Merge remote-tracking branch 'unstable/master'

protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/variantrecalibration/VariantDataManager.java

@@ -110,7 +110,15 @@ public class VariantDataManager {
         return data;
     }
 
-    public void normalizeData(final boolean calculateMeans) {
+    /**
+     * Normalize annotations to mean 0 and standard deviation 1.
+     * Order the variant annotations by the provided list {@code theOrder} or standard deviation.
+     *
+     * @param calculateMeans Boolean indicating whether or not to calculate the means
+     * @param theOrder a list of integers specifying the desired annotation order. If this is null
+     *                 annotations will get sorted in decreasing size of their standard deviations.
+     */
+    public void normalizeData(final boolean calculateMeans, List<Integer> theOrder) {
         boolean foundZeroVarianceAnnotation = false;
         for( int iii = 0; iii < meanVector.length; iii++ ) {
             final double theMean, theSTD;
@@ -150,7 +158,10 @@ public class VariantDataManager {
 
         // re-order the data by increasing standard deviation so that the results don't depend on the order things were specified on the command line
         // standard deviation over the training points is used as a simple proxy for information content, perhaps there is a better thing to use here
-        final List<Integer> theOrder = calculateSortOrder(meanVector);
+        // or use the serialized report's annotation order via the argument theOrder
+        if (theOrder == null){
+            theOrder = calculateSortOrder(meanVector);
+        }
         annotationKeys = reorderList(annotationKeys, theOrder);
         varianceVector = ArrayUtils.toPrimitive(reorderArray(ArrayUtils.toObject(varianceVector), theOrder));
         meanVector = ArrayUtils.toPrimitive(reorderArray(ArrayUtils.toObject(meanVector), theOrder));
@@ -158,7 +169,8 @@ public class VariantDataManager {
             datum.annotations = ArrayUtils.toPrimitive(reorderArray(ArrayUtils.toObject(datum.annotations), theOrder));
             datum.isNull = ArrayUtils.toPrimitive(reorderArray(ArrayUtils.toObject(datum.isNull), theOrder));
         }
-        logger.info("Annotations are now ordered by their information content: " + annotationKeys.toString());
+        logger.info("Annotation order is: " + annotationKeys.toString());
+
     }
 
     public double[] getMeanVector() {

protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/variantrecalibration/VariantRecalibrator.java

@@ -51,6 +51,7 @@
 
 package org.broadinstitute.gatk.tools.walkers.variantrecalibration;
 
+import com.google.common.annotations.VisibleForTesting;
 import htsjdk.variant.variantcontext.Allele;
 import org.broadinstitute.gatk.utils.commandline.*;
 import org.broadinstitute.gatk.engine.CommandLineGATK;
@@ -312,6 +313,9 @@ public class VariantRecalibrator extends RodWalker<ExpandingArrayList<VariantDat
     @Argument(fullName = "trustAllPolymorphic", shortName = "allPoly", doc = "Trust that all the input training sets' unfiltered records contain only polymorphic sites to drastically speed up the computation.", required = false)
     protected Boolean TRUST_ALL_POLYMORPHIC = false;
 
+    @VisibleForTesting
+    protected List<Integer> annotationOrder = null;
+
     /////////////////////////////
     // Private Member Variables
     /////////////////////////////
@@ -372,18 +376,15 @@ public class VariantRecalibrator extends RodWalker<ExpandingArrayList<VariantDat
             final GATKReportTable pPMixTable = reportIn.getTable("GoodGaussianPMix");
             final GATKReportTable anMeansTable = reportIn.getTable("AnnotationMeans");
             final GATKReportTable anStDevsTable = reportIn.getTable("AnnotationStdevs");
-            final int numAnnotations = dataManager.annotationKeys.size();
 
-            if( numAnnotations != pmmTable.getNumColumns()-1 || numAnnotations != nmmTable.getNumColumns()-1 ) { // -1 because the first column is the gaussian number.
+            orderAndValidateAnnotations(anMeansTable, dataManager.annotationKeys);
-                throw new UserException.CommandLineException( "Annotations specified on the command line do not match annotations in the model report." );
-            }
 
             final Map<String, Double> anMeans = getMapFromVectorTable(anMeansTable);
             final Map<String, Double> anStdDevs = getMapFromVectorTable(anStDevsTable);
             dataManager.setNormalization(anMeans, anStdDevs);
 
-            goodModel = GMMFromTables(pmmTable, pmcTable, pPMixTable, numAnnotations);
+            goodModel = GMMFromTables(pmmTable, pmcTable, pPMixTable, annotationOrder.size());
-            badModel = GMMFromTables(nmmTable, nmcTable, nPMixTable, numAnnotations);
+            badModel = GMMFromTables(nmmTable, nmcTable, nPMixTable, annotationOrder.size());
         }
 
         final Set<VCFHeaderLine> hInfo = new HashSet<>();
@@ -401,6 +402,32 @@ public class VariantRecalibrator extends RodWalker<ExpandingArrayList<VariantDat
 
     }
 
+    /**
+     * Order and validate annotations according to the annotations in the serialized model
+     * Annotations on the command line must be the same as those in the model report or this will throw an exception.
+     * Sets the {@code annotationOrder} list to map from command line order to the model report's order.
+     * n^2 because we typically use 7 or less annotations.
+     * @param annotationTable GATKReportTable of annotations read from the serialized model file
+     */
+    protected void orderAndValidateAnnotations(final GATKReportTable annotationTable, final List<String> annotationKeys){
+        annotationOrder = new ArrayList<Integer>(annotationKeys.size());
+
+        for (int i = 0; i < annotationTable.getNumRows(); i++){
+            String serialAnno = (String)annotationTable.get(i, "Annotation");
+            for (int j = 0; j < annotationKeys.size(); j++) {
+                if (serialAnno.equals( annotationKeys.get(j) )){
+                    annotationOrder.add(j);
+                }
+            }
+        }
+
+        if(annotationOrder.size() != annotationTable.getNumRows() || annotationOrder.size() != annotationKeys.size()) {
+            final String errorMsg = "Annotations specified on the command line:"+annotationKeys.toString() +" do not match annotations in the model report:"+inputModel;
+            throw new UserException.CommandLineException(errorMsg);
+        }
+
+    }
+
 
     //---------------------------------------------------------------------------------------------------------------
     //
@@ -518,7 +545,7 @@ public class VariantRecalibrator extends RodWalker<ExpandingArrayList<VariantDat
         for (int i = 1; i <= max_attempts; i++) {
             try {
                 dataManager.setData(reduceSum);
-                dataManager.normalizeData(inputModel.isEmpty()); // Each data point is now (x - mean) / standard deviation
+                dataManager.normalizeData(inputModel.isEmpty(), annotationOrder); // Each data point is now (x - mean) / standard deviation
 
                 final List<VariantDatum> positiveTrainingData = dataManager.getTrainingData();
                 final List<VariantDatum> negativeTrainingData;

protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/bqsr/BQSRIntegrationTest.java

@@ -198,13 +198,13 @@ public class BQSRIntegrationTest extends WalkerTest {
     public Object[][] createPRTestData() {
         List<Object[]> tests = new ArrayList<Object[]>();
 
