Merge branch 'master' of ssh://gsa4/humgen/gsa-scr1/gsa-engineering/git/unstable

protected/java/src/org/broadinstitute/sting/gatk/downsampling/AlleleBiasedDownsamplingUtils.java

@@ -60,6 +60,10 @@ public class AlleleBiasedDownsamplingUtils {
 
         // start by stratifying the reads by the alleles they represent at this position
         for( final PileupElement pe : pileup ) {
+            // abort if we have a reduced read - we do not want to remove it!
+            if ( pe.getRead().isReducedRead() )
+                return pileup;
+
             final int baseIndex = BaseUtils.simpleBaseToBaseIndex(pe.getBase());
             if ( baseIndex != -1 )
                 alleleStratifiedElements[baseIndex].add(pe);

protected/java/src/org/broadinstitute/sting/utils/genotyper/AdvancedPerReadAlleleLikelihoodMap.java

@@ -55,9 +55,12 @@ public class AdvancedPerReadAlleleLikelihoodMap extends StandardPerReadAlleleLik
             alleleReadMap.put(allele, new ArrayList<GATKSAMRecord>());
 
         for ( Map.Entry<GATKSAMRecord, Map<Allele, Double>> entry : likelihoodReadMap.entrySet() ) {
-            final Allele bestAllele = getMostLikelyAllele(entry.getValue());
+            // do not remove reduced reads!
-            if ( bestAllele != Allele.NO_CALL )
+            if ( !entry.getKey().isReducedRead() ) {
-                alleleReadMap.get(bestAllele).add(entry.getKey());
+                final Allele bestAllele = getMostLikelyAllele(entry.getValue());
+                if ( bestAllele != Allele.NO_CALL )
+                    alleleReadMap.get(bestAllele).add(entry.getKey());
+            }
         }
 
         // compute the reads to remove and actually remove them

protected/java/test/org/broadinstitute/sting/gatk/walkers/bqsr/BQSRIntegrationTest.java

@@ -5,7 +5,9 @@ import org.broadinstitute.sting.utils.exceptions.UserException;
 import org.testng.annotations.DataProvider;
 import org.testng.annotations.Test;
 
+import java.util.ArrayList;
 import java.util.Arrays;
+import java.util.List;
 
 /**
  * @author ebanks
@@ -118,20 +120,26 @@ public class BQSRIntegrationTest extends WalkerTest {
 
     @DataProvider(name = "PRTest")
     public Object[][] createPRTestData() {
-        return new Object[][]{
+        List<Object[]> tests = new ArrayList<Object[]>();
-                {new PRTest("", "ab2f209ab98ad3432e208cbd524a4c4a")},
+
-                {new PRTest(" -qq -1", "5226c06237b213b9e9b25a32ed92d09a")},
+        tests.add(new Object[]{1, new PRTest(" -qq -1", "a1d87da5dcbde35170d6ba6bc3ee2812")});
-                {new PRTest(" -qq 6", "b592a5c62b952a012e18adb898ea9c33")},
+        tests.add(new Object[]{1, new PRTest(" -qq 6", "a0fecae6d0e5ab9917862fa306186d10")});
-                {new PRTest(" -DIQ", "8977bea0c57b808e65e9505eb648cdf7")}
+        tests.add(new Object[]{1, new PRTest(" -DIQ", "8977bea0c57b808e65e9505eb648cdf7")});
-        };
+
+        for ( final int nct : Arrays.asList(1, 2, 4) ) {
+            tests.add(new Object[]{nct, new PRTest("", "d1bbb4ce6aa93e866f106f8b11d888ed")});
+        }
+
+        return tests.toArray(new Object[][]{});
     }
 
     @Test(dataProvider = "PRTest")
-    public void testPR(PRTest params) {
+    public void testPR(final int nct, PRTest params) {
         WalkerTestSpec spec = new WalkerTestSpec(
                 "-T PrintReads" +
                         " -R " + hg18Reference +
                         " -I " + privateTestDir + "HiSeq.1mb.1RG.bam" +
+                        " -nct " + nct +
                         " -BQSR " + privateTestDir + "HiSeq.20mb.1RG.table" +
                         params.args +
                         " -o %s",

protected/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperGeneralPloidyIntegrationTest.java

@@ -55,36 +55,36 @@ public class UnifiedGenotyperGeneralPloidyIntegrationTest extends WalkerTest {
 
     @Test(enabled = true)
     public void testSNP_ACS_Pools() {
-        PC_LSV_Test_short(" -maxAltAlleles 1 -ploidy 6 -out_mode EMIT_ALL_CONFIDENT_SITES","LSV_SNP_ACS","SNP","ec19f0b7c7d57493cecfff988a4815c8");
+        PC_LSV_Test_short(" -maxAltAlleles 1 -ploidy 6 -out_mode EMIT_ALL_CONFIDENT_SITES","LSV_SNP_ACS","SNP","df0e67c975ef74d593f1c704daab1705");
     }
 
     @Test(enabled = true)
     public void testBOTH_GGA_Pools() {
-        PC_LSV_Test(String.format(" -maxAltAlleles 2 -ploidy 24 -gt_mode GENOTYPE_GIVEN_ALLELES -out_mode EMIT_ALL_SITES -alleles %s",LSV_ALLELES),"LSV_BOTH_GGA","BOTH","9ce24f4ff787aed9d3754519a60ef49f");
+        PC_LSV_Test(String.format(" -maxAltAlleles 2 -ploidy 24 -gt_mode GENOTYPE_GIVEN_ALLELES -out_mode EMIT_ALL_SITES -alleles %s",LSV_ALLELES),"LSV_BOTH_GGA","BOTH","7e5b28c9e21cc7e45c58c41177d8a0fc");
     }
 
     @Test(enabled = true)
     public void testINDEL_GGA_Pools() {
-        PC_LSV_Test(String.format(" -maxAltAlleles 1 -ploidy 24 -gt_mode GENOTYPE_GIVEN_ALLELES  -out_mode EMIT_ALL_SITES -alleles %s",LSV_ALLELES),"LSV_INDEL_GGA","INDEL","492c8ba9a80a902097ff15bbeb031592");
+        PC_LSV_Test(String.format(" -maxAltAlleles 1 -ploidy 24 -gt_mode GENOTYPE_GIVEN_ALLELES  -out_mode EMIT_ALL_SITES -alleles %s",LSV_ALLELES),"LSV_INDEL_GGA","INDEL","ae6c276cc46785a794acff6f7d10ecf7");
     }
 
     @Test(enabled = true)
     public void testINDEL_maxAltAlleles2_ploidy3_Pools_noRef() {
-        PC_LSV_Test_NoRef(" -maxAltAlleles 2 -ploidy 3","LSV_INDEL_DISC_NOREF_p3","INDEL","848e1092b5cd57b0da5f1187e67134e7");
+        PC_LSV_Test_NoRef(" -maxAltAlleles 2 -ploidy 3","LSV_INDEL_DISC_NOREF_p3","INDEL","481452ad7d6378cffb5cd834cc621d55");
     }
 
     @Test(enabled = true)
     public void testINDEL_maxAltAlleles2_ploidy1_Pools_noRef() {
-        PC_LSV_Test_NoRef(" -maxAltAlleles 2 -ploidy 1","LSV_INDEL_DISC_NOREF_p1","INDEL","51a7b51d82a341adec0e6510f5dfadd8");
+        PC_LSV_Test_NoRef(" -maxAltAlleles 2 -ploidy 1","LSV_INDEL_DISC_NOREF_p1","INDEL","812957e51277aca9925c1a7bb4d9a118");
     }
 
