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Merge pull request #691 from broadinstitute/ldg_update_htsjdk 

Update GATK to work with latest htsjdk
This commit is contained in:
Eric Banks 2014-07-30 14:32:23 -04:00
parent d69af637bf 4373922ee6
commit 66ccc636b8
23 changed files with 49 additions and 71 deletions
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2
public/gatk-queue-extensions-public/src/main/scala/org/broadinstitute/gatk/queue/extensions/picard/PicardBamFunction.scala
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@ -27,7 +27,7 @@ package org.broadinstitute.gatk.queue.extensions.picard
import java.io.File
import org.broadinstitute.gatk.queue.function.JavaCommandLineFunction
import htsjdk.samtools.SAMFileReader.ValidationStringency
import htsjdk.samtools.ValidationStringency
import htsjdk.samtools.SAMFileHeader.SortOrder
/**

2
public/gatk-queue-extensions-public/src/main/scala/org/broadinstitute/gatk/queue/extensions/picard/PicardMetricsFunction.scala
View File

@ -27,7 +27,7 @@ package org.broadinstitute.gatk.queue.extensions.picard
import java.io.File
import org.broadinstitute.gatk.queue.function.JavaCommandLineFunction
import htsjdk.samtools.SAMFileReader.ValidationStringency
import htsjdk.samtools.ValidationStringency
import htsjdk.samtools.SAMFileHeader.SortOrder
/**

4
public/gatk-root/pom.xml
View File

@ -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>1.112.1452</htsjdk.version>
<picard.version>1.112.1452</picard.version>
<htsjdk.version>1.118.1556</htsjdk.version>
<picard.version>1.118.1521</picard.version>
</properties>
<!-- Dependency configuration (versions, etc.) -->

7
public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/ReadProperties.java
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@ -27,6 +27,7 @@ package org.broadinstitute.gatk.engine;
import htsjdk.samtools.SAMFileHeader;
import htsjdk.samtools.SAMFileReader;
import htsjdk.samtools.ValidationStringency;
import org.broadinstitute.gatk.engine.arguments.ValidationExclusion;
import org.broadinstitute.gatk.engine.datasources.reads.SAMReaderID;
import org.broadinstitute.gatk.engine.downsampling.DownsamplingMethod;
@ -56,7 +57,7 @@ public class ReadProperties {
private final Collection<SAMReaderID> readers;
private final SAMFileHeader header;
private final SAMFileHeader.SortOrder sortOrder;
private final SAMFileReader.ValidationStringency validationStringency;
private final ValidationStringency validationStringency;
private final DownsamplingMethod downsamplingMethod;
private final ValidationExclusion exclusionList;
private final Collection<ReadFilter> supplementalFilters;
@ -107,7 +108,7 @@ public class ReadProperties {
* How strict should validation be?
* @return Stringency of validation.
*/
public SAMFileReader.ValidationStringency getValidationStringency() {
public ValidationStringency getValidationStringency() {
return validationStringency;
}
@ -173,7 +174,7 @@ public class ReadProperties {
SAMFileHeader header,
SAMFileHeader.SortOrder sortOrder,
boolean useOriginalBaseQualities,
SAMFileReader.ValidationStringency strictness,
ValidationStringency strictness,
DownsamplingMethod downsamplingMethod,
ValidationExclusion exclusionList,
Collection<ReadFilter> supplementalFilters,

2
public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/alignment/bwa/java/AlignerTestHarness.java
View File

@ -63,7 +63,7 @@ public class AlignerTestHarness {
int count = 0;
SAMFileReader reader = new SAMFileReader(bamFile);
reader.setValidationStringency(SAMFileReader.ValidationStringency.SILENT);
reader.setValidationStringency(ValidationStringency.SILENT);
int mismatches = 0;
int failures = 0;

3
public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/arguments/GATKArgumentCollection.java
View File

@ -26,6 +26,7 @@
package org.broadinstitute.gatk.engine.arguments;
import htsjdk.samtools.SAMFileReader;
import htsjdk.samtools.ValidationStringency;
import org.broadinstitute.gatk.utils.commandline.*;
import org.broadinstitute.gatk.engine.GenomeAnalysisEngine;
import org.broadinstitute.gatk.engine.downsampling.DownsampleType;
@ -361,7 +362,7 @@ public class GATKArgumentCollection {
* Keep in mind that if you set this to LENIENT, we may refuse to provide you with support if anything goes wrong.
*/
@Argument(fullName = "validation_strictness", shortName = "S", doc = "How strict should we be with validation", required = false)
public SAMFileReader.ValidationStringency strictnessLevel = SAMFileReader.ValidationStringency.SILENT;
public ValidationStringency strictnessLevel = ValidationStringency.SILENT;
/**
* Some tools keep program records in the SAM header by default. Use this argument to override that behavior and discard program records for the SAM header.
*/