-        tests.add(new Object[]{1, new PRTest(" -qq -1", "8a38828e3b14ce067614d4248e3ea95a")});
+        tests.add(new Object[]{1, new PRTest(" -qq -1", "e9969c6d7fd35d96b82c691b4ced5443")});
-        tests.add(new Object[]{1, new PRTest(" -qq 6", "e4f23250b2c87f0d68d042cc3d2ec1d3")});
+        tests.add(new Object[]{1, new PRTest(" -qq 6", "b4b271acac003b8504b530c5526d43ad")});
-        tests.add(new Object[]{1, new PRTest(" -DIQ", "2dfa45f004d3a371fd290ed67fbdf573")});
+        tests.add(new Object[]{1, new PRTest(" -DIQ", "ec795d16746c3bdf5e54c57337e6eed6")});
-        tests.add(new Object[]{1, new PRTest(" --useOriginalQualities -SQQ 10 -SQQ 20 -SQQ 30", "4882354d9e603f9bbe7c9591bba0a573")});
+        tests.add(new Object[]{1, new PRTest(" --useOriginalQualities -SQQ 10 -SQQ 20 -SQQ 30", "d50df5a7bcc8f195479f64285c124d18")});
-        tests.add(new Object[]{1, new PRTest(" --useOriginalQualities -SQQ 10 -SQQ 20 -SQQ 30 -RDQ", "6ffdfc4593e83f7c234b6249412433af")});
+        tests.add(new Object[]{1, new PRTest(" --useOriginalQualities -SQQ 10 -SQQ 20 -SQQ 30 -RDQ", "58b9df85e49eb3ee228f0d581c168791")});
         for ( final int nct : Arrays.asList(1, 2, 4) ) {
-            tests.add(new Object[]{nct, new PRTest("", "6451093cadfc14d7359617b2a7ea6db8")});
+            tests.add(new Object[]{nct, new PRTest("", "f4704ba2894ec0aec8a55ce6b361f768")});
         }
 
         return tests.toArray(new Object[][]{});

protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/cancer/m2/MuTect2IntegrationTest.java

@@ -138,7 +138,7 @@ public class MuTect2IntegrationTest extends WalkerTest {
     public void testTruePositivesDream3TrackedDropped() {
         M2TestWithDroppedReads(DREAM3_TUMOR_BAM, DREAM3_NORMAL_BAM, "21:10935369", "",
                 "48a446d47bb10434cb7f0ee726d15721",
-                "6ecaeb74893249dfa5723b2266c957e2");
+                "265a72d3f79bb0fe054a847ab0c01c67");
     }
 
     /**

protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeCallerIntegrationTest.java

@@ -133,7 +133,7 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest {
 
     @Test
     public void testHaplotypeBAMOutFlags() throws IOException {
-        final String md5BAMOut = "69aae17f8cd384666ec7c3c1f3d3eb57";
+        final String md5BAMOut = "0934466fa2b8648af9e6267286a57151";
         HCTestWithBAMOut(NA12878_BAM, " -L 20:10000000-10100000 ", "df622103b0a6917f2299b1acfd0ed0ac", md5BAMOut);
         validateForwardedProgramRecords(new ArrayList<>(Arrays.asList(new File(NA12878_BAM))), md5BAMOut);
     }
@@ -330,7 +330,7 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest {
     @Test
     public void testLeftAlignmentBamOutBugFix() throws IOException {
         final String outputVCF = createTempFile("temp", ".vcf").getAbsolutePath();
-        final String md5BAMOut = "27e729df3b166c81792a62a5b57ef7b3";
+        final String md5BAMOut = "60db3996cd37a863d8b93218fcbf1c8b";
         final String base = String.format("-T HaplotypeCaller -R %s -I %s", REF, LEFT_ALIGNMENT_BAMOUT_TEST_INPUT)
                 + " --no_cmdline_in_header -bamout %s -o " + outputVCF  + " -L 1:11740000-11740700 --allowNonUniqueKmersInRef";
         final WalkerTestSpec spec = new WalkerTestSpec(base, 1, Arrays.asList(md5BAMOut));
@@ -541,7 +541,7 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest {
     public void testHaplotypeCallerReadPosRankSum() throws IOException {
         final File testBAM = new File(privateTestDir + "testReadPos.snippet.bam");
         final String md5Variants = "e664b7a9da71cf81e14648ac7e698eea";
-        final String md5BAMOut = "3ef35732e49980093ad445e3ac5731fa";
+        final String md5BAMOut = "74f2cab2d2d0d999b54456b73e597d6c";
         final String base = String.format("-T HaplotypeCaller -R %s -I %s -L 1:3753063 -ip 100 ", REF, testBAM) +
                 " --no_cmdline_in_header -o %s -bamout %s";
         final WalkerTestSpec spec = new WalkerTestSpec(base, Arrays.asList(md5Variants, md5BAMOut));

protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/rnaseq/SplitNCigarReadsIntegrationTest.java

@@ -87,7 +87,7 @@ public class SplitNCigarReadsIntegrationTest extends WalkerTest {
     public void testSplitsWithOverhangs() {
         WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
                 "-T SplitNCigarReads -R " + b37KGReference + " -I " + privateTestDir + "NA12878.RNAseq.bam -o %s --no_pg_tag -U ALLOW_N_CIGAR_READS", 1,
-                Arrays.asList("72fbeb2043f005e1698e21563f0625a9"));
+                Arrays.asList("b721d997bd09873a244fee97c1e58af1"));
         executeTest("test splits with overhangs", spec);
     }
 
@@ -95,7 +95,7 @@ public class SplitNCigarReadsIntegrationTest extends WalkerTest {
     public void testSplitsFixNDN() {
         WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
                 "-T SplitNCigarReads -R " + b37KGReference + " -I " + privateTestDir + "splitNCigarReadsSnippet.bam -o %s --no_pg_tag -U ALLOW_N_CIGAR_READS -fixNDN", 1,
-                Arrays.asList("add7012d5e814d6cfd32f6cac1eb8ce3"));
+                Arrays.asList("9aa80944c2c7ee8a1f259907e3d8b51c"));
         executeTest("test fix NDN", spec);
     }
 
@@ -103,7 +103,7 @@ public class SplitNCigarReadsIntegrationTest extends WalkerTest {
     public void testSplitsWithOverhangsNotClipping() {
         WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
                 "-T SplitNCigarReads --doNotFixOverhangs -R " + b37KGReference + " -I " + privateTestDir + "NA12878.RNAseq.bam -o %s --no_pg_tag -U ALLOW_N_CIGAR_READS", 1,
-                Arrays.asList("6a55ac0a945e010bf03e1dd8f7749417"));
+                Arrays.asList("4134e1ff0eaaa9986e19526a7c3a8319"));
         executeTest("test splits with overhangs not clipping", spec);
     }
 
@@ -111,7 +111,7 @@ public class SplitNCigarReadsIntegrationTest extends WalkerTest {
     public void testSplitsWithOverhangs0Mismatches() {
         WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
                 "-T SplitNCigarReads --maxMismatchesInOverhang 0 -R " + b37KGReference + " -I " + privateTestDir + "NA12878.RNAseq.bam -o %s --no_pg_tag -U ALLOW_N_CIGAR_READS", 1,
-                Arrays.asList("8a577047955ff9edca3caf1f6e545d3e"));
+                Arrays.asList("94ebc9fbd64684e50c5f54ad5ff042b6"));
         executeTest("test splits with overhangs 0 mismatches", spec);
     }
 
@@ -119,7 +119,7 @@ public class SplitNCigarReadsIntegrationTest extends WalkerTest {
     public void testSplitsWithOverhangs5BasesInOverhang() {
         WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
                 "-T SplitNCigarReads --maxBasesInOverhang 5 -R " + b37KGReference + " -I " + privateTestDir + "NA12878.RNAseq.bam -o %s --no_pg_tag -U ALLOW_N_CIGAR_READS", 1,
-                Arrays.asList("bdd822868b88063cf50c6336ed1a5e64"));
+                Arrays.asList("b737b2dfb22a608ee3def6137fed9414"));
         executeTest("test splits with overhangs 5 bases in overhang", spec);
     }
 }

protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/simulatereads/SimulateReadsForVariantsIntegrationTest.java

