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Merge pull request #563 from broadinstitute/aw_refactor_tribble 

GATK changes to conform to Tribble refactoring as part improving Tabix s...
This commit is contained in:
Eric Banks 2014-03-17 13:35:46 -04:00
parent 2115195d18 0369f93b24
commit 2e34ff7692
19 changed files with 93 additions and 42 deletions
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14
protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/indels/IndelRealignerIntegrationTest.java
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@ -60,8 +60,8 @@ public class IndelRealignerIntegrationTest extends WalkerTest {
private static final String knownIndels = validationDataLocation + "indelRealignerTest.pilot1.ceu.vcf";
private static final String baseCommandPrefix = "-T IndelRealigner -noPG -R " + b36KGReference + " -I " + mainTestBam + " -targetIntervals " + mainTestIntervals + " -compress 0 -L 20:49,500-55,500 ";
private static final String baseCommand = baseCommandPrefix + "-o %s ";
private static final String base_md5 = "a102dd55451799e5f053c784b762087e";
private static final String base_md5_with_SW_or_VCF = "06b8eefcbd785e929027feaa22bb060d";
private static final String base_md5 = "458588d68c8ea7e54443ea722604b265";
private static final String base_md5_with_SW_or_VCF = "d5ed91bd5b2023c69078a0fc00268d3c";
@Test
public void testDefaults() {
@ -84,7 +84,7 @@ public class IndelRealignerIntegrationTest extends WalkerTest {
WalkerTestSpec spec1 = new WalkerTestSpec(
baseCommand + "--consensusDeterminationModel KNOWNS_ONLY -known " + knownIndels,
1,
Arrays.asList("1b24b0f2a20aed1adc726d1b296a3192"));
Arrays.asList("a1b9396f4d5b65f7ae6e0062daf363a3"));
executeTest("realigner known indels only from VCF", spec1);
}
@ -101,7 +101,7 @@ public class IndelRealignerIntegrationTest extends WalkerTest {
public void testLods() {
HashMap<String, String> e = new HashMap<String, String>();
e.put( "-LOD 60", base_md5 );
e.put( "-LOD 1 --consensusDeterminationModel USE_SW", "4bf28d3c0337682d439257874377a681" );
e.put( "-LOD 1 --consensusDeterminationModel USE_SW", "dea9bd14323b33348d9cf28e256415f2" );
for ( Map.Entry<String, String> entry : e.entrySet() ) {
WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
@ -117,7 +117,7 @@ public class IndelRealignerIntegrationTest extends WalkerTest {
WalkerTestSpec spec = new WalkerTestSpec(
"-T IndelRealigner -noPG -R " + b36KGReference + " -I " + validationDataLocation + "NA12878.chrom1.SLX.SRP000032.2009_06.bam -L 1:10,000,000-11,000,000 -targetIntervals " + validationDataLocation + "indelRealignerTest.NA12878.chrom1.intervals -compress 0 -o %s",
1,
Arrays.asList("f4f6c3b2a2be0306a0ecd3def334bafe"));
Arrays.asList("b91c0bf803247f703dc1cb6ccdc4f18f"));
executeTest("realigner long run", spec);
}
@ -126,7 +126,7 @@ public class IndelRealignerIntegrationTest extends WalkerTest {
WalkerTestSpec spec = new WalkerTestSpec(
baseCommand + "--noOriginalAlignmentTags --consensusDeterminationModel USE_SW",
1,
Arrays.asList("71fb521f8febfe2dc683fc636e28ae7d"));
Arrays.asList("041e2254f271261fb46dc3878cf638f6"));
executeTest("realigner no output tags", spec);
}
@ -148,7 +148,7 @@ public class IndelRealignerIntegrationTest extends WalkerTest {
@Test
public void testMaxReadsInMemory() {
HashMap<String, String> e = new HashMap<String, String>();
e.put( "--maxReadsInMemory 10000", base_md5 );
e.put( "--maxReadsInMemory 10000", "0108cd5950f1a4eb90209c3dca8f9e11" );
e.put( "--maxReadsInMemory 40000", base_md5 );
for ( Map.Entry<String, String> entry : e.entrySet() ) {

