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

public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/AlleleBalance.java

@@ -90,7 +90,7 @@ public class AlleleBalance extends InfoFieldAnnotation {
                 }
                 // todo -- actually care about indel length from the pileup (agnostic at the moment)
                 int refCount = indelPileup.size();
-                int altCount = vc.isInsertion() ? indelPileup.getNumberOfInsertions() : indelPileup.getNumberOfDeletions();
+                int altCount = vc.isSimpleInsertion() ? indelPileup.getNumberOfInsertions() : indelPileup.getNumberOfDeletions();
 
                 if ( refCount + altCount == 0 ) {
                     continue;

public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/HomopolymerRun.java

@@ -79,7 +79,7 @@ public class HomopolymerRun extends InfoFieldAnnotation implements StandardAnnot
         GenomeLoc locus = ref.getLocus();
         GenomeLoc window = ref.getWindow();
         int refBasePos = (int) (locus.getStart() - window.getStart())+1;
-        if ( vc.isDeletion() ) {
+        if ( vc.isSimpleDeletion() ) {
             // check that deleted bases are the same
             byte dBase = bases[refBasePos];
             for ( int i = 0; i < vc.getReference().length(); i ++ ) {

public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/IndelType.java

@@ -36,9 +36,9 @@ public class IndelType extends InfoFieldAnnotation implements ExperimentalAnnota
             if (!vc.isBiallelic())
                 type = "MULTIALLELIC_INDEL";
             else {
-                if (vc.isInsertion())
+                if (vc.isSimpleInsertion())
                     type = "INS.";
-                else if (vc.isDeletion())
+                else if (vc.isSimpleDeletion())
                     type = "DEL.";
                 else
                     type = "OTHER.";

public/java/src/org/broadinstitute/sting/gatk/walkers/fasta/FastaAlternateReferenceWalker.java

@@ -101,11 +101,11 @@ public class FastaAlternateReferenceWalker extends FastaReferenceWalker {
             if ( vc.isFiltered() )
                 continue;
 
-            if ( vc.isDeletion()) {
+            if ( vc.isSimpleDeletion()) {
                 deletionBasesRemaining = vc.getReference().length();
                 // delete the next n bases, not this one
                 return new Pair<GenomeLoc, String>(context.getLocation(), refBase);
-            } else if ( vc.isInsertion()) {
+            } else if ( vc.isSimpleInsertion()) {
                 return new Pair<GenomeLoc, String>(context.getLocation(), refBase.concat(vc.getAlternateAllele(0).toString()));
             } else if (vc.isSNP()) {
                 return new Pair<GenomeLoc, String>(context.getLocation(), vc.getAlternateAllele(0).toString());

public/java/src/org/broadinstitute/sting/gatk/walkers/indels/IndelRealigner.java

@@ -886,7 +886,7 @@ public class IndelRealigner extends ReadWalker<Integer, Integer> {
         for ( VariantContext knownIndel : knownIndelsToTry ) {
             if ( knownIndel == null || !knownIndel.isIndel() || knownIndel.isComplexIndel() )
                 continue;
-            byte[] indelStr = knownIndel.isInsertion() ? knownIndel.getAlternateAllele(0).getBases() : Utils.dupBytes((byte)'-', knownIndel.getReference().length());
+            byte[] indelStr = knownIndel.isSimpleInsertion() ? knownIndel.getAlternateAllele(0).getBases() : Utils.dupBytes((byte)'-', knownIndel.getReference().length());
             int start = knownIndel.getStart() - leftmostIndex + 1;
             Consensus c = createAlternateConsensus(start, reference, indelStr, knownIndel);
             if ( c != null )
@@ -1088,11 +1088,11 @@ public class IndelRealigner extends ReadWalker<Integer, Integer> {
         if ( indexOnRef > 0 )
             cigar.add(new CigarElement(indexOnRef, CigarOperator.M));
 
-        if ( indel.isDeletion() ) {
+        if ( indel.isSimpleDeletion() ) {
             refIdx += indelStr.length;
             cigar.add(new CigarElement(indelStr.length, CigarOperator.D));
         }
-        else if ( indel.isInsertion() ) {
+        else if ( indel.isSimpleInsertion() ) {
             for ( byte b : indelStr )
                 sb.append((char)b);
             cigar.add(new CigarElement(indelStr.length, CigarOperator.I));

public/java/src/org/broadinstitute/sting/gatk/walkers/indels/RealignerTargetCreator.java

@@ -178,7 +178,7 @@ public class RealignerTargetCreator extends RodWalker<RealignerTargetCreator.Eve
                 switch ( vc.getType() ) {
                     case INDEL:
                         hasIndel = true;
-                        if ( vc.isInsertion() )
+                        if ( vc.isSimpleInsertion() )
                             hasInsertion = true;
                         break;
                     case SNP:
@@ -187,7 +187,7 @@ public class RealignerTargetCreator extends RodWalker<RealignerTargetCreator.Eve
                     case MIXED:
                         hasPointEvent = true;
                         hasIndel = true;
-                        if ( vc.isInsertion() )
+                        if ( vc.isSimpleInsertion() )
                             hasInsertion = true;
                         break;
                     default:

public/java/src/org/broadinstitute/sting/gatk/walkers/validation/ValidationAmplicons.java

@@ -250,17 +250,17 @@ public class ValidationAmplicons extends RodWalker<Integer,Integer> {
         } else /* (mask != null && validate == null ) */ {
             if ( ! mask.isSNP() && ! mask.isFiltered() && ( ! filterMonomorphic || ! mask.isMonomorphic() )) {
                 logger.warn("Mask Variant Context on the following warning line is not a SNP. Currently we can only mask out SNPs. This probe will not be designed.");
-                logger.warn(String.format("%s:%d-%d\t%s\t%s",mask.getChr(),mask.getStart(),mask.getEnd(),mask.isInsertion() ? "INS" : "DEL", Utils.join(",",mask.getAlleles())));
+                logger.warn(String.format("%s:%d-%d\t%s\t%s",mask.getChr(),mask.getStart(),mask.getEnd(),mask.isSimpleInsertion() ? "INS" : "DEL", Utils.join(",",mask.getAlleles())));
                 sequenceInvalid = true;
-                invReason.add(mask.isInsertion() ? "INSERTION" : "DELETION");
+                invReason.add(mask.isSimpleInsertion() ? "INSERTION" : "DELETION");
                 // note: indelCounter could be > 0 (could have small deletion within larger one). This always selects
                 // the larger event.
-                int indelCounterNew = mask.isInsertion() ? 2 : mask.getEnd()-mask.getStart();
+                int indelCounterNew = mask.isSimpleInsertion() ? 2 : mask.getEnd()-mask.getStart();
                 if ( indelCounterNew > indelCounter ) {
                     indelCounter = indelCounterNew;
                 }
                 //sequence.append((char) ref.getBase());
-                //sequence.append(mask.isInsertion() ? 'I' : 'D');
+                //sequence.append(mask.isSimpleInsertion() ? 'I' : 'D');
                 sequence.append("N");
                 indelCounter--;
                 rawSequence.append(Character.toUpperCase((char) ref.getBase()));

public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalWalker.java

@@ -311,7 +311,8 @@ public class VariantEvalWalker extends RodWalker<Integer, Integer> implements Tr
                         // for each comp track
                         for ( final RodBinding<VariantContext> compRod : comps ) {
                             // no sample stratification for comps
-                            final Set<VariantContext> compSet = compVCs.get(compRod) == null ? new HashSet<VariantContext>(0) : compVCs.get(compRod).values().iterator().next();
+                            final HashMap<String, Set<VariantContext>> compSetHash = compVCs.get(compRod);
+                            final Set<VariantContext> compSet = (compSetHash == null || compSetHash.size() == 0) ? new HashSet<VariantContext>(0) : compVCs.get(compRod).values().iterator().next();
 
