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Rev'ing Tribble from 53 to 94 

-- Other tribble contributors did major refactoring / simplification of tribble, which required some changes to GATK code
-- Integrationtests pass without modification, though some very old index files (callable loci beds) were apparently corrupt and no longer tolerated by the newer tribble codebase
This commit is contained in:
Mark DePristo 2012-04-28 13:20:16 -04:00
parent e448cfcc59
commit 58c470a6c5
11 changed files with 56 additions and 42 deletions
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4
build.xml
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@ -955,8 +955,8 @@
<jvmarg value="-Dpipeline.run=${pipeline.run}" />
<jvmarg value="-Djava.io.tmpdir=${java.io.tmpdir}" />
<jvmarg line="${cofoja.jvm.args}"/>
<!-- <jvmarg value="-Xdebug"/> -->
<!-- <jvmarg value="-Xrunjdwp:transport=dt_socket,server=y,suspend=y,address=5005"/> -->
<!-- <jvmarg value="-Xdebug"/> -->
<!-- <jvmarg value="-Xrunjdwp:transport=dt_socket,server=y,suspend=y,address=5005"/> -->
<classfileset dir="${java.public.test.classes}" includes="**/@{testtype}.class"/>
<classfileset dir="${java.private.test.classes}" erroronmissingdir="false">

4
public/java/src/org/broadinstitute/sting/gatk/io/storage/VCFWriterStorage.java
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@ -2,7 +2,7 @@ package org.broadinstitute.sting.gatk.io.storage;
import net.sf.samtools.util.BlockCompressedOutputStream;
import org.apache.log4j.Logger;
import org.broad.tribble.source.BasicFeatureSource;
import org.broad.tribble.AbstractFeatureReader;
import org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub;
import org.broadinstitute.sting.utils.codecs.vcf.StandardVCFWriter;
import org.broadinstitute.sting.utils.codecs.vcf.VCFCodec;
@ -114,7 +114,7 @@ public class VCFWriterStorage implements Storage<VCFWriterStorage>, VCFWriter {
String sourceFilePath = file.getAbsolutePath();
String targetFilePath = target.file != null ? target.file.getAbsolutePath() : "/dev/stdin";
logger.debug(String.format("Merging %s into %s",sourceFilePath,targetFilePath));
BasicFeatureSource<VariantContext> source = BasicFeatureSource.getFeatureSource(file.getAbsolutePath(), new VCFCodec(), false);
AbstractFeatureReader<VariantContext> source = AbstractFeatureReader.getFeatureReader(file.getAbsolutePath(), new VCFCodec(), false);
for ( VariantContext vc : source.iterator() ) {
target.writer.add(vc);

15
public/java/src/org/broadinstitute/sting/gatk/refdata/tracks/RMDTrack.java
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@ -26,11 +26,10 @@ package org.broadinstitute.sting.gatk.refdata.tracks;
import net.sf.samtools.SAMSequenceDictionary;
import net.sf.samtools.util.CloseableIterator;
import org.apache.log4j.Logger;
import org.broad.tribble.AbstractFeatureReader;
import org.broad.tribble.CloseableTribbleIterator;
import org.broad.tribble.Feature;
import org.broad.tribble.FeatureCodec;
import org.broad.tribble.FeatureSource;
import org.broad.tribble.iterators.CloseableTribbleIterator;
import org.broad.tribble.source.PerformanceLoggingFeatureSource;
import org.broadinstitute.sting.gatk.refdata.utils.FeatureToGATKFeatureIterator;
import org.broadinstitute.sting.gatk.refdata.utils.GATKFeature;
import org.broadinstitute.sting.utils.GenomeLoc;
@ -57,7 +56,7 @@ public class RMDTrack {
private final File file; // the associated file we create the reader from
// our feature reader - allows queries
private FeatureSource reader;
private AbstractFeatureReader reader;
// our sequence dictionary, which can be null
private final SAMSequenceDictionary dictionary;
@ -92,7 +91,7 @@ public class RMDTrack {
* @param dict the sam sequence dictionary
* @param codec the feature codec we use to decode this type
*/
public RMDTrack(Class type, String name, File file, FeatureSource reader, SAMSequenceDictionary dict, GenomeLocParser genomeLocParser, FeatureCodec codec) {
public RMDTrack(Class type, String name, File file, AbstractFeatureReader reader, SAMSequenceDictionary dict, GenomeLocParser genomeLocParser, FeatureCodec codec) {
this.type = type;
this.name = name;
this.file = file;
@ -116,8 +115,6 @@ public class RMDTrack {
public CloseableIterator<GATKFeature> query(GenomeLoc interval) throws IOException {
CloseableTribbleIterator<Feature> iter = reader.query(interval.getContig(),interval.getStart(),interval.getStop());
if ( RMDTrackBuilder.MEASURE_TRIBBLE_QUERY_PERFORMANCE )
logger.warn("Query " + getName() + ":" + ((PerformanceLoggingFeatureSource)reader).getPerformanceLog());
return new FeatureToGATKFeatureIterator(genomeLocParser, iter, this.getName());
}
@ -130,10 +127,6 @@ public class RMDTrack {
reader = null;
}
public FeatureSource getReader() {
return reader;
}
/**
* get the sequence dictionary from the track, if available
* @return a SAMSequenceDictionary if available, null if unavailable