     @Test(enabled = true)
     public void testMT_SNP_DISCOVERY_sp4() {
-         PC_MT_Test(CEUTRIO_BAM, " -maxAltAlleles 1 -ploidy 8", "MT_SNP_DISCOVERY_sp4","0a8c3b06243040b743dd90d497bb3f83");
+         PC_MT_Test(CEUTRIO_BAM, " -maxAltAlleles 1 -ploidy 8", "MT_SNP_DISCOVERY_sp4","dd568dc30be90135a3a8957a45a7321c");
     }
 
     @Test(enabled = true)
     public void testMT_SNP_GGA_sp10() {
-        PC_MT_Test(CEUTRIO_BAM, String.format(" -maxAltAlleles 1 -ploidy 20 -gt_mode GENOTYPE_GIVEN_ALLELES  -out_mode EMIT_ALL_SITES -alleles %s",NA12891_CALLS), "MT_SNP_GGA_sp10", "f8ea18ec6a717a77fdf8c5f2482d8d8d");
+        PC_MT_Test(CEUTRIO_BAM, String.format(" -maxAltAlleles 1 -ploidy 20 -gt_mode GENOTYPE_GIVEN_ALLELES  -out_mode EMIT_ALL_SITES -alleles %s",NA12891_CALLS), "MT_SNP_GGA_sp10", "bf793c43b635a931207170be8035b288");
     }
 }

protected/java/test/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeCallerIntegrationTest.java

@@ -21,17 +21,17 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest {
 
     @Test
     public void testHaplotypeCallerMultiSample() {
-        HCTest(CEUTRIO_BAM, "", "1d826f852ec1457efbfa7ee828c5783a");
+        HCTest(CEUTRIO_BAM, "", "aa1df35d6e64d7ca93feb4d2dd15dd0e");
     }
 
     @Test
     public void testHaplotypeCallerSingleSample() {
-        HCTest(NA12878_BAM, "", "01367428c26d3eaf9297c58bf8677dd3");
+        HCTest(NA12878_BAM, "", "186c7f322978283c01249c6de2829215");
     }
 
     @Test
     public void testHaplotypeCallerMultiSampleGGA() {
-        HCTest(CEUTRIO_BAM, "--max_alternate_alleles 3 -gt_mode GENOTYPE_GIVEN_ALLELES -alleles " + validationDataLocation + "combined.phase1.chr20.raw.indels.sites.vcf", "53caa950535749f99d3c5b9bb61c7b60");
+        HCTest(CEUTRIO_BAM, "--max_alternate_alleles 3 -gt_mode GENOTYPE_GIVEN_ALLELES -alleles " + validationDataLocation + "combined.phase1.chr20.raw.indels.sites.vcf", "de9e78a52207fe62144dba5337965469");
     }
 
     private void HCTestComplexVariants(String bam, String args, String md5) {
@@ -42,7 +42,7 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest {
 
     @Test
     public void testHaplotypeCallerMultiSampleComplex() {
-        HCTestComplexVariants(privateTestDir + "AFR.complex.variants.bam", "", "966d338f423c86a390d685aa6336ec69");
+        HCTestComplexVariants(privateTestDir + "AFR.complex.variants.bam", "", "000dbb1b48f94d017cfec127c6cabe8f");
     }
 
     private void HCTestSymbolicVariants(String bam, String args, String md5) {
@@ -53,7 +53,7 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest {
 
     @Test
     public void testHaplotypeCallerSingleSampleSymbolic() {
-        HCTestSymbolicVariants(NA12878_CHR20_BAM, "", "b4ea70a446e4782bd3700ca14dd726ff");
+        HCTestSymbolicVariants(NA12878_CHR20_BAM, "", "16013a9203367c3d1c4ce1dcdc81ef4a");
     }
 
     private void HCTestIndelQualityScores(String bam, String args, String md5) {
@@ -64,20 +64,20 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest {
 
     @Test
     public void testHaplotypeCallerSingleSampleIndelQualityScores() {
-        HCTestIndelQualityScores(NA12878_RECALIBRATED_BAM, "", "2581e760279291a3901a506d060bfac8");
+        HCTestIndelQualityScores(NA12878_RECALIBRATED_BAM, "", "b369c2a6cb5c99a424551b33bae16f3b");
     }
 
     @Test
     public void HCTestProblematicReadsModifiedInActiveRegions() {
         final String base = String.format("-T HaplotypeCaller -R %s -I %s", REF, privateTestDir + "haplotype-problem-4.bam") + " --no_cmdline_in_header -o %s -minPruning 3";
-        final WalkerTestSpec spec = new WalkerTestSpec(base, Arrays.asList("c54c0c9411054bf629bfd98b616e53fc"));
+        final WalkerTestSpec spec = new WalkerTestSpec(base, Arrays.asList("c306140ad28515ee06c603c225217939"));
         executeTest("HCTestProblematicReadsModifiedInActiveRegions: ", spec);
     }
 
     @Test
     public void HCTestStructuralIndels() {
         final String base = String.format("-T HaplotypeCaller -R %s -I %s", REF, privateTestDir + "AFR.structural.indels.bam") + " --no_cmdline_in_header -o %s -minPruning 6 -L 20:8187565-8187800 -L 20:18670537-18670730";
-        final WalkerTestSpec spec = new WalkerTestSpec(base, Arrays.asList("c642dcd93771f6f084d55de31f180d1b"));
+        final WalkerTestSpec spec = new WalkerTestSpec(base, Arrays.asList("b6c67ee8e99cc8f53a6587bb26028047"));
         executeTest("HCTestStructuralIndels: ", spec);
     }
 
@@ -91,7 +91,7 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest {
     public void HCTestReducedBam() {
         WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
                 "-T HaplotypeCaller -R " + b37KGReference + " --no_cmdline_in_header -I " + privateTestDir + "bamExample.ReducedRead.ADAnnotation.bam -o %s -L 1:67,225,396-67,288,518", 1,
-                Arrays.asList("79af83432dc4a1768b3ebffffc4d2b8f"));
+                Arrays.asList("4beb9f87ab3f316a9384c3d0dca6ebe9"));
         executeTest("HC calling on a ReducedRead BAM", spec);
     }
 }

public/java/src/org/broadinstitute/sting/gatk/arguments/StandardCallerArgumentCollection.java

@@ -75,8 +75,9 @@ public class StandardCallerArgumentCollection {
      * Basically, it will ignore the contamination fraction of reads for each alternate allele.  So if the pileup contains N total bases, then we
      * will try to remove (N * contamination fraction) bases for each alternate allele.
      */
-    @Argument(fullName = "contamination_percentage_to_filter", shortName = "contamination", doc = "Fraction of contamination in sequencing data (for all samples) to aggressively remove", required = false)
+    @Argument(fullName = "contamination_fraction_to_filter", shortName = "contamination", doc = "Fraction of contamination in sequencing data (for all samples) to aggressively remove", required = false)
-    public double CONTAMINATION_FRACTION = 0.0;
+    public double CONTAMINATION_FRACTION = DEFAULT_CONTAMINATION_FRACTION;
+    public static final double DEFAULT_CONTAMINATION_FRACTION = 0.05;
 
