Merge branch 'master' of ssh://gsa1/humgen/gsa-scr1/gsa-engineering/git/unstable

public/c/bwa/build_linux.sh

@@ -1,5 +1,5 @@
 #!/bin/sh
-export BWA_HOME="/humgen/gsa-scr1/hanna/src/bwa-trunk/bwa"
+export BWA_HOME="/humgen/gsa-scr1/hanna/src/bio-bwa/bwa"
 export JAVA_INCLUDE="/broad/tools/Linux/x86_64/pkgs/jdk_1.6.0_12/include -I/broad/tools/Linux/x86_64/pkgs/jdk_1.6.0_12/include/linux"
 export TARGET_LIB="libbwa.so"
 export EXTRA_LIBS="-lc -lz -lstdc++ -lpthread"

public/c/bwa/bwa_gateway.cpp

@@ -233,6 +233,8 @@ void BWA::set_disallow_indel_within_range(int indel_range) { options.indel_end_s
 void BWA::set_mismatch_penalty(int penalty) { options.s_mm = penalty; }
 void BWA::set_gap_open_penalty(int penalty) { options.s_gapo = penalty; }
 void BWA::set_gap_extension_penalty(int penalty) { options.s_gape = penalty; }
+void BWA::set_mode_nonstop() { options.mode |= BWA_MODE_NONSTOP; options.max_top2 = 0x7fffffff; }
+void BWA::set_max_entries_in_queue(int max_entries) { options.max_entries = max_entries; }
 
 /**
  * Create a sequence with a set of reasonable initial defaults.  

public/c/bwa/bwa_gateway.h

@@ -60,6 +60,8 @@ class BWA {
   void set_mismatch_penalty(int penalty);
   void set_gap_open_penalty(int penalty);
   void set_gap_extension_penalty(int penalty);
+  void set_mode_nonstop();
+  void set_max_entries_in_queue(int max_entries);
 
   // Perform the alignment
   Alignment* generate_single_alignment(const char* bases, 

public/c/bwa/org_broadinstitute_sting_alignment_bwa_c_BWACAligner.cpp

@@ -8,11 +8,13 @@
 #include "bwa_gateway.h"
 #include "org_broadinstitute_sting_alignment_bwa_c_BWACAligner.h"
 
+typedef void (BWA::*boolean_setter)();
 typedef void (BWA::*int_setter)(int value);
 typedef void (BWA::*float_setter)(float value);
 
 static jobject convert_to_java_alignment(JNIEnv* env, const jbyte* read_bases, const jsize read_length, const Alignment& alignment);
 static jstring get_configuration_file(JNIEnv* env, jobject configuration, const char* field_name);
+static void set_boolean_configuration_param(JNIEnv* env, jobject configuration, const char* field_name, BWA* bwa, boolean_setter setter);
 static void set_int_configuration_param(JNIEnv* env, jobject configuration, const char* field_name, BWA* bwa, int_setter setter);
 static void set_float_configuration_param(JNIEnv* env, jobject configuration, const char* field_name, BWA* bwa, float_setter setter);
 static void throw_config_value_exception(JNIEnv* env, const char* field_name, const char* message);
@@ -100,6 +102,10 @@ JNIEXPORT void JNICALL Java_org_broadinstitute_sting_alignment_bwa_c_BWACAligner
   if(env->ExceptionCheck()) return; 
   set_int_configuration_param(env, configuration, "gapExtensionPenalty", bwa, &BWA::set_gap_extension_penalty);
   if(env->ExceptionCheck()) return;
+  set_boolean_configuration_param(env, configuration, "nonStopMode", bwa, &BWA::set_mode_nonstop);
+  if(env->ExceptionCheck()) return;
+  set_int_configuration_param(env, configuration, "maxEntriesInQueue", bwa, &BWA::set_max_entries_in_queue);
+  if(env->ExceptionCheck()) return;
 }
 
 JNIEXPORT jobjectArray JNICALL Java_org_broadinstitute_sting_alignment_bwa_c_BWACAligner_getPaths(JNIEnv *env, jobject instance, jlong java_bwa, jbyteArray java_bases) 
@@ -357,6 +363,36 @@ static jstring get_configuration_file(JNIEnv* env, jobject configuration, const
   return path;
 }
 
