zzh
/
gatk-3.8
1
0
Fork 0
Code Issues Pull Requests Packages Projects Releases Wiki Activity

Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable

This commit is contained in:
Ryan Poplin 2012-05-21 16:47:07 -04:00
parent 04000d920c 94cd4e6a7d
commit 08dfd6cab6
11 changed files with 418 additions and 21 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

6
public/java/src/org/broadinstitute/sting/gatk/datasources/rmd/ResourcePool.java
View File

@ -25,6 +25,7 @@
package org.broadinstitute.sting.gatk.datasources.rmd;
import net.sf.samtools.SAMSequenceDictionary;
import net.sf.samtools.util.CloseableIterator;
import org.broadinstitute.sting.utils.GenomeLocParser;
import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
@ -33,7 +34,7 @@ import java.util.*;
/**
* A pool of open resources, all of which can create a closeable iterator.
*/
abstract class ResourcePool <T,I extends Iterator> {
abstract class ResourcePool <T,I extends CloseableIterator> {
/**
* Sequence dictionary.
*/
@ -109,6 +110,9 @@ abstract class ResourcePool <T,I extends Iterator> {
T resource = resourceAssignments.get( iterator );
Object obj = resourceAssignments.remove(iterator);
// Close the iterator.
iterator.close();
// make sure we actually removed the assignment
if (obj == null)
throw new ReviewedStingException("Failed to remove resource assignment; target key had no associated value in the resource assignment map");

4
public/java/src/org/broadinstitute/sting/gatk/refdata/utils/FeatureToGATKFeatureIterator.java
View File

@ -65,6 +65,8 @@ public class FeatureToGATKFeatureIterator implements CloseableIterator<GATKFeatu
@Override
public void close() {
// we don't close them anymore
// The private adapted iterator may not be passed on by the method constructing this object,
// leaving only this adapter to close the wrapped iterator.
iterator.close();
}
}

51
public/java/src/org/broadinstitute/sting/gatk/report/GATKReportTable.java
View File

@ -81,6 +81,13 @@ public class GATKReportTable {
public int index() { return index; }
}
/**
* Construct a new GATK report table from the reader
* Note that the row ID mappings are just the index -> index
*
* @param reader the reader
* @param version the GATK report version
*/
public GATKReportTable(BufferedReader reader, GATKReportVersion version) {
switch ( version ) {
@ -271,8 +278,16 @@ public class GATKReportTable {
}
/**
* Add a column to the report and specify the default value that should be supplied if a given position in the table
* is never explicitly set.
* Remove a mapping from ID to row index.
*
* @param ID the row ID
*/
public void removeRowIDMapping(final Object ID) {
rowIdToIndex.remove(ID);
}
/**
* Add a column to the report
*
* @param columnName the name of the column
*/
@ -281,9 +296,7 @@ public class GATKReportTable {
}
/**
* Add a column to the report, specify the default column value, whether the column should be displayed in the final
* output (useful when intermediate columns are necessary for later calculations, but are not required to be in the
* output file), and the format string used to display the data.
* Add a column to the report and the format string used to display the data.
*
* @param columnName the name of the column
* @param format the format string used to display data
@ -305,7 +318,7 @@ public class GATKReportTable {
}
/**
* Set the value for a given position in the table
* expand the underlying table if needed to include the given row index
*
* @param rowIndex the row index
* @param updateRowIdMap should we update the row ID map?
@ -324,7 +337,8 @@ public class GATKReportTable {
}
/**
* Set the value for a given position in the table
* Set the value for a given position in the table.
* If the row ID doesn't exist, it will create a new row in the table with the given ID.
*
* @param rowID the row ID
* @param columnName the name of the column
@ -338,6 +352,14 @@ public class GATKReportTable {
set(rowIdToIndex.get(rowID), columnNameToIndex.get(columnName), value);
}
/**
* Set the value for a given position in the table.
* If the row index doesn't exist, it will create new rows in the table accordingly.
*
* @param rowIndex the row index
* @param colIndex the column index
* @param value the value to set
*/
public void set(final int rowIndex, final int colIndex, Object value) {
expandTo(rowIndex, true);
verifyEntry(rowIndex, colIndex);
@ -375,11 +397,12 @@ public class GATKReportTable {
}
/**
* Set the value for a given position in the table
*
* @param rowID the row ID
* @param columnName the name of the column
*/
* Increment the value for a given position in the table.
* Throws an exception if the value in the cell is not an integer.
*
* @param rowID the row ID
* @param columnName the name of the column
*/
public void increment(final Object rowID, final String columnName) {
int prevValue;
if ( !rowIdToIndex.containsKey(rowID) ) {
@ -518,6 +541,10 @@ public class GATKReportTable {
// write the table body
if ( sortByRowID ) {
// make sure that there are exactly the correct number of ID mappings
if ( rowIdToIndex.size() != underlyingData.size() )
throw new ReviewedStingException("There isn't a 1-to-1 mapping from row ID to index; this can happen when rows are not created consistently");
final TreeMap<Object, Integer> sortedMap;
try {
sortedMap = new TreeMap<Object, Integer>(rowIdToIndex);