     @Hidden
     @Argument(fullName = "logRemovedReadsFromContaminationFiltering", shortName="contaminationLog", required=false)

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

@@ -47,8 +47,8 @@ public class UnifiedArgumentCollection extends StandardCallerArgumentCollection
     /**
      * Note that calculating the SLOD increases the runtime by an appreciable amount.
      */
-    @Argument(fullName = "noSLOD", shortName = "nosl", doc = "If provided, we will not calculate the SLOD", required = false)
+    @Argument(fullName = "computeSLOD", shortName = "slod", doc = "If provided, we will calculate the SLOD (SB annotation)", required = false)
-    public boolean NO_SLOD = false;
+    public boolean COMPUTE_SLOD = false;
 
     /**
      * Depending on the value of the --max_alternate_alleles argument, we may genotype only a fraction of the alleles being sent on for genotyping.
@@ -204,7 +204,7 @@ public class UnifiedArgumentCollection extends StandardCallerArgumentCollection
         this.GLmodel = uac.GLmodel;
         this.AFmodel = uac.AFmodel;
         this.PCR_error = uac.PCR_error;
-        this.NO_SLOD = uac.NO_SLOD;
+        this.COMPUTE_SLOD = uac.COMPUTE_SLOD;
         this.ANNOTATE_NUMBER_OF_ALLELES_DISCOVERED = uac.ANNOTATE_NUMBER_OF_ALLELES_DISCOVERED;
         this.MIN_BASE_QUALTY_SCORE = uac.MIN_BASE_QUALTY_SCORE;
         this.MAX_DELETION_FRACTION = uac.MAX_DELETION_FRACTION;

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

@@ -28,6 +28,7 @@ package org.broadinstitute.sting.gatk.walkers.genotyper;
 import org.broadinstitute.sting.commandline.*;
 import org.broadinstitute.sting.gatk.CommandLineGATK;
 import org.broadinstitute.sting.gatk.arguments.DbsnpArgumentCollection;
+import org.broadinstitute.sting.gatk.arguments.StandardCallerArgumentCollection;
 import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.gatk.downsampling.DownsampleType;
@@ -238,7 +239,12 @@ public class UnifiedGenotyper extends LocusWalker<List<VariantCallContext>, Unif
             }
 
             if ( UAC.CONTAMINATION_FRACTION > 0.0 ) {
-                throw new UserException.NotSupportedInGATKLite("you cannot enable usage of contamination down-sampling");
+                if ( UAC.CONTAMINATION_FRACTION == StandardCallerArgumentCollection.DEFAULT_CONTAMINATION_FRACTION ) {
+                    UAC.CONTAMINATION_FRACTION = 0.0;
+                    logger.warn("setting contamination down-sampling fraction to 0.0 because it is not enabled in GATK-lite");
+                } else {
+                    throw new UserException.NotSupportedInGATKLite("you cannot enable usage of contamination down-sampling");
+                }
             }
         }
 
@@ -290,7 +296,7 @@ public class UnifiedGenotyper extends LocusWalker<List<VariantCallContext>, Unif
             headerInfo.addAll(annotationEngine.getVCFAnnotationDescriptions());
 
         // annotation (INFO) fields from UnifiedGenotyper
-        if ( !UAC.NO_SLOD )
+        if ( UAC.COMPUTE_SLOD )
             VCFStandardHeaderLines.addStandardInfoLines(headerInfo, true, VCFConstants.STRAND_BIAS_KEY);
 
         if ( UAC.ANNOTATE_NUMBER_OF_ALLELES_DISCOVERED )

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

@@ -451,7 +451,7 @@ public class UnifiedGenotyperEngine {
             attributes.put(VCFConstants.MLE_ALLELE_FREQUENCY_KEY, MLEfrequencies);
         }
 
-        if ( !UAC.NO_SLOD && !limitedContext && !bestGuessIsRef ) {
+        if ( UAC.COMPUTE_SLOD && !limitedContext && !bestGuessIsRef ) {
             //final boolean DEBUG_SLOD = false;
 