                             // find the comp
                             final VariantContext comp = findMatchingComp(eval, compSet);

public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/CountVariants.java

@@ -39,8 +39,10 @@ public class CountVariants extends VariantEvaluator implements StandardEval {
     public long nInsertions = 0;
     @DataPoint(description = "Number of deletions")
     public long nDeletions = 0;
-    @DataPoint(description = "Number of complex loci")
+    @DataPoint(description = "Number of complex indels")
     public long nComplex = 0;
+    @DataPoint(description = "Number of mixed loci (loci that can't be classified as a SNP, Indel or MNP)")
+    public long nMixed = 0;
 
 
     @DataPoint(description = "Number of no calls loci")
@@ -113,11 +115,15 @@ public class CountVariants extends VariantEvaluator implements StandardEval {
                     if (vc1.getAttributeAsBoolean("ISSINGLETON")) nSingletons++;
                     break;
                 case INDEL:
-                    if (vc1.isInsertion()) nInsertions++;
+                    if (vc1.isSimpleInsertion())
-                    else nDeletions++;
+                        nInsertions++;
+                    else if (vc1.isSimpleDeletion())
+                        nDeletions++;
+                    else
+                        nComplex++;
                     break;
                 case MIXED:
-                    nComplex++;
+                    nMixed++;
                     break;
                 default:
                     throw new ReviewedStingException("Unexpected VariantContext type " + vc1.getType());
@@ -180,8 +186,8 @@ public class CountVariants extends VariantEvaluator implements StandardEval {
         heterozygosity = perLocusRate(nHets);
         heterozygosityPerBp = perLocusRInverseRate(nHets);
         hetHomRatio = ratio(nHets, nHomVar);
-        indelRate = perLocusRate(nDeletions + nInsertions);
+        indelRate = perLocusRate(nDeletions + nInsertions + nComplex);
-        indelRatePerBp = perLocusRInverseRate(nDeletions + nInsertions);
+        indelRatePerBp = perLocusRInverseRate(nDeletions + nInsertions + nComplex);
         deletionInsertionRatio = ratio(nDeletions, nInsertions);
     }
 }

public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/IndelLengthHistogram.java

@@ -96,9 +96,9 @@ public class IndelLengthHistogram extends VariantEvaluator {
         }
 
         if ( vc1.isIndel() ) {
-            if ( vc1.isInsertion() ) {
+            if ( vc1.isSimpleInsertion() ) {
                 indelHistogram.update(vc1.getAlternateAllele(0).length());
-            } else if ( vc1.isDeletion() ) {
+            } else if ( vc1.isSimpleDeletion() ) {
                 indelHistogram.update(-vc1.getReference().length());
             } else {
                 throw new ReviewedStingException("Indel type that is not insertion or deletion.");

public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/IndelMetricsByAC.java