@@ -64,7 +64,7 @@ public class SimulateReadsForVariantsIntegrationTest extends WalkerTest {
         WalkerTestSpec spec = new WalkerTestSpec(
                 "-T SimulateReadsForVariants --no_pg_tag -R " + b37KGReference + " -V " + publicTestDir + "forSimulation.vcf -o %s",
                  1,
-                 Arrays.asList("d929369b9095420a8aaff2595ec2f80a"));
+                 Arrays.asList("b5680f835aff1da6e1e60123d39f2371"));
         executeTest("testVariants", spec);
     }
 
@@ -74,7 +74,7 @@ public class SimulateReadsForVariantsIntegrationTest extends WalkerTest {
         WalkerTestSpec spec = new WalkerTestSpec(
                 "-RL 70 -T SimulateReadsForVariants --no_pg_tag -R " + b37KGReference + " -V " + publicTestDir + "forSimulation.vcf -o %s",
                  1,
-                 Arrays.asList("bbc65e4f8bd3a1656616476a1e190ecf"));
+                 Arrays.asList("177d32e0b13bd40aaeef71e8e5ffefe7"));
         executeTest("testReadLength", spec);
     }
 
@@ -84,7 +84,7 @@ public class SimulateReadsForVariantsIntegrationTest extends WalkerTest {
         WalkerTestSpec spec = new WalkerTestSpec(
                 "-ER 40 -T SimulateReadsForVariants --no_pg_tag -R " + b37KGReference + " -V " + publicTestDir + "forSimulation.vcf -o %s",
                  1,
-                 Arrays.asList("cb0e4b11bbd1b5a154ad6c99541cd017"));
+                 Arrays.asList("7353b4d148221f4f4975f07712413e18"));
         executeTest("testErrorRate", spec);
     }
 
@@ -94,7 +94,7 @@ public class SimulateReadsForVariantsIntegrationTest extends WalkerTest {
         WalkerTestSpec spec = new WalkerTestSpec(
                 "-RGPL SOLID -T SimulateReadsForVariants --no_pg_tag -R " + b37KGReference + " -V " + publicTestDir + "forSimulation.vcf -o %s",
                 1,
-                Arrays.asList("2b5c6cda9a434c9e25e5da5599eeae51"));
+                Arrays.asList("6f7a2ff3aa3c2e24a00f04dc770a4140"));
         executeTest("testPlatformTag", spec);
     }
 
@@ -105,7 +105,7 @@ public class SimulateReadsForVariantsIntegrationTest extends WalkerTest {
         WalkerTestSpec spec = new WalkerTestSpec(
                 "-T SimulateReadsForVariants --no_pg_tag --useAFAsAlleleFraction -DP 100 -R " + b37KGReference + " -V " + publicTestDir + "forAlleleFractionSimulation.vcf -o %s",
                 1,
-                Arrays.asList("1ae2c354718b470e30b44d5e59cb9944"));
+                Arrays.asList("f19d4b62269512fff0dcce21874c0d43"));
         executeTest("testAlleleFraction", spec);
 
     }
@@ -116,7 +116,7 @@ public class SimulateReadsForVariantsIntegrationTest extends WalkerTest {
         WalkerTestSpec spec = new WalkerTestSpec(
                 "-T SimulateReadsForVariants --no_pg_tag -R " + b37KGReference + " -V " + publicTestDir + "forLongInsert.vcf -o %s",
                 1,
-                Arrays.asList("5c069bff8efb988660c7f6d28a3117fc"));
+                Arrays.asList("052f1b644848cfd058cd2aeb0b6f2fd2"));
         executeTest("testLongInsertFailure", spec);
     }
 
@@ -126,7 +126,7 @@ public class SimulateReadsForVariantsIntegrationTest extends WalkerTest {
         WalkerTestSpec spec = new WalkerTestSpec(
                 "-RL 269 -T SimulateReadsForVariants --no_pg_tag -R " + b37KGReference + " -V " + publicTestDir + "forLongInsert.vcf -o %s",
                 1,
-                Arrays.asList("0657f6a692d22b5e2b7f5832710042e4"));
+                Arrays.asList("33f7da2e0b711a9ad28cb49c60e648be"));
         executeTest("testLongInsertSuccess", spec);
     }
 

protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantrecalibration/VariantRecalibrationWalkersIntegrationTest.java

@@ -51,6 +51,8 @@
 
 package org.broadinstitute.gatk.tools.walkers.variantrecalibration;
 
+import org.broadinstitute.gatk.utils.exceptions.UserException;
+import org.broadinstitute.gatk.utils.exceptions.UserException.CommandLineException;
 import org.broadinstitute.gatk.utils.variant.VCIterable;
 import org.broadinstitute.gatk.engine.walkers.WalkerTest;
 import htsjdk.variant.variantcontext.VariantContext;
@@ -60,6 +62,7 @@ import org.testng.annotations.DataProvider;
 import org.testng.annotations.Test;
 
 import java.io.File;
+import java.io.IOException;
 import java.util.Arrays;
 import java.util.List;
 
@@ -390,5 +393,73 @@ public class VariantRecalibrationWalkersIntegrationTest extends WalkerTest {
             new File(outputFile.getAbsolutePath() + ".pdf").deleteOnExit();
         }
     }
+
+    @Test
+    public void testVQSRAnnotationOrder() throws IOException {
+        final String inputFile = privateTestDir + "oneSNP.vcf";
+        final String exacModelReportFilename = privateTestDir + "subsetExAC.snps_model.report";
+        final String annoOrderRecal = privateTestDir + "anno_order.recal";
+        final String annoOrderTranches = privateTestDir + "anno_order.tranches";
+        final String goodMd5 = "d41d8cd98f00b204e9800998ecf8427e";
+        final String base = "-R " + b37KGReference +
+                        " -T VariantRecalibrator" +
+                        " -input " + inputFile +
+                        " -L 1:110201699" +
+                        " -resource:truth=true,training=true,prior=15.0 " + inputFile +
+                        " -an FS -an ReadPosRankSum -an MQ -an MQRankSum -an QD -an SOR"+
+                        " --recal_file " + annoOrderRecal +
+                        " -tranchesFile " + annoOrderTranches +
+                        " --input_model " + exacModelReportFilename +
+                        " -ignoreAllFilters -mode SNP" +
+                        " --no_cmdline_in_header" ;
+
+        final WalkerTestSpec spec = new WalkerTestSpec(base, 1, Arrays.asList(goodMd5));
+        spec.disableShadowBCF(); // TODO -- enable when we support symbolic alleles
+
+        List<File> outputFiles = executeTest("testVQSRAnnotationOrder", spec).getFirst();
+        setPDFsForDeletion(outputFiles);
+
+
+        final String base2 = "-R " + b37KGReference +
+                " -T VariantRecalibrator" +
+                " -input " + inputFile +
+                " -L 1:110201699" +
+                " -resource:truth=true,training=true,prior=15.0 " + inputFile +
+                " -an ReadPosRankSum -an MQ -an MQRankSum -an QD -an SOR -an FS "+
+                " --recal_file " + annoOrderRecal +
+                " -tranchesFile " + annoOrderTranches +
+                " --input_model " + exacModelReportFilename +
+                " -ignoreAllFilters -mode SNP" +
+                " --no_cmdline_in_header" ;
+
+        final WalkerTestSpec spec2 = new WalkerTestSpec(base2, 1, Arrays.asList(goodMd5));
+        spec2.disableShadowBCF(); // TODO -- enable when we support symbolic alleles
+        outputFiles = executeTest("testVQSRAnnotationOrder2", spec2).getFirst();
+        setPDFsForDeletion(outputFiles);
+    }
+
+    @Test(expectedExceptions={RuntimeException.class, CommandLineException.class})
+    public void testVQSRAnnotationMismatch() throws IOException {
+        final String inputFile = privateTestDir + "oneSNP.vcf";
+        final String exacModelReportFilename = privateTestDir + "subsetExAC.snps_model.report";
+        final String annoOrderRecal = privateTestDir + "anno_order.recal";
+        final String annoOrderTranches = privateTestDir + "anno_order.tranches";
+        final String goodMd5 = "d41d8cd98f00b204e9800998ecf8427e";
+        final String base = "-R " + b37KGReference +
+                " -T VariantRecalibrator" +
+                " -input " + inputFile +
+                " -L 1:110201699" +
+                " -resource:truth=true,training=true,prior=15.0 " + inputFile +
+                " -an FS -an ReadPosRankSum -an MQ -an MQRankSum -an QD -an SOR -an BaseQRankSum"+
+                " --recal_file " + annoOrderRecal +
+                " -tranchesFile " + annoOrderTranches +
+                " --input_model " + exacModelReportFilename +
+                " -ignoreAllFilters -mode SNP" +
+                " --no_cmdline_in_header" ;
+
+        final WalkerTestSpec spec = new WalkerTestSpec(base, 1, Arrays.asList(goodMd5));
+        spec.disableShadowBCF(); // TODO -- enable when we support symbolic alleles
+        executeTest("testVQSRAnnotationMismatch", spec).getFirst();
+    }
 }
 

protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantrecalibration/VariantRecalibratorModelOutputUnitTest.java

@@ -276,4 +276,52 @@ public class VariantRecalibratorModelOutputUnitTest  extends BaseTest {
         return new GaussianMixtureModel(badGaussianList, shrinkage, dirichlet, priorCounts);
     }
 
+    @Test
+    public void testAnnotationOrderAndValidate() {
+        final VariantRecalibrator vqsr = new VariantRecalibrator();
+        final List<String> annotationList = new ArrayList<>();
+        annotationList.add("QD");
+        annotationList.add("FS");
+        annotationList.add("ReadPosRankSum");
+        annotationList.add("MQ");
+        annotationList.add("MQRankSum");
+        annotationList.add("SOR");
+
+        double[] meanVector = {16.13, 2.45, 0.37, 59.08, 0.14, 0.91};
+        final String columnName = "Mean";
+        final String formatString = "%.3f";
+        GATKReportTable annotationTable = vqsr.makeVectorTable("AnnotationMeans", "Mean for each annotation, used to normalize data", annotationList, meanVector, columnName, formatString);
+        vqsr.orderAndValidateAnnotations(annotationTable, annotationList);
+
+        for (int i = 0; i < vqsr.annotationOrder.size(); i++){
+            Assert.assertEquals(i, (int)vqsr.annotationOrder.get(i));
+        }
+
+        annotationList.remove(0);
+        annotationList.add("QD");
+        vqsr.orderAndValidateAnnotations(annotationTable, annotationList);
+        for (int i = 0; i < vqsr.annotationOrder.size(); i++) {
+            if (i == 0) {
+                Assert.assertEquals(annotationList.size()-1, (int)vqsr.annotationOrder.get(i));
+            } else {
+                Assert.assertEquals(i - 1, (int)vqsr.annotationOrder.get(i));
+            }
+        }
+
+        final List<String> annotationList2 = new ArrayList<>();
+        annotationList2.add("ReadPosRankSum");
+        annotationList2.add("MQRankSum");
+        annotationList2.add("MQ");
+        annotationList2.add("SOR");
+        annotationList2.add("QD");
+        annotationList2.add("FS");
+
+        final VariantRecalibrator vqsr2 = new VariantRecalibrator();
+        vqsr2.orderAndValidateAnnotations(annotationTable, annotationList2);
+        for (int i = 0; i < vqsr2.annotationOrder.size(); i++){
+            Assert.assertEquals(annotationList.get(vqsr.annotationOrder.get(i)), annotationList2.get(vqsr2.annotationOrder.get(i)));
+        }
+
+    }
+
 }

protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/LeftAlignAndTrimVariantsIntegrationTest.java

@@ -154,7 +154,7 @@ public class LeftAlignAndTrimVariantsIntegrationTest extends WalkerTest {
         WalkerTestSpec spec = new WalkerTestSpec(
                 "-T LeftAlignAndTrimVariants -o %s -R " + b37KGReference + " --variant:vcf " + privateTestDir + "multiallele-gt.vcf --no_cmdline_in_header -split",
                 1,
-                Arrays.asList("80b4a994a569ecfbd628121b85e64339"));
+                Arrays.asList("a7dcd0cf9542bf58153023d26deec06e"));
         executeTest("test left alignment of multiple alleles with genoptypes", spec);
     }
 
@@ -172,7 +172,7 @@ public class LeftAlignAndTrimVariantsIntegrationTest extends WalkerTest {
         WalkerTestSpec spec = new WalkerTestSpec(
                 "-T LeftAlignAndTrimVariants -o %s -R " + b37KGReference + " --variant:vcf " + privateTestDir + "multiallele-gt.vcf --no_cmdline_in_header -split -keepOriginalAC",
                 1,
-                Arrays.asList("6774b43d9446278e716d7198717a5f85"));
+                Arrays.asList("26e67892c75ded1756709476520d4264"));
         executeTest("test left alignment of multiple alleles with genoptypes, keep original AC", spec);
     }
 

protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/SelectVariantsIntegrationTest.java

@@ -494,7 +494,7 @@ public class SelectVariantsIntegrationTest extends WalkerTest {
                 { privateTestDir+"forHardLeftAlignVariantsTest.vcf", "", "a835454cbd132f2d56defb55ba13b2dd"},
                 { privateTestDir+"multi-allelic-ordering.vcf", "-sn SAMPLE-CC -sn SAMPLE-CT", "b19e508640a89f176f7ea347babfcc66"},
                 { privateTestDir+"multi-allelic-ordering.vcf", "-sn SAMPLE-CC -sn SAMPLE-CT -env", "15d982a280754804fa384ccc0f3a2ccf"},
-                { privateTestDir+"multi-allelic-ordering.vcf", "-sn SAMPLE-CC -sn SAMPLE-CT -trimAlternates", "cbad00c0722a94c382f75b428f2a8e6c"},
+                { privateTestDir+"multi-allelic-ordering.vcf", "-sn SAMPLE-CC -sn SAMPLE-CT -trimAlternates", "41ffddc776a2af55db297dbefc6d2097"},
                 { privateTestDir+"multi-allelic-ordering.vcf", "-sn SAMPLE-CC -sn SAMPLE-CT -env -trimAlternates", "a9f448502a27e777b3112cf98e1d325f"}
         };
     }
@@ -782,7 +782,7 @@ public class SelectVariantsIntegrationTest extends WalkerTest {
         WalkerTestSpec spec = new WalkerTestSpec(
                 "-T SelectVariants -R " + b37KGReference + " --variant " + testfile + " -o %s --no_cmdline_in_header -sn NA12891 -trimAlternates",
                 1,
-                Arrays.asList("c8203bea524cdb66717abbbc50a234b5"));
+                Arrays.asList("f068e449cf3c142c8c5758c5eab38780"));
         spec.disableShadowBCF();
         executeTest("testSACDiploid", spec);
     }
@@ -794,7 +794,7 @@ public class SelectVariantsIntegrationTest extends WalkerTest {
         WalkerTestSpec spec = new WalkerTestSpec(
                 "-T SelectVariants -R " + b37KGReference + " --variant " + testfile + " -o %s --no_cmdline_in_header -sn NA12891 -trimAlternates",
                 1,
-                Arrays.asList("f48a3c789898e24fbec6db9c6e8d800a"));
+                Arrays.asList("ade30e246b807e45cf6c54db96fc8627"));
         spec.disableShadowBCF();
         executeTest("testSACNonDiploid", spec);
     }

protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/SelectVariantsParallelIntegrationTest.java

