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Merge pull request #431 from broadinstitute/jt_custom_vcf_idx 

Add engine options to override the default VCF/BCF indexing strategy
This commit is contained in:
droazen 2013-12-03 19:32:36 -08:00
parent d90b295570 fd0a02e52e
commit 61b50a02b1
21 changed files with 352 additions and 18 deletions
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23
public/java/src/org/broadinstitute/sting/gatk/arguments/GATKArgumentCollection.java
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@ -35,6 +35,8 @@ import org.broadinstitute.sting.gatk.samples.PedigreeValidationType;
import org.broadinstitute.sting.utils.QualityUtils;
import org.broadinstitute.sting.utils.baq.BAQ;
import org.broadinstitute.sting.utils.exceptions.UserException;
import org.broadinstitute.sting.utils.variant.GATKVCFIndexType;
import org.broadinstitute.sting.utils.variant.GATKVCFUtils;
import java.io.File;
import java.util.ArrayList;
@ -454,5 +456,26 @@ public class GATKArgumentCollection {
@Hidden
public boolean generateShadowBCF = false;
// TODO -- remove all code tagged with TODO -- remove me when argument generateShadowBCF is removed
// --------------------------------------------------------------------------------------------------------------
//
// VCF/BCF index parameters
//
// --------------------------------------------------------------------------------------------------------------
/**
* Specify the Tribble indexing strategy to use for VCFs.
*
* LINEAR creates a LinearIndex with bins of equal width, specified by the Bin Width parameter
* INTERVAL creates an IntervalTreeIndex with bins with an equal amount of features, specified by the Features Per Bin parameter
* DYNAMIC_SEEK attempts to optimize for minimal seek time by choosing an appropriate strategy and parameter (user-supplied parameter is ignored)
* DYNAMIC_SIZE attempts to optimize for minimal index size by choosing an appropriate strategy and parameter (user-supplied parameter is ignored)
*/
@Argument(fullName="variant_index_type",shortName = "variant_index_type",doc="which type of IndexCreator to use for VCF/BCF indices",required=false)
public GATKVCFIndexType variant_index_type = GATKVCFUtils.DEFAULT_INDEX_TYPE;
@Argument(fullName="variant_index_parameter",shortName = "variant_index_parameter",doc="the parameter (bin width or features per bin) to pass to the VCF/BCF IndexCreator",required=false)
public int variant_index_parameter = GATKVCFUtils.DEFAULT_INDEX_PARAMETER;
}

2
public/java/src/org/broadinstitute/sting/gatk/io/storage/StorageFactory.java
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@ -62,7 +62,7 @@ public class StorageFactory {
* @param <T> Type of the stream to create.
* @return Storage object with a facade of type T.
*/
public static <T> Storage<T> createStorage( Stub<T> stub, File file ) {
public static <T> Storage<T> createStorage( Stub<T> stub, File file ) {
Storage storage;
if(stub instanceof OutputStreamStub) {

11
public/java/src/org/broadinstitute/sting/gatk/io/storage/VariantContextWriterStorage.java
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@ -133,14 +133,21 @@ public class VariantContextWriterStorage implements Storage<VariantContextWriter
// The GATK/Tribble can't currently index block-compressed files on the fly. Disable OTF indexing even if the user explicitly asked for it.
EnumSet<Options> options = stub.getWriterOptions(indexOnTheFly);
VariantContextWriter writer = VariantContextWriterFactory.create(file, this.stream, stub.getMasterSequenceDictionary(), options);
VariantContextWriter writer = VariantContextWriterFactory.create(file, this.stream, stub.getMasterSequenceDictionary(), stub.getIndexCreator(), options);
// if the stub says to test BCF, create a secondary writer to BCF and an 2 way out writer to send to both
// TODO -- remove me when argument generateShadowBCF is removed
if ( stub.alsoWriteBCFForTest() && ! VariantContextWriterFactory.isBCFOutput(file, options)) {
final File bcfFile = BCF2Utils.shadowBCF(file);
if ( bcfFile != null ) {
VariantContextWriter bcfWriter = VariantContextWriterFactory.create(bcfFile, stub.getMasterSequenceDictionary(), options);
FileOutputStream bcfStream;
try {
bcfStream = new FileOutputStream(bcfFile);
} catch (FileNotFoundException e) {
throw new RuntimeException(bcfFile + ": Unable to create BCF writer", e);
}
VariantContextWriter bcfWriter = VariantContextWriterFactory.create(bcfFile, bcfStream, stub.getMasterSequenceDictionary(), stub.getIndexCreator(), options);
writer = new TestWriter(writer, bcfWriter);
}
}