@@ -1,221 +0,0 @@
-package org.broadinstitute.sting.gatk.walkers.varianteval.evaluators;
-
-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.varianteval.VariantEvalWalker;
-import org.broadinstitute.sting.gatk.walkers.varianteval.util.Analysis;
-import org.broadinstitute.sting.gatk.walkers.varianteval.util.DataPoint;
-import org.broadinstitute.sting.gatk.walkers.varianteval.util.TableType;
-import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
-import org.broadinstitute.sting.utils.variantcontext.VariantContext;
-
-import java.util.ArrayList;
-
-/*
- * Copyright (c) 2010 The Broad Institute
- *
- * Permission is hereby granted, free of charge, to any person
- * obtaining a copy of this software and associated documentation
- * files (the "Software"), to deal in the Software without
- * restriction, including without limitation the rights to use,
- * copy, modify, merge, publish, distribute, sublicense, and/or sell
- * copies of the Software, and to permit persons to whom the
- * Software is furnished to do so, subject to the following
- * conditions:
- *
- * The above copyright notice and this permission notice shall be
- * included in all copies or substantial portions of the Software.
- *
- * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
- * EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
- * OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
- * NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
- * HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
- * WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
- * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
- * OTHER DEALINGS IN THE SOFTWARE.
- */
-
-/**
- * @author delangel
- * @since Apr 11, 2010
- */
-
-@Analysis(name = "Indel Metrics by allele count", description = "Shows various stats binned by allele count")
-public class IndelMetricsByAC extends VariantEvaluator {
-    // a mapping from quality score histogram bin to Ti/Tv ratio
-    @DataPoint(description = "Indel Metrics by allele count")
-    IndelMetricsByAc metrics = null;
-
-    int numSamples = 0;
-
-    public void initialize(VariantEvalWalker walker) {
-        numSamples = walker.getNumSamples();
-    }
-
-    //@DataPoint(name="Quality by Allele Count", description = "average variant quality for each allele count")
-    //AlleleCountStats alleleCountStats = null;
-    private static final int INDEL_SIZE_LIMIT = 100;
-    private static final int NUM_SCALAR_COLUMNS = 6;
-    static int len2Index(int ind) {
-        return ind+INDEL_SIZE_LIMIT;
-    }
-
-    static int index2len(int ind) {
-        return ind-INDEL_SIZE_LIMIT-NUM_SCALAR_COLUMNS;
-    }
-
-    protected final static String[] METRIC_COLUMNS;
-    static {
-        METRIC_COLUMNS= new String[NUM_SCALAR_COLUMNS+2*INDEL_SIZE_LIMIT+1];
-        METRIC_COLUMNS[0] = "AC";
-        METRIC_COLUMNS[1] = "nIns";
-        METRIC_COLUMNS[2] = "nDels";
-        METRIC_COLUMNS[3] = "n";
-        METRIC_COLUMNS[4] = "nComplex";
-        METRIC_COLUMNS[5] = "nLong";
-
-        for (int k=NUM_SCALAR_COLUMNS; k < NUM_SCALAR_COLUMNS+ 2*INDEL_SIZE_LIMIT+1; k++)
-            METRIC_COLUMNS[k] = "indel_size_len"+Integer.valueOf(index2len(k));
-    }
-
-    class IndelMetricsAtAC {
-        public int ac = -1, nIns =0, nDel = 0, nComplex = 0, nLong;
-        public int sizeCount[] = new int[2*INDEL_SIZE_LIMIT+1];
-
-        public IndelMetricsAtAC(int ac) { this.ac = ac; }
-
-        public void update(VariantContext eval) {
-            int eventLength = 0;
-            if ( eval.isInsertion() ) {
-                eventLength = eval.getAlternateAllele(0).length();
-                nIns++;
-            } else if ( eval.isDeletion() ) {
-                eventLength = -eval.getReference().length();
-                nDel++;
-            }
-            else {
-                nComplex++;
-            }
-            if (Math.abs(eventLength) < INDEL_SIZE_LIMIT)
-                sizeCount[len2Index(eventLength)]++;
-            else
-                nLong++;
-
-
-
-         }
-
-        // corresponding to METRIC_COLUMNS
-        public String getColumn(int i) {
-            if (i >= NUM_SCALAR_COLUMNS && i <=NUM_SCALAR_COLUMNS+ 2*INDEL_SIZE_LIMIT)
-                return String.valueOf(sizeCount[i-NUM_SCALAR_COLUMNS]);
-
-            switch (i) {
-                case 0: return String.valueOf(ac);
-                case 1: return String.valueOf(nIns);
-                case 2: return String.valueOf(nDel);
-                case 3: return String.valueOf(nIns + nDel);
-                case 4: return String.valueOf(nComplex);
-                case 5: return String.valueOf(nLong);
-
-                default:
-                    throw new ReviewedStingException("Unexpected column " + i);
-            }
-        }
-    }
-
-    class IndelMetricsByAc implements TableType {
-        ArrayList<IndelMetricsAtAC> metrics = new ArrayList<IndelMetricsAtAC>();
-        Object[] rows = null;
-
-        public IndelMetricsByAc( int nchromosomes ) {
-            rows = new Object[nchromosomes+1];
-            metrics = new ArrayList<IndelMetricsAtAC>(nchromosomes+1);
-            for ( int i = 0; i < nchromosomes + 1; i++ ) {
-                metrics.add(new IndelMetricsAtAC(i));
-                rows[i] = "ac" + i;
-            }
-        }
-
-        public Object[] getRowKeys() {
-            return rows;
-        }
-
-        public Object[] getColumnKeys() {
-            return METRIC_COLUMNS;
-        }
-
-        public String getName() {
-            return "IndelMetricsByAc";
-        }
-
-        //
-        public String getCell(int ac, int y) {
-            return metrics.get(ac).getColumn(y);
-        }
-
-        public String toString() {
-            return "";
-        }
-
-        public void incrValue( VariantContext eval ) {
-            int ac = -1;
-
-            if ( eval.hasGenotypes() )
-                ac = eval.getChromosomeCount(eval.getAlternateAllele(0));
-            else if ( eval.hasAttribute("AC") ) {
-                ac = Integer.valueOf(eval.getAttributeAsString("AC"));
-            }
-
-            if ( ac != -1 )
-                metrics.get(ac).update(eval);
-        }
-    }
-
-    //public IndelMetricsByAC(VariantEvalWalker parent) {
-        //super(parent);
-        // don't do anything
-    //}
-
-    public String getName() {
-        return "IndelMetricsByAC";
-    }
-
-    public int getComparisonOrder() {
-        return 1;   // we only need to see each eval track
-    }
-
-    public boolean enabled() {
-        return true;
-    }
-
-    public String toString() {
-        return getName();
-    }
-
-    public String update1(VariantContext eval, RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) {
-        final String interesting = null;
-
-        if (eval != null ) {
-            if ( metrics == null ) {
-                int nSamples = numSamples;
-                //int nSamples = 2;
-                if ( nSamples != -1 )
-                    metrics = new IndelMetricsByAc(2 * nSamples);
-            }
-
-            if ( eval.isIndel() && eval.isBiallelic() &&
-                    metrics != null ) {
-                metrics.incrValue(eval);
-            }
-        }
-
-        return interesting; // This module doesn't capture any interesting sites, so return null
-    }
-
-    //public void finalizeEvaluation() {
-    //
-    //}
-}

public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/IndelStatistics.java

@@ -44,7 +44,7 @@ public class IndelStatistics extends VariantEvaluator {
     @DataPoint(description = "Indel Statistics")
     IndelStats indelStats = null;
 
-    @DataPoint(description = "Indel Classification")
+   // @DataPoint(description = "Indel Classification")
     IndelClasses indelClasses = null;
 
     int numSamples = 0;
@@ -57,13 +57,13 @@ public class IndelStatistics extends VariantEvaluator {
     private static final int IND_HET = 0;
     private static final int IND_INS = 1;
     private static final int IND_DEL = 2;
-    private static final int IND_AT_CG_RATIO = 3;
+    private static final int IND_COMPLEX = 3;
     private static final int IND_HET_INS = 4;
     private static final int IND_HOM_INS = 5;
     private static final int IND_HET_DEL = 6;
     private static final int IND_HOM_DEL = 7;
     private static final int IND_HOM_REF = 8;
-    private static final int IND_COMPLEX = 9;
+    private static final int IND_MIXED = 9;
     private static final int IND_LONG = 10;
     private static final int IND_AT_EXP = 11;
     private static final int IND_CG_EXP = 12;
@@ -79,15 +79,14 @@ public class IndelStatistics extends VariantEvaluator {
     }
 
     static class IndelStats implements TableType {
-        protected final static String ALL_SAMPLES_KEY = "allSamples";
+         protected final static String[] COLUMN_KEYS;
-        protected final static String[] COLUMN_KEYS;
 
          static {
             COLUMN_KEYS= new String[NUM_SCALAR_COLUMNS+2*INDEL_SIZE_LIMIT+1];
             COLUMN_KEYS[0] = "heterozygosity";
             COLUMN_KEYS[1] = "insertions";
             COLUMN_KEYS[2] = "deletions";
-            COLUMN_KEYS[3] = "AT_CG_expansion_ratio";
+            COLUMN_KEYS[3] = "complex";
             COLUMN_KEYS[4] = "het_insertions";
             COLUMN_KEYS[5] = "homozygous_insertions";
             COLUMN_KEYS[6] = "het_deletions";
@@ -104,13 +103,10 @@ public class IndelStatistics extends VariantEvaluator {
         }
 
         // map of sample to statistics
-        protected final HashMap<String, int[]> indelSummary = new HashMap<String, int[]>();
+        protected final  int[] indelSummary;
 
         public IndelStats(final VariantContext vc) {
-            indelSummary.put(ALL_SAMPLES_KEY, new int[COLUMN_KEYS.length]);
+            indelSummary = new int[COLUMN_KEYS.length];
-            for( final String sample : vc.getGenotypes().keySet() ) {
-                indelSummary.put(sample, new int[COLUMN_KEYS.length]);
-            }
         }
 