@@ -100,7 +100,7 @@ public class SelectVariantsParallelIntegrationTest extends WalkerTest {
             { // AD and PL decoding race condition
                 final String testfile = privateTestDir + "race_condition.vcf";
                 final String args = "-env -trimAlternates -sn SAMPLE -L 1:1-10,000,000 -V " + testfile;
-                new ParallelSelectTestProvider(b37KGReference, args, "9983e6a41472e8956dd32f967bf87f05", nt);
+                new ParallelSelectTestProvider(b37KGReference, args, "6bd8bf3ebd72e91eba9b4e0a44d1744f", nt);
             }
         }
 

public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/EngineFeaturesIntegrationTest.java

@@ -324,12 +324,12 @@ public class EngineFeaturesIntegrationTest extends WalkerTest {
 
     @Test()
     public void testDefaultBaseQualities20() {
-        executeTest("testDefaultBaseQualities20", testDefaultBaseQualities(20, "90a450f74554bbd2cc3a9e0f9de68e26"));
+        executeTest("testDefaultBaseQualities20", testDefaultBaseQualities(20, "da5a4293e125f00ecbdfd450b80d8357"));
     }
 
     @Test()
     public void testDefaultBaseQualities30() {
-        executeTest("testDefaultBaseQualities30", testDefaultBaseQualities(30, "ec11db4173ce3b8e43997f00dab5ae26"));
+        executeTest("testDefaultBaseQualities30", testDefaultBaseQualities(30, "c82e72ee08d545266927a7f2e8ab24c3"));
     }
 
     @Test(expectedExceptions = Exception.class)
@@ -732,10 +732,10 @@ public class EngineFeaturesIntegrationTest extends WalkerTest {
     public void testSAMWriterFeatures() {
         testBAMFeatures("-compress 0", "49228d4f5b14c4cfed4a09372eb71139");
         testBAMFeatures("-compress 9", "bc61a1b2b53a2ec7c63b533fa2f8701b");
-        testBAMFeatures("-simplifyBAM", "a1127bab46674b165496b79bb9fa7964");
+        testBAMFeatures("-simplifyBAM", "f66b671b32d1bbbf65a88585a64b556a");
 
         //Validate MD5
-        final String expectedMD5 = "c58b9114fc15b53655f2c03c819c29fd";
+        final String expectedMD5 = "a0c0f1fafc248ac82a84b8ca71292caf";
         final File md5Target = testBAMFeatures("--generate_md5", expectedMD5);
         final File md5File = new File(md5Target.getAbsoluteFile() + ".md5");
         md5File.deleteOnExit();

public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/arguments/CramIntegrationTest.java

@@ -41,16 +41,16 @@ public class CramIntegrationTest extends WalkerTest {
         return new Object[][] {
                 {"PrintReads", "exampleBAM.bam", "", "cram", ""}, // Bypass MD5 check since the CRAM header stores the file name
                 {"PrintReads", "exampleCRAM.cram", "", "cram", ""},
-                {"PrintReads", "exampleCRAM.cram", "", "bam", "e7834d5992a69143d7c463275213bbf8"},
+                {"PrintReads", "exampleCRAM.cram", "", "bam", "50c55e1040aa0ffd4036aa581fcfe8af"},
-                {"PrintReads", "exampleCRAM.cram", " -L chr1:200", "bam", "d362fbf30a2c77a2653f1c8eb2dd8fc1"},
+                {"PrintReads", "exampleCRAM.cram", " -L chr1:200", "bam", "f74f78bd16aed8a395f0e79e3898ab19"},
                 {"CountLoci", "exampleCRAM.cram", "", "txt", "ade93df31a6150321c1067e749cae9be"},
                 {"CountLoci", "exampleCRAM.cram", " -L chr1:200", "txt", "b026324c6904b2a9cb4b88d6d61c81d1"},
                 {"CountReads", "exampleCRAM.cram", "", "txt", "4fbafd6948b6529caa2b78e476359875"},
                 {"CountReads", "exampleCRAM.cram", " -L chr1:200", "txt", "b026324c6904b2a9cb4b88d6d61c81d1"},
-                {"PrintReads", "exampleCRAM.cram", " -L chr1:200 -L chr1:89597", "bam", "a11bd125b69f651aaa2ae68c8ccab22f"},
+                {"PrintReads", "exampleCRAM.cram", " -L chr1:200 -L chr1:89597", "bam", "1a6331f0e7afdccd07425df251d28811"},
                 {"CountLoci", "exampleCRAM.cram", " -L chr1:200 -L chr1:89597", "txt", "26ab0db90d72e28ad0ba1e22ee510510"},
                 {"CountReads", "exampleCRAM.cram", " -L chr1:200 -L chr1:89597", "txt", "6d7fce9fee471194aa8b5b6e47267f03"},
-                {"PrintReads", "exampleCRAM-nobai-withcrai.cram", " -L chr1:200 -L chr1:89597", "bam", "9e3e8b5a58dfcb50f5b270547c01d56a"},
+                {"PrintReads", "exampleCRAM-nobai-withcrai.cram", " -L chr1:200 -L chr1:89597", "bam", "41f8ebb256120befc6ea7d228915b349"},
                 {"CountLoci", "exampleCRAM-nobai-withcrai.cram", " -L chr1:200 -L chr1:89597", "txt", "26ab0db90d72e28ad0ba1e22ee510510"},
                 {"CountReads", "exampleCRAM-nobai-withcrai.cram", " -L chr1:200 -L chr1:89597", "txt", "6d7fce9fee471194aa8b5b6e47267f03"},
         };

public/gatk-engine/src/test/java/org/broadinstitute/gatk/engine/arguments/IntervalIntegrationTest.java

@@ -62,7 +62,7 @@ public class IntervalIntegrationTest extends WalkerTest {
         // our base file
         File baseOutputFile = createTempFile("testUnmappedReadInclusion",".bam");
         spec.setOutputFileLocation(baseOutputFile);
-        spec.addAuxFile("c66bb2c3c5382e2acff09b2b359562bb",createTempFileFromBase(baseOutputFile.getAbsolutePath()));
+        spec.addAuxFile("4eeb9b07d3c9ddd4ea9eada7805903a2",createTempFileFromBase(baseOutputFile.getAbsolutePath()));
         spec.addAuxFile("fadcdf88597b9609c5f2a17f4c6eb455", createTempFileFromBase(baseOutputFile.getAbsolutePath().substring(0,baseOutputFile.getAbsolutePath().indexOf(".bam"))+".bai"));
 