24
public/java/src/org/broadinstitute/sting/gatk/io/stubs/VariantContextWriterStub.java
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@ -26,6 +26,7 @@
package org.broadinstitute.sting.gatk.io.stubs;
import net.sf.samtools.SAMSequenceDictionary;
import org.broad.tribble.index.IndexCreator;
import org.broadinstitute.sting.gatk.GenomeAnalysisEngine;
import org.broadinstitute.sting.gatk.io.OutputTracker;
import org.broadinstitute.sting.utils.variant.GATKVCFUtils;
@ -70,6 +71,17 @@ public class VariantContextWriterStub implements Stub<VariantContextWriter>, Var
*/
private final PrintStream genotypeStream;
/**
* A hack: push the argument sources into the VCF header so that the VCF header
* can rebuild the command-line arguments.
*/
private final Collection<Object> argumentSources;
/**
* Which IndexCreator to use
*/
private final IndexCreator indexCreator;
/**
* The cached VCF header (initialized to null)
*/
@ -80,12 +92,6 @@ public class VariantContextWriterStub implements Stub<VariantContextWriter>, Var
*/
private boolean isCompressed = false;
/**
* A hack: push the argument sources into the VCF header so that the VCF header
* can rebuild the command-line arguments.
*/
private final Collection<Object> argumentSources;
/**
* Should the header be written out? A hidden argument.
*/
@ -118,6 +124,7 @@ public class VariantContextWriterStub implements Stub<VariantContextWriter>, Var
this.engine = engine;
this.genotypeFile = genotypeFile;
this.genotypeStream = null;
this.indexCreator = GATKVCFUtils.getIndexCreator(engine.getArguments().variant_index_type, engine.getArguments().variant_index_parameter, genotypeFile);
this.argumentSources = argumentSources;
}
@ -132,6 +139,7 @@ public class VariantContextWriterStub implements Stub<VariantContextWriter>, Var
this.engine = engine;
this.genotypeFile = null;
this.genotypeStream = new PrintStream(genotypeStream);
this.indexCreator = null;
this.argumentSources = argumentSources;
}
@ -175,6 +183,10 @@ public class VariantContextWriterStub implements Stub<VariantContextWriter>, Var
this.forceBCF = forceBCF;
}
public IndexCreator getIndexCreator() {
return indexCreator;
}
/**
* Gets the master sequence dictionary from the engine associated with this stub
* @link GenomeAnalysisEngine.getMasterSequenceDictionary

12
public/java/src/org/broadinstitute/sting/tools/CatVariants.java
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@ -31,12 +31,15 @@ import org.apache.log4j.BasicConfigurator;
import org.apache.log4j.Level;
import org.broad.tribble.AbstractFeatureReader;
import org.broad.tribble.FeatureReader;
import org.broad.tribble.index.IndexCreator;
import org.broadinstitute.sting.commandline.Argument;
import org.broadinstitute.sting.commandline.Input;
import org.broadinstitute.sting.commandline.Output;
import org.broadinstitute.sting.commandline.CommandLineProgram;
import org.broadinstitute.sting.utils.help.DocumentedGATKFeature;
import org.broadinstitute.sting.utils.help.HelpConstants;
import org.broadinstitute.sting.utils.variant.GATKVCFIndexType;
import org.broadinstitute.sting.utils.variant.GATKVCFUtils;
import org.broadinstitute.variant.bcf2.BCF2Codec;
import org.broadinstitute.sting.utils.collections.Pair;
import org.broadinstitute.variant.vcf.VCFCodec;
@ -123,6 +126,12 @@ public class CatVariants extends CommandLineProgram {
@Argument(fullName = "assumeSorted", shortName = "assumeSorted", doc = "assumeSorted should be true if he input files are already sorted (based on the position of the variants", required = false)
private Boolean assumeSorted = false;
@Argument(fullName = "variant_index_type", doc = "which type of IndexCreator to use for VCF/BCF indices", required = false)
private GATKVCFIndexType variant_index_type = GATKVCFUtils.DEFAULT_INDEX_TYPE;
@Argument(fullName = "variant_index_parameter", doc = "the parameter (bin width or features per bin) to pass to the VCF/BCF IndexCreator", required = false)
private Integer variant_index_parameter = GATKVCFUtils.DEFAULT_INDEX_PARAMETER;
/*
* print usage information
*/
@ -204,7 +213,8 @@ public class CatVariants extends CommandLineProgram {
FileOutputStream outputStream = new FileOutputStream(outputFile);
EnumSet<Options> options = EnumSet.of(Options.INDEX_ON_THE_FLY);
final VariantContextWriter outputWriter = VariantContextWriterFactory.create(outputFile, outputStream, ref.getSequenceDictionary(), options);
final IndexCreator idxCreator = GATKVCFUtils.getIndexCreator(variant_index_type, variant_index_parameter, outputFile);
final VariantContextWriter outputWriter = VariantContextWriterFactory.create(outputFile, outputStream, ref.getSequenceDictionary(), idxCreator, options);
boolean firstFile = true;
int count =0;

