忽略target子文件夹

Order annotations by the order in the model report.

.gitignore

@@ -1,5 +1,6 @@
 .idea/
 .queue/
+**/target/
 /*.bam
 /*.bai
 /*.bed

pom.xml

@@ -13,7 +13,7 @@
     <parent>
         <groupId>org.broadinstitute.gatk</groupId>
         <artifactId>gatk-root</artifactId>
-        <version>3.9-SNAPSHOT</version>
+        <version>3.8-1</version>
         <relativePath>public/gatk-root</relativePath>
     </parent>
 

protected/gatk-package-distribution/pom.xml

@@ -5,7 +5,7 @@
     <parent>
         <groupId>org.broadinstitute.gatk</groupId>
         <artifactId>gatk-aggregator</artifactId>
-        <version>3.9-SNAPSHOT</version>
+        <version>3.8-1</version>
         <relativePath>../..</relativePath>
     </parent>
 

protected/gatk-queue-extensions-distribution/pom.xml

@@ -5,7 +5,7 @@
     <parent>
         <groupId>org.broadinstitute.gatk</groupId>
         <artifactId>gatk-aggregator</artifactId>
-        <version>3.9-SNAPSHOT</version>
+        <version>3.8-1</version>
         <relativePath>../..</relativePath>
     </parent>
 

protected/gatk-queue-package-distribution/pom.xml

@@ -5,7 +5,7 @@
     <parent>
         <groupId>org.broadinstitute.gatk</groupId>
         <artifactId>gatk-aggregator</artifactId>
-        <version>3.9-SNAPSHOT</version>
+        <version>3.8-1</version>
         <relativePath>../..</relativePath>
     </parent>
 

protected/gatk-tools-protected/pom.xml

@@ -5,7 +5,7 @@
     <parent>
         <groupId>org.broadinstitute.gatk</groupId>
         <artifactId>gatk-aggregator</artifactId>
-        <version>3.9-SNAPSHOT</version>
+        <version>3.8-1</version>
         <relativePath>../..</relativePath>
     </parent>
 

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.
-                throw new UserException.CommandLineException( "Annotations specified on the command line do not match annotations in the model report." );
-            }
+            orderAndValidateAnnotations(anMeansTable, dataManager.annotationKeys);
 
             final Map<String, Double> anMeans = getMapFromVectorTable(anMeansTable);
             final Map<String, Double> anStdDevs = getMapFromVectorTable(anStDevsTable);
             dataManager.setNormalization(anMeans, anStdDevs);
 
-            goodModel = GMMFromTables(pmmTable, pmcTable, pPMixTable, numAnnotations);
-            badModel = GMMFromTables(nmmTable, nmcTable, nPMixTable, numAnnotations);
+            goodModel = GMMFromTables(pmmTable, pmcTable, pPMixTable, annotationOrder.size());
+            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 6", "e4f23250b2c87f0d68d042cc3d2ec1d3")});
-        tests.add(new Object[]{1, new PRTest(" -DIQ", "2dfa45f004d3a371fd290ed67fbdf573")});
-        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 -RDQ", "6ffdfc4593e83f7c234b6249412433af")});
+        tests.add(new Object[]{1, new PRTest(" -qq -1", "e9969c6d7fd35d96b82c691b4ced5443")});
+        tests.add(new Object[]{1, new PRTest(" -qq 6", "b4b271acac003b8504b530c5526d43ad")});
+        tests.add(new Object[]{1, new PRTest(" -DIQ", "ec795d16746c3bdf5e54c57337e6eed6")});
+        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", "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/pom.xml

@@ -5,7 +5,7 @@
     <parent>
         <groupId>org.broadinstitute.gatk</groupId>
         <artifactId>gatk-root</artifactId>
-        <version>3.9-SNAPSHOT</version>
+        <version>3.8-1</version>
         <relativePath>../public/gatk-root</relativePath>
     </parent>
 

public/external-example/pom.xml

@@ -9,7 +9,7 @@
     <name>External Example</name>
 
     <properties>
-        <gatk.version>3.9-SNAPSHOT</gatk.version>
+        <gatk.version>3.8-1</gatk.version>
         <!--
         gatk.basedir property must point to your checkout of GATK/GATK until we can get all the
         dependencies out of the committed gatk repo and into central.

public/gatk-engine/pom.xml

@@ -5,7 +5,7 @@
     <parent>
         <groupId>org.broadinstitute.gatk</groupId>
         <artifactId>gatk-aggregator</artifactId>
-        <version>3.9-SNAPSHOT</version>
+        <version>3.8-1</version>
         <relativePath>../..</relativePath>
     </parent>
 