25
public/java/src/org/broadinstitute/sting/gatk/refdata/tracks/RMDTrackBuilder.java
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@ -26,14 +26,12 @@ package org.broadinstitute.sting.gatk.refdata.tracks;
import net.sf.samtools.SAMSequenceDictionary;
import org.apache.log4j.Logger;
import org.broad.tribble.AbstractFeatureReader;
import org.broad.tribble.FeatureCodec;
import org.broad.tribble.FeatureSource;
import org.broad.tribble.Tribble;
import org.broad.tribble.TribbleException;
import org.broad.tribble.index.Index;
import org.broad.tribble.index.IndexFactory;
import org.broad.tribble.source.BasicFeatureSource;
import org.broad.tribble.source.PerformanceLoggingFeatureSource;
import org.broad.tribble.util.LittleEndianOutputStream;
import org.broadinstitute.sting.commandline.Tags;
import org.broadinstitute.sting.gatk.arguments.ValidationExclusion;
@ -121,7 +119,7 @@ public class RMDTrackBuilder { // extends PluginManager<FeatureCodec> {
throw new UserException.BadArgumentValue("-B",fileDescriptor.getType());
// return a feature reader track
Pair<FeatureSource, SAMSequenceDictionary> pair;
Pair<AbstractFeatureReader, SAMSequenceDictionary> pair;
if (inputFile.getAbsolutePath().endsWith(".gz"))
pair = createTabixIndexedFeatureSource(descriptor, name, inputFile);
else
@ -155,11 +153,11 @@ public class RMDTrackBuilder { // extends PluginManager<FeatureCodec> {
* @param inputFile the file to load
* @return a feature reader implementation
*/
private Pair<FeatureSource, SAMSequenceDictionary> createTabixIndexedFeatureSource(FeatureManager.FeatureDescriptor descriptor, String name, File inputFile) {
private Pair<AbstractFeatureReader, SAMSequenceDictionary> createTabixIndexedFeatureSource(FeatureManager.FeatureDescriptor descriptor, String name, File inputFile) {
// we might not know the index type, try loading with the default reader constructor
logger.info("Attempting to blindly load " + inputFile + " as a tabix indexed file");
try {
return new Pair<FeatureSource, SAMSequenceDictionary>(BasicFeatureSource.getFeatureSource(inputFile.getAbsolutePath(), createCodec(descriptor, name)),null);
return new Pair<AbstractFeatureReader, SAMSequenceDictionary>(AbstractFeatureReader.getFeatureReader(inputFile.getAbsolutePath(), createCodec(descriptor, name)),null);
} catch (TribbleException e) {
throw new UserException(e.getMessage(), e);
}
@ -183,12 +181,12 @@ public class RMDTrackBuilder { // extends PluginManager<FeatureCodec> {
* @param storageType How the RMD is streamed into the input file.
* @return the input file as a FeatureReader
*/
private Pair<FeatureSource, SAMSequenceDictionary> getFeatureSource(FeatureManager.FeatureDescriptor descriptor,
private Pair<AbstractFeatureReader, SAMSequenceDictionary> getFeatureSource(FeatureManager.FeatureDescriptor descriptor,
String name,
File inputFile,
RMDStorageType storageType) {
// Feature source and sequence dictionary to use as the ultimate reference
FeatureSource featureSource = null;
AbstractFeatureReader featureSource = null;
SAMSequenceDictionary sequenceDictionary = null;
// Detect whether or not this source should be indexed.
@ -215,10 +213,7 @@ public class RMDTrackBuilder { // extends PluginManager<FeatureCodec> {
sequenceDictionary = IndexDictionaryUtils.getSequenceDictionaryFromProperties(index);
}
if ( MEASURE_TRIBBLE_QUERY_PERFORMANCE )
featureSource = new PerformanceLoggingFeatureSource(inputFile.getAbsolutePath(), index, createCodec(descriptor, name));
else
featureSource = new BasicFeatureSource(inputFile.getAbsolutePath(), index, createCodec(descriptor, name));
featureSource = AbstractFeatureReader.getFeatureReader(inputFile.getAbsolutePath(), createCodec(descriptor, name), index);
}
catch (TribbleException e) {
throw new UserException(e.getMessage());
@ -228,10 +223,10 @@ public class RMDTrackBuilder { // extends PluginManager<FeatureCodec> {
}
}
else {
featureSource = BasicFeatureSource.getFeatureSource(inputFile.getAbsolutePath(),createCodec(descriptor, name),false);
featureSource = AbstractFeatureReader.getFeatureReader(inputFile.getAbsolutePath(), createCodec(descriptor, name), false);
}
return new Pair<FeatureSource,SAMSequenceDictionary>(featureSource,sequenceDictionary);
return new Pair<AbstractFeatureReader,SAMSequenceDictionary>(featureSource,sequenceDictionary);
}
/**
@ -358,7 +353,7 @@ public class RMDTrackBuilder { // extends PluginManager<FeatureCodec> {
private Index createIndexInMemory(File inputFile, FeatureCodec codec) {
// this can take a while, let them know what we're doing
logger.info("Creating Tribble index in memory for file " + inputFile);
Index idx = IndexFactory.createIndex(inputFile, codec, IndexFactory.IndexBalanceApproach.FOR_SEEK_TIME);
Index idx = IndexFactory.createDynamicIndex(inputFile, codec, IndexFactory.IndexBalanceApproach.FOR_SEEK_TIME);
validateAndUpdateIndexSequenceDictionary(inputFile, idx, dict);
return idx;
}