38
public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/SAMDataSource.java
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@ -86,7 +86,7 @@ public class SAMDataSource {
/**
* How strict are the readers driving this data source.
*/
private final SAMFileReader.ValidationStringency validationStringency;
private final ValidationStringency validationStringency;
/**
* Do we want to remove the program records from this data source?
@ -183,7 +183,7 @@ public class SAMDataSource {
numFileHandles,
genomeLocParser,
false,
SAMFileReader.ValidationStringency.STRICT,
ValidationStringency.STRICT,
null,
null,
new ValidationExclusion(),
@ -202,7 +202,7 @@ public class SAMDataSource {
Integer numFileHandles,
GenomeLocParser genomeLocParser,
boolean useOriginalBaseQualities,
SAMFileReader.ValidationStringency strictness,
ValidationStringency strictness,
Integer readBufferSize,
DownsamplingMethod downsamplingMethod,
ValidationExclusion exclusionList,
@ -251,7 +251,7 @@ public class SAMDataSource {
Integer numFileHandles,
GenomeLocParser genomeLocParser,
boolean useOriginalBaseQualities,
SAMFileReader.ValidationStringency strictness,
ValidationStringency strictness,
Integer readBufferSize,
DownsamplingMethod downsamplingMethod,
ValidationExclusion exclusionList,
@ -800,7 +800,7 @@ public class SAMDataSource {
* @param reader Reader for which to determine the id.
* @return id of the given reader.
*/
protected synchronized SAMReaderID getReaderID(SAMFileReader reader) {
protected synchronized SAMReaderID getReaderID(SamReader reader) {
for(SAMReaders readers: allResources) {
SAMReaderID id = readers.getReaderID(reader);
if(id != null)
@ -845,7 +845,7 @@ public class SAMDataSource {
* @param validationStringency validation stringency.
* @param removeProgramRecords indicate whether to clear program records from the readers
*/
public SAMReaders(Collection<SAMReaderID> readerIDs, SAMFileReader.ValidationStringency validationStringency, boolean removeProgramRecords) {
public SAMReaders(Collection<SAMReaderID> readerIDs, ValidationStringency validationStringency, boolean removeProgramRecords) {
final int totalNumberOfFiles = readerIDs.size();
int readerNumber = 1;
final SimpleTimer timer = new SimpleTimer().start();
@ -1028,7 +1028,7 @@ public class SAMDataSource {
* @param reader Reader for which to search.
* @return The id associated the given reader, or null if the reader is not present in this collection.
*/
protected SAMReaderID getReaderID(SAMFileReader reader) {
protected SAMReaderID getReaderID(SamReader reader) {
for(Map.Entry<SAMReaderID,SAMFileReader> entry: readers.entrySet()) {
if(reader == entry.getValue())
return entry.getKey();
@ -1132,33 +1132,11 @@ public class SAMDataSource {
/**
* Locates the index file alongside the given BAM, if present.
* TODO: This is currently a hachetjob that reaches into Picard and pulls out its index file locator. Replace with something more permanent.
* @param bamFile The data file to use.
* @return A File object if the index file is present; null otherwise.
*/
private File findIndexFile(File bamFile) {
File indexFile;
try {
Class bamFileReaderClass = Class.forName("htsjdk.samtools.BAMFileReader");
Method indexFileLocator = bamFileReaderClass.getDeclaredMethod("findIndexFile",File.class);
indexFileLocator.setAccessible(true);
indexFile = (File)indexFileLocator.invoke(null,bamFile);
}
catch(ClassNotFoundException ex) {
throw new ReviewedGATKException("Unable to locate BAMFileReader class, used to check for index files");
}
catch(NoSuchMethodException ex) {
throw new ReviewedGATKException("Unable to locate Picard index file locator.");
}
catch(IllegalAccessException ex) {
throw new ReviewedGATKException("Unable to access Picard index file locator.");
}
catch(InvocationTargetException ex) {
throw new ReviewedGATKException("Unable to invoke Picard index file locator.");
}
return indexFile;
return SamFiles.findIndex(bamFile);
}
/**