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", " -L chr1:200", "bam", "d362fbf30a2c77a2653f1c8eb2dd8fc1"},
+                {"PrintReads", "exampleCRAM.cram", "", "bam", "50c55e1040aa0ffd4036aa581fcfe8af"},
+                {"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("fa90ff91ac0cc689c71a3460a3530b8b", createTempFileFromBase(baseOutputFile.getAbsolutePath().substring(0,baseOutputFile.getAbsolutePath().indexOf(".bam"))+".bai"));
+        spec.addAuxFile("70ac0317c0c13d885e6c2de4f837cdd3",createTempFileFromBase(baseOutputFile.getAbsolutePath()));
+        spec.addAuxFile("df469db01610ddb731868dfb28917142", createTempFileFromBase(baseOutputFile.getAbsolutePath().substring(0,baseOutputFile.getAbsolutePath().indexOf(".bam"))+".bai"));
 
         executeTest("testMixedMappedAndUnmapped",spec);
     }

public/gatk-queue-extensions-generator/pom.xml

@@ -5,7 +5,7 @@
     <parent>
         <groupId>org.broadinstitute.gatk</groupId>
         <artifactId>gatk-aggregator</artifactId>
-        <version>3.9-SNAPSHOT</version>
+        <version>3.8-1</version>
         <relativePath>../..</relativePath>
     </parent>
 

public/gatk-queue-extensions-public/pom.xml

@@ -5,7 +5,7 @@
     <parent>
         <groupId>org.broadinstitute.gatk</groupId>
         <artifactId>gatk-aggregator</artifactId>
-        <version>3.9-SNAPSHOT</version>
+        <version>3.8-1</version>
         <relativePath>../..</relativePath>
     </parent>
 

public/gatk-queue/pom.xml

@@ -5,7 +5,7 @@
     <parent>
         <groupId>org.broadinstitute.gatk</groupId>
         <artifactId>gatk-aggregator</artifactId>
-        <version>3.9-SNAPSHOT</version>
+        <version>3.8-1</version>
         <relativePath>../..</relativePath>
     </parent>
 

public/gatk-root/pom.xml

@@ -12,7 +12,7 @@
 
     <groupId>org.broadinstitute.gatk</groupId>
     <artifactId>gatk-root</artifactId>
-    <version>3.9-SNAPSHOT</version>
+    <version>3.8-1</version>
     <packaging>pom</packaging>
     <name>GATK Root</name>
 
@@ -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/pom.xml

@@ -5,7 +5,7 @@
     <parent>
         <groupId>org.broadinstitute.gatk</groupId>
         <artifactId>gatk-aggregator</artifactId>
-        <version>3.9-SNAPSHOT</version>
+        <version>3.8-1</version>
         <relativePath>../..</relativePath>
     </parent>
 

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 testQClip2() { testClipper("clipQSum2", "-QT 2", Q10ClipOutput, "27847d330b962e60650df23b6efc8c3c"); }
-    @Test public void testQClip10() { testClipper("clipQSum10", "-QT 10", "b29c5bc1cb9006ed9306d826a11d444f", "27847d330b962e60650df23b6efc8c3c"); }
-    @Test public void testQClip20() { testClipper("clipQSum20", "-QT 20", "6c3434dce66ae5c9eeea502f10fb9bee", "f89ec5439e88f5a75433150da0069034"); }
+    @Test public void testQClip0() { testClipper("clipQSum0", "-QT 0", "117a4760b54308f81789c39b1c9de578", "2e617e0f0b4a1bf45dbb666da0a6a16c"); }
+    @Test public void testQClip2() { testClipper("clipQSum2", "-QT 2", Q10ClipOutput, "1b0d2317dfd1fd5a4d14eea3f560ac17"); }
+    @Test public void testQClip10() { testClipper("clipQSum10", "-QT 10", "b29c5bc1cb9006ed9306d826a11d444f", "1b0d2317dfd1fd5a4d14eea3f560ac17"); }
+    @Test public void testQClip20() { testClipper("clipQSum20", "-QT 20", "6c3434dce66ae5c9eeea502f10fb9bee", "3a9a10966cce58baf9e9400a2c5f99ca"); }
 
