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Merge pull request #1555 from broadinstitute/rhl_htsjdk_2.9.0_picard_2.8.3 

Move htsjdk to ver 2.9.0 and picard to ver 2.8.3
This commit is contained in:
Ron Levine 2017-02-17 13:54:17 -05:00 committed by GitHub
parent 67baa9046c ab75b08ea7
commit c55c77ab27
5 changed files with 18 additions and 133 deletions
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36
protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/VariantsToVCFIntegrationTest.java
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@ -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>();

29
public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/utilities/UnzipSingleBlock.java
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@ -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.
@ -42,23 +39,13 @@ public class UnzipSingleBlock extends CommandLineProgram {
@Input(fullName = "block_file", shortName = "b", doc = "block file over which to test unzipping", required = true)
private File blockFile;
@Input(fullName = "compressed_block_size", shortName = "cbs", doc = "size of compressed block", required = true)
private int compressedBufferSize;
public int execute() throws IOException {
final byte[] uncompressedBuffer = new byte[65536];
public int execute() throws IOException, NoSuchMethodException, IllegalAccessException, InvocationTargetException {
byte[] compressedBuffer = new byte[(int)blockFile.length()];
byte[] uncompressedBuffer = new byte[65536];
FileInputStream fis = new FileInputStream(blockFile);
fis.read(compressedBuffer);
fis.close();
BlockGunzipper gunzipper = new BlockGunzipper();
final BlockCompressedInputStream gunzipper = new BlockCompressedInputStream(blockFile);
gunzipper.setCheckCrcs(true);
Method unzipBlock = BlockGunzipper.class.getDeclaredMethod("unzipBlock",byte[].class,byte[].class,Integer.TYPE);
unzipBlock.setAccessible(true);
unzipBlock.invoke(gunzipper,uncompressedBuffer,compressedBuffer,compressedBufferSize);
gunzipper.read(uncompressedBuffer);
gunzipper.close();
System.out.printf("SUCCESS!%n");
@ -70,10 +57,10 @@ 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;
}

4
public/gatk-root/pom.xml
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@ -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>
<picard.version>2.7.2</picard.version>
<htsjdk.version>2.9.0</htsjdk.version>
<picard.version>2.8.3</picard.version>
</properties>
<!-- Dependency configuration (versions, etc.) -->

74
public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/refdata/VariantContextAdaptors.java
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@ -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 ) {

8
public/gatk-utils/src/test/java/org/broadinstitute/gatk/utils/codecs/hapmap/HapMapUnitTest.java
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@ -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);
}