FilterSamReadsTest.java

/*
 * The MIT License
 *
 * Pierre Lindenbaum - Institut du Thorax - 2016
 *
 * 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 picard.sam;

import htsjdk.samtools.*;
import org.testng.Assert;
import org.testng.annotations.BeforeTest;
import org.testng.annotations.DataProvider;
import org.testng.annotations.Test;

import picard.cmdline.CommandLineProgramTest;

import java.io.File;
import java.util.stream.StreamSupport;

public class FilterSamReadsTest extends CommandLineProgramTest {
    @Override
    public String getCommandLineProgramName() {
        return FilterSamReads.class.getSimpleName();
    }

    private static final int READ_LENGTH = 151;
    private final SAMRecordSetBuilder builder = new SAMRecordSetBuilder();
    private final static File TEST_DIR = new File("testdata/picard/sam/FilterSamReads/");


    @BeforeTest
    public void setUp() {
        builder.setReadLength(READ_LENGTH);
        builder.addPair("mapped_pair_chr1", 0, 1, 151); //should be kept in first test, filtered out in third
        builder.addPair("mapped_pair_chr2", 1, 1, 151); //should be filtered out for first test, and kept in third
        builder.addPair("prove_one_of_pair", 0, 1000, 1000); //neither of these will be kept in any test
        builder.addPair("one_of_pair", 0, 1, 1000); //first read should pass, second should not, but both will be kept in first test
    }

    @DataProvider(name = "dataTestJsFilter")
    public Object[][] dataTestJsFilter() {
        return new Object[][]{
                {"testdata/picard/sam/aligned.sam", "testdata/picard/sam/FilterSamReads/filterOddStarts.js",3},
                {"testdata/picard/sam/aligned.sam", "testdata/picard/sam/FilterSamReads/filterReadsWithout5primeSoftClip.js", 0}
        };
    }

    @DataProvider(name = "dataTestPairedIntervalFilter")
    public Object[][] dataTestPairedIntervalFilter() {
        return new Object[][]{
                {"testdata/picard/sam/FilterSamReads/filter1.interval_list", 4},
                {"testdata/picard/sam/FilterSamReads/filter2.interval_list", 0}
        };
    }
    
    /**
     * filters a SAM using a javascript filter
     */
    @Test(dataProvider = "dataTestJsFilter")
    public void testJavaScriptFilters(final String samFilename, final String javascriptFilename,final int expectNumber) throws Exception {
        // input as SAM file 
        final File inputSam = new File(samFilename);
        final File javascriptFile = new File(javascriptFilename);

        FilterSamReads filterTest = setupProgram(javascriptFile, inputSam, FilterSamReads.Filter.includeJavascript);
        Assert.assertEquals(filterTest.doWork(),0);

        long count = getReadCount(filterTest);

        Assert.assertEquals(count, expectNumber);
    }

    /**
     * filters a SAM using an interval filter
     */
    @Test(dataProvider = "dataTestPairedIntervalFilter")
    public void testPairedIntervalFilter(final String intervalFilename, final int expectNumber) throws Exception {
        // Build a sam file for testing
        final File inputSam = File.createTempFile("testSam", ".sam", TEST_DIR);
        inputSam.deleteOnExit();

        final SAMFileWriter writer = new SAMFileWriterFactory()
                .setCreateIndex(true).makeBAMWriter(builder.getHeader(), false, inputSam);

        for (final SAMRecord record : builder) {
            writer.addAlignment(record);
        }
        writer.close();

        final File intervalFile = new File(intervalFilename);

        FilterSamReads filterTest = setupProgram(intervalFile, inputSam, FilterSamReads.Filter.includePairedIntervals);
        Assert.assertEquals(filterTest.doWork(),0);

        long count = getReadCount(filterTest);

        Assert.assertEquals(count, expectNumber);
    }

    private FilterSamReads setupProgram(final File inputFile, final File inputSam, final FilterSamReads.Filter filter) throws Exception {
        final FilterSamReads program = new FilterSamReads();
        program.INPUT = inputSam;
        program.OUTPUT = File.createTempFile("FilterSamReads.output.", ".sam");
        program.OUTPUT.deleteOnExit();
        program.FILTER = filter;

        if(filter == FilterSamReads.Filter.includePairedIntervals) {
            program.INTERVAL_LIST = inputFile;
        }
        else {
            program.JAVASCRIPT_FILE = inputFile;
        }

        return program;
    }

    private long getReadCount(FilterSamReads filterTest) throws Exception {
        final SamReader samReader = SamReaderFactory.makeDefault().open(filterTest.OUTPUT);

        long count = StreamSupport.stream(samReader.spliterator(), false)
                .count();

        samReader.close();
        return count;
    }
}