         /**
@@ -118,19 +114,10 @@ public class IndelStatistics extends VariantEvaluator {
          * @return one row per sample
          */
         public Object[] getRowKeys() {
-            return indelSummary.keySet().toArray(new String[indelSummary.size()]);
+            return new String[]{"all"};
         }
         public Object getCell(int x, int y) {
-            final Object[] rowKeys = getRowKeys();
+            return String.format("%d",indelSummary[y]);
-            if (y == IND_AT_CG_RATIO) {
-
-                int at = indelSummary.get(rowKeys[x])[IND_AT_EXP];
-                int cg = indelSummary.get(rowKeys[x])[IND_CG_EXP];
-                return String.format("%4.2f",((double)at) / (Math.max(cg, 1)));
-            }
-            else
-                return String.format("%d",indelSummary.get(rowKeys[x])[y]);
-
         }
 
         /**
@@ -160,96 +147,49 @@ public class IndelStatistics extends VariantEvaluator {
             int eventLength = 0;
             boolean isInsertion = false, isDeletion = false;
 
-            if ( vc.isInsertion() ) {
+            if ( vc.isSimpleInsertion() ) {
                 eventLength = vc.getAlternateAllele(0).length();
-                indelSummary.get(ALL_SAMPLES_KEY)[IND_INS]++;
+                indelSummary[IND_INS]++;
                 isInsertion = true;
-            } else if ( vc.isDeletion() ) {
+            } else if ( vc.isSimpleDeletion() ) {
-                indelSummary.get(ALL_SAMPLES_KEY)[IND_DEL]++;
+                indelSummary[IND_DEL]++;
                 eventLength = -vc.getReference().length();
                 isDeletion = true;
             }
-            else {
+            else if (vc.isComplexIndel()) {
-                indelSummary.get(ALL_SAMPLES_KEY)[IND_COMPLEX]++;
+                indelSummary[IND_COMPLEX]++;
             }
+            else if (vc.isMixed())
+                indelSummary[IND_MIXED]++;
+
             if (IndelUtils.isATExpansion(vc,ref))
-                indelSummary.get(ALL_SAMPLES_KEY)[IND_AT_EXP]++;
+                indelSummary[IND_AT_EXP]++;
             if (IndelUtils.isCGExpansion(vc,ref))
-                 indelSummary.get(ALL_SAMPLES_KEY)[IND_CG_EXP]++;
+                 indelSummary[IND_CG_EXP]++;
 
             // make sure event doesn't overstep array boundaries
-            if (Math.abs(eventLength) < INDEL_SIZE_LIMIT) {
+            if (vc.isSimpleDeletion() || vc.isSimpleInsertion()) {
-                indelSummary.get(ALL_SAMPLES_KEY)[len2Index(eventLength)]++;
+                if (Math.abs(eventLength) < INDEL_SIZE_LIMIT) {
-                if (eventLength % 3 != 0)
+                    indelSummary[len2Index(eventLength)]++;
-                    indelSummary.get(ALL_SAMPLES_KEY)[IND_FRAMESHIFT]++;
+                    if (eventLength % 3 != 0)
-            }
+                        indelSummary[IND_FRAMESHIFT]++;
-            else
-                indelSummary.get(ALL_SAMPLES_KEY)[IND_LONG]++;
-
-
-            for( final String sample : vc.getGenotypes().keySet() ) {
-                if ( indelSummary.containsKey(sample) ) {
-                    Genotype g = vc.getGenotype(sample);
-                    boolean isVariant = (g.isCalled() && !g.isHomRef());
-                    if (isVariant) {
-                        // update ins/del count
-                        if (isInsertion) {
-                            indelSummary.get(sample)[IND_INS]++;
-                        }
-                        else if (isDeletion)
-                            indelSummary.get(sample)[IND_DEL]++;
-                        else
-                            indelSummary.get(sample)[IND_COMPLEX]++;
-
-                        // update histogram
-                        if (Math.abs(eventLength) < INDEL_SIZE_LIMIT) {
-                            indelSummary.get(sample)[len2Index(eventLength)]++;
-                            if (eventLength % 3 != 0)
-                                indelSummary.get(sample)[IND_FRAMESHIFT]++;    
-                        }
-                        else
-                            indelSummary.get(sample)[IND_LONG]++;
-
-                        if (g.isHet())
-                            if (isInsertion)
-                                indelSummary.get(sample)[IND_HET_INS]++;
-                            else if (isDeletion)
-                                indelSummary.get(sample)[IND_HET_DEL]++;
-                        else
-                            if (isInsertion)
-                                indelSummary.get(sample)[IND_HOM_INS]++;
-                            else if (isDeletion)
-                                indelSummary.get(sample)[IND_HOM_DEL]++;
-
-                        if (IndelUtils.isATExpansion(vc,ref))
-                            indelSummary.get(sample)[IND_AT_EXP]++;
-                        if (IndelUtils.isCGExpansion(vc,ref))
-                             indelSummary.get(sample)[IND_CG_EXP]++;
-
-
-                    }
-                    else
-                        indelSummary.get(sample)[IND_HOM_REF]++;
                 }
+                else
+                    indelSummary[IND_LONG]++;
             }
 
-
         }
     }
 
     static class IndelClasses implements TableType {
-        protected final static String ALL_SAMPLES_KEY = "allSamples";
         protected final static String[] columnNames = IndelUtils.getIndelClassificationNames();
 
 
         // map of sample to statistics
-        protected final HashMap<String, int[]> indelClassSummary = new HashMap<String, int[]>();
+        protected final int[] indelClassSummary;
 
         public IndelClasses(final VariantContext vc) {
-            indelClassSummary.put(ALL_SAMPLES_KEY, new int[columnNames.length]);
+            indelClassSummary = new int[columnNames.length];
-            for( final String sample : vc.getGenotypes().keySet() ) {
-                indelClassSummary.put(sample, new int[columnNames.length]);
-            }
         }
 
         /**
@@ -257,11 +197,10 @@ public class IndelStatistics extends VariantEvaluator {
          * @return one row per sample
          */
         public Object[] getRowKeys() {
-            return indelClassSummary.keySet().toArray(new String[indelClassSummary.size()]);
+            return new String[]{"all"};
         }
         public Object getCell(int x, int y) {
-            final Object[] rowKeys = getRowKeys();
+            return String.format("%d",indelClassSummary[y]);
-            return String.format("%d",indelClassSummary.get(rowKeys[x])[y]);
         }
 
         /**
@@ -285,18 +224,7 @@ public class IndelStatistics extends VariantEvaluator {
         }
 
         private void incrementSampleStat(VariantContext vc, int index) {
-            indelClassSummary.get(ALL_SAMPLES_KEY)[index]++;
+            indelClassSummary[index]++;
-            for( final String sample : vc.getGenotypes().keySet() ) {
-                 if ( indelClassSummary.containsKey(sample) ) {
-                     Genotype g = vc.getGenotype(sample);
-                     boolean isVariant = (g.isCalled() && !g.isHomRef());
-                     if (isVariant)
-                         // update  count
-                         indelClassSummary.get(sample)[index]++;
-
-                 }
-             }
-
         }
         /*
          * increment the specified value
@@ -344,16 +272,13 @@ public class IndelStatistics extends VariantEvaluator {
 
         if (eval != null ) {
             if ( indelStats == null ) {
-                int nSamples = numSamples;
+                indelStats = new IndelStats(eval);
-
-                if ( nSamples != -1 )
-                    indelStats = new IndelStats(eval);
             }
             if ( indelClasses == null ) {
                 indelClasses = new IndelClasses(eval);
             }
 