3
public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/utilities/BAMFileStat.java
View File

@ -27,6 +27,7 @@ package org.broadinstitute.gatk.engine.datasources.reads.utilities;
import htsjdk.samtools.BAMIndex;
import htsjdk.samtools.SAMFileReader;
import htsjdk.samtools.ValidationStringency;
import org.broadinstitute.gatk.utils.commandline.Argument;
import org.broadinstitute.gatk.utils.commandline.CommandLineProgram;
import org.broadinstitute.gatk.utils.exceptions.ReviewedGATKException;
@ -85,7 +86,7 @@ public class BAMFileStat extends CommandLineProgram {
BAMIndex index;
reader = new SAMFileReader(bamFile);
reader.setValidationStringency(SAMFileReader.ValidationStringency.SILENT);
reader.setValidationStringency(ValidationStringency.SILENT);
reader.enableIndexCaching(true);
index = reader.getIndex();

7
public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/datasources/reads/utilities/PrintBAMRegion.java
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@ -25,10 +25,7 @@
package org.broadinstitute.gatk.engine.datasources.reads.utilities;
import htsjdk.samtools.GATKBAMFileSpan;
import htsjdk.samtools.GATKChunk;
import htsjdk.samtools.SAMFileReader;
import htsjdk.samtools.SAMRecordIterator;
import htsjdk.samtools.*;
import org.broadinstitute.gatk.utils.commandline.Argument;
import org.broadinstitute.gatk.utils.commandline.CommandLineProgram;
import org.broadinstitute.gatk.utils.exceptions.UserException;
@ -58,7 +55,7 @@ public class PrintBAMRegion extends CommandLineProgram {
public int execute() {
SAMFileReader reader = new SAMFileReader(input);
reader.setValidationStringency(SAMFileReader.ValidationStringency.SILENT);
reader.setValidationStringency(ValidationStringency.SILENT);
Pattern regionPattern = Pattern.compile("(\\d+):(\\d+)-(\\d+):(\\d+)");
Matcher matcher = regionPattern.matcher(region);

3
public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/io/OutputTracker.java
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@ -26,6 +26,7 @@
package org.broadinstitute.gatk.engine.io;
import htsjdk.samtools.SAMFileReader;
import htsjdk.samtools.ValidationStringency;
import org.broadinstitute.gatk.utils.commandline.ArgumentSource;
import org.broadinstitute.gatk.engine.io.storage.Storage;
import org.broadinstitute.gatk.engine.io.storage.StorageFactory;
@ -77,7 +78,7 @@ public abstract class OutputTracker {
*/
public abstract <T> T getStorage( Stub<T> stub );
public void prepareWalker( Walker walker, SAMFileReader.ValidationStringency strictnessLevel ) {
public void prepareWalker( Walker walker, ValidationStringency strictnessLevel ) {
for( Map.Entry<ArgumentSource,Object> io: inputs.entrySet() ) {
ArgumentSource targetField = io.getKey();
Object targetValue = io.getValue();

3
public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/engine/walkers/diffengine/BAMDiffableReader.java
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@ -28,6 +28,7 @@ package org.broadinstitute.gatk.engine.walkers.diffengine;
import htsjdk.samtools.SAMFileReader;
import htsjdk.samtools.SAMRecord;
import htsjdk.samtools.SAMRecordIterator;
import htsjdk.samtools.ValidationStringency;
import htsjdk.samtools.util.BlockCompressedInputStream;
import java.io.*;
@ -49,7 +50,7 @@ public class BAMDiffableReader implements DiffableReader {
@Override
public DiffElement readFromFile(File file, int maxElementsToRead) {
final SAMFileReader reader = new SAMFileReader(file, null); // null because we don't want it to look for the index
reader.setValidationStringency(SAMFileReader.ValidationStringency.SILENT);
reader.setValidationStringency(ValidationStringency.SILENT);
DiffNode root = DiffNode.rooted(file.getName());
SAMRecordIterator iterator = reader.iterator();