39
public/java/src/org/broadinstitute/sting/utils/variant/GATKVCFIndexType.java 100644
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@ -0,0 +1,39 @@
/*
* Copyright (c) 2012 The Broad Institute
*
* Permission is hereby granted, free of charge, to any person
* obtaining a copy of this software and associated documentation
* files (the "Software"), to deal in the Software without
* restriction, including without limitation the rights to use,
* copy, modify, merge, publish, distribute, sublicense, and/or sell
* copies of the Software, and to permit persons to whom the
* Software is furnished to do so, subject to the following
* conditions:
*
* The above copyright notice and this permission notice shall be
* included in all copies or substantial portions of the Software.
*
* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
* EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
* OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
* NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
* HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
* WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
* FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR
* THE USE OR OTHER DEALINGS IN THE SOFTWARE.
*/
package org.broadinstitute.sting.utils.variant;
import org.broadinstitute.sting.commandline.EnumerationArgumentDefault;
/**
* Choose the Tribble indexing strategy
*/
public enum GATKVCFIndexType {
@EnumerationArgumentDefault
DYNAMIC_SEEK, // use DynamicIndexCreator(IndexFactory.IndexBalanceApproach.FOR_SEEK_TIME)
DYNAMIC_SIZE, // use DynamicIndexCreator(IndexFactory.IndexBalanceApproach.FOR_SIZE)
LINEAR, // use LinearIndexCreator()
INTERVAL // use IntervalIndexCreator()
}

30
public/java/src/org/broadinstitute/sting/utils/variant/GATKVCFUtils.java
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@ -28,6 +28,11 @@ package org.broadinstitute.sting.utils.variant;
import org.broad.tribble.Feature;
import org.broad.tribble.FeatureCodec;
import org.broad.tribble.FeatureCodecHeader;
import org.broad.tribble.index.DynamicIndexCreator;
import org.broad.tribble.index.IndexCreator;
import org.broad.tribble.index.IndexFactory;
import org.broad.tribble.index.interval.IntervalIndexCreator;
import org.broad.tribble.index.linear.LinearIndexCreator;
import org.broad.tribble.readers.LineIterator;
import org.broad.tribble.readers.PositionalBufferedStream;
import org.broadinstitute.sting.commandline.RodBinding;
@ -43,6 +48,7 @@ import java.io.FileInputStream;
import java.io.IOException;
import java.util.*;
/**
* A set of GATK-specific static utility methods for common operations on VCF files/records.
*/
@ -55,6 +61,9 @@ public class GATKVCFUtils {
public final static String GATK_COMMAND_LINE_KEY = "GATKCommandLine";
public final static GATKVCFIndexType DEFAULT_INDEX_TYPE = GATKVCFIndexType.DYNAMIC_SEEK; // by default, optimize for seek time. All indices prior to Nov 2013 used this type.
public final static Integer DEFAULT_INDEX_PARAMETER = -1; // the default DYNAMIC_SEEK does not use a parameter
/**
* Gets the appropriately formatted header for a VCF file describing this GATK run
*
@ -175,6 +184,27 @@ public class GATKVCFUtils {
return VCFUtils.withUpdatedContigs(header, engine.getArguments().referenceFile, engine.getMasterSequenceDictionary());
}
/**
* Create and return an IndexCreator
* @param type
* @param parameter
* @param outFile
* @return
*/
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;
default: throw new IllegalArgumentException("Unknown IndexCreator type: " + type);
}
idxCreator.initialize(outFile, parameter);
return idxCreator;
}
/**
* Utility class to read all of the VC records from a file
*