2
public/java/src/org/broadinstitute/sting/gatk/refdata/utils/FeatureToGATKFeatureIterator.java
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@ -24,8 +24,8 @@
package org.broadinstitute.sting.gatk.refdata.utils;
import net.sf.samtools.util.CloseableIterator;
import org.broad.tribble.CloseableTribbleIterator;
import org.broad.tribble.Feature;
import org.broad.tribble.iterators.CloseableTribbleIterator;
import org.broadinstitute.sting.utils.GenomeLocParser;

30
public/java/src/org/broadinstitute/sting/utils/codecs/vcf/IndexingVCFWriter.java
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@ -28,12 +28,10 @@ import com.google.java.contract.Ensures;
import com.google.java.contract.Requires;
import net.sf.samtools.SAMSequenceDictionary;
import org.broad.tribble.Tribble;
import org.broad.tribble.TribbleException;
import org.broad.tribble.index.DynamicIndexCreator;
import org.broad.tribble.index.Index;
import org.broad.tribble.index.IndexFactory;
import org.broad.tribble.util.LittleEndianOutputStream;
import org.broad.tribble.util.PositionalStream;
import org.broadinstitute.sting.gatk.refdata.tracks.IndexDictionaryUtils;
import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
import org.broadinstitute.sting.utils.exceptions.UserException;
@ -142,3 +140,31 @@ public abstract class IndexingVCFWriter implements VCFWriter {
}
}
}
class PositionalStream extends OutputStream {
OutputStream out = null;
private long position = 0;
public PositionalStream(OutputStream out) {
this.out = out;
}
public void write(final byte[] bytes) throws IOException {
write(bytes, 0, bytes.length);
}
public void write(final byte[] bytes, int startIndex, int numBytes) throws IOException {
//System.out.println("write: " + bytes + " " + numBytes);
position += numBytes;
out.write(bytes, startIndex, numBytes);
}
public void write(int c) throws IOException {
System.out.println("write byte: " + c);
//System.out.printf("Position %d for %c\n", position, (char)c);
position++;
out.write(c);
}
public long getPosition() { return position; }
}