-            if ( eval.isIndel() && eval.isBiallelic() ) {
+            if ( eval.isIndel() || eval.isMixed() ) {
                 if (indelStats != null )
                     indelStats.incrValue(eval, ref);
 

public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/util/VariantEvalUtils.java

@@ -347,9 +347,9 @@ public class VariantEvalUtils {
                         }
                     }
                 }
-
-                bindings.put(track, mapping);
             }
+
+            bindings.put(track, mapping);
         }
 
         return bindings;

public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/LeftAlignVariants.java

@@ -133,7 +133,7 @@ public class LeftAlignVariants extends RodWalker<Integer, Integer> {
 
         // get the indel length
         int indelLength;
-        if ( vc.isDeletion() )
+        if ( vc.isSimpleDeletion() )
             indelLength = vc.getReference().length();
         else
             indelLength = vc.getAlternateAllele(0).length();
@@ -150,7 +150,7 @@ public class LeftAlignVariants extends RodWalker<Integer, Integer> {
         // create a CIGAR string to represent the event
         ArrayList<CigarElement> elements = new ArrayList<CigarElement>();
         elements.add(new CigarElement(originalIndex, CigarOperator.M));
-        elements.add(new CigarElement(indelLength, vc.isDeletion() ? CigarOperator.D : CigarOperator.I));
+        elements.add(new CigarElement(indelLength, vc.isSimpleDeletion() ? CigarOperator.D : CigarOperator.I));
         elements.add(new CigarElement(refSeq.length - originalIndex, CigarOperator.M));
         Cigar originalCigar = new Cigar(elements);
 
@@ -165,8 +165,8 @@ public class LeftAlignVariants extends RodWalker<Integer, Integer> {
 
             int indelIndex = originalIndex-difference;
             byte[] newBases = new byte[indelLength];
-            System.arraycopy((vc.isDeletion() ? refSeq : originalIndel), indelIndex, newBases, 0, indelLength);
+            System.arraycopy((vc.isSimpleDeletion() ? refSeq : originalIndel), indelIndex, newBases, 0, indelLength);
-            Allele newAllele = Allele.create(newBases, vc.isDeletion());
+            Allele newAllele = Allele.create(newBases, vc.isSimpleDeletion());
             newVC = updateAllele(newVC, newAllele, refSeq[indelIndex-1]);
 
             writer.add(newVC);
@@ -178,14 +178,14 @@ public class LeftAlignVariants extends RodWalker<Integer, Integer> {
     }
 
     private static byte[] makeHaplotype(VariantContext vc, byte[] ref, int indexOfRef, int indelLength) {
-        byte[] hap = new byte[ref.length + (indelLength * (vc.isDeletion() ? -1 : 1))];
+        byte[] hap = new byte[ref.length + (indelLength * (vc.isSimpleDeletion() ? -1 : 1))];
 
         // add the bases before the indel
         System.arraycopy(ref, 0, hap, 0, indexOfRef);
         int currentPos = indexOfRef;
 
         // take care of the indel
-        if ( vc.isDeletion() ) {
+        if ( vc.isSimpleDeletion() ) {
             indexOfRef += indelLength;
         } else {
             System.arraycopy(vc.getAlternateAllele(0).getBases(), 0, hap, currentPos, indelLength);

public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariants.java

@@ -209,7 +209,7 @@ public class SelectVariants extends RodWalker<Integer, Integer> {
      * Note that sample exclusion takes precedence over inclusion, so that if a sample is in both lists it will be excluded.
      */
     @Argument(fullName="exclude_sample_file", shortName="xl_sf", doc="File containing a list of samples (one per line) to exclude. Can be specified multiple times", required=false)
-    public Set<File> XLsampleFiles;
+    public Set<File> XLsampleFiles = new HashSet<File>(0);
 
     /**
      * Note that these expressions are evaluated *after* the specified samples are extracted and the INFO field annotations are updated.
@@ -348,7 +348,7 @@ public class SelectVariants extends RodWalker<Integer, Integer> {
         samples.removeAll(XLsamplesFromFile);
         samples.removeAll(XLsampleNames);
 
-        if ( samples.size() == 0 )
+        if ( samples.size() == 0 && !NO_SAMPLES_SPECIFIED )
             throw new UserException("All samples requested to be included were also requested to be excluded.");
 
         for ( String sample : samples )

public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/ValidateVariants.java

@@ -137,11 +137,11 @@ public class ValidateVariants extends RodWalker<Integer, Integer> {
         Allele reportedRefAllele = vc.getReference();
         Allele observedRefAllele;
         // insertions
-        if ( vc.isInsertion() ) {
+        if ( vc.isSimpleInsertion() ) {
             observedRefAllele = Allele.create(Allele.NULL_ALLELE_STRING);
         }
         // deletions
-        else if ( vc.isDeletion() || vc.isMixed() || vc.isMNP() ) {
+        else if ( vc.isSimpleDeletion() || vc.isMixed() || vc.isMNP() ) {
             // we can't validate arbitrarily long deletions
             if ( reportedRefAllele.length() > 100 ) {
                 logger.info(String.format("Reference allele is too long (%d) at position %s:%d; skipping that record.", reportedRefAllele.length(), vc.getChr(), vc.getStart()));

public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToVCF.java

@@ -167,8 +167,8 @@ public class VariantsToVCF extends RodWalker<Integer, Integer> {
                             continue;
 
                         Map<String, Allele> alleleMap = new HashMap<String, Allele>(2);
-                        alleleMap.put(RawHapMapFeature.DELETION, Allele.create(Allele.NULL_ALLELE_STRING, dbsnpVC.isInsertion()));
+                        alleleMap.put(RawHapMapFeature.DELETION, Allele.create(Allele.NULL_ALLELE_STRING, dbsnpVC.isSimpleInsertion()));
-                        alleleMap.put(RawHapMapFeature.INSERTION, Allele.create(((RawHapMapFeature)record).getAlleles()[1], !dbsnpVC.isInsertion()));
+                        alleleMap.put(RawHapMapFeature.INSERTION, Allele.create(((RawHapMapFeature)record).getAlleles()[1], !dbsnpVC.isSimpleInsertion()));
                         hapmap.setActualAlleles(alleleMap);
 
                         // also, use the correct positioning for insertions

public/java/src/org/broadinstitute/sting/queue/extensions/gatk/ArgumentDefinitionField.java

@@ -144,6 +144,9 @@ public abstract class ArgumentDefinitionField extends ArgumentField {
         } else if ("input_file".equals(argumentDefinition.fullName) && argumentDefinition.ioType == ArgumentIOType.INPUT) {
             return Arrays.asList(new InputTaggedFileDefinitionField(argumentDefinition), new InputIndexesArgumentField(argumentDefinition, BAMIndex.BAMIndexSuffix, ".bam"));
 