36
public/java/test/org/broadinstitute/sting/ExampleToCopyUnitTest.java
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@ -104,6 +104,42 @@ public class ExampleToCopyUnitTest extends BaseTest {
Assert.assertTrue(size >= 0);
}
/**
* DataProvider example using a class-based data structure
*/
private class MyDataProviderClass extends TestDataProvider {
private int start;
private int size;
private MyDataProviderClass(int start, int size) {
super(MyDataProviderClass.class);
this.start = start;
this.size = size;
}
}
@DataProvider(name = "MyClassBasedDataProvider")
public Object[][] makeMyDataProviderClass() {
// this functionality can be adapted to provide input data for whatever you might want in your data
for ( final int start : Arrays.asList(1, 10, 100) ) {
for ( final int size : Arrays.asList(1, 10, 100, 1000) ) {
new MyDataProviderClass(start, size);
}
}
return TestDataProvider.getTests(MyDataProviderClass.class);
}
/**
* Example testng test using MyClassBasedDataProvider
*/
@Test(dataProvider = "MyClassBasedDataProvider")
public void testMyDataProviderClass(MyDataProviderClass testSpec) {
// adaptor this code to do whatever testing you want given the arguments start and size
Assert.assertTrue(testSpec.start >= 0);
Assert.assertTrue(testSpec.size >= 0);
}
/**
* A unit test that creates an artificial read for testing some code that uses reads
*/

43
public/java/test/org/broadinstitute/sting/utils/variant/GATKVCFUtilsUnitTest.java
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@ -25,6 +25,10 @@
package org.broadinstitute.sting.utils.variant;
import org.broad.tribble.index.DynamicIndexCreator;
import org.broad.tribble.index.IndexCreator;
import org.broad.tribble.index.interval.IntervalIndexCreator;
import org.broad.tribble.index.linear.LinearIndexCreator;
import org.broadinstitute.sting.BaseTest;
import org.broadinstitute.sting.gatk.GenomeAnalysisEngine;
import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
@ -35,8 +39,10 @@ import org.broadinstitute.sting.gatk.walkers.Walker;
import org.broadinstitute.variant.vcf.VCFHeader;
import org.broadinstitute.variant.vcf.VCFHeaderLine;
import org.testng.Assert;
import org.testng.annotations.DataProvider;
import org.testng.annotations.Test;
import java.io.File;
import java.util.Arrays;
import java.util.Collections;
import java.util.Set;
@ -83,4 +89,41 @@ public class GATKVCFUtilsUnitTest extends BaseTest {
Assert.assertTrue(lines2.contains(line1));
Assert.assertTrue(lines2.contains(line2));
}
private class IndexCreatorTest extends TestDataProvider {
private final GATKVCFIndexType type;
private final int parameter;
private final Class expectedClass;
private final int expectedDefaultBinSize;
private final int expectedBinSize;
private IndexCreatorTest(GATKVCFIndexType type, int parameter, Class expectedClass, int expectedDefaultBinSize, int expectedBinSize) {
super(IndexCreatorTest.class);
this.type = type;
this.parameter = parameter;
this.expectedClass = expectedClass;
this.expectedDefaultBinSize = expectedDefaultBinSize;
this.expectedBinSize = expectedBinSize;
}
}
@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);
return IndexCreatorTest.getTests(IndexCreatorTest.class);
}
@Test(dataProvider = "indexCreator")
public void testGetIndexCreator(IndexCreatorTest spec) {
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");
}
}

