/*
* 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.datasources.providers;
import htsjdk.tribble.Feature;
import org.broadinstitute.gatk.utils.commandline.RodBinding;
import org.broadinstitute.gatk.utils.commandline.Tags;
import org.broadinstitute.gatk.engine.datasources.reads.MockLocusShard;
import org.broadinstitute.gatk.engine.datasources.rmd.ReferenceOrderedDataSource;
import org.broadinstitute.gatk.engine.refdata.tracks.RMDTrackBuilder;
import org.broadinstitute.gatk.engine.refdata.utils.RMDTriplet;
import org.testng.Assert;
import org.broadinstitute.gatk.utils.BaseTest;
import org.broadinstitute.gatk.engine.datasources.reads.Shard;
import org.broadinstitute.gatk.engine.refdata.RefMetaDataTracker;
import org.broadinstitute.gatk.utils.codecs.table.TableFeature;
import org.broadinstitute.gatk.engine.refdata.utils.RMDTriplet.RMDStorageType;
import org.broadinstitute.gatk.utils.GenomeLocParser;
import org.broadinstitute.gatk.utils.fasta.CachingIndexedFastaSequenceFile;
import org.testng.annotations.BeforeClass;
import org.testng.annotations.Test;
import java.io.File;
import java.io.FileNotFoundException;
import java.util.Arrays;
import java.util.Collections;
import htsjdk.samtools.reference.IndexedFastaSequenceFile;
/**
* User: hanna
* Date: May 27, 2009
* Time: 3:07:23 PM
* BROAD INSTITUTE SOFTWARE COPYRIGHT NOTICE AND AGREEMENT
* Software and documentation are copyright 2005 by the Broad Institute.
* All rights are reserved.
*
* Users acknowledge that this software is supplied without any warranty or support.
* The Broad Institute is not responsible for its use, misuse, or
* functionality.
*/
/**
* Test the transparent view into the reference-ordered data. At the moment, just do some basic bindings and make
* sure the data comes through correctly.
*/
public class ReferenceOrderedViewUnitTest extends BaseTest {
/**
* Sequence file.
*/
private static IndexedFastaSequenceFile seq;
private GenomeLocParser genomeLocParser;
/**
* our track builder
*/
RMDTrackBuilder builder = null;
@BeforeClass
public void init() throws FileNotFoundException {
// sequence
seq = new CachingIndexedFastaSequenceFile(new File(hg18Reference));
genomeLocParser = new GenomeLocParser(seq);
// disable auto-index creation/locking in the RMDTrackBuilder for tests
builder = new RMDTrackBuilder(seq.getSequenceDictionary(),genomeLocParser,null,true,null);
}
/**
* Make sure binding to an empty list produces an empty tracker.
*/
@Test
public void testNoBindings() {
Shard shard = new MockLocusShard(genomeLocParser,Collections.singletonList(genomeLocParser.createGenomeLoc("chrM",1,30)));
LocusShardDataProvider provider = new LocusShardDataProvider(shard, null, genomeLocParser, shard.getGenomeLocs().get(0), null, seq, Collections.<ReferenceOrderedDataSource>emptyList());
ReferenceOrderedView view = new ManagingReferenceOrderedView( provider );
RefMetaDataTracker tracker = view.getReferenceOrderedDataAtLocus(genomeLocParser.createGenomeLoc("chrM",10));
Assert.assertEquals(tracker.getValues(Feature.class).size(), 0, "The tracker should not have produced any data");
}
/**
* Test a single ROD binding.
*/
@Test
public void testSingleBinding() {
String fileName = privateTestDir + "TabularDataTest.dat";
RMDTriplet triplet = new RMDTriplet("tableTest","Table",fileName,RMDStorageType.FILE,new Tags());
ReferenceOrderedDataSource dataSource = new ReferenceOrderedDataSource(triplet,builder,seq.getSequenceDictionary(),genomeLocParser,false);
Shard shard = new MockLocusShard(genomeLocParser,Collections.singletonList(genomeLocParser.createGenomeLoc("chrM",1,30)));
LocusShardDataProvider provider = new LocusShardDataProvider(shard, null, genomeLocParser, shard.getGenomeLocs().get(0), null, seq, Collections.singletonList(dataSource));
ReferenceOrderedView view = new ManagingReferenceOrderedView( provider );
RefMetaDataTracker tracker = view.getReferenceOrderedDataAtLocus(genomeLocParser.createGenomeLoc("chrM",20));
TableFeature datum = tracker.getFirstValue(new RodBinding<TableFeature>(TableFeature.class, "tableTest"));
Assert.assertEquals(datum.get("COL1"),"C","datum parameter for COL1 is incorrect");
Assert.assertEquals(datum.get("COL2"),"D","datum parameter for COL2 is incorrect");
Assert.assertEquals(datum.get("COL3"),"E","datum parameter for COL3 is incorrect");
}
/**
* Make sure multiple bindings are visible from the view.
*/
@Test
public void testMultipleBinding() {
File file = new File(privateTestDir + "TabularDataTest.dat");
RMDTriplet testTriplet1 = new RMDTriplet("tableTest1","Table",file.getAbsolutePath(),RMDStorageType.FILE,new Tags());
ReferenceOrderedDataSource dataSource1 = new ReferenceOrderedDataSource(testTriplet1,builder,seq.getSequenceDictionary(),genomeLocParser,false);
RMDTriplet testTriplet2 = new RMDTriplet("tableTest2","Table",file.getAbsolutePath(),RMDStorageType.FILE,new Tags());
ReferenceOrderedDataSource dataSource2 = new ReferenceOrderedDataSource(testTriplet2,builder,seq.getSequenceDictionary(),genomeLocParser,false);
Shard shard = new MockLocusShard(genomeLocParser,Collections.singletonList(genomeLocParser.createGenomeLoc("chrM",1,30)));
LocusShardDataProvider provider = new LocusShardDataProvider(shard, null, genomeLocParser, shard.getGenomeLocs().get(0), null, seq, Arrays.asList(dataSource1,dataSource2));
ReferenceOrderedView view = new ManagingReferenceOrderedView( provider );
RefMetaDataTracker tracker = view.getReferenceOrderedDataAtLocus(genomeLocParser.createGenomeLoc("chrM",20));
TableFeature datum1 = tracker.getFirstValue(new RodBinding<TableFeature>(TableFeature.class, "tableTest1"));
Assert.assertEquals(datum1.get("COL1"),"C","datum1 parameter for COL1 is incorrect");
Assert.assertEquals(datum1.get("COL2"),"D","datum1 parameter for COL2 is incorrect");
Assert.assertEquals(datum1.get("COL3"),"E","datum1 parameter for COL3 is incorrect");
TableFeature datum2 = tracker.getFirstValue(new RodBinding<TableFeature>(TableFeature.class, "tableTest2"));
Assert.assertEquals(datum2.get("COL1"),"C","datum2 parameter for COL1 is incorrect");
Assert.assertEquals(datum2.get("COL2"),"D","datum2 parameter for COL2 is incorrect");
Assert.assertEquals(datum2.get("COL3"),"E","datum2 parameter for COL3 is incorrect");
}
}