             // the overall lod

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

@@ -0,0 +1,169 @@
+package org.broadinstitute.sting.gatk.walkers.qc;
+
+import org.broadinstitute.sting.commandline.Argument;
+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.GenomeLoc;
+import org.broadinstitute.sting.utils.MathUtils;
+import org.broadinstitute.sting.utils.pileup.PileupElement;
+import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
+
+import java.io.PrintStream;
+import java.util.List;
+
+/**
+ * Emits intervals in which the differences between the original and reduced bam quals are bigger epsilon (unless the quals of
+ * the reduced bam are above sufficient threshold)
+ *
+ * <h2>Input</h2>
+ * <p>
+ * The original and reduced BAM files.
+ * </p>
+ *
+ * <h2>Output</h2>
+ * <p>
+ * A list of intervals in which the differences between the original and reduced bam quals are bigger epsilon.
+ * </p>
+ *
+ * <h2>Examples</h2>
+ * <pre>
+ * java -Xmx2g -jar GenomeAnalysisTK.jar \
+ *   -I:original original.bam \
+ *   -I:reduced reduced.bam \
+ *   -R ref.fasta \
+ *   -T AssessReducedQuals \
+ *   -o output.intervals
+ * </pre>
+ *
+ * @author ami
+ */
+
+public class AssessReducedQuals extends LocusWalker<GenomeLoc, GenomeLoc> implements TreeReducible<GenomeLoc> {
+
+    private static final String reduced = "reduced";
+    private static final String original = "original";
+    private static final int originalQualsIndex = 0;
+    private static final int reducedQualsIndex = 1;
+
+    @Argument(fullName = "sufficientQualSum", shortName = "sufficientQualSum", doc = "When a reduced bam qual sum is above this threshold, it passes even without comparing to the non-reduced bam ", required = false)
+    public int sufficientQualSum = 600;
+
+    @Argument(fullName = "qual_epsilon", shortName = "epsilon", doc = "when |Quals_reduced_bam - Quals_original_bam| > epsilon*Quals_original_bam we output this interval", required = false)
+    public int qual_epsilon = 0;
+
+    @Argument(fullName = "debugLevel", shortName = "debug", doc = "debug mode on")
+    public int debugLevel = 0;
+
+    @Output
+    protected PrintStream out;
+
+    public void initialize() {
+        if (debugLevel != 0)
+            out.println("  Debug mode" +
+                        "Debug:\tsufficientQualSum: "+sufficientQualSum+ "\n " +
+                        "Debug:\tqual_epsilon: "+qual_epsilon);
+    }
+
+    @Override
+    public boolean includeReadsWithDeletionAtLoci() { return true; }
+
+    @Override
+    public GenomeLoc map(RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) {
+        if ( tracker == null )
+            return null;
+
+        boolean reportLocus;
+        final int[] quals = getPileupQuals(context.getBasePileup());
+        if (debugLevel != 0)
+            out.println("Debug:\tLocus Quals\t"+ref.getLocus()+"\toriginal\t"+quals[originalQualsIndex]+"\treduced\t"+quals[reducedQualsIndex]);
+        final int epsilon = MathUtils.fastRound(quals[originalQualsIndex]*qual_epsilon);
+        final int calcOriginalQuals = Math.min(quals[originalQualsIndex],sufficientQualSum);
+        final int calcReducedQuals = Math.min(quals[reducedQualsIndex],sufficientQualSum);
+        final int OriginalReducedQualDiff = calcOriginalQuals - calcReducedQuals;
+        reportLocus = OriginalReducedQualDiff > epsilon || OriginalReducedQualDiff < -1*epsilon;
+        if(debugLevel != 0 && reportLocus)
+            out.println("Debug:\tEmited Locus\t"+ref.getLocus()+"\toriginal\t"+quals[originalQualsIndex]+"\treduced\t"+quals[reducedQualsIndex]+"\tepsilon\t"+epsilon+"\tdiff\t"+OriginalReducedQualDiff);
+
+        return reportLocus ? ref.getLocus() : null;
+    }
+
+    private final int[] getPileupQuals(final ReadBackedPileup readPileup) {
+
+        final int[] quals = new int[2];
+        String[] printPileup = {"Debug 2:\toriginal pileup:\t"+readPileup.getLocation()+"\nDebug 2:----------------------------------\n",
+                                "Debug 2:\t reduced pileup:\t"+readPileup.getLocation()+"\nDebug 2:----------------------------------\n"};
+
+        for( PileupElement p : readPileup ){
+            final List<String> tags = getToolkit().getReaderIDForRead(p.getRead()).getTags().getPositionalTags();
+            if ( isGoodRead(p,tags) ){
+                final int tempQual = (int)(p.getQual()) * p.getRepresentativeCount();
+                final int tagIndex = getTagIndex(tags);
+                quals[tagIndex] += tempQual;
+                if(debugLevel == 2)
+                    printPileup[tagIndex] += "\tDebug 2: ("+p+")\tMQ="+p.getMappingQual()+":QU="+p.getQual()+":RC="+p.getRepresentativeCount()+":OS="+p.getOffset()+"\n";
+            }
+        }
+        if(debugLevel == 2){
+            out.println(printPileup[originalQualsIndex]);
+            out.println(printPileup[reducedQualsIndex]);
+        }
+        return quals;
+    }
+
+    private final boolean isGoodRead(PileupElement p, List<String> tags){
+        return !p.isDeletion() && (tags.contains(reduced) || (tags.contains(original) && (int)p.getQual() >= 20 && p.getMappingQual() >= 20));
+    }
+
+    private final int getTagIndex(List<String> tags){
+        return tags.contains(reduced) ? 1 : 0;
+    }
+
+    @Override
+    public void onTraversalDone(GenomeLoc sum) {
+        if ( sum != null )
+            out.println(sum);
+    }
+
+    @Override
+    public GenomeLoc treeReduce(GenomeLoc lhs, GenomeLoc rhs) {
+        if ( lhs == null )
+            return rhs;
+
+        if ( rhs == null )
+            return lhs;
+
+        // if contiguous, just merge them
+        if ( lhs.contiguousP(rhs) )
+            return getToolkit().getGenomeLocParser().createGenomeLoc(lhs.getContig(), lhs.getStart(), rhs.getStop());
+
+        // otherwise, print the lhs and start over with the rhs
+        out.println(lhs);
+        return rhs;
+    }
+
+    @Override
+    public GenomeLoc reduceInit() {
+        return null;
+    }
+
+    @Override
+    public GenomeLoc reduce(GenomeLoc value, GenomeLoc sum) {
+        if ( value == null )
+            return sum;
+
+        if ( sum == null )
+            return value;
+
+        // if contiguous, just merge them
+        if ( sum.contiguousP(value) )
+            return getToolkit().getGenomeLocParser().createGenomeLoc(sum.getContig(), sum.getStart(), value.getStop());
+
+        // otherwise, print the sum and start over with the value
+        out.println(sum);
+        return value;
+    }
+}

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

@@ -459,7 +459,6 @@ public class SelectVariants extends RodWalker<Integer, Integer> implements TreeR
             UAC.GLmodel = GenotypeLikelihoodsCalculationModel.Model.BOTH;
             UAC.OutputMode = UnifiedGenotyperEngine.OUTPUT_MODE.EMIT_ALL_SITES;
             UAC.GenotypingMode = GenotypeLikelihoodsCalculationModel.GENOTYPING_MODE.GENOTYPE_GIVEN_ALLELES;
-            UAC.NO_SLOD = true;
             UG_engine = new UnifiedGenotyperEngine(getToolkit(), UAC, logger, null, null, samples, VariantContextUtils.DEFAULT_PLOIDY);
             headerLines.addAll(UnifiedGenotyper.getHeaderInfo(UAC, null, null));
         }

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

@@ -346,7 +346,7 @@ public abstract class ArgumentDefinitionField extends ArgumentField {
 
         @Override
         protected String getFreezeFields() {
-            return String.format("if (num_threads.isDefined) nCoresRequest = num_threads%n");
+            return String.format("if (num_threads.isDefined) nCoresRequest = num_threads%nif (num_cpu_threads_per_data_thread.isDefined) nCoresRequest = Some(nCoresRequest.getOrElse(1) * num_cpu_threads_per_data_thread.getOrElse(1))%n");
         }
     }
 

public/java/src/org/broadinstitute/sting/utils/collections/NestedIntegerArray.java

@@ -25,9 +25,11 @@
 
 package org.broadinstitute.sting.utils.collections;
 
+import org.apache.log4j.Logger;
 import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 
 import java.util.ArrayList;
+import java.util.Arrays;
 import java.util.List;
 
 /**
@@ -38,39 +40,50 @@ import java.util.List;
 
 public class NestedIntegerArray<T> {
 
+    private static Logger logger = Logger.getLogger(NestedIntegerArray.class);
+
     protected final Object[] data;
 
     protected final int numDimensions;
     protected final int[] dimensions;
 
+    // Preallocate the first two dimensions to limit contention during tree traversals in put()
+    private static final int NUM_DIMENSIONS_TO_PREALLOCATE = 2;
+
     public NestedIntegerArray(final int... dimensions) {
         numDimensions = dimensions.length;
         if ( numDimensions == 0 )
             throw new ReviewedStingException("There must be at least one dimension to an NestedIntegerArray");
         this.dimensions = dimensions.clone();
 
+        int dimensionsToPreallocate = Math.min(dimensions.length, NUM_DIMENSIONS_TO_PREALLOCATE);
+
+        logger.info(String.format("Creating NestedIntegerArray with dimensions %s", Arrays.toString(dimensions)));
+        logger.info(String.format("Pre-allocating first %d dimensions", dimensionsToPreallocate));
+
         data = new Object[dimensions[0]];
-        prepopulateArray(data, 0);
+        preallocateArray(data, 0, dimensionsToPreallocate);
+
+        logger.info(String.format("Done pre-allocating first %d dimensions", dimensionsToPreallocate));
     }
 