131
public/java/test/org/broadinstitute/sting/utils/variant/VCFIntegrationTest.java
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@ -25,11 +25,24 @@
package org.broadinstitute.sting.utils.variant;
import org.broad.tribble.index.AbstractIndex;
import org.broad.tribble.index.ChrIndex;
import org.broad.tribble.index.Index;
import org.broad.tribble.index.IndexFactory;
import org.broad.tribble.index.interval.IntervalTreeIndex;
import org.broad.tribble.index.linear.LinearIndex;
import org.broadinstitute.sting.WalkerTest;
import org.broadinstitute.variant.vcf.VCFCodec;
import org.testng.Assert;
import org.testng.TestException;
import org.testng.annotations.DataProvider;
import org.testng.annotations.Test;
import java.io.File;
import java.lang.reflect.Field;
import java.util.Arrays;
import java.util.Collections;
import java.util.LinkedHashMap;
import java.util.List;
public class VCFIntegrationTest extends WalkerTest {
@ -141,4 +154,122 @@ public class VCFIntegrationTest extends WalkerTest {
spec1.disableShadowBCF();
executeTest("Test reading VCF without header lines with additional args " + moreArgs, spec1);
}
//
//
// IndexCreator tests
//
//
private class VCFIndexCreatorTest extends TestDataProvider {
private final GATKVCFIndexType type;
private final int parameter;
private VCFIndexCreatorTest(GATKVCFIndexType type, int parameter) {
super(VCFIndexCreatorTest.class);
this.type = type;
this.parameter = parameter;
}
public String toString() {
return String.format("Index Type %s, Index Parameter %s", type, parameter);
}
public Index getIndex(final File vcfFile) {
switch (type) {
case DYNAMIC_SEEK : return IndexFactory.createDynamicIndex(vcfFile, new VCFCodec(), IndexFactory.IndexBalanceApproach.FOR_SEEK_TIME);
case DYNAMIC_SIZE : return IndexFactory.createDynamicIndex(vcfFile, new VCFCodec(), IndexFactory.IndexBalanceApproach.FOR_SIZE);
case LINEAR : return IndexFactory.createLinearIndex(vcfFile, new VCFCodec(), parameter);
case INTERVAL : return IndexFactory.createIntervalIndex(vcfFile, new VCFCodec(), parameter);
default : throw new TestException("Invalid index type");
}
}
}
@DataProvider(name = "IndexDataProvider")
public Object[][] indexCreatorData() {
new VCFIndexCreatorTest(GATKVCFIndexType.DYNAMIC_SEEK, 0);
new VCFIndexCreatorTest(GATKVCFIndexType.DYNAMIC_SIZE, 0);
new VCFIndexCreatorTest(GATKVCFIndexType.LINEAR, 100);
new VCFIndexCreatorTest(GATKVCFIndexType.LINEAR, 10000);
new VCFIndexCreatorTest(GATKVCFIndexType.INTERVAL, 20);
new VCFIndexCreatorTest(GATKVCFIndexType.INTERVAL, 2000);
return TestDataProvider.getTests(VCFIndexCreatorTest.class);
}
@Test(dataProvider = "IndexDataProvider")
public void testVCFIndexCreation(VCFIndexCreatorTest testSpec) throws NoSuchFieldException, IllegalAccessException {
final String commandLine = " -T SelectVariants" +
" -R " + b37KGReference +
" --no_cmdline_in_header" +
" -L 20" +
" -V " + b37_NA12878_OMNI +
" --variant_index_type " + testSpec.type +
" --variant_index_parameter " + testSpec.parameter +
" -o %s ";
final String name = "testVCFIndexCreation: " + testSpec.toString();
final WalkerTestSpec spec = new WalkerTestSpec(commandLine, 1, Arrays.asList(""));
spec.disableShadowBCF();
File outVCF = executeTest(name, spec).first.get(0);
File outIdx = new File(outVCF.getAbsolutePath() + ".idx");
final Index actualIndex = IndexFactory.loadIndex(outIdx.getAbsolutePath());
final Index expectedIndex = testSpec.getIndex(outVCF);
if (testSpec.type.equals("LINEAR"))
Assert.assertTrue(actualIndex instanceof LinearIndex, "Index is not a LinearIndex");
else if (testSpec.type.equals("INTERVAL"))
Assert.assertTrue(actualIndex instanceof IntervalTreeIndex, "Index is not a IntervalTreeIndex");
// dynamic indices ultimately resolve to one of LinearIndex or IntervalTreeIndex
Assert.assertTrue(equivalentAbstractIndices((AbstractIndex)actualIndex, (AbstractIndex)expectedIndex), "Indices are not equivalent");
if (actualIndex instanceof LinearIndex && expectedIndex instanceof LinearIndex) {
Assert.assertTrue(equivalentLinearIndices((LinearIndex)actualIndex, (LinearIndex)expectedIndex, "20"), "Linear indices are not equivalent");
}
else if (actualIndex instanceof IntervalTreeIndex && expectedIndex instanceof IntervalTreeIndex) {
Assert.assertTrue(equivalentIntervalIndices((IntervalTreeIndex)actualIndex, (IntervalTreeIndex)expectedIndex, "20"), "Interval indices are not equivalent");
}
else {
Assert.fail("Indices are not of the same type");
}
}
private static boolean equivalentAbstractIndices(AbstractIndex thisIndex, AbstractIndex otherIndex){
return thisIndex.getVersion() == otherIndex.getVersion() &&
thisIndex.getIndexedFile().equals(otherIndex.getIndexedFile()) &&
thisIndex.getIndexedFileSize() == otherIndex.getIndexedFileSize() &&
thisIndex.getIndexedFileMD5().equals(otherIndex.getIndexedFileMD5()) &&
thisIndex.getFlags() == otherIndex.getFlags();
}
private static boolean equivalentLinearIndices(LinearIndex thisIndex, LinearIndex otherIndex, String chr) throws NoSuchFieldException, IllegalAccessException {
org.broad.tribble.index.linear.LinearIndex.ChrIndex thisChr = (org.broad.tribble.index.linear.LinearIndex.ChrIndex)getChrIndex(thisIndex, chr);
org.broad.tribble.index.linear.LinearIndex.ChrIndex otherChr = (org.broad.tribble.index.linear.LinearIndex.ChrIndex)getChrIndex(otherIndex, chr);
return thisChr.getName().equals(otherChr.getName()) &&
//thisChr.getTotalSize() == otherChr.getTotalSize() && TODO: why does this differ?
thisChr.getNFeatures() == otherChr.getNFeatures() &&
thisChr.getNBlocks() == otherChr.getNBlocks();
}
private static boolean equivalentIntervalIndices(IntervalTreeIndex thisIndex, IntervalTreeIndex otherIndex, String chr) throws NoSuchFieldException, IllegalAccessException {
org.broad.tribble.index.interval.IntervalTreeIndex.ChrIndex thisChr = (org.broad.tribble.index.interval.IntervalTreeIndex.ChrIndex)getChrIndex(thisIndex, chr);
org.broad.tribble.index.interval.IntervalTreeIndex.ChrIndex otherChr = (org.broad.tribble.index.interval.IntervalTreeIndex.ChrIndex)getChrIndex(otherIndex, chr);
// TODO: compare trees?
return thisChr.getName().equals(otherChr.getName());
}
private static ChrIndex getChrIndex(AbstractIndex index, String chr) throws NoSuchFieldException, IllegalAccessException {
Field f = AbstractIndex.class.getDeclaredField("chrIndices");
f.setAccessible(true);
LinkedHashMap<String, ChrIndex> chrIndices = (LinkedHashMap<String, ChrIndex>) f.get(index);
return chrIndices.get(chr);
}
}