+        } else if ((RodBinding.class.equals(argumentDefinition.argumentType) || RodBinding.class.equals(argumentDefinition.componentType)) && argumentDefinition.ioType == ArgumentIOType.INPUT) {
+            return Arrays.asList(new InputTaggedFileDefinitionField(argumentDefinition), new InputIndexesArgumentField(argumentDefinition, Tribble.STANDARD_INDEX_EXTENSION));
+
         } else if (argumentDefinition.ioType == ArgumentIOType.INPUT) {
             return Collections.singletonList(new InputArgumentField(argumentDefinition));
 
@@ -196,7 +199,7 @@ public abstract class ArgumentDefinitionField extends ArgumentField {
     }
 
     // if (intervalFields.contains(argumentDefinition.fullName) && argumentDefinition.ioType == ArgumentIOType.INPUT)
-    // Change intervals exclusize of intervalsString.
+    // Change intervals exclusive of intervalsString.
     private static class IntervalFileArgumentField extends InputArgumentField {
         public IntervalFileArgumentField(ArgumentDefinition argumentDefinition) {
             super(argumentDefinition);
@@ -332,9 +335,7 @@ public abstract class ArgumentDefinitionField extends ArgumentField {
         }
     }
 
-    /**
+    // Allows the user to specify the track name, track type, and the file.
-     * The other extreme of a NamedRodBindingField, allows the user to specify the track name, track type, and the file.
-     */
     public static class RodBindArgumentField extends ArgumentDefinitionField {
         public RodBindArgumentField(ArgumentDefinition argumentDefinition) {
             super(argumentDefinition);
@@ -347,25 +348,28 @@ public abstract class ArgumentDefinitionField extends ArgumentField {
         }
     }
 
-    /**
+    // Tagged input_files or other rods.
-     * Named input_files.
-     */
     public static class InputTaggedFileDefinitionField extends ArgumentDefinitionField {
         public InputTaggedFileDefinitionField(ArgumentDefinition argumentDefinition) {
             super(argumentDefinition);
         }
         @Override protected Class<?> getInnerType() { return null; } // TaggedFile does not need to be imported.
-        @Override protected String getFieldType() { return "List[File]"; }
+        @Override protected String getFieldType() { return argumentDefinition.isMultiValued ? "List[File]" :  "File"; }
-        @Override protected String getDefaultValue() { return "Nil"; }
+        @Override protected String getDefaultValue() { return argumentDefinition.isMultiValued ? "Nil" : "_"; }
         @Override protected String getCommandLineTemplate() {
-            return " + repeat(\"\", %3$s, format=TaggedFile.formatCommandLine(\"%1$s\"))";
+            if (argumentDefinition.isMultiValued) {
+                return " + repeat(\"\", %3$s, format=TaggedFile.formatCommandLine(\"%1$s\"))";
+            } else if (!argumentDefinition.required) {
+                return " + optional(\"\", %3$s, format=TaggedFile.formatCommandLine(\"%1$s\"))";
+            } else {
+                return " + TaggedFile.formatCommandLine(\"%1$s\")(\"\", %3$s, \"\")";
+            }
         }
     }
 
-    /**
+    // Adds optional inputs for the indexes of any rods added to this function.
-     * Adds optional inputs for the indexes of any bams or sams added to this function.
-     */
     private static class InputIndexesArgumentField extends ArgumentField {
+        private final boolean originalIsMultiValued;
         private final String indexFieldName;
         private final String originalFieldName;
         private final String indexSuffix;
@@ -374,14 +378,19 @@ public abstract class ArgumentDefinitionField extends ArgumentField {
             this(originalArgumentDefinition, indexSuffix, null);
         }
         public InputIndexesArgumentField(ArgumentDefinition originalArgumentDefinition, String indexSuffix, String originalSuffix) {
-            this.indexFieldName = originalArgumentDefinition.fullName + "Indexes";
+            this.originalIsMultiValued = originalArgumentDefinition.isMultiValued;
+            this.indexFieldName = originalArgumentDefinition.fullName + "Index" + (originalIsMultiValued ? "es" : "");
             this.originalFieldName = originalArgumentDefinition.fullName;
             this.indexSuffix = indexSuffix;
             this.originalSuffix = originalSuffix;
         }
         @Override protected Class<? extends Annotation> getAnnotationIOClass() { return Input.class; }
         @Override public String getCommandLineAddition() { return ""; }
-        @Override protected String getDoc() { return "Dependencies on any indexes of " + this.originalFieldName; }
+        @Override protected String getDoc() {
+            return originalIsMultiValued
+                    ? "Dependencies on any indexes of " + this.originalFieldName
+                    : "Dependencies on the index of " + this.originalFieldName;
+        }
         @Override protected String getFullName() { return this.indexFieldName; }
         @Override protected boolean isRequired() { return false; }
         @Override protected String getFieldType() { return "List[File]"; }
@@ -389,24 +398,41 @@ public abstract class ArgumentDefinitionField extends ArgumentField {
         @Override protected Class<?> getInnerType() { return File.class; }
         @Override protected String getRawFieldName() { return this.indexFieldName; }
         @Override protected String getFreezeFields() {
-            if (originalSuffix == null) {
+            if (originalIsMultiValued) {
-                return String.format(
+                if (originalSuffix == null) {
-                        ("%1$s ++= %2$s" +
+                    return String.format(
-                                ".filter(orig => orig != null)" +
+                            ("%1$s ++= %2$s" +
-                                ".map(orig => new File(orig.getPath + \"%3$s\"))%n"),
+                                    ".filter(orig => orig != null)" +
-                        indexFieldName, originalFieldName, indexSuffix);
+                                    ".map(orig => new File(orig.getPath + \"%3$s\"))%n"),
+                            indexFieldName, originalFieldName, indexSuffix);
+                } else {
+                    return String.format(
+                            ("%1$s ++= %2$s" +
+                                    ".filter(orig => orig != null && orig.getName.endsWith(\"%4$s\"))" +
+                                    ".flatMap(orig => Array(" +
+                                    " new File(orig.getPath + \"%3$s\")," +
+                                    " new File(orig.getPath.stripSuffix(\"%4$s\") + \"%3$s\") ))%n"),
+                            indexFieldName, originalFieldName, indexSuffix, originalSuffix);
+                }
             } else {
-                return String.format(
+                if (originalSuffix == null) {
-                        ("%1$s ++= %2$s" +
+                    return String.format(
-                                ".filter(orig => orig != null && orig.getName.endsWith(\"%4$s\"))" +
+                            ("if (%2$s != null)%n  " +
-                                ".flatMap(orig => Array(" +
+                                    "%1$s :+= new File(%2$s.getPath + \"%3$s\")%n"),
-                                " new File(orig.getPath + \"%3$s\")," +
+                            indexFieldName, originalFieldName, indexSuffix);
-                                " new File(orig.getPath.stripSuffix(\"%4$s\") + \"%3$s\") ))%n"),
+                } else {
-                        indexFieldName, originalFieldName, indexSuffix, originalSuffix);
+                    return String.format(
+                            ("if (%2$s != null && %2$s.getName.endsWith(\"%4$s\"))%n  " +
+                                    "%1$s ++= Array(" +
+                                    " new File(%2$s.getPath + \"%3$s\")," +
+                                    " new File(%2$s.getPath.stripSuffix(\"%4$s\") + \"%3$s\") )%n"),
+                            indexFieldName, originalFieldName, indexSuffix, originalSuffix);
+                }
             }
         }
     }
 
