Move htsjdk to ver 2.9.0 and picard to ver 2.8.3

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

@@ -67,42 +67,6 @@ import java.util.ArrayList;
  */
 public class VariantsToVCFIntegrationTest extends WalkerTest {
 
-    @Test
-    public void testVariantsToVCFUsingGeliInput() {
-        List<String> md5 = new ArrayList<String>();
-        md5.add("c73bcc3658b4a4d8bd9d794069d41dbd");
-
-        WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
-                "-R " + b36KGReference +
-                        " --variant:GeliText " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.lod5.variants.geli.calls" +
-                        " -T VariantsToVCF" +
-                        " -L 1:10,000,000-11,000,000" +
-                        " -sample NA123AB" +
-                        " -o %s" +
-                        " --no_cmdline_in_header",
-                1, // just one output file
-                md5);
-        executeTest("testVariantsToVCFUsingGeliInput - calls", spec).getFirst();
-    }
-
-    @Test
-    public void testGenotypesToVCFUsingGeliInput() {
-        List<String> md5 = new ArrayList<String>();
-        md5.add("a1771924b58dd633620114ef0f462acb");
-
-        WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
-                "-R " + b36KGReference +
-                        " --variant:GeliText " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.lod5.genotypes.geli.calls" +
-                        " -T VariantsToVCF" +
-                        " -L 1:10,100,000-10,200,000" +
-                        " -sample NA123AB" +
-                        " -o %s" +
-                        " --no_cmdline_in_header",
-                1, // just one output file
-                md5);
-        executeTest("testVariantsToVCFUsingGeliInput - genotypes", spec).getFirst();
-    }
-
     @Test
     public void testGenotypesToVCFUsingHapMapInput() {
         List<String> md5 = new ArrayList<String>();

public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/utilities/UnzipSingleBlock.java

@@ -25,15 +25,12 @@
 
 package org.broadinstitute.gatk.engine.datasources.reads.utilities;
 
-import htsjdk.samtools.util.BlockGunzipper;
+import htsjdk.samtools.util.BlockCompressedInputStream;
 import org.broadinstitute.gatk.utils.commandline.CommandLineProgram;
 import org.broadinstitute.gatk.utils.commandline.Input;
 
 import java.io.File;
-import java.io.FileInputStream;
 import java.io.IOException;
-import java.lang.reflect.InvocationTargetException;
-import java.lang.reflect.Method;
 
 /**
  * Test decompression of a single BGZF block.
@@ -45,20 +42,12 @@ public class UnzipSingleBlock extends CommandLineProgram {
     @Input(fullName = "compressed_block_size", shortName = "cbs", doc = "size of compressed block", required = true)
     private int compressedBufferSize;
 
-    public int execute() throws IOException, NoSuchMethodException, IllegalAccessException, InvocationTargetException {
+    public int execute() throws IOException {
-        byte[] compressedBuffer = new byte[(int)blockFile.length()];
+        final byte[] uncompressedBuffer = new byte[65536];
-        byte[] uncompressedBuffer = new byte[65536];
 
-        FileInputStream fis = new FileInputStream(blockFile);
+        final BlockCompressedInputStream gunzipper = new BlockCompressedInputStream(blockFile);
-        fis.read(compressedBuffer);
-        fis.close();
-
-        BlockGunzipper gunzipper = new BlockGunzipper();
         gunzipper.setCheckCrcs(true);
-        Method unzipBlock = BlockGunzipper.class.getDeclaredMethod("unzipBlock",byte[].class,byte[].class,Integer.TYPE);
+        gunzipper.read(uncompressedBuffer);
-        unzipBlock.setAccessible(true);
-
-        unzipBlock.invoke(gunzipper,uncompressedBuffer,compressedBuffer,compressedBufferSize);
 
         System.out.printf("SUCCESS!%n");
 