+static void set_boolean_configuration_param(JNIEnv* env, jobject configuration, const char* field_name, BWA* bwa, boolean_setter setter) {
+  jclass configuration_class = env->GetObjectClass(configuration);
+  if(configuration_class == NULL) return;
+
+  jfieldID configuration_field = env->GetFieldID(configuration_class, field_name, "Ljava/lang/Boolean;");
+  if(configuration_field == NULL) return;
+
+  jobject boxed_value = env->GetObjectField(configuration,configuration_field);
+  if(env->ExceptionCheck()) return;
+
+  if(boxed_value != NULL) {
+    jclass boolean_box_class = env->FindClass("java/lang/Boolean");
+    if(boolean_box_class == NULL) return;
+
+    jmethodID boolean_extractor = env->GetMethodID(boolean_box_class,"booleanValue", "()Z");
+    if(boolean_extractor == NULL) return;
+
+    jboolean value = env->CallBooleanMethod(boxed_value,boolean_extractor);
+    if(env->ExceptionCheck()) return;
+
+    if(value)
+      (bwa->*setter)();
+
+    env->DeleteLocalRef(boolean_box_class);
+  }
+
+  env->DeleteLocalRef(boxed_value);
+  env->DeleteLocalRef(configuration_class);
+}
+
 static void set_int_configuration_param(JNIEnv* env, jobject configuration, const char* field_name, BWA* bwa, int_setter setter) {
   jclass configuration_class = env->GetObjectClass(configuration);
   if(configuration_class == NULL) return;

public/java/src/org/broadinstitute/sting/alignment/bwa/BWAConfiguration.java

@@ -41,4 +41,14 @@ public class BWAConfiguration {
      * What is the scoring penalty for a gap extension?
      */
     public Integer gapExtensionPenalty = null;
+
+    /**
+     * Enter bwa's 'non-stop' mode (equivalent to bwa aln -N parameter).
+     */
+    public Boolean nonStopMode = false;
+
+    /**
+     * Set the max queue size that bwa will use when searching for matches (equivalent to bwa aln -m parameter).
+     */
+    public Integer maxEntriesInQueue = null;
 }

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

@@ -88,7 +88,7 @@ public class GATKBAMIndex {
         seek(0);
         final byte[] buffer = readBytes(4);
         if (!Arrays.equals(buffer, BAM_INDEX_MAGIC)) {
-            throw new RuntimeException("Invalid file header in BAM index " + mFile +
+            throw new ReviewedStingException("Invalid file header in BAM index " + mFile +
                                        ": " + new String(buffer));
         }
 
@@ -112,7 +112,7 @@ public class GATKBAMIndex {
         openIndexFile();
 
         if (referenceSequence >= sequenceCount)
-            throw new ReviewedStingException("Invalid sequence number " + referenceSequence);
+            throw new ReviewedStingException("Invalid sequence number " + referenceSequence + " in index file " + mFile);
 
         skipToSequence(referenceSequence);
 
@@ -183,12 +183,12 @@ public class GATKBAMIndex {
     public int getLevelForBin(final Bin bin) {
         GATKBin gatkBin = new GATKBin(bin);
         if(gatkBin.getBinNumber() >= MAX_BINS)
-            throw new SAMException("Tried to get level for invalid bin.");
+            throw new ReviewedStingException("Tried to get level for invalid bin in index file " + mFile);
         for(int i = getNumIndexLevels()-1; i >= 0; i--) {
             if(gatkBin.getBinNumber() >= LEVEL_STARTS[i])
                 return i;
         }
-        throw new SAMException("Unable to find correct bin for bin "+bin);
+        throw new ReviewedStingException("Unable to find correct bin for bin " + bin + " in index file " + mFile);
     }
 
     /**
@@ -352,7 +352,7 @@ public class GATKBAMIndex {
             fileChannel.read(buffer);
         }
         catch(IOException ex) {
-            throw new ReviewedStingException("Index: unable to read bytes from index file.");
+            throw new ReviewedStingException("Index: unable to read bytes from index file " + mFile);
         }
     }
 
@@ -379,7 +379,7 @@ public class GATKBAMIndex {
             fileChannel.position(fileChannel.position() + count);
         }
         catch(IOException ex) {
-            throw new ReviewedStingException("Index: unable to reposition file channel.");
+            throw new ReviewedStingException("Index: unable to reposition file channel of index file " + mFile);
         }
     }
 