     /**
-     * Recursively allocate the entire tree of arrays in all its dimensions.
+     * Recursively allocate the first dimensionsToPreallocate dimensions of the tree
      *
-     * Doing this upfront uses more memory initially, but saves time over the course of the run
+     * Pre-allocating the first few dimensions helps limit contention during tree traversals in put()
-     * and (crucially) avoids having to make threads wait while traversing the tree to check
-     * whether branches exist or not.
      *
      * @param subarray current node in the tree
      * @param dimension current level in the tree
+     * @param dimensionsToPreallocate preallocate only this many dimensions (starting from the first)
      */
-    private void prepopulateArray( Object[] subarray, int dimension ) {
+    private void preallocateArray( Object[] subarray, int dimension, int dimensionsToPreallocate ) {
-        if ( dimension >= numDimensions - 1 ) {
+        if ( dimension >= dimensionsToPreallocate - 1 ) {
             return;
         }
 
         for ( int i = 0; i < subarray.length; i++ ) {
             subarray[i] = new Object[dimensions[dimension + 1]];
-            prepopulateArray((Object[])subarray[i], dimension + 1);
+            preallocateArray((Object[])subarray[i], dimension + 1, dimensionsToPreallocate);
         }
     }
 
@@ -82,8 +95,9 @@ public class NestedIntegerArray<T> {
             if ( keys[i] >= dimensions[i] )
                 return null;
 
-            myData = (Object[])myData[keys[i]];  // interior nodes in the tree will never be null, so we can safely traverse
+            myData = (Object[])myData[keys[i]];
-                                                 // down to the leaves
+            if ( myData == null )
+                return null;
         }
 
         return (T)myData[keys[numNestedDimensions]];
@@ -92,8 +106,8 @@ public class NestedIntegerArray<T> {
     /**
      * Insert a value at the position specified by the given keys.
      *
-     * This method is THREAD-SAFE despite not being synchronized, however the caller MUST
+     * This method is thread-safe, however the caller MUST check the
-     * check the return value to see if the put succeeded. This method RETURNS FALSE if
+     * return value to see if the put succeeded. This method RETURNS FALSE if
      * the value could not be inserted because there already was a value present
      * at the specified location. In this case the caller should do a get() to get
      * the already-existing value and (potentially) update it.
@@ -113,8 +127,17 @@ public class NestedIntegerArray<T> {
             if ( keys[i] >= dimensions[i] )
                 throw new ReviewedStingException("Key " + keys[i] + " is too large for dimension " + i + " (max is " + (dimensions[i]-1) + ")");
 
-            myData = (Object[])myData[keys[i]];  // interior nodes in the tree will never be null, so we can safely traverse
+            // If we're at or beyond the last dimension that was pre-allocated, we need to do a synchronized
-                                                 // down to the leaves
+            // check to see if the next branch exists, and if it doesn't, create it
+            if ( i >= NUM_DIMENSIONS_TO_PREALLOCATE - 1 ) {
+                synchronized ( myData ) {
+                    if ( myData[keys[i]] == null ) {
+                        myData[keys[i]] = new Object[dimensions[i + 1]];
+                    }
+                }
+            }
+
+            myData = (Object[])myData[keys[i]];
         }
 
         synchronized ( myData ) {   // lock the bottom row while we examine and (potentially) update it

public/java/src/org/broadinstitute/sting/utils/recalibration/BaseRecalibration.java

@@ -61,17 +61,6 @@ public class BaseRecalibration {
 //            qualityScoreByFullCovariateKey[i] = new NestedHashMap();
 //    }
 
-    /**
-     * Thread local cache to allow multi-threaded use of this class
-     */
-    private ThreadLocal<ReadCovariates> readCovariatesCache;
-    {
-        readCovariatesCache = new ThreadLocal<ReadCovariates> () {
-            @Override protected ReadCovariates initialValue() {
-                return new ReadCovariates(MAXIMUM_RECALIBRATED_READ_LENGTH, requestedCovariates.length);
-            }
-        };
-    }
 
     /**
      * Constructor using a GATK Report file
@@ -113,13 +102,7 @@ public class BaseRecalibration {
             }
         }
 
-        // Compute all covariates for the read
+        final ReadCovariates readCovariates = RecalUtils.computeCovariates(read, requestedCovariates);
-        // TODO -- the need to clear here suggests there's an error in the indexing / assumption code
-        // TODO -- for BI and DI. Perhaps due to the indel buffer size on the ends of the reads?
-        // TODO -- the output varies with -nt 1 and -nt 2 if you don't call clear here
-        // TODO -- needs to be fixed.
-        final ReadCovariates readCovariates = readCovariatesCache.get().clear();
-        RecalUtils.computeCovariates(read, requestedCovariates, readCovariates);
 
         for (final EventType errorModel : EventType.values()) { // recalibrate all three quality strings
             if (disableIndelQuals && errorModel != EventType.BASE_SUBSTITUTION) {

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

@@ -193,6 +193,8 @@ class JEXLMap implements Map<VariantContextUtils.JexlVCMatchExp, Boolean> {
                 infoMap.put("isHet", g.isHet() ? "1" : "0");
                 infoMap.put("isHomVar", g.isHomVar() ? "1" : "0");
                 infoMap.put(VCFConstants.GENOTYPE_QUALITY_KEY, g.getGQ());
+                if ( g.hasDP() )
+                    infoMap.put(VCFConstants.DEPTH_KEY, g.getDP());
                 for ( Map.Entry<String, Object> e : g.getExtendedAttributes().entrySet() ) {
                     if ( e.getValue() != null && !e.getValue().equals(VCFConstants.MISSING_VALUE_v4) )
                         infoMap.put(e.getKey(), e.getValue());

public/java/test/org/broadinstitute/sting/gatk/walkers/filters/VariantFiltrationIntegrationTest.java

@@ -108,4 +108,22 @@ public class VariantFiltrationIntegrationTest extends WalkerTest {
                 Arrays.asList("8ed32a2272bab8043a255362335395ef"));
         executeTest("testUnfilteredBecomesFilteredAndPass", spec);
     }
+
+    @Test
+    public void testFilteringDPfromINFO() {
+        WalkerTestSpec spec = new WalkerTestSpec(
+                "-T VariantFiltration -o %s --no_cmdline_in_header -R " + b37KGReference
+                        + " --filterExpression 'DP < 8' --filterName lowDP -V " + privateTestDir + "filteringDepthInFormat.vcf", 1,
+                Arrays.asList("a01f7cce53ea556c9741aa60b6124c41"));
+        executeTest("testFilteringDPfromINFO", spec);
+    }
+
+    @Test
+    public void testFilteringDPfromFORMAT() {
+        WalkerTestSpec spec = new WalkerTestSpec(
+                "-T VariantFiltration -o %s --no_cmdline_in_header -R " + b37KGReference
+                        + " --genotypeFilterExpression 'DP < 8' --genotypeFilterName lowDP -V " + privateTestDir + "filteringDepthInFormat.vcf", 1,
+                Arrays.asList("e10485c7c33d9211d0c1294fd7858476"));
+        executeTest("testFilteringDPfromFORMAT", spec);
+    }
 }

public/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperIntegrationTest.java