5
public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/sam/SAMFileReaderBuilder.java
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@ -26,6 +26,7 @@
package org.broadinstitute.gatk.utils.sam;
import htsjdk.samtools.SAMFileReader;
import htsjdk.samtools.ValidationStringency;
import org.broadinstitute.gatk.utils.exceptions.ReviewedGATKException;
import java.io.File;
@ -47,7 +48,7 @@ public class SAMFileReaderBuilder {
/**
* What compression level should be used when building this file?
*/
private SAMFileReader.ValidationStringency validationStringency = null;
private ValidationStringency validationStringency = null;
/**
* Sets the handle of the sam file to which data should be written.
@ -61,7 +62,7 @@ public class SAMFileReaderBuilder {
* Sets the validation stringency to apply when reading this sam file.
* @param validationStringency Stringency to apply. Must not be null.
*/
public void setValidationStringency( SAMFileReader.ValidationStringency validationStringency ) {
public void setValidationStringency( ValidationStringency validationStringency ) {
this.validationStringency = validationStringency;
}

7
public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/EngineFeaturesIntegrationTest.java
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@ -25,10 +25,7 @@
package org.broadinstitute.gatk.engine;
import htsjdk.samtools.SAMFileReader;
import htsjdk.samtools.SAMReadGroupRecord;
import htsjdk.samtools.SAMRecord;
import htsjdk.samtools.SAMSequenceDictionary;
import htsjdk.samtools.*;
import htsjdk.samtools.util.CloseableIterator;
import htsjdk.tribble.readers.LineIterator;
import org.broadinstitute.gatk.engine.walkers.WalkerTest;
@ -308,7 +305,7 @@ public class EngineFeaturesIntegrationTest extends WalkerTest {
final File outputBam = executeTest("testGATKEngineConsolidatesCigars", spec).first.get(0);
final SAMFileReader reader = new SAMFileReader(outputBam);
reader.setValidationStringency(SAMFileReader.ValidationStringency.SILENT);
reader.setValidationStringency(ValidationStringency.SILENT);
reader.setSAMRecordFactory(new GATKSamRecordFactory());
final SAMRecord read = reader.iterator().next();

8
public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/ReadMetricsUnitTest.java
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@ -152,7 +152,7 @@ public class ReadMetricsUnitTest extends BaseTest {
final SAMDataSource dataSource = new SAMDataSource(samFiles, new ThreadAllocation(), null, genomeLocParser,
false,
SAMFileReader.ValidationStringency.STRICT,
ValidationStringency.STRICT,
null,
null,
new ValidationExclusion(),
@ -187,7 +187,7 @@ public class ReadMetricsUnitTest extends BaseTest {
final SAMDataSource dataSource = new SAMDataSource(samFiles, new ThreadAllocation(), null, genomeLocParser,
false,
SAMFileReader.ValidationStringency.STRICT,
ValidationStringency.STRICT,
null,
null,
new ValidationExclusion(),
@ -228,7 +228,7 @@ public class ReadMetricsUnitTest extends BaseTest {
final SAMDataSource dataSource = new SAMDataSource(samFiles, new ThreadAllocation(), null, genomeLocParser,
false,
SAMFileReader.ValidationStringency.STRICT,
ValidationStringency.STRICT,
null,
null,
new ValidationExclusion(),
@ -275,7 +275,7 @@ public class ReadMetricsUnitTest extends BaseTest {
final SAMDataSource dataSource = new SAMDataSource(samFiles, new ThreadAllocation(), null, genomeLocParser,
false,
SAMFileReader.ValidationStringency.STRICT,
ValidationStringency.STRICT,
null,
null,
new ValidationExclusion(),

2
public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/datasources/reads/ReadShardBalancerUnitTest.java
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@ -88,7 +88,7 @@ public class ReadShardBalancerUnitTest extends BaseTest {
null,
new GenomeLocParser(header.getSequenceDictionary()),
false,
SAMFileReader.ValidationStringency.SILENT,
ValidationStringency.SILENT,
ReadShard.DEFAULT_MAX_READS, // reset ReadShard.MAX_READS to ReadShard.DEFAULT_MAX_READS for each test
downsamplingMethod,
new ValidationExclusion(),

