/*
* 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.gatk.engine.refdata.tracks;
import htsjdk.samtools.reference.IndexedFastaSequenceFile;
import htsjdk.tribble.Tribble;
import htsjdk.tribble.index.Index;
import htsjdk.tribble.util.LittleEndianOutputStream;
import htsjdk.variant.vcf.VCFCodec;
import org.broadinstitute.gatk.utils.exceptions.UserException;
import org.testng.Assert;
import org.broadinstitute.gatk.utils.BaseTest;
import org.broadinstitute.gatk.utils.GenomeLocParser;
import org.broadinstitute.gatk.utils.fasta.CachingIndexedFastaSequenceFile;
import org.testng.annotations.BeforeMethod;
import org.testng.annotations.Test;
import java.io.*;
import java.nio.channels.FileChannel;
/**
* @author aaron
* <p/>
* Class RMDTrackBuilderUnitTest
* <p/>
* Testing out the builder for tribble Tracks
*/
public class RMDTrackBuilderUnitTest extends BaseTest {
private RMDTrackBuilder builder;
private IndexedFastaSequenceFile seq;
private GenomeLocParser genomeLocParser;
@BeforeMethod
public void setup() {
File referenceFile = new File(b37KGReference);
try {
seq = new CachingIndexedFastaSequenceFile(referenceFile);
}
catch(FileNotFoundException ex) {
throw new UserException.CouldNotReadInputFile(referenceFile,ex);
}
genomeLocParser = new GenomeLocParser(seq);
// We have to disable auto-index creation/locking in the RMDTrackBuilder for tests,
// as the lock acquisition calls were intermittently hanging on our farm. This unfortunately
// means that we can't include tests for the auto-index creation feature.
builder = new RMDTrackBuilder(seq.getSequenceDictionary(),genomeLocParser,null,true,null);
}
@Test
public void testBuilder() {
Assert.assertTrue(builder.getFeatureManager().getFeatureDescriptors().size() > 0);
}
@Test
public void testDisableAutoIndexGeneration() throws IOException {
final File unindexedVCF = new File(privateTestDir + "unindexed.vcf");
final File unindexedVCFIndex = Tribble.indexFile(unindexedVCF);
Index index = builder.loadIndex(unindexedVCF, new VCFCodec());
Assert.assertFalse(unindexedVCFIndex.exists());
Assert.assertNotNull(index);
}
@Test
public void testLoadOnDiskIndex() {
final File originalVCF = new File(privateTestDir + "vcf4.1.example.vcf");
final File tempVCFWithCorrectIndex = createTempVCFFileAndIndex(originalVCF, false);
final File tempVCFIndexFile = Tribble.indexFile(tempVCFWithCorrectIndex);
final Index index = builder.loadFromDisk(tempVCFWithCorrectIndex, tempVCFIndexFile);
Assert.assertNotNull(index);
Assert.assertTrue(tempVCFIndexFile.exists());
final Index inMemoryIndex = builder.createIndexInMemory(tempVCFWithCorrectIndex, new VCFCodec());
Assert.assertTrue(index.equalsIgnoreProperties(inMemoryIndex));
}
@Test
public void testLoadOnDiskOutdatedIndex() {
final File originalVCF = new File(privateTestDir + "vcf4.1.example.vcf");
final File tempVCFWithOutdatedIndex = createTempVCFFileAndIndex(originalVCF, true);
final File tempVCFIndexFile = Tribble.indexFile(tempVCFWithOutdatedIndex);
final Index index = builder.loadFromDisk(tempVCFWithOutdatedIndex, tempVCFIndexFile);
// loadFromDisk() should return null to indicate that the index is outdated and should not be used,
// but should not delete the index since our builder has disableAutoIndexCreation set to true
Assert.assertNull(index);
Assert.assertTrue(tempVCFIndexFile.exists());
}
/**
* Create a temporary vcf file and an associated index file, which may be set to be out-of-date
* relative to the vcf
*
* @param vcfFile the vcf file
* @param createOutOfDateIndex if true, ensure that the temporary vcf file is modified after the index
* @return a file pointing to the new tmp location, with accompanying index
*/
private File createTempVCFFileAndIndex( final File vcfFile, final boolean createOutOfDateIndex ) {
try {
final File tmpFile = createTempFile("RMDTrackBuilderUnitTest", "");
final File tmpIndex = Tribble.indexFile(tmpFile);
tmpIndex.deleteOnExit();
copyFile(vcfFile, tmpFile);
final Index inMemoryIndex = builder.createIndexInMemory(tmpFile, new VCFCodec());
final LittleEndianOutputStream indexOutputStream = new LittleEndianOutputStream(new FileOutputStream(tmpIndex));
// If requested, modify the tribble file after the index. Otherwise, modify the index last.
if ( createOutOfDateIndex ) {
inMemoryIndex.write(indexOutputStream);
indexOutputStream.close();
Thread.sleep(2000);
copyFile(vcfFile, tmpFile);
}
else {
copyFile(vcfFile, tmpFile);
Thread.sleep(2000);
inMemoryIndex.write(indexOutputStream);
indexOutputStream.close();
}
return tmpFile;
} catch (IOException e) {
Assert.fail("Unable to create temperary file");
} catch (InterruptedException e) {
Assert.fail("Somehow our thread got interrupted");
}
return null;
}
/**
* copy a file, from http://www.exampledepot.com/egs/java.nio/File2File.html
*
* @param srFile the source file
* @param dtFile the destination file
*/
private static void copyFile(File srFile, File dtFile) {
try {
// Create channel on the source
FileChannel srcChannel = new FileInputStream(srFile).getChannel();
// Create channel on the destination
FileChannel dstChannel = new FileOutputStream(dtFile).getChannel();
// Copy file contents from source to destination
dstChannel.transferFrom(srcChannel, 0, srcChannel.size());
// Close the channels
srcChannel.close();
dstChannel.close();
} catch (IOException e) {
e.printStackTrace();
Assert.fail("Unable to process copy " + e.getMessage());
}
}
}