         executeTest("testUnmappedReadInclusion",spec);
@@ -109,8 +109,8 @@ public class IntervalIntegrationTest extends WalkerTest {
         // our base file
         File baseOutputFile = createTempFile("testMixedMappedAndUnmapped",".bam");
         spec.setOutputFileLocation(baseOutputFile);
-        spec.addAuxFile("c64cff3ed376bc8f2977078dbdac4518",createTempFileFromBase(baseOutputFile.getAbsolutePath()));
+        spec.addAuxFile("70ac0317c0c13d885e6c2de4f837cdd3",createTempFileFromBase(baseOutputFile.getAbsolutePath()));
-        spec.addAuxFile("fa90ff91ac0cc689c71a3460a3530b8b", createTempFileFromBase(baseOutputFile.getAbsolutePath().substring(0,baseOutputFile.getAbsolutePath().indexOf(".bam"))+".bai"));
+        spec.addAuxFile("df469db01610ddb731868dfb28917142", createTempFileFromBase(baseOutputFile.getAbsolutePath().substring(0,baseOutputFile.getAbsolutePath().indexOf(".bam"))+".bai"));
 
         executeTest("testMixedMappedAndUnmapped",spec);
     }

public/gatk-root/pom.xml

@@ -89,7 +89,7 @@
             <dependency>
                 <groupId>com.intel.gkl</groupId>
                 <artifactId>gkl</artifactId>
-                <version>0.5.2</version>
+                <version>0.6.0</version>
             </dependency>
             <dependency>
                 <groupId>log4j</groupId>

public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/variantutils/VariantsToTable.java

@@ -98,7 +98,7 @@ import java.util.*;
  *
  * <h3>Caveats</h3>
  * <ul>
- *     <li>Some annotations cannot be applied to all variant sites, so VCFs typically contain records where some annotation values are missing. By default this tool the tool will emit the special value NA for the missing annotations if you request export of an annotation for which not all records have values. You can override this behavior by setting --errorIfMissingData in the command line. As a result, the tool will throw an error if a record is missing a value.</li>
+ *     <li>Some annotations cannot be applied to all variant sites, so VCFs typically contain records where some annotation values are missing. By default this tool will emit the special value NA for the missing annotations if you request export of an annotation for which not all records have values. You can override this behavior by setting --errorIfMissingData in the command line. As a result, the tool will throw an error if a record is missing a value.</li>
  *     <li>When you request export of sample-level annotations (FORMAT field annotations such as GT), the annotations will be identified per-sample. If multiple samples are present in the VCF, the columns will be ordered alphabetically by sample name (SM tag).</li>
  * </ul>
  *
@@ -181,7 +181,7 @@ public class VariantsToTable extends RodWalker<Integer, Integer> {
 
     /**
      * By default, this tool will write out NA values indicating missing data when it encounters a field without a value in a record.
-     * If this flag is added to the command, the tool will instead exit with an error if missing data is encountered..
+     * If this flag is added to the command, the tool will instead exit with an error if missing data is encountered.
      */
     @Advanced
     @Argument(fullName="errorIfMissingData", shortName="EMD", doc="If provided, we will require every record to contain every field", required=false)

public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/BAQIntegrationTest.java

@@ -44,13 +44,13 @@ public class BAQIntegrationTest extends WalkerTest {
     // --------------------------------------------------------------------------------------------------------------
     @Test
     public void testPrintReadsNoBAQ() {
-        WalkerTestSpec spec = new WalkerTestSpec( baseCommand +" -baq OFF",  1, Arrays.asList("e33187ca383c7f5c75c5d547ec79e1cb"));
+        WalkerTestSpec spec = new WalkerTestSpec( baseCommand +" -baq OFF",  1, Arrays.asList("526dbbb390dbd36daa70ac35a8eddc36"));
         executeTest(String.format("testPrintReadsNoBAQ"), spec);
     }
 
     @Test
     public void testPrintReadsRecalBAQ() {
-        WalkerTestSpec spec = new WalkerTestSpec( baseCommand +" -baq RECALCULATE",  1, Arrays.asList("a25043edfbfa4f21a13cc21064b460df"));
+        WalkerTestSpec spec = new WalkerTestSpec( baseCommand +" -baq RECALCULATE",  1, Arrays.asList("25cb8f91e31a07cca2e141a119c9e020"));
         executeTest(String.format("testPrintReadsRecalBAQ"), spec);
     }
 }

public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/readutils/ClipReadsWalkersIntegrationTest.java

@@ -47,22 +47,22 @@ public class ClipReadsWalkersIntegrationTest extends WalkerTest {
     }
 
     final static String Q10ClipOutput = "b29c5bc1cb9006ed9306d826a11d444f";
-    @Test public void testQClip0() { testClipper("clipQSum0", "-QT 0", "117a4760b54308f81789c39b1c9de578", "bcf0d1e13537f764f006ef6d9b401ea7"); }
+    @Test public void testQClip0() { testClipper("clipQSum0", "-QT 0", "117a4760b54308f81789c39b1c9de578", "2e617e0f0b4a1bf45dbb666da0a6a16c"); }
-    @Test public void testQClip2() { testClipper("clipQSum2", "-QT 2", Q10ClipOutput, "27847d330b962e60650df23b6efc8c3c"); }
+    @Test public void testQClip2() { testClipper("clipQSum2", "-QT 2", Q10ClipOutput, "1b0d2317dfd1fd5a4d14eea3f560ac17"); }
-    @Test public void testQClip10() { testClipper("clipQSum10", "-QT 10", "b29c5bc1cb9006ed9306d826a11d444f", "27847d330b962e60650df23b6efc8c3c"); }
+    @Test public void testQClip10() { testClipper("clipQSum10", "-QT 10", "b29c5bc1cb9006ed9306d826a11d444f", "1b0d2317dfd1fd5a4d14eea3f560ac17"); }
-    @Test public void testQClip20() { testClipper("clipQSum20", "-QT 20", "6c3434dce66ae5c9eeea502f10fb9bee", "f89ec5439e88f5a75433150da0069034"); }
+    @Test public void testQClip20() { testClipper("clipQSum20", "-QT 20", "6c3434dce66ae5c9eeea502f10fb9bee", "3a9a10966cce58baf9e9400a2c5f99ca"); }
 
-    @Test public void testClipRange1() { testClipper("clipRange1", "-CT 1-5", "b5acd753226e25b1e088838c1aab9117", "987007f6e430cad4cb4a8d1cc1f45d91"); }
+    @Test public void testClipRange1() { testClipper("clipRange1", "-CT 1-5", "b5acd753226e25b1e088838c1aab9117", "701f03388ffaeb0f92be1e719e2477df"); }
-    @Test public void testClipRange2() { testClipper("clipRange2", "-CT 1-5,11-15", "be4fcad5b666a5540028b774169cbad7", "ec4cf54ed50a6baf69dbf98782c19aeb"); }
+    @Test public void testClipRange2() { testClipper("clipRange2", "-CT 1-5,11-15", "be4fcad5b666a5540028b774169cbad7", "7dc5da735c437b6523e0823a1ed0e981"); }
 
-    @Test public void testClipSeq() { testClipper("clipSeqX", "-X CCCCC", "db199bd06561c9f2122f6ffb07941fbc", "a9cf540e4ed2514061248a878e09a09c"); }
+    @Test public void testClipSeq() { testClipper("clipSeqX", "-X CCCCC", "db199bd06561c9f2122f6ffb07941fbc", "daa41acd8c9f1a75c8107d0fd0db8cf0"); }
-    @Test public void testClipSeqFile() { testClipper("clipSeqXF", "-XF " + privateTestDir + "seqsToClip.fasta", "22cd33dbd06cc425ce3626360367bfca", "906871df304dd966682e5798d59fc86b"); }
+    @Test public void testClipSeqFile() { testClipper("clipSeqXF", "-XF " + privateTestDir + "seqsToClip.fasta", "22cd33dbd06cc425ce3626360367bfca", "b1812de69c967059362139a269044362"); }
 