12
public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/datasources/reads/SAMDataSourceUnitTest.java
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@ -105,7 +105,7 @@ public class SAMDataSourceUnitTest extends BaseTest {
null,
genomeLocParser,
false,
SAMFileReader.ValidationStringency.SILENT,
ValidationStringency.SILENT,
null,
null,
new ValidationExclusion(),
@ -159,7 +159,7 @@ public class SAMDataSourceUnitTest extends BaseTest {
null,
genomeLocParser,
false,
SAMFileReader.ValidationStringency.SILENT,
ValidationStringency.SILENT,
null,
null,
new ValidationExclusion(),
@ -175,7 +175,7 @@ public class SAMDataSourceUnitTest extends BaseTest {
null,
genomeLocParser,
false,
SAMFileReader.ValidationStringency.SILENT,
ValidationStringency.SILENT,
null,
null,
new ValidationExclusion(),
@ -196,7 +196,7 @@ public class SAMDataSourceUnitTest extends BaseTest {
null,
genomeLocParser,
false,
SAMFileReader.ValidationStringency.SILENT,
ValidationStringency.SILENT,
null,
null,
new ValidationExclusion(),
@ -221,7 +221,7 @@ public class SAMDataSourceUnitTest extends BaseTest {
null,
genomeLocParser,
false,
SAMFileReader.ValidationStringency.SILENT,
ValidationStringency.SILENT,
null,
null,
new ValidationExclusion(),
@ -238,7 +238,7 @@ public class SAMDataSourceUnitTest extends BaseTest {
null,
genomeLocParser,
false,
SAMFileReader.ValidationStringency.SILENT,
ValidationStringency.SILENT,
null,
null,
new ValidationExclusion(),

2
public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/filters/ReadFilterTest.java
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@ -317,7 +317,7 @@ public class ReadFilterTest extends BaseTest {
final ThreadAllocation ta = new ThreadAllocation();
final Integer numFileHandles = 1; // I believe that any value would do but need to confirm.
final boolean useOriginalBaseQualities = true;
final SAMFileReader.ValidationStringency strictness = SAMFileReader.ValidationStringency.LENIENT;
final ValidationStringency strictness = ValidationStringency.LENIENT;
final Integer readBufferSize = 1; // not relevant.
final DownsamplingMethod downsamplingMethod = DownsamplingMethod.NONE;
final ValidationExclusion exclusionList = composeValidationExclusion();

2
public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/engine/traversals/TraverseActiveRegionsUnitTest.java
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@ -473,7 +473,7 @@ public class TraverseActiveRegionsUnitTest extends BaseTest {
SAMDataSource dataSource = new SAMDataSource(samFiles, new ThreadAllocation(), null, genomeLocParser,
false,
SAMFileReader.ValidationStringency.STRICT,
ValidationStringency.STRICT,
null,
null,
new ValidationExclusion(),

2
public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/utils/locusiterator/LocusIteratorByStateBaseTest.java
View File

@ -75,7 +75,7 @@ public class LocusIteratorByStateBaseTest extends BaseTest {
new SAMFileHeader(),
SAMFileHeader.SortOrder.coordinate,
false,
SAMFileReader.ValidationStringency.STRICT,
ValidationStringency.STRICT,
downsamplingMethod,
new ValidationExclusion(),
Collections.<ReadFilter>emptyList(),

BIN
public/repo/picard/picard/1.112.1452/picard-1.112.1452.jar → public/repo/picard/picard/1.118.1521/picard-1.118.1521.jar
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4
public/repo/picard/picard/1.112.1452/picard-1.112.1452.pom → public/repo/picard/picard/1.118.1521/picard-1.118.1521.pom
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@ -3,13 +3,13 @@
<modelVersion>4.0.0</modelVersion>
<groupId>picard</groupId>
<artifactId>picard</artifactId>
<version>1.112.1452</version>
<version>1.118.1521</version>
<name>picard</name>
<dependencies>
<dependency>
<groupId>samtools</groupId>
<artifactId>htsjdk</artifactId>
<version>1.112.1452</version>
<version>1.118.1556</version>
</dependency>
<!-- TODO: Picard is using a custom zip with just ant's BZip2 classes. See also: http://www.kohsuke.org/bzip2 -->
<dependency>

BIN
public/repo/samtools/htsjdk/1.112.1452/htsjdk-1.112.1452.jar → public/repo/samtools/htsjdk/1.118.1556/htsjdk-1.118.1556.jar
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2
public/repo/samtools/htsjdk/1.112.1452/htsjdk-1.112.1452.pom → public/repo/samtools/htsjdk/1.118.1556/htsjdk-1.118.1556.pom
View File

@ -3,7 +3,7 @@
<modelVersion>4.0.0</modelVersion>
<groupId>samtools</groupId>
<artifactId>htsjdk</artifactId>
<version>1.112.1452</version>
<version>1.118.1556</version>
<name>htsjdk</name>
<dependencies>
<dependency>