@@ -388,7 +388,7 @@ public class GATKBAMIndex {
             fileChannel.position(position);
         }
         catch(IOException ex) {
-            throw new ReviewedStingException("Index: unable to reposition of file channel.");
+            throw new ReviewedStingException("Index: unable to reposition of file channel of index file " + mFile);
         }
     }
 

public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperEngine.java

@@ -858,171 +858,4 @@ public class UnifiedGenotyperEngine {
 
         return calls;
     }
-
-    /**
-     * @param vc            variant context with genotype likelihoods
-     * @param allelesToUse  bit vector describing which alternate alleles from the vc are okay to use
-     * @param exactAC       integer array describing the AC from the exact model for the corresponding alleles
-     * @return genotypes
-     */
-    public static GenotypesContext constrainedAssignGenotypes(VariantContext vc, boolean[] allelesToUse, int[] exactAC ) {
-
-        final GenotypesContext GLs = vc.getGenotypes();
-
-        // samples
-        final List<String> sampleIndices = GLs.getSampleNamesOrderedByName();
-
-        // we need to determine which of the alternate alleles (and hence the likelihoods) to use and carry forward
-        final int numOriginalAltAlleles = allelesToUse.length;
-        final List<Allele> newAlleles = new ArrayList<Allele>(numOriginalAltAlleles+1);
-        newAlleles.add(vc.getReference());
-        final HashMap<Allele,Integer> alleleIndexMap = new HashMap<Allele,Integer>(); // need this for skipping dimensions
-        int[] alleleCount = new int[exactAC.length];
-        for ( int i = 0; i < numOriginalAltAlleles; i++ ) {
-            if ( allelesToUse[i] ) {
-                newAlleles.add(vc.getAlternateAllele(i));
-                alleleIndexMap.put(vc.getAlternateAllele(i),i);
-                alleleCount[i] = exactAC[i];
-            } else {
-                alleleCount[i] = 0;
-            }
-        }
-        final List<Allele> newAltAlleles = newAlleles.subList(1,newAlleles.size());
-        final int numNewAltAlleles = newAltAlleles.size();
-        ArrayList<Integer> likelihoodIndexesToUse = null;
-
-        // an optimization: if we are supposed to use all (or none in the case of a ref call) of the alleles,
-        // then we can keep the PLs as is; otherwise, we determine which ones to keep
-        final int[][] PLcache;
-        if ( numNewAltAlleles != numOriginalAltAlleles && numNewAltAlleles > 0 ) {
-            likelihoodIndexesToUse = new ArrayList<Integer>(30);
-            PLcache = PLIndexToAlleleIndex[numOriginalAltAlleles];
-
-            for ( int PLindex = 0; PLindex < PLcache.length; PLindex++ ) {
-                int[] alleles = PLcache[PLindex];
-                // consider this entry only if both of the alleles are good
-                if ( (alleles[0] == 0 || allelesToUse[alleles[0] - 1]) && (alleles[1] == 0 || allelesToUse[alleles[1] - 1]) )
-                    likelihoodIndexesToUse.add(PLindex);
-            }
-        } else {
-            PLcache = PLIndexToAlleleIndex[numOriginalAltAlleles];
-        }
-
-        // set up the trellis dimensions
-        // SAMPLE x alt 1 x alt 2 x alt 3
-        // todo -- check that exactAC has alt counts at [1],[2],[3] (and not [0],[1],[2])
-        double[][][][] transitionTrellis = new double[sampleIndices.size()+1][exactAC[1]][exactAC[2]][exactAC[3]];
-        // N x AC1 x AC2 x AC3; worst performance in multi-allelic where all alleles are moderate frequency
-        // capped at the MLE ACs*
-        // todo -- there's an optimization: not all states in the rectangular matrix will be reached, in fact
-        // todo -- for tT[0] we only care about tT[0][0][0][0], and for tT[1], only combinations of 0,1,2.
-        int idx = 1; // index of which sample we're on
-        int prevMaxState = 0; // the maximum state (e.g. AC) reached by the previous sample. Symmetric. (AC capping handled by logic in loop)
-        // iterate over each sample
-        for ( String sample : sampleIndices ) {
-            // push the likelihoods into the next possible states, that is to say
-            // L[state] = L[prev state] + L[genotype getting into state]
-            // iterate over each previous state, by dimension
-            // and contribute the likelihoods for transitions to this state
-            double[][][] prevState = transitionTrellis[idx-1];
-            double[][][] thisState = transitionTrellis[idx];
-            Genotype genotype = GLs.get(sample);
-            if ( genotype.isNoCall() || genotype.isFiltered() ) {
-                thisState = prevState.clone();
-            } else {