-    @Test public void testClipMulti() { testClipper("clipSeqMulti", "-QT 10 -CT 1-5 -XF " + privateTestDir + "seqsToClip.fasta -X CCCCC", "e4a88276a6f76ccc2b05a06c76305a1c", "b41995fea04034ca0427c4a71504ef83"); }
+    @Test public void testClipMulti() { testClipper("clipSeqMulti", "-QT 10 -CT 1-5 -XF " + privateTestDir + "seqsToClip.fasta -X CCCCC", "e4a88276a6f76ccc2b05a06c76305a1c", "9f999ed70684fdfb8dba019ff71741fe"); }
 
-    @Test public void testClipNs() { testClipper("testClipNs", "-QT 10 -CR WRITE_NS", Q10ClipOutput, "27847d330b962e60650df23b6efc8c3c"); }
+    @Test public void testClipNs() { testClipper("testClipNs", "-QT 10 -CR WRITE_NS", Q10ClipOutput, "1b0d2317dfd1fd5a4d14eea3f560ac17"); }
-    @Test public void testClipQ0s() { testClipper("testClipQs", "-QT 10 -CR WRITE_Q0S", Q10ClipOutput, "195b8bdfc0186fdca742764aa9b06363"); }
+    @Test public void testClipQ0s() { testClipper("testClipQs", "-QT 10 -CR WRITE_Q0S", Q10ClipOutput, "b7ce95f277d5f66b7f5a60ffbf9692cf"); }
-    @Test public void testClipSoft() { testClipper("testClipSoft", "-QT 10 -CR SOFTCLIP_BASES", Q10ClipOutput, "08d16051be0b3fa3453eb1e6ca48b098"); }
+    @Test public void testClipSoft() { testClipper("testClipSoft", "-QT 10 -CR SOFTCLIP_BASES", Q10ClipOutput, "55c9d86c18c5a59a98429e8a5076e871"); }
 
     @Test
     public void testUseOriginalQuals() {
@@ -74,7 +74,7 @@ public class ClipReadsWalkersIntegrationTest extends WalkerTest {
                         " -OQ -QT 4 -CR WRITE_Q0S" +
                         " -o %s -os %s",
                 2,
-                Arrays.asList("a2819d54b2110150e38511f5a55db91d", "55c01ccc2e84481b22d3632cdb06c8ba"));
+                Arrays.asList("0e4c116fa07c3d8190eefe6968a0b819", "55c01ccc2e84481b22d3632cdb06c8ba"));
         executeTest("clipOriginalQuals", spec);
     }
 }

public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/readutils/PrintReadsIntegrationTest.java

@@ -59,27 +59,27 @@ public class PrintReadsIntegrationTest extends WalkerTest {
     @DataProvider(name = "PRTest")
     public Object[][] createPrintReadsTestData() {
         return new Object[][]{
-                {new PRTest(hg18Reference, new String[]{"HiSeq.1mb.bam"}, "", "0aa3505ba61e05663e629011dd54e423")},
+                {new PRTest(hg18Reference, new String[]{"HiSeq.1mb.bam"}, "", "83d1454dc01cd2e7458dad4012695f64")},
                 {new PRTest(hg18Reference, new String[]{"HiSeq.1mb.bam"}, " -compress 0", "0aec10d19e0dbdfe1d0cbb3eddaf623a")},
-                {new PRTest(hg18Reference, new String[]{"HiSeq.1mb.bam"}, " -simplifyBAM", "c565d9cd4838a313e7bdb30530c0cf71")},
+                {new PRTest(hg18Reference, new String[]{"HiSeq.1mb.bam"}, " -simplifyBAM", "60255a68df1b8f2fbba373d75274f0de")},
-                {new PRTest(hg18Reference, new String[]{"HiSeq.1mb.bam"}, " -n 10", "917440a38aba707ec0e012168590981a")},
+                {new PRTest(hg18Reference, new String[]{"HiSeq.1mb.bam"}, " -n 10", "eb7c6bacca5fee09b8df50880eb81ee6")},
                 // See: GATKBAMIndex.getStartOfLastLinearBin(), BAMScheduler.advance(), IntervalOverlapFilteringIterator.advance()
-                {new PRTest(b37KGReference, new String[]{"unmappedFlagReadsInLastLinearBin.bam"}, "", "0b58c903f54e8543a8b2ce1439aa769b")},
+                {new PRTest(b37KGReference, new String[]{"unmappedFlagReadsInLastLinearBin.bam"}, "", "3d67c398ce2ac1deeddbccbd850380a7")},
-                {new PRTest(b37KGReference, new String[]{"unmappedFlagReadsInLastLinearBin.bam"}, " -L 1", "5b1154cc81dba6bcfe76188e4df8d79c")},
+                {new PRTest(b37KGReference, new String[]{"unmappedFlagReadsInLastLinearBin.bam"}, " -L 1", "37cdd8871843693f2650d7b48c8ae1d4")},
-                {new PRTest(b37KGReference, new String[]{"unmappedFlagReadsInLastLinearBin.cram"}, " -L 1:10001 -L GL000192.1:500204", "a84efdc3d4a8d6329b5f0b494dd280d2")},
+                {new PRTest(b37KGReference, new String[]{"unmappedFlagReadsInLastLinearBin.cram"}, " -L 1:10001 -L GL000192.1:500204", "4d63fd6e977a53e5d9590bd030b40bd0")},
-                {new PRTest(b37KGReference, new String[]{"unmappedFlagReadsInLastLinearBin.bam"}, " -L unmapped", "cbd3d1d50c8674f79033aa8c36aa3cd1")},
+                {new PRTest(b37KGReference, new String[]{"unmappedFlagReadsInLastLinearBin.bam"}, " -L unmapped", "a834400e3bd69045eb8a9e94131633f5")},
-                {new PRTest(b37KGReference, new String[]{"unmappedFlagReadsInLastLinearBin.bam"}, " -L 1 -L unmapped", "5b1154cc81dba6bcfe76188e4df8d79c")},
+                {new PRTest(b37KGReference, new String[]{"unmappedFlagReadsInLastLinearBin.bam"}, " -L 1 -L unmapped", "37cdd8871843693f2650d7b48c8ae1d4")},
-                {new PRTest(b37KGReference, new String[]{"oneReadAllInsertion.bam"}, "",  "e212d1799ae797e781b17e630656a9a1")},
+                {new PRTest(b37KGReference, new String[]{"oneReadAllInsertion.bam"}, "",  "6c04aac25e2136fee395897aac96bea8")},
-                {new PRTest(b37KGReference, new String[]{"NA12878.1_10mb_2_10mb.bam"}, "",  "0387c61303140d8899fcbfdd3e72ed80")},
+                {new PRTest(b37KGReference, new String[]{"NA12878.1_10mb_2_10mb.bam"}, "",  "57a9bc1f7dd4e7717ee796c484bcf45a")},
                 // Tests for filtering options
                 {new PRTest(b37KGReference, new String[]{"NA12878.1_10mb_2_10mb.bam", "NA20313.highCoverageRegion.bam"},
-                        "",  "ad56da66be0bdab5a8992de9617ae6a5")},
+                        "",  "e691d61df10f7614d73c8ecb46c75ee1")},
                 {new PRTest(b37KGReference, new String[]{"NA12878.1_10mb_2_10mb.bam", "NA20313.highCoverageRegion.bam"},
-                        " -readGroup SRR359098",  "c3bfe28722a665e666098dbb7048a9f1")},
+                        " -readGroup SRR359098",  "7644eab114bf537411218f782d75a6a6")},
                 {new PRTest(b37KGReference, new String[]{"NA12878.1_10mb_2_10mb.bam", "NA20313.highCoverageRegion.bam"},
-                        " -readGroup 20FUK.3 -sn NA12878",  "8191f8d635d00b1f4d0993b785cc46c5")},
+                        " -readGroup 20FUK.3 -sn NA12878",  "351d5da29874033e50d29c5c36575a6c")},
                 {new PRTest(b37KGReference, new String[]{"NA12878.1_10mb_2_10mb.bam", "NA20313.highCoverageRegion.bam"},
-                        " -sn na12878",  "92a85b4223ec45e114f12a1fe6ebbaeb")},
+                        " -sn na12878",  "9056d852418dd2083f38e3eac1551fcd")},
         };
     }
 

public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/readutils/SplitSamFileIntegrationTest.java