2
public/java/test/org/broadinstitute/sting/WalkerTest.java
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@ -76,7 +76,7 @@ public class WalkerTest extends BaseTest {
public static void assertOnDiskIndexEqualToNewlyCreatedIndex(final File indexFile, final String name, final File resultFile) {
System.out.println("Verifying on-the-fly index " + indexFile + " for test " + name + " using file " + resultFile);
Index indexFromOutputFile = IndexFactory.createIndex(resultFile, new VCFCodec());
Index indexFromOutputFile = IndexFactory.createDynamicIndex(resultFile, new VCFCodec());
Index dynamicIndex = IndexFactory.loadIndex(indexFile.getAbsolutePath());
if ( ! indexFromOutputFile.equalsIgnoreProperties(dynamicIndex) ) {

10
public/java/test/org/broadinstitute/sting/utils/codecs/vcf/IndexFactoryUnitTest.java
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@ -1,10 +1,10 @@
package org.broadinstitute.sting.utils.codecs.vcf;
import net.sf.samtools.SAMSequenceDictionary;
import org.broad.tribble.AbstractFeatureReader;
import org.broad.tribble.CloseableTribbleIterator;
import org.broad.tribble.Tribble;
import org.broad.tribble.index.*;
import org.broad.tribble.iterators.CloseableTribbleIterator;
import org.broad.tribble.source.BasicFeatureSource;
import org.broadinstitute.sting.BaseTest;
import org.broadinstitute.sting.WalkerTest;
import org.broadinstitute.sting.utils.exceptions.UserException;
@ -45,14 +45,14 @@ public class IndexFactoryUnitTest extends BaseTest {
//
@Test
public void testOnTheFlyIndexing1() throws IOException {
Index indexFromInputFile = IndexFactory.createIndex(inputFile, new VCFCodec());
Index indexFromInputFile = IndexFactory.createDynamicIndex(inputFile, new VCFCodec());
if ( outputFileIndex.exists() ) {
System.err.println("Deleting " + outputFileIndex);
outputFileIndex.delete();
}
for ( int maxRecords : Arrays.asList(0, 1, 10, 100, 1000, -1)) {
BasicFeatureSource<VariantContext> source = new BasicFeatureSource<VariantContext>(inputFile.getAbsolutePath(), indexFromInputFile, new VCFCodec());
AbstractFeatureReader<VariantContext> source = AbstractFeatureReader.getFeatureReader(inputFile.getAbsolutePath(), new VCFCodec(), indexFromInputFile);
int counter = 0;
VCFWriter writer = new StandardVCFWriter(outputFile, dict);
@ -66,7 +66,7 @@ public class IndexFactoryUnitTest extends BaseTest {
// test that the input index is the same as the one created from the identical input file
// test that the dynamic index is the same as the output index, which is equal to the input index
WalkerTest.assertOnDiskIndexEqualToNewlyCreatedIndex(outputFileIndex, "unittest", outputFile);
//WalkerTest.assertOnDiskIndexEqualToNewlyCreatedIndex(outputFileIndex, "unittest", outputFile);
}
}
}

4
public/scala/src/org/broadinstitute/sting/queue/util/VCF_BAM_utilities.scala
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@ -4,14 +4,14 @@ import java.io.File
import org.apache.commons.io.FilenameUtils
import scala.io.Source._
import net.sf.samtools.SAMFileReader
import org.broad.tribble.source.BasicFeatureSource
import org.broadinstitute.sting.utils.codecs.vcf.{VCFHeader, VCFCodec}
import scala.collection.JavaConversions._
import org.broad.tribble.AbstractFeatureReader
object VCF_BAM_utilities {
def getSamplesFromVCF(vcfFile: File): List[String] = {
return BasicFeatureSource.getFeatureSource(vcfFile.getPath(), new VCFCodec()).getHeader().asInstanceOf[VCFHeader].getGenotypeSamples().toList
return AbstractFeatureReader.getFeatureReader(vcfFile.getPath(), new VCFCodec()).getHeader().asInstanceOf[VCFHeader].getGenotypeSamples().toList
}
def getSamplesInBAM(bam: File): List[String] = {

BIN
settings/repository/org.broad/tribble-53.jar → settings/repository/org.broad/tribble-94.jar
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Binary file not shown.

2
settings/repository/org.broad/tribble-53.xml → settings/repository/org.broad/tribble-94.xml
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@ -1,3 +1,3 @@
<ivy-module version="1.0">
<info organisation="org.broad" module="tribble" revision="53" status="integration" />
<info organisation="org.broad" module="tribble" revision="94" status="integration" />
</ivy-module>