4
public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/AlleleFrequencyCalculationModel.java
View File

@ -52,17 +52,17 @@ public abstract class AlleleFrequencyCalculationModel implements Cloneable {
protected int N;
protected int MAX_ALTERNATE_ALLELES_TO_GENOTYPE;
protected boolean CAP_MAX_ALTERNATE_ALLELES_FOR_INDELS;
protected Logger logger;
protected PrintStream verboseWriter;
protected enum GenotypeType { AA, AB, BB }
protected static final double VALUE_NOT_CALCULATED = Double.NEGATIVE_INFINITY;
protected AlleleFrequencyCalculationModel(final UnifiedArgumentCollection UAC, final int N, final Logger logger, final PrintStream verboseWriter) {
this.N = N;
this.MAX_ALTERNATE_ALLELES_TO_GENOTYPE = UAC.MAX_ALTERNATE_ALLELES;
this.CAP_MAX_ALTERNATE_ALLELES_FOR_INDELS = UAC.CAP_MAX_ALTERNATE_ALLELES_FOR_INDELS;
this.logger = logger;
this.verboseWriter = verboseWriter;
}

12
public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/ExactAFCalculationModel.java
View File

@ -49,13 +49,15 @@ public class ExactAFCalculationModel extends AlleleFrequencyCalculationModel {
GenotypesContext GLs = vc.getGenotypes();
List<Allele> alleles = vc.getAlleles();
// don't try to genotype too many alternate alleles
if ( vc.getAlternateAlleles().size() > MAX_ALTERNATE_ALLELES_TO_GENOTYPE ) {
logger.warn("this tool is currently set to genotype at most " + MAX_ALTERNATE_ALLELES_TO_GENOTYPE + " alternate alleles in a given context, but the context at " + vc.getChr() + ":" + vc.getStart() + " has " + (vc.getAlternateAlleles().size()) + " alternate alleles so only the top alleles will be used; see the --max_alternate_alleles argument");
final int myMaxAltAllelesToGenotype = CAP_MAX_ALTERNATE_ALLELES_FOR_INDELS && vc.getType().equals(VariantContext.Type.INDEL) ? 2 : MAX_ALTERNATE_ALLELES_TO_GENOTYPE;
alleles = new ArrayList<Allele>(MAX_ALTERNATE_ALLELES_TO_GENOTYPE + 1);
// don't try to genotype too many alternate alleles
if ( vc.getAlternateAlleles().size() > myMaxAltAllelesToGenotype ) {
logger.warn("this tool is currently set to genotype at most " + myMaxAltAllelesToGenotype + " alternate alleles in a given context, but the context at " + vc.getChr() + ":" + vc.getStart() + " has " + (vc.getAlternateAlleles().size()) + " alternate alleles so only the top alleles will be used; see the --max_alternate_alleles argument");
alleles = new ArrayList<Allele>(myMaxAltAllelesToGenotype + 1);
alleles.add(vc.getReference());
alleles.addAll(chooseMostLikelyAlternateAlleles(vc, MAX_ALTERNATE_ALLELES_TO_GENOTYPE));
alleles.addAll(chooseMostLikelyAlternateAlleles(vc, myMaxAltAllelesToGenotype));
GLs = VariantContextUtils.subsetDiploidAlleles(vc, alleles, false);
}

5
public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedArgumentCollection.java
View File