@@ -43,9 +43,9 @@ public class SplitSamFileIntegrationTest extends WalkerTest {
                         " --outputRoot " + prefix,
                 Collections.<String>emptyList()
         );
-        addSplitOutput(spec, prefix, "NA12878", "3e28b666fb673be138eca9bd3db9520b");
+        addSplitOutput(spec, prefix, "NA12878", "356bddf614a44a0234f7b116f5cde998");
-        addSplitOutput(spec, prefix, "NA12891", "af01069bc3da4252ce8417a03d11f48b");
+        addSplitOutput(spec, prefix, "NA12891", "5dd92a0089e3f781e77d94010264b9fd");
-        addSplitOutput(spec, prefix, "NA12892", "cfa1cb6aaca03900160bd5627f4f698b");
+        addSplitOutput(spec, prefix, "NA12892", "ea8f16c18c89b49ce9d32d76c6af75f9");
         executeTest("testSplitSamFile", spec);
     }
 

public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/variant/GATKVariantContextUtils.java

@@ -851,9 +851,13 @@ public class GATKVariantContextUtils {
 
                 if ( newLikelihoods == null || (originalVC.getAttributeAsInt(VCFConstants.DEPTH_KEY, 0) == 0 && likelihoodsAreUninformative(newLikelihoods) )) {
                     gb.noPL();
+                    gb.noGQ();
                 } else {
                     gb.PL(newLikelihoods);
+                    final int PLindex = MathUtils.maxElementIndex(newLikelihoods);
+                    gb.log10PError(GenotypeLikelihoods.getGQLog10FromLikelihoods(PLindex, newLikelihoods));
                 }
+
             }
 
             // create the new strand allele counts array from the used alleles

public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/variant/GATKVariantContextUtilsUnitTest.java

@@ -1503,7 +1503,7 @@ public class GATKVariantContextUtilsUnitTest extends BaseTest {
                         attribute(GATKVCFConstants.STRAND_COUNT_BY_SAMPLE_KEY, homC3AllelesSAC).make()).make(),
                 new VariantContextBuilder(vcBase).alleles(AG).make(),
                 Arrays.asList(new GenotypeBuilder(base).alleles(Arrays.asList(Aref)).PL(new double[]{-20, 0}).AD(new int[]{0, 1}).
-                        attribute(GATKVCFConstants.STRAND_COUNT_BY_SAMPLE_KEY, new int[]{0, 0, 1, 1}).GQ(100).make())});
+                        attribute(GATKVCFConstants.STRAND_COUNT_BY_SAMPLE_KEY, new int[]{0, 0, 1, 1}).GQ(200).make())});
 
         tests.add(new Object[]{
                 new VariantContextBuilder(vcBase).alleles(ACG).genotypes(new GenotypeBuilder(base).alleles(Arrays.asList(Aref, Aref, Aref)).AD(homRef3AllelesAD).PL(triploidRef3AllelesPL).
@@ -1522,7 +1522,7 @@ public class GATKVariantContextUtilsUnitTest extends BaseTest {
                         attribute(GATKVCFConstants.STRAND_COUNT_BY_SAMPLE_KEY, homC3AllelesSAC).make()).make(),
                 new VariantContextBuilder(vcBase).alleles(AG).make(),
                 Arrays.asList(new GenotypeBuilder(base).alleles(Arrays.asList(Aref, Aref, G)).PL(new double[]{0, -40, -70, -90}).AD(new int[]{20, 1}).
-                        attribute(GATKVCFConstants.STRAND_COUNT_BY_SAMPLE_KEY, new int[]{0, 0, 1, 1}).GQ(100).make())});
+                        attribute(GATKVCFConstants.STRAND_COUNT_BY_SAMPLE_KEY, new int[]{0, 0, 1, 1}).GQ(400).make())});
 
         tests.add(new Object[]{
                 new VariantContextBuilder(vcBase).alleles(ACG).genotypes(new GenotypeBuilder(base).alleles(AA).AD(homRef3AllelesAD).PL(homRef3AllelesPL).
@@ -1547,19 +1547,19 @@ public class GATKVariantContextUtilsUnitTest extends BaseTest {
                         attribute(GATKVCFConstants.STRAND_COUNT_BY_SAMPLE_KEY, hetRefG3AllelesSAC).make()).make(),
                 new VariantContextBuilder(vcBase).alleles(AG).make(),
                 Arrays.asList(new GenotypeBuilder(base).alleles(AA).PL(new double[]{-20, 0, -50}).AD(new int[]{10, 11}).
-                        attribute(GATKVCFConstants.STRAND_COUNT_BY_SAMPLE_KEY, new int[]{10, 10, 11, 11}).GQ(100).make())});
+                        attribute(GATKVCFConstants.STRAND_COUNT_BY_SAMPLE_KEY, new int[]{10, 10, 11, 11}).GQ(200).make())});
         tests.add(new Object[]{
                 new VariantContextBuilder(vcBase).alleles(ACG).genotypes(new GenotypeBuilder(base).alleles(AA).AD(hetCG3AllelesAD).PL(hetCG3AllelesPL).
                         attribute(GATKVCFConstants.STRAND_COUNT_BY_SAMPLE_KEY, hetCG3AllelesSAC).make()).make(),
                 new VariantContextBuilder(vcBase).alleles(AG).make(),
                 Arrays.asList(new GenotypeBuilder(base).alleles(AA).PL(new double[]{0, -20, -30}).AD(new int[]{0, 11}).
-                        attribute(GATKVCFConstants.STRAND_COUNT_BY_SAMPLE_KEY, new int[]{0, 0, 11, 11}).GQ(100).make())});
+                        attribute(GATKVCFConstants.STRAND_COUNT_BY_SAMPLE_KEY, new int[]{0, 0, 11, 11}).GQ(200).make())});
         tests.add(new Object[]{
                 new VariantContextBuilder(vcBase).alleles(ACG).genotypes(new GenotypeBuilder(base).alleles(AA).AD(homG3AllelesAD).PL(homG3AllelesPL).
                         attribute(GATKVCFConstants.STRAND_COUNT_BY_SAMPLE_KEY, homG3AllelesSAC).make()).make(),
                 new VariantContextBuilder(vcBase).alleles(AG).make(),
                 Arrays.asList(new GenotypeBuilder(base).alleles(AA).PL(new double[]{-20, -40, 0}).AD(new int[]{0, 21}).
-                        attribute(GATKVCFConstants.STRAND_COUNT_BY_SAMPLE_KEY, new int[]{0, 0, 21, 21}).GQ(100).make())});
+                        attribute(GATKVCFConstants.STRAND_COUNT_BY_SAMPLE_KEY, new int[]{0, 0, 21, 21}).GQ(200).make())});
 
         return tests.toArray(new Object[][]{});
     }