-    @Test public void testClipRange1() { testClipper("clipRange1", "-CT 1-5", "b5acd753226e25b1e088838c1aab9117", "987007f6e430cad4cb4a8d1cc1f45d91"); }
-    @Test public void testClipRange2() { testClipper("clipRange2", "-CT 1-5,11-15", "be4fcad5b666a5540028b774169cbad7", "ec4cf54ed50a6baf69dbf98782c19aeb"); }
+    @Test public void testClipRange1() { testClipper("clipRange1", "-CT 1-5", "b5acd753226e25b1e088838c1aab9117", "701f03388ffaeb0f92be1e719e2477df"); }
+    @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 testClipSeqFile() { testClipper("clipSeqXF", "-XF " + privateTestDir + "seqsToClip.fasta", "22cd33dbd06cc425ce3626360367bfca", "906871df304dd966682e5798d59fc86b"); }
+    @Test public void testClipSeq() { testClipper("clipSeqX", "-X CCCCC", "db199bd06561c9f2122f6ffb07941fbc", "daa41acd8c9f1a75c8107d0fd0db8cf0"); }
+    @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 testClipQ0s() { testClipper("testClipQs", "-QT 10 -CR WRITE_Q0S", Q10ClipOutput, "195b8bdfc0186fdca742764aa9b06363"); }
-    @Test public void testClipSoft() { testClipper("testClipSoft", "-QT 10 -CR SOFTCLIP_BASES", Q10ClipOutput, "08d16051be0b3fa3453eb1e6ca48b098"); }
+    @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, "b7ce95f277d5f66b7f5a60ffbf9692cf"); }
+    @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"}, " -n 10", "917440a38aba707ec0e012168590981a")},
+                {new PRTest(hg18Reference, new String[]{"HiSeq.1mb.bam"}, " -simplifyBAM", "60255a68df1b8f2fbba373d75274f0de")},
+                {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"}, " -L 1", "5b1154cc81dba6bcfe76188e4df8d79c")},
-                {new PRTest(b37KGReference, new String[]{"unmappedFlagReadsInLastLinearBin.cram"}, " -L 1:10001 -L GL000192.1:500204", "a84efdc3d4a8d6329b5f0b494dd280d2")},
-                {new PRTest(b37KGReference, new String[]{"unmappedFlagReadsInLastLinearBin.bam"}, " -L unmapped", "cbd3d1d50c8674f79033aa8c36aa3cd1")},
-                {new PRTest(b37KGReference, new String[]{"unmappedFlagReadsInLastLinearBin.bam"}, " -L 1 -L unmapped", "5b1154cc81dba6bcfe76188e4df8d79c")},
-                {new PRTest(b37KGReference, new String[]{"oneReadAllInsertion.bam"}, "",  "e212d1799ae797e781b17e630656a9a1")},
-                {new PRTest(b37KGReference, new String[]{"NA12878.1_10mb_2_10mb.bam"}, "",  "0387c61303140d8899fcbfdd3e72ed80")},
+                {new PRTest(b37KGReference, new String[]{"unmappedFlagReadsInLastLinearBin.bam"}, "", "3d67c398ce2ac1deeddbccbd850380a7")},
+                {new PRTest(b37KGReference, new String[]{"unmappedFlagReadsInLastLinearBin.bam"}, " -L 1", "37cdd8871843693f2650d7b48c8ae1d4")},
+                {new PRTest(b37KGReference, new String[]{"unmappedFlagReadsInLastLinearBin.cram"}, " -L 1:10001 -L GL000192.1:500204", "4d63fd6e977a53e5d9590bd030b40bd0")},
+                {new PRTest(b37KGReference, new String[]{"unmappedFlagReadsInLastLinearBin.bam"}, " -L unmapped", "a834400e3bd69045eb8a9e94131633f5")},
+                {new PRTest(b37KGReference, new String[]{"unmappedFlagReadsInLastLinearBin.bam"}, " -L 1 -L unmapped", "37cdd8871843693f2650d7b48c8ae1d4")},
+                {new PRTest(b37KGReference, new String[]{"oneReadAllInsertion.bam"}, "",  "6c04aac25e2136fee395897aac96bea8")},
+                {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, "NA12891", "af01069bc3da4252ce8417a03d11f48b");
-        addSplitOutput(spec, prefix, "NA12892", "cfa1cb6aaca03900160bd5627f4f698b");
+        addSplitOutput(spec, prefix, "NA12878", "356bddf614a44a0234f7b116f5cde998");
+        addSplitOutput(spec, prefix, "NA12891", "5dd92a0089e3f781e77d94010264b9fd");
+        addSplitOutput(spec, prefix, "NA12892", "ea8f16c18c89b49ce9d32d76c6af75f9");
         executeTest("testSplitSamFile", spec);
     }
 

public/gatk-utils/pom.xml

@@ -5,7 +5,7 @@
     <parent>
         <groupId>org.broadinstitute.gatk</groupId>
         <artifactId>gatk-aggregator</artifactId>
-        <version>3.9-SNAPSHOT</version>
+        <version>3.8-1</version>
         <relativePath>../..</relativePath>
     </parent>
 

public/gsalib/pom.xml

@@ -5,7 +5,7 @@
     <parent>
         <groupId>org.broadinstitute.gatk</groupId>
         <artifactId>gatk-aggregator</artifactId>
-        <version>3.9-SNAPSHOT</version>
+        <version>3.8-1</version>
         <relativePath>../..</relativePath>
     </parent>
 

public/package-tests/pom.xml

@@ -9,7 +9,7 @@
     <parent>
         <groupId>org.broadinstitute.gatk</groupId>
         <artifactId>gatk-root</artifactId>
-        <version>3.9-SNAPSHOT</version>
+        <version>3.8-1</version>
         <relativePath>../gatk-root</relativePath>
     </parent>
 

public/pom.xml

@@ -5,7 +5,7 @@
     <parent>
         <groupId>org.broadinstitute.gatk</groupId>
         <artifactId>gatk-root</artifactId>
-        <version>3.9-SNAPSHOT</version>
+        <version>3.8-1</version>
         <relativePath>gatk-root</relativePath>
     </parent>