5
public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/io/storage/SAMFileWriterStorage.java
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@ -27,6 +27,7 @@ package org.broadinstitute.sting.gatk.io.storage;
import net.sf.samtools.*;
import net.sf.samtools.util.CloseableIterator;
import net.sf.samtools.util.ProgressLoggerInterface;
import net.sf.samtools.util.RuntimeIOException;
import org.apache.log4j.Logger;
import org.broadinstitute.sting.gatk.io.stubs.SAMFileWriterStub;
@ -149,4 +150,8 @@ public class SAMFileWriterStorage implements SAMFileWriter, Storage<SAMFileWrite
return writer;
}
@Override
public void setProgressLogger(final ProgressLoggerInterface logger) {
writer.setProgressLogger(logger);
}
}

9
public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/io/stubs/SAMFileWriterStub.java
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@ -28,6 +28,7 @@ package org.broadinstitute.sting.gatk.io.stubs;
import net.sf.samtools.SAMFileHeader;
import net.sf.samtools.SAMFileWriter;
import net.sf.samtools.SAMRecord;
import net.sf.samtools.util.ProgressLoggerInterface;
import org.broadinstitute.sting.gatk.GenomeAnalysisEngine;
import org.broadinstitute.sting.gatk.io.OutputTracker;
import org.broadinstitute.sting.gatk.io.StingSAMFileWriter;
@ -313,4 +314,12 @@ public class SAMFileWriterStub implements Stub<SAMFileWriter>, StingSAMFileWrite
public void close() {
outputTracker.getStorage(this).close();
}
/**
* @throws java.lang.UnsupportedOperationException No progress logging in this implementation.
*/
@Override
public void setProgressLogger(final ProgressLoggerInterface logger) {
throw new UnsupportedOperationException("Progress logging not supported");
}
}

2
public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/io/stubs/VariantContextWriterStub.java
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@ -205,7 +205,7 @@ public class VariantContextWriterStub implements Stub<VariantContextWriter>, Var
if ( doNotWriteGenotypes ) options.add(Options.DO_NOT_WRITE_GENOTYPES);
if ( engine.lenientVCFProcessing() ) options.add(Options.ALLOW_MISSING_FIELDS_IN_HEADER);
if ( indexOnTheFly && ! isCompressed() ) options.add(Options.INDEX_ON_THE_FLY);
if ( indexOnTheFly) options.add(Options.INDEX_ON_THE_FLY);
if ( forceBCF || (getOutputFile() != null && VariantContextWriterFactory.isBCFOutput(getOutputFile())) )
options.add(Options.FORCE_BCF);

17
public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/refdata/tracks/IndexDictionaryUtils.java
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@ -29,10 +29,11 @@ import net.sf.samtools.SAMSequenceDictionary;
import net.sf.samtools.SAMSequenceRecord;
import org.apache.log4j.Logger;
import org.broad.tribble.index.Index;
import org.broad.tribble.index.MutableIndex;
import org.broadinstitute.sting.gatk.arguments.ValidationExclusion;
import org.broadinstitute.sting.utils.SequenceDictionaryUtils;
import java.util.LinkedHashSet;
import java.util.List;
import java.util.Map;
import java.util.Set;
import java.util.TreeSet;
@ -70,23 +71,29 @@ public class IndexDictionaryUtils {
* @param dict the sequence dictionary to add contigs to
* @return the filled-in sequence dictionary
*/
static SAMSequenceDictionary createSequenceDictionaryFromContigList(Index index, SAMSequenceDictionary dict) {
LinkedHashSet<String> seqNames = index.getSequenceNames();
static SAMSequenceDictionary createSequenceDictionaryFromContigList(final Index index, final SAMSequenceDictionary dict) {
final List<String> seqNames = index.getSequenceNames();
if (seqNames == null) {
return dict;
}
for (String name : seqNames) {
for (final String name : seqNames) {
SAMSequenceRecord seq = new SAMSequenceRecord(name, 0);
dict.addSequence(seq);
}
return dict;
}
/**
* Sets the sequence dictionary of the given index. THE INDEX MUST BE MUTABLE (i.e. not Tabix).
*
* @param index the (mutable) index file to use
* @param dict the dictionary to use
*/
public static void setIndexSequenceDictionary(Index index, SAMSequenceDictionary dict) {
for ( SAMSequenceRecord seq : dict.getSequences() ) {
final String contig = IndexDictionaryUtils.SequenceDictionaryPropertyPredicate + seq.getSequenceName();
final String length = String.valueOf(seq.getSequenceLength());
index.addProperty(contig,length);
((MutableIndex)index).addProperty(contig, length);
}
}