+    // Tracks an automatically generated index
     private static abstract class OutputIndexArgumentField extends ArgumentField {
         protected final String indexFieldName;
         protected final String originalFieldName;
@@ -456,6 +482,7 @@ public abstract class ArgumentDefinitionField extends ArgumentField {
         }
     }
 
+    // Allows setting the format for floats and doubles
     private static class FormatterArgumentField extends ArgumentField {
         private final ArgumentField argumentField;
         public FormatterArgumentField(ArgumentField argumentField) {

public/java/src/org/broadinstitute/sting/utils/IndelUtils.java

@@ -121,9 +121,9 @@ public class IndelUtils {
         boolean done = false;
 
         ArrayList<Integer> inds = new ArrayList<Integer>();
-        if ( vc.isInsertion() ) {
+        if ( vc.isSimpleInsertion() ) {
             indelAlleleString = vc.getAlternateAllele(0).getDisplayString();
-        } else if ( vc.isDeletion() ) {
+        } else if ( vc.isSimpleDeletion() ) {
             indelAlleleString = vc.getReference().getDisplayString();
         }
         else {

public/java/src/org/broadinstitute/sting/utils/variantcontext/VariantContext.java

@@ -583,24 +583,24 @@ public class VariantContext implements Feature { // to enable tribble intergrati
     /**
      * @return true if the alleles indicate a simple insertion (i.e., the reference allele is Null)
      */
-    public boolean isInsertion() {
+    public boolean isSimpleInsertion() {
-        // can't just call !isDeletion() because of complex indels
+        // can't just call !isSimpleDeletion() because of complex indels
-        return getType() == Type.INDEL && getReference().isNull();
+        return getType() == Type.INDEL && getReference().isNull() && isBiallelic();
     }
 
     /**
      * @return true if the alleles indicate a simple deletion (i.e., a single alt allele that is Null)
      */
-    public boolean isDeletion() {
+    public boolean isSimpleDeletion() {
-        // can't just call !isInsertion() because of complex indels
+        // can't just call !isSimpleInsertion() because of complex indels
-        return getType() == Type.INDEL && getAlternateAllele(0).isNull();
+        return getType() == Type.INDEL && getAlternateAllele(0).isNull() && isBiallelic();
     }
 
     /**
      * @return true if the alleles indicate neither a simple deletion nor a simple insertion
      */
     public boolean isComplexIndel() {
-        return isIndel() && !isDeletion() && !isInsertion();
+        return isIndel() && !isSimpleDeletion() && !isSimpleInsertion();
     }
 
     public boolean isSymbolic() {

public/java/test/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalIntegrationTest.java

@@ -29,7 +29,7 @@ public class VariantEvalIntegrationTest extends WalkerTest {
                                         "-o %s"
                                 ),
                                 1,
-                                Arrays.asList("bced1842c78fbabb089dd12b7087050d")
+                                Arrays.asList("1fefd6cf9c2554d5f886c3998defd4d0")
                               );
         executeTest("testFundamentalsCountVariantsSNPsandIndels", spec);
     }
@@ -50,7 +50,7 @@ public class VariantEvalIntegrationTest extends WalkerTest {
                         "-o %s"
                 ),
                 1,
-                Arrays.asList("06510bd37ffaa39e817ca0dcaf8f8ac2")
+                Arrays.asList("d470e00a368b5a0468012818994c6a89")
         );
         executeTest("testFundamentalsCountVariantsSNPsandIndelsWithNovelty", spec);
     }
@@ -72,7 +72,7 @@ public class VariantEvalIntegrationTest extends WalkerTest {
                         "-o %s"
                 ),
                 1,
-                Arrays.asList("19c5b1b6396921c5b1059a2849ae4fcc")
+                Arrays.asList("12856e52c2682328f91594089328596c")
         );
         executeTest("testFundamentalsCountVariantsSNPsandIndelsWithNoveltyAndFilter", spec);
     }
@@ -93,7 +93,7 @@ public class VariantEvalIntegrationTest extends WalkerTest {
                         "-o %s"
                 ),
                 1,
-                Arrays.asList("a71f8d81cf166cd97ac628092650964a")
+                Arrays.asList("91610b9240f64e0eb03cfd2602cf57af")
         );
         executeTest("testFundamentalsCountVariantsSNPsandIndelsWithCpG", spec);
     }
@@ -114,7 +114,7 @@ public class VariantEvalIntegrationTest extends WalkerTest {
                         "-o %s"
                 ),
                 1,
-                Arrays.asList("4dabe0658232f6174188515db6dfe112")
+                Arrays.asList("e40b77e7ed6581328e373a24b93cd170")
         );
         executeTest("testFundamentalsCountVariantsSNPsandIndelsWithFunctionalClass", spec);
     }
@@ -135,7 +135,7 @@ public class VariantEvalIntegrationTest extends WalkerTest {
                         "-o %s"
                 ),
                 1,
-                Arrays.asList("3340587f10ceff83e5567ddfd1a9a60e")
+                Arrays.asList("15beaf3823c131cabc5fb0445239f978")
         );
         executeTest("testFundamentalsCountVariantsSNPsandIndelsWithDegeneracy", spec);
     }
@@ -156,7 +156,7 @@ public class VariantEvalIntegrationTest extends WalkerTest {
                         "-o %s"
                 ),
                 1,
-                Arrays.asList("c730c7ee31c8138cef6efd8dd04fbbfc")
+                Arrays.asList("7ddd4ee74938d229ce5cb7b9b9104abe")
         );
         executeTest("testFundamentalsCountVariantsSNPsandIndelsWithSample", spec);
     }
@@ -179,7 +179,7 @@ public class VariantEvalIntegrationTest extends WalkerTest {
                         "-o %s"
                 ),
                 1,
-                Arrays.asList("2559ca8f454b03e81561f6947f79df18")
+                Arrays.asList("a90f33906a732ef5eb346e559c96ccc1")
         );
         executeTest("testFundamentalsCountVariantsSNPsandIndelsWithJexlExpression", spec);
     }
@@ -204,7 +204,7 @@ public class VariantEvalIntegrationTest extends WalkerTest {
                         "-o %s"
                 ),
                 1,
-                Arrays.asList("23aa5f97641d2fd033095f21c51d2f37")
+                Arrays.asList("2567f90d3d7354850c5a59730ecc6e4f")
         );
         executeTest("testFundamentalsCountVariantsSNPsandIndelsWithMultipleJexlExpressions", spec);
     }
@@ -223,7 +223,7 @@ public class VariantEvalIntegrationTest extends WalkerTest {
                         "-o %s"
                 ),
                 1,
-                Arrays.asList("a69dd3f06903b3f374c6d6f010c653e0")
+                Arrays.asList("fa091aa8967893389c51102fd9f0bebb")
         );
         executeTest("testFundamentalsCountVariantsNoCompRod", spec);
     }
@@ -236,7 +236,7 @@ public class VariantEvalIntegrationTest extends WalkerTest {
                 " --eval " + validationDataLocation + "yri.trio.gatk_glftrio.intersection.annotated.filtered.chr1.vcf" +
                 " --comp:comp_genotypes,VCF3 " + validationDataLocation + "yri.trio.gatk.ug.head.vcf";
         WalkerTestSpec spec = new WalkerTestSpec(withSelect(tests, "DP < 50", "DP50") + " " + extraArgs + " -ST CpG -o %s",
-                1, Arrays.asList("125fe0a04b5d933cc14016598b2791cd"));
+                1, Arrays.asList("2df4f8911ffc3c8d042298723ed465f8"));
         executeTestParallel("testSelect1", spec);
     }
 
