gatk-3.8/java/test/org/broadinstitute/sting/gatk/traversals/TraverseReadsTest.java

package org.broadinstitute.sting.gatk.traversals;

import org.broadinstitute.sting.BaseTest;
import org.broadinstitute.sting.gatk.Reads;
import org.broadinstitute.sting.gatk.datasources.providers.ShardDataProvider;
import org.broadinstitute.sting.gatk.datasources.shards.Shard;
import org.broadinstitute.sting.gatk.datasources.shards.ShardStrategy;
import org.broadinstitute.sting.gatk.datasources.shards.ShardStrategyFactory;
import org.broadinstitute.sting.gatk.datasources.simpleDataSources.SAMDataSource;
import org.broadinstitute.sting.gatk.refdata.ReferenceOrderedData;
import org.broadinstitute.sting.gatk.refdata.ReferenceOrderedDatum;
import org.broadinstitute.sting.gatk.walkers.CountReadsWalker;
import org.broadinstitute.sting.gatk.walkers.Walker;
import org.broadinstitute.sting.utils.GenomeLocParser;
import org.broadinstitute.sting.utils.fasta.FastaSequenceFile2;
import org.broadinstitute.sting.utils.fasta.IndexedFastaSequenceFile;
import static org.junit.Assert.fail;
import org.junit.Before;
import org.junit.Test;

import java.io.File;
import java.io.FileNotFoundException;
import java.io.FileOutputStream;
import java.io.PrintStream;
import java.lang.reflect.Field;
import java.util.ArrayList;
import java.util.List;

/**
 *
 * User: aaron
 * Date: Apr 24, 2009
 * Time: 3:42:16 PM
 *
 * The Broad Institute
 * SOFTWARE COPYRIGHT NOTICE AGREEMENT 
 * This software and its documentation are copyright 2009 by the
 * Broad Institute/Massachusetts Institute of Technology. All rights are reserved.
 *
 * This software is supplied without any warranty or guaranteed support whatsoever. Neither
 * the Broad Institute nor MIT can be responsible for its use, misuse, or functionality.
 *
 */


/**
 * @author aaron
 * @version 1.0
 * @date Apr 24, 2009
 * <p/>
 * Class TraverseReadsTest
 * <p/>
 * test traversing reads
 */
public class TraverseReadsTest extends BaseTest {

    private FastaSequenceFile2 seq;
    private File bam = new File("/humgen/gsa-scr1/GATK_Data/Validation_Data/index_test.bam"); // TCGA-06-0188.aligned.duplicates_marked.bam");
    private File refFile = new File("/humgen/gsa-scr1/GATK_Data/Validation_Data/Homo_sapiens_assembly17.fasta");
    private List<File> bamList;
    private Walker countReadWalker;
    private File output;
    private long readSize = 100000;
    private TraverseReads traversalEngine = null;

    /**
     * This function does the setup of our parser, before each method call.
     * <p/>
     * Called before every test case method.
     */
    @Before
    public void doForEachTest() {
        output = new File("testOut.txt");
        FileOutputStream out = null;
        PrintStream ps; // declare a print stream object

        try {
            out = new FileOutputStream(output);
        } catch (FileNotFoundException e) {
            e.printStackTrace();  //To change body of catch statement use File | Settings | File Templates.
            fail("Couldn't open the output file");
        }

        // Connect print stream to the output stream
        ps = new PrintStream(out);
        bamList = new ArrayList<File>();
        bamList.add(bam);
        countReadWalker = new CountReadsWalker();
        try {
            Field f = Walker.class.getDeclaredField("out");
            f.setAccessible(true);
            f.set(countReadWalker, ps);

        } catch (IllegalAccessException e) {
            e.printStackTrace();  //To change body of catch statement use File | Settings | File Templates.
        } catch (NoSuchFieldException e) {
            e.printStackTrace();  //To change body of catch statement use File | Settings | File Templates.
            fail("Couldn't set the walkers printstream");
        }
        List<ReferenceOrderedData<? extends ReferenceOrderedDatum>> rods = new ArrayList<ReferenceOrderedData<? extends ReferenceOrderedDatum>>();

        traversalEngine = new TraverseReads(bamList, refFile, rods);


    }


    /** Test out that we can shard the file and iterate over every read */
    @Test
    public void testMappedReadCount() {

        IndexedFastaSequenceFile ref = null;
        try {
            ref = new IndexedFastaSequenceFile(refFile);
        }
        catch (FileNotFoundException ex) {
            throw new RuntimeException("File not found opening fasta file; please do this check before MicroManaging", ex);
        }
        GenomeLocParser.setupRefContigOrdering(ref);

        ShardStrategy shardStrategy = ShardStrategyFactory.shatter(ShardStrategyFactory.SHATTER_STRATEGY.READS,
                ref.getSequenceDictionary(),
                readSize);

        SAMDataSource dataSource = new SAMDataSource(new Reads(bamList),true);
        dataSource.viewUnmappedReads(false);

        countReadWalker.initialize();
        Object accumulator = countReadWalker.reduceInit();

        while (shardStrategy.hasNext()) {
            Shard shard = shardStrategy.next();

            if (shard == null) {
                fail("Shard == null");
            }

            ShardDataProvider dataProvider = new ShardDataProvider(shard,dataSource,null,null);
            accumulator = traversalEngine.traverse(countReadWalker, shard, dataProvider, accumulator);
            dataProvider.close();

        }

        traversalEngine.printOnTraversalDone("loci", accumulator);
        countReadWalker.onTraversalDone(accumulator);

        if (!(accumulator instanceof Integer)) {
            fail("Count read walker should return an interger.");
        }
        if (((Integer) accumulator) != 9721) {
            fail("there should be 9721 mapped reads in the index file, there was " + ((Integer) accumulator) );
        }
    }


    /** Test out that we can shard the file and iterate over every read */
    @Test
    public void testUnmappedReadCount() {
        IndexedFastaSequenceFile ref = null;
        try {
            ref = new IndexedFastaSequenceFile(refFile);
        }
        catch (FileNotFoundException ex) {
            throw new RuntimeException("File not found opening fasta file; please do this check before MicroManaging", ex);
        }
        GenomeLocParser.setupRefContigOrdering(ref);

        ShardStrategy shardStrategy = ShardStrategyFactory.shatter(ShardStrategyFactory.SHATTER_STRATEGY.READS,
                ref.getSequenceDictionary(),
                readSize);

        SAMDataSource dataSource = new SAMDataSource(new Reads(bamList),true);
        dataSource.viewUnmappedReads(true);

        countReadWalker.initialize();
        Object accumulator = countReadWalker.reduceInit();

        while (shardStrategy.hasNext()) {
            Shard shard = shardStrategy.next();

            if (shard == null) {
                fail("Shard == null");
            }

            ShardDataProvider dataProvider = new ShardDataProvider(shard,dataSource,null,null);
            accumulator = traversalEngine.traverse(countReadWalker, shard, dataProvider, accumulator);
            dataProvider.close();
        }

        traversalEngine.printOnTraversalDone("loci", accumulator);
        countReadWalker.onTraversalDone(accumulator);

        if (!(accumulator instanceof Integer)) {
            fail("Count read walker should return an interger.");
        }
        if (((Integer) accumulator) != 10000) {
            fail("there should be 10000 mapped reads in the index file, there was " + ((Integer) accumulator));
        }
    }

}