10
public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/sam/ArtificialStingSAMFileWriter.java
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@ -26,8 +26,8 @@
package org.broadinstitute.sting.utils.sam;
import net.sf.samtools.SAMFileHeader;
import net.sf.samtools.SAMFileWriter;
import net.sf.samtools.SAMRecord;
import net.sf.samtools.util.ProgressLoggerInterface;
import org.broadinstitute.sting.gatk.io.StingSAMFileWriter;
import java.util.ArrayList;
@ -119,4 +119,12 @@ public class ArtificialStingSAMFileWriter implements StingSAMFileWriter {
@Override
public void setMaxRecordsInRam(int maxRecordsInRam) {
}
/**
* @throws java.lang.UnsupportedOperationException No progress logging in this implementation.
*/
@Override
public void setProgressLogger(final ProgressLoggerInterface logger) {
throw new UnsupportedOperationException("Progress logging not supported");
}
}

8
public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/sam/NWaySAMFileWriter.java
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@ -26,6 +26,7 @@
package org.broadinstitute.sting.utils.sam;
import net.sf.samtools.*;
import net.sf.samtools.util.ProgressLoggerInterface;
import org.broadinstitute.sting.gatk.GenomeAnalysisEngine;
import org.broadinstitute.sting.gatk.datasources.reads.SAMReaderID;
import org.broadinstitute.sting.utils.Utils;
@ -174,4 +175,11 @@ public class NWaySAMFileWriter implements SAMFileWriter {
public void close() {
for ( SAMFileWriter w : writerMap.values() ) w.close();
}
@Override
public void setProgressLogger(final ProgressLoggerInterface logger) {
for (final SAMFileWriter writer: writerMap.values()) {
writer.setProgressLogger(logger);
}
}
}

6
public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/sam/SimplifyingSAMFileWriter.java
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@ -28,6 +28,7 @@ package org.broadinstitute.sting.utils.sam;
import net.sf.samtools.SAMFileHeader;
import net.sf.samtools.SAMFileWriter;
import net.sf.samtools.SAMRecord;
import net.sf.samtools.util.ProgressLoggerInterface;
/**
* XXX
@ -77,4 +78,9 @@ public class SimplifyingSAMFileWriter implements SAMFileWriter {
read.setAttribute("RG", rg);
return read;
}
@Override
public void setProgressLogger(final ProgressLoggerInterface logger) {
dest.setProgressLogger(logger);
}
}

9
public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/variant/GATKVCFUtils.java
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@ -194,14 +194,13 @@ public class GATKVCFUtils {
public static IndexCreator getIndexCreator(GATKVCFIndexType type, int parameter, File outFile) {
IndexCreator idxCreator;
switch (type) {
case DYNAMIC_SEEK: idxCreator = new DynamicIndexCreator(IndexFactory.IndexBalanceApproach.FOR_SEEK_TIME); break;
case DYNAMIC_SIZE: idxCreator = new DynamicIndexCreator(IndexFactory.IndexBalanceApproach.FOR_SIZE); break;
case LINEAR: idxCreator = new LinearIndexCreator(); break;
case INTERVAL: idxCreator = new IntervalIndexCreator(); break;
case DYNAMIC_SEEK: idxCreator = new DynamicIndexCreator(outFile, IndexFactory.IndexBalanceApproach.FOR_SEEK_TIME); break;
case DYNAMIC_SIZE: idxCreator = new DynamicIndexCreator(outFile, IndexFactory.IndexBalanceApproach.FOR_SIZE); break;
case LINEAR: idxCreator = new LinearIndexCreator(outFile, parameter); break;
case INTERVAL: idxCreator = new IntervalIndexCreator(outFile, parameter); break;
default: throw new IllegalArgumentException("Unknown IndexCreator type: " + type);
}
idxCreator.initialize(outFile, parameter);
return idxCreator;
}