@ -117,6 +117,10 @@ public class UnifiedArgumentCollection {
@Argument(fullName = "max_alternate_alleles", shortName = "maxAlleles", doc = "Maximum number of alternate alleles to genotype", required = false)
public int MAX_ALTERNATE_ALLELES = 3;
@Hidden
@Argument(fullName = "cap_max_alternate_alleles_for_indels", shortName = "capMaxAllelesForIndels", doc = "Cap the maximum number of alternate alleles to genotype for indel calls at 2; overrides the --max_alternate_alleles argument; GSA production use only", required = false)
public boolean CAP_MAX_ALTERNATE_ALLELES_FOR_INDELS = false;
// indel-related arguments
/**
* A candidate indel is genotyped (and potentially called) if there are this number of reads with a consensus indel at a site.
@ -192,6 +196,7 @@ public class UnifiedArgumentCollection {
uac.INDEL_HAPLOTYPE_SIZE = INDEL_HAPLOTYPE_SIZE;
uac.alleles = alleles;
uac.MAX_ALTERNATE_ALLELES = MAX_ALTERNATE_ALLELES;
uac.CAP_MAX_ALTERNATE_ALLELES_FOR_INDELS = CAP_MAX_ALTERNATE_ALLELES_FOR_INDELS;
// todo- arguments to remove
uac.IGNORE_SNP_ALLELES = IGNORE_SNP_ALLELES;

88
public/java/test/org/broadinstitute/sting/gatk/datasources/rmd/ReferenceOrderedQueryDataPoolUnitTest.java 100644
View File

@ -0,0 +1,88 @@
/*
* 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.gatk.datasources.rmd;
import net.sf.picard.reference.IndexedFastaSequenceFile;
import org.broad.tribble.Feature;
import org.broadinstitute.sting.BaseTest;
import org.broadinstitute.sting.commandline.Tags;
import org.broadinstitute.sting.gatk.refdata.utils.*;
import org.broadinstitute.sting.utils.GenomeLoc;
import org.broadinstitute.sting.utils.GenomeLocParser;
import org.broadinstitute.sting.utils.fasta.CachingIndexedFastaSequenceFile;
import org.testng.Assert;
import org.testng.annotations.Test;
import java.io.File;
import java.io.IOException;
import java.util.List;
public class ReferenceOrderedQueryDataPoolUnitTest extends BaseTest{
@Test
public void testCloseFilePointers() throws IOException {
// Build up query parameters
File file = new File(BaseTest.validationDataLocation + "NA12878.hg19.example1.vcf");
RMDTriplet triplet = new RMDTriplet("test", "VCF", file.getAbsolutePath(), RMDTriplet.RMDStorageType.FILE, new Tags());
IndexedFastaSequenceFile seq = new CachingIndexedFastaSequenceFile(new File(BaseTest.hg19Reference));
GenomeLocParser parser = new GenomeLocParser(seq);
GenomeLoc loc = parser.createGenomeLoc("20", 1, 100000);
TestRMDTrackBuilder builder = new TestRMDTrackBuilder(seq.getSequenceDictionary(), parser);
// Create the query data pool
ReferenceOrderedQueryDataPool pool = new ReferenceOrderedQueryDataPool(triplet, builder, seq.getSequenceDictionary(), parser);
for (int i = 0; i < 3; i++) {
// Ensure our tribble iterators are closed.
CheckableCloseableTribbleIterator.clearThreadIterators();
Assert.assertTrue(CheckableCloseableTribbleIterator.getThreadIterators().isEmpty(), "Tribble iterators list was not cleared.");
// Request the the rodIterator
LocationAwareSeekableRODIterator rodIterator = pool.iterator(new MappedStreamSegment(loc));
// Run normal iteration over rodIterator
Assert.assertTrue(rodIterator.hasNext(), "Rod iterator does not have a next value.");
GenomeLoc rodIteratorLocation = rodIterator.next().getLocation();
Assert.assertEquals(rodIteratorLocation.getContig(), "20", "Instead of chr 20 rod iterator was at location " + rodIteratorLocation);
// Check that the underlying tribbleIterators are still open.
List<CheckableCloseableTribbleIterator<? extends Feature>> tribbleIterators = CheckableCloseableTribbleIterator.getThreadIterators();
Assert.assertFalse(tribbleIterators.isEmpty(), "Tribble iterators list is empty");
for (CheckableCloseableTribbleIterator<? extends Feature> tribbleIterator: tribbleIterators) {
Assert.assertFalse(tribbleIterator.isClosed(), "Tribble iterator is closed but should be still open.");
}
// Releasing the rodIterator should close the underlying tribbleIterator.
pool.release(rodIterator);
// Check that the underlying tribbleIterators are now closed.
for (CheckableCloseableTribbleIterator<? extends Feature> tribbleIterator: tribbleIterators) {
Assert.assertTrue(tribbleIterator.isClosed(), "Tribble iterator is open but should be now closed.");
}
}
// Extra cleanup.
CheckableCloseableTribbleIterator.clearThreadIterators();
}
}