-                double[] likelihoods = genotype.getLikelihoods().getAsVector();
-                int dim1min = Math.max(0, alleleCount[0]-2*(sampleIndices.size()-idx+1));
-                int dim1max = Math.min(prevMaxState,alleleCount[0]);
-                int dim2min = Math.max(0,alleleCount[1]-2*(sampleIndices.size()-idx+1));
-                int dim2max = Math.min(prevMaxState,alleleCount[1]);
-                int dim3min = Math.max(0,alleleCount[2]-2*(sampleIndices.size()-idx+1));
-                int dim3max = Math.min(prevMaxState,alleleCount[2]);
-                // cue annoying nested for loop
-                for ( int a1 = dim1min ; a1 <= dim1max; a1++ ) {
-                    for ( int a2 = dim2min; a2 <= dim2max; a2++ ) {
-                        for ( int a3 = dim3min; a3 <= dim3max; a3++ ) {
-                            double base = prevState[a1][a2][a3];
-                            for ( int likIdx : likelihoodIndexesToUse ) {
-                                int[] offsets = calculateOffsets(PLcache[likIdx]);
-                                thisState[a1+offsets[1]][a2+offsets[2]][a3+offsets[3]] = base + likelihoods[likIdx];
-                            }
-                        }
-                    }
-                }
-                prevMaxState += 2;
-            }
-            idx++;
-        }
-
-        // after all that pain, we have a fully calculated trellis. Now just march backwards from the EAC state and
-        // assign genotypes along the greedy path
-
-        GenotypesContext calls = GenotypesContext.create(sampleIndices.size());
-        int[] state = alleleCount;
-        for ( String sample : Utils.reverse(sampleIndices) ) {
-            --idx;
-            // the next state will be the maximum achievable state
-            Genotype g = GLs.get(sample);
-            if ( g.isNoCall() || ! g.hasLikelihoods() ) {
-                calls.add(g);
-                continue;
-            }
-
-            // subset to the new likelihoods. These are not used except for subsetting in the context iself.
-            // i.e. they are not a part of the calculation.
-            final double[] originalLikelihoods = GLs.get(sample).getLikelihoods().getAsVector();
-            double[] newLikelihoods;
-            if ( likelihoodIndexesToUse == null ) {
-                newLikelihoods = originalLikelihoods;
-            } else {
-                newLikelihoods = new double[likelihoodIndexesToUse.size()];
-                int newIndex = 0;
-                for ( int oldIndex : likelihoodIndexesToUse )
-                    newLikelihoods[newIndex++] = originalLikelihoods[oldIndex];
-
-                // might need to re-normalize
-                newLikelihoods = MathUtils.normalizeFromLog10(newLikelihoods, false, true);
-            }
-
-            // todo -- alter this. For ease of programming, likelihood indeces are
-            // todo -- used to iterate over achievable states.
-            double max = Double.NEGATIVE_INFINITY;
-            int[] bestState = null;
-            int[] bestAlleles = null;
-            int bestLikIdx = -1;
-            for ( int likIdx : likelihoodIndexesToUse ) {
-                int[] offsets = calculateOffsets(PLcache[likIdx]);
-                double val = transitionTrellis[idx-1][state[0]-offsets[0]][state[1]-offsets[1]][state[2]-offsets[2]];
-                if ( val > max ) {
-                    max = val;
-                    bestState = new int[] { state[0]-offsets[0],state[1]-offsets[1],state[2]-offsets[2]};
-                    bestAlleles = PLcache[likIdx];
-                    bestLikIdx = likIdx;
-                }
-            }
-            state = bestState;
-            List<Allele> gtAlleles = new ArrayList<Allele>(2);
-            gtAlleles.add(newAlleles.get(bestAlleles[0]));
-            gtAlleles.add(newAlleles.get(bestAlleles[1]));
-
-            final double qual = numNewAltAlleles == 0 ? Genotype.NO_LOG10_PERROR : GenotypeLikelihoods.getQualFromLikelihoods(bestLikIdx, newLikelihoods);
-            Map<String, Object> attrs = new HashMap<String, Object>(g.getAttributes());
-            if ( numNewAltAlleles == 0 )
-                attrs.remove(VCFConstants.PHRED_GENOTYPE_LIKELIHOODS_KEY);
-            else
-                attrs.put(VCFConstants.PHRED_GENOTYPE_LIKELIHOODS_KEY, GenotypeLikelihoods.fromLog10Likelihoods(newLikelihoods));
-            calls.add(new Genotype(sample, gtAlleles, qual, null, attrs, false));
-
-        }
-        return calls;
-    }
-
-    private static int[] calculateOffsets(int[] alleleIndeces) {
-        int[] offsets = new int[4];
-        for ( int i = 0; i < alleleIndeces.length; i++ ) {
-            offsets[alleleIndeces[i]]++;
-        }
-
-        return offsets;
-    }
 }