33
public/gatk-framework/src/test/java/org/broadinstitute/sting/utils/variant/GATKVCFUtilsUnitTest.java
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@ -43,6 +43,7 @@ import org.testng.annotations.DataProvider;
import org.testng.annotations.Test;
import java.io.File;
import java.lang.reflect.Method;
import java.util.Arrays;
import java.util.Collections;
import java.util.Set;
@ -94,36 +95,44 @@ public class GATKVCFUtilsUnitTest extends BaseTest {
private final GATKVCFIndexType type;
private final int parameter;
private final Class expectedClass;
private final int expectedDefaultBinSize;
private final int expectedBinSize;
private final Integer expectedDimension;
private final Method dimensionGetter;
private IndexCreatorTest(GATKVCFIndexType type, int parameter, Class expectedClass, int expectedDefaultBinSize, int expectedBinSize) {
private IndexCreatorTest(GATKVCFIndexType type, int parameter, Class expectedClass, Integer expectedDimension,
String dimensionGetterName) {
super(IndexCreatorTest.class);
this.type = type;
this.parameter = parameter;
this.expectedClass = expectedClass;
this.expectedDefaultBinSize = expectedDefaultBinSize;
this.expectedBinSize = expectedBinSize;
this.expectedDimension = expectedDimension;
try {
// Conditional matches testGetIndexCreator's if-statement
this.dimensionGetter = this.expectedDimension == null ? null : expectedClass.getDeclaredMethod(dimensionGetterName);
} catch (NoSuchMethodException e) {
throw new RuntimeException(e);
}
}
}
@DataProvider(name = "indexCreator")
public Object[][] indexCreatorData() {
new IndexCreatorTest(GATKVCFIndexType.DYNAMIC_SEEK, 0, DynamicIndexCreator.class, -1, -1);
new IndexCreatorTest(GATKVCFIndexType.DYNAMIC_SIZE, 0, DynamicIndexCreator.class, -1, -1);
new IndexCreatorTest(GATKVCFIndexType.LINEAR, 100, LinearIndexCreator.class, LinearIndexCreator.DEFAULT_BIN_WIDTH, 100);
new IndexCreatorTest(GATKVCFIndexType.INTERVAL, 200, IntervalIndexCreator.class, IntervalIndexCreator.DEFAULT_FEATURE_COUNT, 200);
new IndexCreatorTest(GATKVCFIndexType.DYNAMIC_SEEK, 0, DynamicIndexCreator.class, null, null);
new IndexCreatorTest(GATKVCFIndexType.DYNAMIC_SIZE, 0, DynamicIndexCreator.class, null, null);
new IndexCreatorTest(GATKVCFIndexType.LINEAR, 100, LinearIndexCreator.class, 100, "getBinSize");
new IndexCreatorTest(GATKVCFIndexType.INTERVAL, 200, IntervalIndexCreator.class, 200, "getFeaturesPerInterval");
return IndexCreatorTest.getTests(IndexCreatorTest.class);
}
@Test(dataProvider = "indexCreator")
public void testGetIndexCreator(IndexCreatorTest spec) {
public void testGetIndexCreator(IndexCreatorTest spec) throws Exception{
File dummy = new File("");
IndexCreator ic = GATKVCFUtils.getIndexCreator(spec.type, spec.parameter, dummy);
Assert.assertEquals(ic.getClass(), spec.expectedClass, "Wrong IndexCreator type");
Assert.assertEquals(ic.defaultBinSize(), spec.expectedDefaultBinSize, "Wrong default bin size");
Assert.assertEquals(ic.getBinSize(), spec.expectedBinSize, "Wrong bin size");
if (spec.expectedDimension != null) {
Integer dimension = (int)spec.dimensionGetter.invoke(ic);
Assert.assertEquals(dimension, spec.expectedDimension, "Wrong dimension");
}
}
}