89
public/java/test/org/broadinstitute/sting/gatk/refdata/utils/CheckableCloseableTribbleIterator.java 100644
View File

@ -0,0 +1,89 @@
/*
* 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.gatk.refdata.utils;
import org.broad.tribble.CloseableTribbleIterator;
import org.broad.tribble.Feature;
import java.util.ArrayList;
import java.util.Iterator;
import java.util.List;
/**
* Adapter to allow checking if the wrapped iterator was closed.
* Creating an CCTI also adds it to the list returned from getThreadIterators().
* @param <T> feature
*/
public class CheckableCloseableTribbleIterator<T extends Feature> implements CloseableTribbleIterator<T> {
private final CloseableTribbleIterator<T> iterator;
private boolean closed = false;
private static ThreadLocal<List<CheckableCloseableTribbleIterator<? extends Feature>>> threadIterators =
new ThreadLocal<List<CheckableCloseableTribbleIterator<? extends Feature>>>() {
@Override
protected List<CheckableCloseableTribbleIterator<? extends Feature>> initialValue() {
return new ArrayList<CheckableCloseableTribbleIterator<? extends Feature>>();
}
};
public CheckableCloseableTribbleIterator(CloseableTribbleIterator<T> iterator) {
this.iterator = iterator;
threadIterators.get().add(this);
}
/**
* Returns the list of iterators created on this thread since the last time clearCreatedIterators() was called.
* @return the list of iterators created on this thread since the last time clearCreatedIterators() was called.
*/
public static List<CheckableCloseableTribbleIterator<? extends Feature>> getThreadIterators() {
return threadIterators.get();
}
/**
* Clears the tracked list of iterators created on this thread.
*/
public static void clearThreadIterators() {
threadIterators.get().clear();
}
@Override
public void close() {
iterator.close();
this.closed = true;
}
/**
* Returns true if this iterator was properly closed.
* @return true if this iterator was properly closed.
*/
public boolean isClosed() {
return closed;
}
@Override public Iterator<T> iterator() { return this; }
@Override public boolean hasNext() { return iterator.hasNext(); }
@Override public T next() { return iterator.next(); }
@Override public void remove() { iterator.remove(); }
}

59
public/java/test/org/broadinstitute/sting/gatk/refdata/utils/FeatureToGATKFeatureIteratorUnitTest.java 100644
View File

@ -0,0 +1,59 @@
/*
* 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.gatk.refdata.utils;
import net.sf.picard.reference.IndexedFastaSequenceFile;
import org.broad.tribble.Feature;
import org.broadinstitute.sting.BaseTest;
import org.broadinstitute.sting.utils.GenomeLoc;
import org.broadinstitute.sting.utils.GenomeLocParser;
import org.broadinstitute.sting.utils.codecs.vcf.VCFCodec;
import org.broadinstitute.sting.utils.fasta.CachingIndexedFastaSequenceFile;
import org.testng.Assert;
import org.testng.annotations.Test;
import java.io.File;
import java.io.IOException;
public class FeatureToGATKFeatureIteratorUnitTest extends BaseTest {
@Test
@SuppressWarnings("unchecked")
public void testCloseFilePointers() throws IOException {
IndexedFastaSequenceFile seq = new CachingIndexedFastaSequenceFile(new File(BaseTest.hg19Reference));
GenomeLocParser parser = new GenomeLocParser(seq);
File file = new File(validationDataLocation + "NA12878.hg19.example1.vcf");
VCFCodec codec = new VCFCodec();
TestFeatureReader reader = new TestFeatureReader(file.getAbsolutePath(), codec);
CheckableCloseableTribbleIterator<Feature> tribbleIterator = reader.query("20", 1, 100000);
FeatureToGATKFeatureIterator gatkIterator = new FeatureToGATKFeatureIterator(parser, tribbleIterator, "test");
Assert.assertTrue(gatkIterator.hasNext(), "GATK feature iterator does not have a next value.");
GenomeLoc gatkLocation = gatkIterator.next().getLocation();
Assert.assertEquals(gatkLocation.getContig(), "20", "Instead of chr 20 rod iterator was at location " + gatkLocation);
Assert.assertFalse(tribbleIterator.isClosed(), "Tribble iterator is closed but should be still open.");
gatkIterator.close();
Assert.assertTrue(tribbleIterator.isClosed(), "Tribble iterator is open but should be now closed.");
reader.close();
}
}

