigarString("1M75I");
-
-        SAMRecord indelOnlyRead = ArtificialSAMUtils.createArtificialRead(header,"indelOnly",0,secondLocus,76);
-        indelOnlyRead.setReadBases(Utils.dupBytes((byte)'A',76));
-        indelOnlyRead.setBaseQualities(Utils.dupBytes((byte)'@',76));
-        indelOnlyRead.setCigarString("76I");
-
-        SAMRecord fullMatchAfterIndel = ArtificialSAMUtils.createArtificialRead(header,"fullMatch",0,secondLocus,1);
-        fullMatchAfterIndel.setReadBases(Utils.dupBytes((byte)'A',1));
-        fullMatchAfterIndel.setBaseQualities(Utils.dupBytes((byte)'@',1));
-        fullMatchAfterIndel.setCigarString("1M");
-
-        List<SAMRecord> reads = Arrays.asList(leadingRead,indelOnlyRead,fullMatchAfterIndel);
-
-        // create the iterator by state with the fake reads and fake records
-        li = makeLTBS(reads,readAttributes);
-
-        Assert.assertTrue(li.hasNext(),"Missing first locus at " + firstLocus);
-        AlignmentContext alignmentContext = li.next();
-        Assert.assertEquals(alignmentContext.getLocation().getStart(),firstLocus,"Incorrect locus at this position; should be " + firstLocus);
-        List<GATKSAMRecord> readsAtLocus = alignmentContext.getBasePileup().getReads();
-        Assert.assertEquals(readsAtLocus.size(),1,"Wrong number of reads at locus " + firstLocus);
-        Assert.assertSame(readsAtLocus.get(0),leadingRead,"leadingRead absent from pileup at locus " + firstLocus);
-
-        Assert.assertTrue(li.hasNext(),"Missing extended event at " + firstLocus);
-        alignmentContext = li.next();        
-        Assert.assertEquals(alignmentContext.getLocation().getStart(),firstLocus,"Incorrect extended event locus at this position; should be " + firstLocus);
-        readsAtLocus = alignmentContext.getExtendedEventPileup().getReads();
-        Assert.assertEquals(readsAtLocus.size(),3,"Wrong number of reads at extended event locus " + firstLocus);
-        Assert.assertSame(readsAtLocus.get(0),leadingRead,"leadingRead absent from pileup at extended event locus " + firstLocus);
-        Assert.assertSame(readsAtLocus.get(1),indelOnlyRead,"indelOnlyRead absent from pileup at extended event locus " + firstLocus);
-        // Weird, but as above, reads immediately after the indel are included in the extended event pileup
-        Assert.assertSame(readsAtLocus.get(2),fullMatchAfterIndel,"fullMatchAfterIndel absent from pileup at extended event locus " + firstLocus);
-
-        // Traditionally, reads that end with indels bleed into the pileup at the following locus.  Verify that the next pileup contains this read
-        // and considers it to be an indel-containing read.        
-        Assert.assertTrue(li.hasNext(),"Missing base pileup at " + secondLocus);
-        alignmentContext = li.next();
-        Assert.assertEquals(alignmentContext.getLocation().getStart(),secondLocus,"Incorrect extended event locus at this position; should be " + secondLocus);
-        readsAtLocus = alignmentContext.getBasePileup().getReads();
-        Assert.assertEquals(readsAtLocus.size(),3,"Wrong number of reads at extended event locus " + secondLocus);
-        Assert.assertSame(readsAtLocus.get(0),leadingRead,"leadingRead absent from pileup at extended event locus " + secondLocus);
-        Assert.assertSame(readsAtLocus.get(1),indelOnlyRead,"indelOnlyRead absent from pileup at extended event locus " + secondLocus);
-        // Weird, but as above, reads immediately after the indel are included in the extended event pileup
-        Assert.assertSame(readsAtLocus.get(2),fullMatchAfterIndel,"fullMatchAfterIndel absent from pileup at extended event locus " + secondLocus);
-
-        Assert.assertFalse(li.hasNext(),"Too many alignment contexts");
-    }
-
     private static ReadProperties createTestReadProperties() {
         return new ReadProperties(
                 Collections.<SAMReaderID>emptyList(),
@@ -354,7 +182,6 @@ public class LocusIteratorByStateUnitTest extends BaseTest {
                 new ValidationExclusion(),
                 Collections.<ReadFilter>emptyList(),
                 false,
-                false,
                 BAQ.CalculationMode.OFF,
                 BAQ.QualityMode.DONT_MODIFY,
                 null, // no BAQ

public/java/test/org/broadinstitute/sting/gatk/walkers/PileupWalkerIntegrationTest.java

@@ -23,16 +23,4 @@ public class PileupWalkerIntegrationTest extends WalkerTest {
         WalkerTestSpec spec = new WalkerTestSpec(gatk_args, 1, Arrays.asList(expected_md5));
         executeTest("Testing the standard (no-indel) pileup on three merged FHS pools with 27 deletions in 969 bases", spec);
     }
-
-    @Test
-    public void testExtendedEventPileup() {
-        String gatk_args = "-T Pileup -I " + validationDataLocation + "OV-0930.normal.chunk.bam "
-                 + "-R " + hg18Reference
-                + " -show_indels -o %s";
-        String expected_md5="06eedc2e7927650961d99d703f4301a4";
-        WalkerTestSpec spec = new WalkerTestSpec(gatk_args,1,Arrays.asList(expected_md5));
-        executeTest("Testing the extended pileup with indel records included on a small chunk of Ovarian dataset with 20 indels (1 D, 19 I)", spec);
-
-
-    }
 }