BIN
public/repo/net/sf/picard/1.107.1683/picard-1.107.1683.jar → public/repo/net/sf/picard/1.109.1722/picard-1.109.1722.jar
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8
public/repo/net/sf/picard/1.107.1683/picard-1.107.1683.pom → public/repo/net/sf/picard/1.109.1722/picard-1.109.1722.pom
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@ -3,23 +3,23 @@
<modelVersion>4.0.0</modelVersion>
<groupId>net.sf</groupId>
<artifactId>picard</artifactId>
<version>1.107.1683</version>
<version>1.109.1722</version>
<name>picard</name>
<dependencies>
<dependency>
<groupId>net.sf</groupId>
<artifactId>sam</artifactId>
<version>1.107.1683</version>
<version>1.109.1722</version>
</dependency>
<dependency>
<groupId>org.broadinstitute</groupId>
<artifactId>variant</artifactId>
<version>1.107.1683</version>
<version>1.109.1722</version>
</dependency>
<dependency>
<groupId>org.broad</groupId>
<artifactId>tribble</artifactId>
<version>1.107.1683</version>
<version>1.109.1722</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/net/sf/sam/1.107.1683/sam-1.107.1683.jar → public/repo/net/sf/sam/1.109.1722/sam-1.109.1722.jar
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2
public/repo/net/sf/sam/1.107.1683/sam-1.107.1683.pom → public/repo/net/sf/sam/1.109.1722/sam-1.109.1722.pom
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@ -3,7 +3,7 @@
<modelVersion>4.0.0</modelVersion>
<groupId>net.sf</groupId>
<artifactId>sam</artifactId>
<version>1.107.1683</version>
<version>1.109.1722</version>
<name>sam-jdk</name>
<dependencies>
<dependency>

BIN
public/repo/org/broad/tribble/1.107.1683/tribble-1.107.1683.jar → public/repo/org/broad/tribble/1.109.1722/tribble-1.109.1722.jar
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4
public/repo/org/broad/tribble/1.107.1683/tribble-1.107.1683.pom → public/repo/org/broad/tribble/1.109.1722/tribble-1.109.1722.pom
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@ -3,13 +3,13 @@
<modelVersion>4.0.0</modelVersion>
<groupId>org.broad</groupId>
<artifactId>tribble</artifactId>
<version>1.107.1683</version>
<version>1.109.1722</version>
<name>tribble</name>
<dependencies>
<dependency>
<groupId>net.sf</groupId>
<artifactId>sam</artifactId>
<version>1.107.1683</version>
<version>1.109.1722</version>
</dependency>
</dependencies>
</project>

BIN
public/repo/org/broadinstitute/variant/1.107.1683/variant-1.107.1683.jar → public/repo/org/broadinstitute/variant/1.109.1722/variant-1.109.1722.jar
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6
public/repo/org/broadinstitute/variant/1.107.1683/variant-1.107.1683.pom → public/repo/org/broadinstitute/variant/1.109.1722/variant-1.109.1722.pom
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@ -3,18 +3,18 @@
<modelVersion>4.0.0</modelVersion>
<groupId>org.broadinstitute</groupId>
<artifactId>variant</artifactId>
<version>1.107.1683</version>
<version>1.109.1722</version>
<name>variant</name>
<dependencies>
<dependency>
<groupId>org.broad</groupId>
<artifactId>tribble</artifactId>
<version>1.107.1683</version>
<version>1.109.1722</version>
</dependency>
<dependency>
<groupId>net.sf</groupId>
<artifactId>sam</artifactId>
<version>1.107.1683</version>
<version>1.109.1722</version>
</dependency>
<dependency>
<groupId>org.apache.commons</groupId>

2
public/sting-root/pom.xml
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@ -43,7 +43,7 @@
<test.args>-Xmx${test.maxmemory} -XX:+UseParallelOldGC -XX:ParallelGCThreads=${java.gc.threads} -XX:GCTimeLimit=${java.gc.timeLimit} -XX:GCHeapFreeLimit=${java.gc.heapFreeLimit}</test.args>
<!-- Version numbers for picard sam-jdk. Usually kept in sync. -->
<picard.public.version>1.107.1683</picard.public.version>
<picard.public.version>1.109.1722</picard.public.version>
<sam.version>${picard.public.version}</sam.version>
<picard.version>${picard.public.version}</picard.version>
<variant.version>${picard.public.version}</variant.version>