@@ -70,10 +59,10 @@ public class UnzipSingleBlock extends CommandLineProgram {
      * @param argv Command-line argument text.
      * @throws Exception on error.
      */
-    public static void main(String[] argv) throws Exception {
+    public static void main(final String[] argv) throws Exception {
         int returnCode = 0;
         try {
-            UnzipSingleBlock instance = new UnzipSingleBlock();
+            final UnzipSingleBlock instance = new UnzipSingleBlock();
             start(instance, argv);
             returnCode = 0;
         }

public/gatk-root/pom.xml

@@ -44,8 +44,8 @@
         <test.listeners>org.testng.reporters.FailedReporter,org.testng.reporters.JUnitXMLReporter,org.broadinstitute.gatk.utils.TestNGTestTransformer,org.broadinstitute.gatk.utils.GATKTextReporter,org.uncommons.reportng.HTMLReporter</test.listeners>
 
         <!-- Version numbers for picard and htsjdk -->
-        <htsjdk.version>2.8.1</htsjdk.version>
+        <htsjdk.version>2.9.0</htsjdk.version>
-        <picard.version>2.7.2</picard.version>
+        <picard.version>2.8.3</picard.version>
     </properties>
 
     <!-- Dependency configuration (versions, etc.) -->

public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/refdata/VariantContextAdaptors.java

@@ -25,15 +25,10 @@
 
 package org.broadinstitute.gatk.utils.refdata;
 
-import htsjdk.samtools.util.SequenceUtil;
 import htsjdk.tribble.Feature;
-import htsjdk.tribble.annotation.Strand;
-import htsjdk.tribble.gelitext.GeliTextFeature;
 import org.broadinstitute.gatk.utils.contexts.ReferenceContext;
-import org.broadinstitute.gatk.utils.GenomeLoc;
 import org.broadinstitute.gatk.utils.classloader.PluginManager;
 import org.broadinstitute.gatk.utils.codecs.hapmap.RawHapMapFeature;
-import org.broadinstitute.gatk.utils.variant.GATKVariantContextUtils;
 import htsjdk.variant.variantcontext.*;
 
 import java.util.*;
@@ -59,10 +54,10 @@ public class VariantContextAdaptors {
     //
     // --------------------------------------------------------------------------------------------------------------
 
-    private static Map<Class<? extends Feature>,VCAdaptor> adaptors = new HashMap<Class<? extends Feature>,VCAdaptor>();
+    private static Map<Class<? extends Feature>,VCAdaptor> adaptors = new HashMap<>();
 
     static {
-        PluginManager<VCAdaptor> vcAdaptorManager = new PluginManager<VCAdaptor>(VCAdaptor.class);
+        PluginManager<VCAdaptor> vcAdaptorManager = new PluginManager<>(VCAdaptor.class);
         List<VCAdaptor> adaptorInstances = vcAdaptorManager.createAllTypes();
         for(VCAdaptor adaptor: adaptorInstances)
             adaptors.put(adaptor.getAdaptableFeatureType(),adaptor);
@@ -110,67 +105,6 @@ public class VariantContextAdaptors {
         }
     }
 