52
public/java/test/org/broadinstitute/sting/gatk/refdata/utils/TestFeatureReader.java 100644
View File

@ -0,0 +1,52 @@
/*
* 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.gatk.refdata.utils;
import org.broad.tribble.Feature;
import org.broad.tribble.FeatureCodec;
import org.broad.tribble.TribbleIndexedFeatureReader;
import java.io.IOException;
/**
* Feature reader with additional test utilities. The iterators can be checked to see if they are closed.
*/
public class TestFeatureReader extends TribbleIndexedFeatureReader<Feature> {
public TestFeatureReader(String featurePath, FeatureCodec codec) throws IOException {
super(featurePath, codec, true);
}
@Override
@SuppressWarnings("unchecked")
public CheckableCloseableTribbleIterator<Feature> iterator() throws IOException {
return new CheckableCloseableTribbleIterator<Feature>(super.iterator());
}
@Override
@SuppressWarnings("unchecked")
public CheckableCloseableTribbleIterator<Feature> query(String chr, int start, int end) throws IOException {
return new CheckableCloseableTribbleIterator<Feature>(super.query(chr, start, end));
}
}

69
public/java/test/org/broadinstitute/sting/gatk/refdata/utils/TestRMDTrackBuilder.java 100644
View File

@ -0,0 +1,69 @@
/*
* 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.gatk.refdata.utils;
import net.sf.samtools.SAMSequenceDictionary;
import org.broad.tribble.FeatureCodec;
import org.broad.tribble.Tribble;
import org.broad.tribble.index.Index;
import org.broadinstitute.sting.gatk.refdata.tracks.FeatureManager;
import org.broadinstitute.sting.gatk.refdata.tracks.IndexDictionaryUtils;
import org.broadinstitute.sting.gatk.refdata.tracks.RMDTrack;
import org.broadinstitute.sting.gatk.refdata.tracks.RMDTrackBuilder;
import org.broadinstitute.sting.utils.GenomeLocParser;
import java.io.File;
import java.io.IOException;
/**
* Extension of RMDTrackBuilder that creates TestFeatureReader's which in turn create CheckableCloseableTribbleIterator's.
*/
public class TestRMDTrackBuilder extends RMDTrackBuilder {
private GenomeLocParser genomeLocParser;
public TestRMDTrackBuilder(SAMSequenceDictionary dict, GenomeLocParser genomeLocParser) {
super(dict, genomeLocParser, null);
this.genomeLocParser = genomeLocParser;
}
@Override
public RMDTrack createInstanceOfTrack(RMDTriplet fileDescriptor) {
String name = fileDescriptor.getName();
File inputFile = new File(fileDescriptor.getFile());
FeatureManager.FeatureDescriptor descriptor = getFeatureManager().getByTriplet(fileDescriptor);
FeatureCodec codec = getFeatureManager().createCodec(descriptor, name, genomeLocParser);
TestFeatureReader featureReader;
Index index;
try {
// Create a feature reader that creates checkable tribble iterators.
featureReader = new TestFeatureReader(inputFile.getAbsolutePath(), codec);
index = loadFromDisk(inputFile, Tribble.indexFile(inputFile));
} catch (IOException e) {
throw new RuntimeException(e);
}
SAMSequenceDictionary sequenceDictionary = IndexDictionaryUtils.getSequenceDictionaryFromProperties(index);
return new RMDTrack(descriptor.getCodecClass(), name, inputFile, featureReader, sequenceDictionary, genomeLocParser, codec);
}
}