3
public/scala/src/org/broadinstitute/sting/queue/extensions/gatk/CatVariantsGatherer.scala
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@ -48,6 +48,9 @@ class CatVariantsGatherer extends CatVariants with GatherFunction with RetryMemo
this.variant = this.gatherParts.zipWithIndex map { case (input, index) => new TaggedFile(input, "input"+index) }
this.outputFile = this.originalOutput
this.assumeSorted = true
this.variant_index_type = originalGATK.variant_index_type
this.variant_index_parameter = originalGATK.variant_index_parameter
super.freezeFieldValues()
}

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settings/repository/org.broad/tribble-1.96.1534.xml → settings/repository/org.broad/tribble-1.102.1595.xml
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<ivy-module version="1.0">
<info organisation="org.broad" module="tribble" revision="1.96.1534" status="integration" />
<info organisation="org.broad" module="tribble" revision="1.102.1595" status="integration" />
</ivy-module>

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settings/repository/org.broadinstitute/variant-1.96.1534.jar → settings/repository/org.broadinstitute/variant-1.102.1595.jar
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2
settings/repository/org.broadinstitute/variant-1.96.1534.xml → settings/repository/org.broadinstitute/variant-1.102.1595.xml
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@ -1,3 +1,3 @@
<ivy-module version="1.0">
<info organisation="org.broadinstitute" module="variant" revision="1.96.1534" status="integration" />
<info organisation="org.broadinstitute" module="variant" revision="1.102.1595" status="integration" />
</ivy-module>