-
-    // --------------------------------------------------------------------------------------------------------------
-    //
-    // GELI to VariantContext
-    //
-    // --------------------------------------------------------------------------------------------------------------
-
-    private static class GeliTextAdaptor implements VCAdaptor {
-        /**
-         * Converts Geli text records to VariantContext. 
-         * @return GeliTextFeature.
-         */
-        @Override
-        public Class<? extends Feature> getAdaptableFeatureType() { return GeliTextFeature.class; }
-
-        /**
-         * convert to a Variant Context, given:
-         * @param name  the name of the ROD
-         * @param input the Rod object, in this case a RodGeliText
-         * @param ref   the reference context
-         * @return a VariantContext object
-         */
-        @Override
-        public VariantContext convert(String name, Object input, ReferenceContext ref) {
-            GeliTextFeature geli = (GeliTextFeature)input;
-            if ( ! Allele.acceptableAlleleBases(String.valueOf(geli.getRefBase())) )
-                return null;
-            Allele refAllele = Allele.create(String.valueOf(geli.getRefBase()), true);
-
-            // make sure we can convert it
-            if ( geli.getGenotype().isHet() || !geli.getGenotype().containsBase(geli.getRefBase())) {
-                // add the reference allele
-                List<Allele> alleles = new ArrayList<Allele>();
-                List<Allele> genotypeAlleles = new ArrayList<Allele>();
-                // add all of the alt alleles
-                for ( char alt : geli.getGenotype().toString().toCharArray() ) {
-                    if ( ! Allele.acceptableAlleleBases(String.valueOf(alt)) ) {
-                        return null;
-                    }
-                    Allele allele = Allele.create(String.valueOf(alt), false);
-                    if (!alleles.contains(allele) && !refAllele.basesMatch(allele.getBases())) alleles.add(allele);
-
-                    // add the allele, first checking if it's reference or not
-                    if (!refAllele.basesMatch(allele.getBases())) genotypeAlleles.add(allele);
-                    else genotypeAlleles.add(refAllele);
-                }
-
-                Map<String, Object> attributes = new HashMap<String, Object>();
-                Collection<Genotype> genotypes = new ArrayList<Genotype>();
-                Genotype call = GenotypeBuilder.create(name, genotypeAlleles);
-
-                // add the call to the genotype list, and then use this list to create a VariantContext
-                genotypes.add(call);
-                alleles.add(refAllele);
-                GenomeLoc loc = ref.getGenomeLocParser().createGenomeLoc(geli.getChr(),geli.getStart());
-                return new VariantContextBuilder(name, loc.getContig(), loc.getStart(), loc.getStop(), alleles).genotypes(genotypes).log10PError(-1 * geli.getLODBestToReference()).attributes(attributes).make();
-            } else
-                return null; // can't handle anything else
-        }
-    }
-
     // --------------------------------------------------------------------------------------------------------------
     //
     // HapMap to VariantContext
@@ -203,7 +137,7 @@ public class VariantContextAdaptors {
             if ( index < 0 )
                 return null; // we weren't given enough reference context to create the VariantContext
 
-            HashSet<Allele> alleles = new HashSet<Allele>();
+            HashSet<Allele> alleles = new HashSet<>();
             Allele refSNPAllele = Allele.create(ref.getBase(), true);
             int deletionLength = -1;
 
@@ -231,7 +165,7 @@ public class VariantContextAdaptors {
 
                 String a1 = genotypeStrings[i].substring(0,1);
                 String a2 = genotypeStrings[i].substring(1);
-                ArrayList<Allele> myAlleles = new ArrayList<Allele>(2);
+                ArrayList<Allele> myAlleles = new ArrayList<>(2);
 
                 // use the mapping to actual alleles, if available
                 if ( alleleMap != null ) {

public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/codecs/hapmap/HapMapUnitTest.java

@@ -28,7 +28,7 @@ package org.broadinstitute.gatk.utils.codecs.hapmap;
 import htsjdk.tribble.annotation.Strand;
 import htsjdk.tribble.readers.LineIterator;
 import htsjdk.tribble.readers.LineIteratorImpl;
-import htsjdk.tribble.readers.LineReaderUtil;
+import htsjdk.tribble.readers.SynchronousLineReader;
 import htsjdk.tribble.readers.PositionalBufferedStream;
 import org.broadinstitute.gatk.utils.BaseTest;
 import org.testng.Assert;
@@ -160,11 +160,11 @@ public class HapMapUnitTest extends BaseTest {
         Assert.assertFalse(codec.canDecode("filename." + RawHapMapCodec.FILE_EXT + EXTRA_CHAR));
         Assert.assertFalse(codec.canDecode("filename" + RawHapMapCodec.FILE_EXT));
     }
-
+    
-
     public LineIterator getLineIterator() {
         try {
-            return new LineIteratorImpl(LineReaderUtil.fromBufferedStream(new PositionalBufferedStream(new FileInputStream(hapMapFile))));
+
+            return new LineIteratorImpl(new SynchronousLineReader(new PositionalBufferedStream(new FileInputStream(hapMapFile))));
         } catch (FileNotFoundException e) {
             Assert.fail("Unable to open hapmap file : " + hapMapFile);
         }