public/java/src/org/broadinstitute/sting/utils/codecs/vcf/AbstractVCFCodec.java

@@ -18,6 +18,7 @@ import java.util.zip.GZIPInputStream;
 
 
 public abstract class AbstractVCFCodec implements FeatureCodec, NameAwareCodec {
+    public final static int MAX_ALLELE_SIZE_BEFORE_WARNING = (int)Math.pow(2, 20);
 
     protected final static Logger log = Logger.getLogger(VCFCodec.class);
     protected final static int NUM_STANDARD_FIELDS = 8;  // INFO is the 8th column
@@ -252,7 +253,7 @@ public abstract class AbstractVCFCodec implements FeatureCodec, NameAwareCodec {
 
         // if we have don't have a header, or we have a header with no genotyping data check that we have eight columns.  Otherwise check that we have nine (normal colummns + genotyping data)
         if (( (header == null || !header.hasGenotypingData()) && nParts != NUM_STANDARD_FIELDS) ||
-             (header != null && header.hasGenotypingData() && nParts != (NUM_STANDARD_FIELDS + 1)) )
+                (header != null && header.hasGenotypingData() && nParts != (NUM_STANDARD_FIELDS + 1)) )
             throw new UserException.MalformedVCF("there aren't enough columns for line " + line + " (we expected " + (header == null ? NUM_STANDARD_FIELDS : NUM_STANDARD_FIELDS + 1) +
                     " tokens, and saw " + nParts + " )", lineNo);
 
@@ -518,8 +519,11 @@ public abstract class AbstractVCFCodec implements FeatureCodec, NameAwareCodec {
      * @param lineNo  the line number for this record
      */
     private static void checkAllele(String allele, boolean isRef, int lineNo) {
-	if ( allele == null || allele.length() == 0 )
+        if ( allele == null || allele.length() == 0 )
-	    generateException("Empty alleles are not permitted in VCF records", lineNo);
+            generateException("Empty alleles are not permitted in VCF records", lineNo);
+
+        if ( MAX_ALLELE_SIZE_BEFORE_WARNING != -1 && allele.length() > MAX_ALLELE_SIZE_BEFORE_WARNING )
+            log.warn(String.format("Allele detected with length %d exceeding max size %d at approximately line %d, likely resulting in degraded VCF processing performance", allele.length(), MAX_ALLELE_SIZE_BEFORE_WARNING, lineNo));
 
         if ( isSymbolicAllele(allele) ) {
             if ( isRef ) {
@@ -572,12 +576,13 @@ public abstract class AbstractVCFCodec implements FeatureCodec, NameAwareCodec {
 
     public static int computeForwardClipping(List<Allele> unclippedAlleles, String ref) {
         boolean clipping = true;
+        final byte ref0 = (byte)ref.charAt(0);
 
         for ( Allele a : unclippedAlleles ) {
             if ( a.isSymbolic() )
                 continue;
 
-            if ( a.length() < 1 || (a.getBases()[0] != ref.getBytes()[0]) ) {
+            if ( a.length() < 1 || (a.getBases()[0] != ref0) ) {
                 clipping = false;
                 break;
             }
@@ -604,7 +609,7 @@ public abstract class AbstractVCFCodec implements FeatureCodec, NameAwareCodec {
                     stillClipping = false;
                 else if ( ref.length() == clipping )
                     generateException("bad alleles encountered", lineNo);
-                else if ( a.getBases()[a.length()-clipping-1] != ref.getBytes()[ref.length()-clipping-1] )
+                else if ( a.getBases()[a.length()-clipping-1] != ((byte)ref.charAt(ref.length()-clipping-1)) )
                     stillClipping = false;
             }
             if ( stillClipping )
@@ -613,6 +618,7 @@ public abstract class AbstractVCFCodec implements FeatureCodec, NameAwareCodec {
 
