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Update GATK to work with latest htsjdk 

ValidationStringency was moved from htsjdk.samtools.SAMFileReader to htsjdk.samtools
samtools find BAM index file method was also moved (and made public!)
This commit is contained in:
Laura Gauthier 2014-07-29 09:09:55 -04:00
parent d69af637bf
commit 4373922ee6
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
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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
/**

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>