@@ -16,9 +16,9 @@ import java.util.List;
 
 public class UnifiedGenotyperIntegrationTest extends WalkerTest {
 
-    private final static String baseCommand = "-T UnifiedGenotyper -R " + b36KGReference + " -nosl --no_cmdline_in_header -glm BOTH -minIndelFrac 0.0 --dbsnp " + b36dbSNP129;
+    private final static String baseCommand = "-T UnifiedGenotyper -R " + b36KGReference + " --no_cmdline_in_header -glm BOTH -minIndelFrac 0.0 --dbsnp " + b36dbSNP129;
-    private final static String baseCommandIndels = "-T UnifiedGenotyper -R " + b36KGReference + " -nosl --no_cmdline_in_header -glm INDEL -mbq 20 -minIndelFrac 0.0 --dbsnp " + b36dbSNP129;
+    private final static String baseCommandIndels = "-T UnifiedGenotyper -R " + b36KGReference + " --no_cmdline_in_header -glm INDEL -mbq 20 -minIndelFrac 0.0 --dbsnp " + b36dbSNP129;
-    private final static String baseCommandIndelsb37 = "-T UnifiedGenotyper -R " + b37KGReference + " -nosl --no_cmdline_in_header -glm INDEL -mbq 20 --dbsnp " + b37dbSNP132;
+    private final static String baseCommandIndelsb37 = "-T UnifiedGenotyper -R " + b37KGReference + " --no_cmdline_in_header -glm INDEL -mbq 20 --dbsnp " + b37dbSNP132;
     private final static String baseCommandNoCmdLineHeaderStdout = "-T UnifiedGenotyper -R " + b37KGReference + " --no_cmdline_in_header -I " + privateTestDir + "bamExample.ReducedRead.ADAnnotation.bam";
 
     // --------------------------------------------------------------------------------------------------------------
@@ -30,7 +30,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
     public void testMultiSamplePilot1() {
         WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
                 baseCommand + " -I " + validationDataLocation + "low_coverage_CEU.chr1.10k-11k.bam -o %s -L 1:10,022,000-10,025,000", 1,
-                Arrays.asList("847605f4efafef89529fe0e496315edd"));
+                Arrays.asList("cdec335abc9ad8e59335e39a73e0e95a"));
         executeTest("test MultiSample Pilot1", spec);
     }
 
@@ -38,7 +38,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
     public void testWithAllelesPassedIn1() {
         WalkerTest.WalkerTestSpec spec1 = new WalkerTest.WalkerTestSpec(
                 baseCommand + " --genotyping_mode GENOTYPE_GIVEN_ALLELES -alleles " + privateTestDir + "allelesForUG.vcf -I " + validationDataLocation + "pilot2_daughters.chr20.10k-11k.bam -o %s -L 20:10,000,000-10,025,000", 1,
-                Arrays.asList("bc15123620e1134f799005d71d1180fe"));
+                Arrays.asList("efddb5e258f97fd4f6661cff9eaa57de"));
         executeTest("test MultiSample Pilot2 with alleles passed in", spec1);
     }
 
@@ -46,7 +46,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
     public void testWithAllelesPassedIn2() {
         WalkerTest.WalkerTestSpec spec2 = new WalkerTest.WalkerTestSpec(
                 baseCommand + " --output_mode EMIT_ALL_SITES --genotyping_mode GENOTYPE_GIVEN_ALLELES -alleles " + privateTestDir + "allelesForUG.vcf -I " + validationDataLocation + "pilot2_daughters.chr20.10k-11k.bam -o %s -L 20:10,000,000-10,025,000", 1,
-                Arrays.asList("1ba7afccc8552f20d72d0b62237558e3"));
+                Arrays.asList("24532eb381724cd74e99370da28d49ed"));
         executeTest("test MultiSample Pilot2 with alleles passed in and emitting all sites", spec2);
     }
 
@@ -54,22 +54,22 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
     public void testSingleSamplePilot2() {
         WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
                 baseCommand + " -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -o %s -L 1:10,000,000-10,100,000", 1,
-                Arrays.asList("afb8768f31ab57eb43f75c1115eadc99"));
+                Arrays.asList("062a946160eec1d0fc135d58ca654ff4"));
         executeTest("test SingleSample Pilot2", spec);
     }
 
     @Test
     public void testMultipleSNPAlleles() {
         WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
-                "-T UnifiedGenotyper -R " + b37KGReference + " -nosl --no_cmdline_in_header -glm BOTH --dbsnp " + b37dbSNP129 + " -I " + privateTestDir + "multiallelic.snps.bam -o %s -L " + privateTestDir + "multiallelic.snps.intervals", 1,
+                "-T UnifiedGenotyper -R " + b37KGReference + " --no_cmdline_in_header -glm BOTH --dbsnp " + b37dbSNP129 + " -I " + privateTestDir + "multiallelic.snps.bam -o %s -L " + privateTestDir + "multiallelic.snps.intervals", 1,
-                Arrays.asList("543f68e42034bf44cfb24da8c9204320"));
+                Arrays.asList("94dc17d76d841f1d3a36160767ffa034"));
         executeTest("test Multiple SNP alleles", spec);
     }
 
     @Test
     public void testBadRead() {
         WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
-                "-T UnifiedGenotyper -R " + b37KGReference + " -nosl --no_cmdline_in_header -glm BOTH -I " + privateTestDir + "badRead.test.bam -o %s -L 1:22753424-22753464", 1,
+                "-T UnifiedGenotyper -R " + b37KGReference + " --no_cmdline_in_header -glm BOTH -I " + privateTestDir + "badRead.test.bam -o %s -L 1:22753424-22753464", 1,
                 Arrays.asList("d915535c1458733f09f82670092fcab6"));
         executeTest("test bad read", spec);
     }
@@ -77,16 +77,16 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
     @Test
     public void testReverseTrim() {
         WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
-                "-T UnifiedGenotyper -R " + b37KGReference + " -nosl --no_cmdline_in_header -glm INDEL -I " + validationDataLocation + "CEUTrio.HiSeq.b37.chr20.10_11mb.bam -o %s -L 20:10289124 -L 20:10090289", 1,
+                "-T UnifiedGenotyper -R " + b37KGReference + " --no_cmdline_in_header -glm INDEL -I " + validationDataLocation + "CEUTrio.HiSeq.b37.chr20.10_11mb.bam -o %s -L 20:10289124 -L 20:10090289", 1,
-                Arrays.asList("5ce03dd9ca2d9324c1d4a9d64389beb5"));
+                Arrays.asList("9106d01ca0d0a8fedd068e72d509f380"));
         executeTest("test reverse trim", spec);
     }
 
     @Test
     public void testMismatchedPLs() {
         WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
-                "-T UnifiedGenotyper -R " + b37KGReference + " -nosl --no_cmdline_in_header -glm INDEL -I " + privateTestDir + "mismatchedPLs.bam -o %s -L 1:24020341", 1,
+                "-T UnifiedGenotyper -R " + b37KGReference + " --no_cmdline_in_header -glm INDEL -I " + privateTestDir + "mismatchedPLs.bam -o %s -L 1:24020341", 1,
-                Arrays.asList("3c006b06b17bbe8e787d64eff6a63a19"));
+                Arrays.asList("d847acf841ba8ba653f996ce4869f439"));
         executeTest("test mismatched PLs", spec);
     }
 
@@ -96,7 +96,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
     //
     // --------------------------------------------------------------------------------------------------------------
 
-    private final static String COMPRESSED_OUTPUT_MD5 = "fd236bd635d514e4214d364f45ec4d10";
+    private final static String COMPRESSED_OUTPUT_MD5 = "6792419c482e767a3deb28913ed2b1ad";
 
     @Test
     public void testCompressedOutput() {
@@ -117,7 +117,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
 
         // Note that we need to turn off any randomization for this to work, so no downsampling and no annotations
 
-        String md5 = "d408b4661b820ed86272415b8ea08780";
+        String md5 = "3d25ea660275a455ca443a786bff3d32";
 