         return clipping;
     }
+
     /**
      * clip the alleles, based on the reference
      *

public/java/test/org/broadinstitute/sting/utils/codecs/vcf/VCFCodecUnitTest.java

@@ -0,0 +1,91 @@
+/*
+ * Copyright (c) 2012, 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.
+ */
+
+// our package
+package org.broadinstitute.sting.utils.codecs.vcf;
+
+
+// the imports for unit testing.
+
+
+import org.broadinstitute.sting.BaseTest;
+import org.broadinstitute.sting.utils.variantcontext.*;
+import org.testng.Assert;
+import org.testng.annotations.BeforeSuite;
+import org.testng.annotations.DataProvider;
+import org.testng.annotations.Test;
+
+import java.util.*;
+
+
+public class VCFCodecUnitTest extends BaseTest {
+
+    // --------------------------------------------------------------------------------
+    //
+    // Provider
+    //
+    // --------------------------------------------------------------------------------
+
+    private class AlleleClippingTestProvider extends TestDataProvider {
+        final String ref;
+        final List<Allele> alleles = new ArrayList<Allele>();
+        final int expectedClip;
+
+        private AlleleClippingTestProvider(final int expectedClip, final String ref, final String ... alleles) {
+            super(AlleleClippingTestProvider.class);
+            this.ref = ref;
+            for ( final String allele : alleles )
+                this.alleles.add(Allele.create(allele));
+            this.expectedClip = expectedClip;
+        }
+
+        @Override
+        public String toString() {
+            return String.format("ref=%s allele=%s reverse clip %d", ref, alleles, expectedClip);
+        }
+    }
+
+    @DataProvider(name = "AlleleClippingTestProvider")
+    public Object[][] MakeAlleleClippingTest() {
+        // pair clipping
+        new AlleleClippingTestProvider(0, "ATT", "CCG");
+        new AlleleClippingTestProvider(1, "ATT", "CCT");
+        new AlleleClippingTestProvider(2, "ATT", "CTT");
+        new AlleleClippingTestProvider(2, "ATT", "ATT");  // cannot completely clip allele
+
+        // triplets
+        new AlleleClippingTestProvider(0, "ATT", "CTT", "CGG");
+        new AlleleClippingTestProvider(1, "ATT", "CTT", "CGT"); // the T can go
+        new AlleleClippingTestProvider(2, "ATT", "CTT", "CTT"); // both Ts can go
+
+        return AlleleClippingTestProvider.getTests(AlleleClippingTestProvider.class);
+    }
+
+
+    @Test(dataProvider = "AlleleClippingTestProvider")
+    public void TestAlleleClipping(AlleleClippingTestProvider cfg) {
+        int result = AbstractVCFCodec.computeReverseClipping(cfg.alleles, cfg.ref, 0, 1);
+        Assert.assertEquals(result, cfg.expectedClip);
+    }
+}

public/scala/qscript/org/broadinstitute/sting/queue/qscripts/GATKResourcesBundle.scala

@@ -134,8 +134,8 @@ class GATKResourcesBundle extends QScript {
     addResource(new Resource("/humgen/1kg/processing/official_release/phase1/ALL.wgs.VQSR_consensus_biallelic.20101123.indels.sites.vcf",
       "1000G_biallelic.indels", b37, true, false))
 
-    addResource(new Resource("/humgen/gsa-hpprojects/GATK/data/Comparisons/Validated/Mills_Devine_Indels_2011/ALL.wgs.indels_mills_devine_hg19_leftAligned_collapsed_double_hit.sites.vcf",
+    addResource(new Resource("/humgen/gsa-hpprojects/GATK/data/Comparisons/Unvalidated/GoldStandardIndel/gold.standard.indel.MillsAnd1000G.b37.vcf",
-      "Mills_Devine_2hit.indels", b37, true, true))
+      "Mills_and_1000G_gold_standard.indels", b37, true, true))
     
     //
     // example call set for wiki tutorial

settings/repository/org.broad/tribble-53.xml

@@ -1,3 +1,3 @@
 <ivy-module version="1.0">
-    <info organisation="org.broad" module="tribble" revision="46" status="integration" />
+    <info organisation="org.broad" module="tribble" revision="53" status="integration" />
 </ivy-module>