@@ -253,7 +253,7 @@ public class VariantEvalIntegrationTest extends WalkerTest {
     @Test
     public void testCompVsEvalAC() {
         String extraArgs = "-T VariantEval -R "+b36KGReference+" -o %s -ST CpG -EV GenotypeConcordance --eval:evalYRI,VCF3 " + validationDataLocation + "yri.trio.gatk.ug.very.few.lines.vcf --comp:compYRI,VCF3 " + validationDataLocation + "yri.trio.gatk.fake.genotypes.ac.test.vcf";
-        WalkerTestSpec spec = new WalkerTestSpec(extraArgs,1,Arrays.asList("d1932be3748fcf6da77dc51aec323710"));
+        WalkerTestSpec spec = new WalkerTestSpec(extraArgs,1,Arrays.asList("ed54aa127b173d8ad8b6482f2a929a42"));
         executeTestParallel("testCompVsEvalAC",spec);
     }
 
@@ -283,7 +283,7 @@ public class VariantEvalIntegrationTest extends WalkerTest {
                            " --dbsnp " + b37dbSNP132 +
                            " --eval:evalBI " + validationDataLocation + "VariantEval/ALL.20100201.chr20.bi.sites.vcf" +
                            " -noST -ST Novelty -o %s";
-        WalkerTestSpec spec = new WalkerTestSpec(extraArgs,1,Arrays.asList("cbea5f9f8c046d4c014d261db352c43b"));
+        WalkerTestSpec spec = new WalkerTestSpec(extraArgs,1,Arrays.asList("18c44636e36d6657110bf984f8eac181"));
         executeTestParallel("testEvalTrackWithoutGenotypes",spec);
     }
 
@@ -295,7 +295,7 @@ public class VariantEvalIntegrationTest extends WalkerTest {
                 " --eval:evalBI " + validationDataLocation + "VariantEval/ALL.20100201.chr20.bi.sites.vcf" +
                 " --eval:evalBC " + validationDataLocation + "VariantEval/ALL.20100201.chr20.bc.sites.vcf" +
                 " -noST -ST Novelty -o %s";
-        WalkerTestSpec spec = new WalkerTestSpec(extraArgs,1,Arrays.asList("d07a246963ae609643620c839b20cd1e"));
+        WalkerTestSpec spec = new WalkerTestSpec(extraArgs,1,Arrays.asList("1b8ae4fd10de0888bd843f833859d990"));
         executeTestParallel("testMultipleEvalTracksWithoutGenotypes",spec);
     }
 
@@ -373,7 +373,7 @@ public class VariantEvalIntegrationTest extends WalkerTest {
                                         "-o %s"
                                 ),
                                 1,
-                                Arrays.asList("44464fe7c89a56cf128a932ef640f7da")
+                                Arrays.asList("da65fc8f0d0eeaf0a0b06a07f444bb8e")
                               );
         executeTest("testAlleleCountStrat", spec);
     }

public/java/test/org/broadinstitute/sting/utils/variantcontext/VariantContextUnitTest.java

@@ -146,8 +146,8 @@ public class VariantContextUnitTest {
         Assert.assertEquals(vc.getType(), VariantContext.Type.SNP);
         Assert.assertTrue(vc.isSNP());
         Assert.assertFalse(vc.isIndel());
-        Assert.assertFalse(vc.isInsertion());
+        Assert.assertFalse(vc.isSimpleInsertion());
-        Assert.assertFalse(vc.isDeletion());
+        Assert.assertFalse(vc.isSimpleDeletion());
         Assert.assertFalse(vc.isMixed());
         Assert.assertTrue(vc.isBiallelic());
         Assert.assertEquals(vc.getNAlleles(), 2);
@@ -173,8 +173,8 @@ public class VariantContextUnitTest {
         Assert.assertEquals(VariantContext.Type.NO_VARIATION, vc.getType());
         Assert.assertFalse(vc.isSNP());
         Assert.assertFalse(vc.isIndel());
-        Assert.assertFalse(vc.isInsertion());
+        Assert.assertFalse(vc.isSimpleInsertion());
-        Assert.assertFalse(vc.isDeletion());
+        Assert.assertFalse(vc.isSimpleDeletion());
         Assert.assertFalse(vc.isMixed());
         Assert.assertFalse(vc.isBiallelic());
         Assert.assertEquals(vc.getNAlleles(), 1);
@@ -199,8 +199,8 @@ public class VariantContextUnitTest {
         Assert.assertEquals(vc.getType(), VariantContext.Type.INDEL);
         Assert.assertFalse(vc.isSNP());
         Assert.assertTrue(vc.isIndel());
-        Assert.assertFalse(vc.isInsertion());
+        Assert.assertFalse(vc.isSimpleInsertion());
-        Assert.assertTrue(vc.isDeletion());
+        Assert.assertTrue(vc.isSimpleDeletion());
         Assert.assertFalse(vc.isMixed());
         Assert.assertTrue(vc.isBiallelic());
         Assert.assertEquals(vc.getNAlleles(), 2);
@@ -226,8 +226,8 @@ public class VariantContextUnitTest {
         Assert.assertEquals(vc.getType(), VariantContext.Type.INDEL);
         Assert.assertFalse(vc.isSNP());
         Assert.assertTrue(vc.isIndel());
-        Assert.assertTrue(vc.isInsertion());
+        Assert.assertTrue(vc.isSimpleInsertion());
-        Assert.assertFalse(vc.isDeletion());
+        Assert.assertFalse(vc.isSimpleDeletion());
         Assert.assertFalse(vc.isMixed());
         Assert.assertTrue(vc.isBiallelic());
         Assert.assertEquals(vc.getNAlleles(), 2);
@@ -433,7 +433,7 @@ public class VariantContextUnitTest {
         Assert.assertFalse(vc14.isBiallelic());
 
         Assert.assertTrue(vc5.isIndel());
-        Assert.assertTrue(vc5.isDeletion());
+        Assert.assertTrue(vc5.isSimpleDeletion());
         Assert.assertTrue(vc5.isVariant());
         Assert.assertTrue(vc5.isBiallelic());