         WalkerTest.WalkerTestSpec spec1 = new WalkerTest.WalkerTestSpec(
                 baseCommand + " -dt NONE -G none -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -o %s -L 1:10,000,000-10,075,000", 1,
@@ -149,15 +149,15 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
     public void testMinBaseQualityScore() {
         WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
                 baseCommand + " -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -o %s -L 1:10,000,000-10,010,000 --min_base_quality_score 26", 1,
-                Arrays.asList("839ecd30d354a36b5dfa2b5e99859765"));
+                Arrays.asList("56157d930da6ccd224bce1ca93f11e41"));
         executeTest("test min_base_quality_score 26", spec);
     }
 
     @Test
     public void testSLOD() {
         WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
-                "-T UnifiedGenotyper -R " + b36KGReference + " --no_cmdline_in_header -glm BOTH --dbsnp " + b36dbSNP129 + " -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -o %s -L 1:10,000,000-10,010,000", 1,
+                "-T UnifiedGenotyper -R " + b36KGReference + " --computeSLOD --no_cmdline_in_header -glm BOTH --dbsnp " + b36dbSNP129 + " -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -o %s -L 1:10,000,000-10,010,000", 1,
-                Arrays.asList("c7429e670ba477bf9a6bbee2fb41c5a9"));
+                Arrays.asList("9f95cfe14d53a697c58247833bfd72a6"));
         executeTest("test SLOD", spec);
     }
 
@@ -165,7 +165,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
     public void testNDA() {
         WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
                 baseCommand + " --annotateNDA -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -o %s -L 1:10,000,000-10,010,000", 1,
-                Arrays.asList("abd8e33e649cc11b55e200d3940cc7e2"));
+                Arrays.asList("480437dd6e2760f4ab3194431519f331"));
         executeTest("test NDA", spec);
     }
 
@@ -173,7 +173,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
     public void testCompTrack() {
         WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
                 "-T UnifiedGenotyper -R " + b36KGReference + " --no_cmdline_in_header -glm BOTH -comp:FOO " + b36dbSNP129 + " -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -o %s -L 1:10,000,000-10,010,000", 1,
-                Arrays.asList("8a9b424e00cdbe6b5e73d517335b2186"));
+                Arrays.asList("22c039412fd387dde6125b07c9a74a25"));
         executeTest("test using comp track", spec);
     }
 
@@ -187,17 +187,17 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
 
     @Test
     public void testOutputParameterSitesOnly() {
-        testOutputParameters("-sites_only", "97ba874eafc9884a4de027a84c036311");
+        testOutputParameters("-sites_only", "40aeb4c9e31fe7046b72afc58e7599cb");
     }
 
     @Test
     public void testOutputParameterAllConfident() {
-        testOutputParameters("--output_mode EMIT_ALL_CONFIDENT_SITES", "f9ea04d96eeef29e71d37e60518c2579");
+        testOutputParameters("--output_mode EMIT_ALL_CONFIDENT_SITES", "c706ca93b25ff83613cb4e95dcac567c");
     }
 
     @Test
     public void testOutputParameterAllSites() {
-        testOutputParameters("--output_mode EMIT_ALL_SITES", "41c046d38ea328421df924e37e017645");
+        testOutputParameters("--output_mode EMIT_ALL_SITES", "8a263fd0a94463ce1de9990f2b8ec841");
     }
 
     private void testOutputParameters(final String args, final String md5) {
@@ -211,18 +211,10 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
     public void testConfidence() {
         WalkerTest.WalkerTestSpec spec1 = new WalkerTest.WalkerTestSpec(
                 baseCommand + " -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -o %s -L 1:10,000,000-10,010,000 -stand_call_conf 10 ", 1,
-                Arrays.asList("9addd225a985178339a0c49dc5fdc220"));
+                Arrays.asList("df524e98903d96ab9353bee7c16a69de"));
         executeTest("test confidence 1", spec1);
     }
 
-    @Test
-    public void testConfidence2() {
-        WalkerTest.WalkerTestSpec spec2 = new WalkerTest.WalkerTestSpec(
-                baseCommand + " -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -o %s -L 1:10,000,000-10,010,000 -stand_emit_conf 10 ", 1,
-                Arrays.asList("9addd225a985178339a0c49dc5fdc220"));
-        executeTest("test confidence 2", spec2);
-    }
-
     // --------------------------------------------------------------------------------------------------------------
     //
     // testing heterozygosity
@@ -230,12 +222,12 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
     // --------------------------------------------------------------------------------------------------------------
     @Test
     public void testHeterozyosity1() {
-        testHeterozosity( 0.01, "986923de51c71635d47e3d06fe3794a1" );
+        testHeterozosity( 0.01, "8e61498ca03a8d805372a64c466b3b42" );
     }
 
     @Test
     public void testHeterozyosity2() {
-        testHeterozosity( 1.0 / 1850, "fb12b1553f813004a394a391a8540873" );
+        testHeterozosity( 1.0 / 1850, "668d06b5173cf3b97d052726988e1d7b" );
     }
 
     private void testHeterozosity(final double arg, final String md5) {
@@ -259,7 +251,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
                         " -o %s" +
                         " -L 1:10,000,000-10,100,000",
                 1,
-                Arrays.asList("04a87b87ee4323eba853c78f25551d1a"));
+                Arrays.asList("908eb5e21fa39e7fb377cf4a9c4c7835"));
 
         executeTest(String.format("test multiple technologies"), spec);
     }
@@ -278,7 +270,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
                         " -L 1:10,000,000-10,100,000" +
                         " -baq CALCULATE_AS_NECESSARY",
                 1,
-                Arrays.asList("98058fc913b61c22d44875da1f5ea89c"));
+                Arrays.asList("c814558bb0ed2e19b12e1a2bf4465d52"));
 
         executeTest(String.format("test calling with BAQ"), spec);
     }
@@ -297,7 +289,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
                         " -o %s" +
                         " -L 1:10,000,000-10,500,000",
                 1,
-                Arrays.asList("650c53774afacfc07a595675e8cdde17"));
+                Arrays.asList("3593495aab5f6204c65de0b073a6ff65"));
 
         executeTest(String.format("test indel caller in SLX"), spec);
     }
@@ -312,7 +304,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
                         " -minIndelCnt 1" +
                         " -L 1:10,000,000-10,100,000",
                 1,
-                Arrays.asList("6a0c2a3a7bcc56ad01428c71408055aa"));
+                Arrays.asList("8b486a098029d5a106b0a37eff541c15"));
 
         executeTest(String.format("test indel caller in SLX with low min allele count"), spec);
     }
@@ -325,7 +317,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
                          " -o %s" +
                          " -L 1:10,000,000-10,500,000",
                  1,
-                 Arrays.asList("5f2721c3323de5390d2d47446139f32b"));
+                 Arrays.asList("18efedc50cae2aacaba372265e38310b"));
 
          executeTest(String.format("test indel calling, multiple technologies"), spec);
      }
@@ -335,7 +327,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
         WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
                 baseCommandIndels + " --genotyping_mode GENOTYPE_GIVEN_ALLELES -alleles " + privateTestDir + "indelAllelesForUG.vcf -I " + validationDataLocation +
                         "pilot2_daughters.chr20.10k-11k.bam -o %s -L 20:10,000,000-10,100,000", 1,
-                Arrays.asList("7e3f67bf371112be5dbadb4fe6faa52a"));
+                Arrays.asList("3ff8c7c80a518aa3eb8671a21479de5f"));
         executeTest("test MultiSample Pilot2 indels with alleles passed in", spec);
     }
 
@@ -345,7 +337,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
                 baseCommandIndels + " --output_mode EMIT_ALL_SITES --genotyping_mode GENOTYPE_GIVEN_ALLELES -alleles "
                         + privateTestDir + "indelAllelesForUG.vcf -I " + validationDataLocation +
                         "pilot2_daughters.chr20.10k-11k.bam -o %s -L 20:10,000,000-10,100,000", 1,
-                Arrays.asList("bc31c4977cb7e563ddf9c8dea27f3f4f"));
+                Arrays.asList("578c0540f4f2052a634a829bcb9cc27d"));
         executeTest("test MultiSample Pilot2 indels with alleles passed in and emitting all sites", spec);
     }
 
@@ -353,13 +345,13 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
     public void testMultiSampleIndels1() {
         WalkerTest.WalkerTestSpec spec1 = new WalkerTest.WalkerTestSpec(
                 baseCommandIndels + " -I " + validationDataLocation + "low_coverage_CEU.chr1.10k-11k.bam -o %s -L 1:10450700-10551000", 1,
-                Arrays.asList("a4761d7f25e7a62f34494801c98a0da7"));
+                Arrays.asList("f7d0d0aee603df25c1f0525bb8df189e"));
         List<File> result = executeTest("test MultiSample Pilot1 CEU indels", spec1).getFirst();
 
         WalkerTest.WalkerTestSpec spec2 = new WalkerTest.WalkerTestSpec(
                 baseCommandIndels + " --genotyping_mode GENOTYPE_GIVEN_ALLELES -alleles " + result.get(0).getAbsolutePath() + " -I " + validationDataLocation +
                         "low_coverage_CEU.chr1.10k-11k.bam -o %s -L 1:10450700-10551000", 1,
-                Arrays.asList("c526c234947482d1cd2ffc5102083a08"));
+                Arrays.asList("fc91d457a16b4ca994959c2b5f3f0352"));
         executeTest("test MultiSample Pilot1 CEU indels using GENOTYPE_GIVEN_ALLELES", spec2);
     }
 
@@ -415,7 +407,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
     public void testMinIndelFraction0() {
         WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
                 assessMinIndelFraction + " -minIndelFrac 0.0", 1,
-                Arrays.asList("ba4fafec383fb988f20c8cf53dd3e9a0"));
+                Arrays.asList("857b8e5df444463ac27f665c4f67fbe2"));
         executeTest("test minIndelFraction 0.0", spec);
     }
 
@@ -423,7 +415,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
     public void testMinIndelFraction25() {
         WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
                 assessMinIndelFraction + " -minIndelFrac 0.25", 1,
-                Arrays.asList("4c57a88de275105156aaafc6f9041365"));
+                Arrays.asList("81d4c7d9010fd6733b2997bc378e7471"));
         executeTest("test minIndelFraction 0.25", spec);
     }
 
@@ -444,8 +436,8 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
     @Test
     public void testNsInCigar() {
         WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
-                "-T UnifiedGenotyper -R " + b37KGReference + " -nosl --no_cmdline_in_header -I " + validationDataLocation + "testWithNs.bam -o %s -L 8:141799600-141814700", 1,
+                "-T UnifiedGenotyper -R " + b37KGReference + " --no_cmdline_in_header -I " + validationDataLocation + "testWithNs.bam -o %s -L 8:141799600-141814700", 1,
-                Arrays.asList("e8ebfaac0804b782f22ab8ea35152735"));
+                Arrays.asList("bd7984a374f0ae5d277bd5fc5065f64f"));
         executeTest("test calling on reads with Ns in CIGAR", spec);
     }
 
@@ -458,25 +450,25 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
     @Test
     public void testReducedBam() {
         WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
-                "-T UnifiedGenotyper -R " + b37KGReference + " -nosl --no_cmdline_in_header -I " + privateTestDir + "bamExample.ReducedRead.ADAnnotation.bam -o %s -L 1:67,225,396-67,288,518", 1,
+                "-T UnifiedGenotyper -R " + b37KGReference + " --no_cmdline_in_header -I " + privateTestDir + "bamExample.ReducedRead.ADAnnotation.bam -o %s -L 1:67,225,396-67,288,518", 1,
-                Arrays.asList("da9c05f87bd6415e97f90c49cf68ed19"));
+                Arrays.asList("1b711c0966a2f76eb21801e73b76b758"));
         executeTest("test calling on a ReducedRead BAM", spec);
     }
 
     @Test
     public void testReducedBamSNPs() {
-        testReducedCalling("SNP", "1d4a826b144723ff0766c36aa0239287");
+        testReducedCalling("SNP", "9ba4867cadb366746ee63e7a4afdb95e");
     }
 
     @Test
     public void testReducedBamINDELs() {
-        testReducedCalling("INDEL", "68ef51d5c98480e0c0192e0eecb95bca");
+        testReducedCalling("INDEL", "132a4e0ccf9230b5bb4b56c649e2bdd5");
     }
 
 
     private void testReducedCalling(final String model, final String md5) {
         WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
-                "-T UnifiedGenotyper -R " + b37KGReference + " -nosl --no_cmdline_in_header -I " + privateTestDir + "NA12878.HiSeq.b37.chr20.10_11mb.reduced.bam -o %s -L 20:10,000,000-11,000,000 -glm " + model, 1,
+                "-T UnifiedGenotyper -R " + b37KGReference + " --no_cmdline_in_header -I " + privateTestDir + "NA12878.HiSeq.b37.chr20.10_11mb.reduced.bam -o %s -L 20:10,000,000-11,000,000 -glm " + model, 1,
                 Arrays.asList(md5));
         executeTest("test calling on a ReducedRead BAM with " + model, spec);
     }
@@ -490,7 +482,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
     @Test
     public void testContaminationDownsampling() {
         WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
-                baseCommand + " -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -o %s -L 1:10,000,000-10,010,000 --contamination_percentage_to_filter 0.20", 1,
+                baseCommand + " -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -o %s -L 1:10,000,000-10,010,000 --contamination_fraction_to_filter 0.20", 1,
                 Arrays.asList("27dd04159e06d9524fb8a4eef41f96ae"));
         executeTest("test contamination_percentage_to_filter 0.20", spec);
     }

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

@@ -137,6 +137,13 @@ class GATKResourcesBundle extends QScript {
     addResource(new Resource("/humgen/gsa-hpprojects/GATK/data/Comparisons/Unvalidated/GoldStandardIndel/gold.standard.indel.MillsAnd1000G.b37.vcf",
       "Mills_and_1000G_gold_standard.indels", b37, true, false))
 
+    //
+    // CEU trio (NA12878,NA12891,NA12892) best practices results (including PBT)
+    //
+
+    addResource(new Resource("/humgen/gsa-hpprojects/NA12878Collection/callsets/CEUtrio_BestPractices/current/CEUTrio.HiSeq.WGS.b37.UG.snps_and_indels.recalibrated.filtered.phaseByTransmission.vcf",
+      "CEUTrio.HiSeq.WGS.b37.UG.bestPractices.phaseByTransmission",b37,true,false))
+
     //
     // example call set for wiki tutorial
     //