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/*
* The MIT License
*
* Copyright (c) 2016 Nils Homer
*
* 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.vcf;
import htsjdk.samtools.util.CloserUtil;
import htsjdk.variant.vcf.VCFFileReader;
import htsjdk.variant.vcf.VCFHeader;
import org.testng.Assert;
import org.testng.annotations.BeforeTest;
import org.testng.annotations.DataProvider;
import org.testng.annotations.Test;
import picard.PicardException;
import picard.nio.PicardHtsPath;
import java.io.File;
import java.io.IOException;
/**
* Tests for FixVcfHeader.
*
* @author Nils Homer
*/
public class FixVcfHeaderTest {
private PicardHtsPath INPUT_VCF;
private File OUTPUT_VCF;
private PicardHtsPath HEADER_VCF;
private PicardHtsPath HEADER_VCF_WITH_EXTRA_SAMPLE;
@BeforeTest
void setup() {
final File testDataPath = new File("testdata/picard/vcf/FixVcfHeaderTest/");
INPUT_VCF = new PicardHtsPath(new File(testDataPath, "input.vcf"));
OUTPUT_VCF = new File(testDataPath, "output.vcf");
HEADER_VCF = new PicardHtsPath(new File(testDataPath, "header.vcf"));
HEADER_VCF_WITH_EXTRA_SAMPLE = new PicardHtsPath(new File(testDataPath, "header_with_extra_sample.vcf"));
}
private void runFixVcfHeader(final int checkFirstNRecords,
final PicardHtsPath replacementHeader,
final boolean enforceSampleSamples) throws IOException {
final FixVcfHeader program = new FixVcfHeader();
final File outputVcf = VcfTestUtils.createTemporaryIndexedFile("output.", ".vcf");
program.INPUT = INPUT_VCF;
program.OUTPUT = outputVcf;
if (replacementHeader == null) {
program.CHECK_FIRST_N_RECORDS = checkFirstNRecords;
}
else {
program.HEADER = replacementHeader;
program.ENFORCE_SAME_SAMPLES = enforceSampleSamples;
}
Assert.assertEquals(program.instanceMain(new String[0]), 0);
final VCFFileReader actualReader = new VCFFileReader(OUTPUT_VCF, false);
final VCFFileReader expectedReader = new VCFFileReader(outputVcf, false);
// Check that the headers match (order does not matter
final VCFHeader actualHeader = actualReader.getFileHeader();
final VCFHeader expectedHeader = expectedReader.getFileHeader();
Assert.assertEquals(actualHeader.getFilterLines().size(), expectedHeader.getFilterLines().size());
Assert.assertEquals(actualHeader.getInfoHeaderLines().size(), expectedHeader.getInfoHeaderLines().size());
Assert.assertEquals(actualHeader.getFormatHeaderLines().size(), expectedHeader.getFormatHeaderLines().size());
// Check the number of records match, since we don't touch them
Assert.assertEquals(actualReader.iterator().stream().count(), expectedReader.iterator().stream().count(), "The wrong number of variants was found.");
CloserUtil.close(actualReader);
CloserUtil.close(expectedReader);
}
@Test(dataProvider = "testFixVcfHeaderDataProvider")
public void testFixVcfHeader(final int checkFirstNRecords,
final PicardHtsPath replacementHeader,
final boolean enforceSampleSamples) throws IOException {
runFixVcfHeader(checkFirstNRecords, replacementHeader, enforceSampleSamples);
}
@DataProvider(name="testFixVcfHeaderDataProvider")
public Object[][] testFixVcfHeaderDataProvider() {
return new Object[][] {
{-1, HEADER_VCF, true}, // tests replacing with a new header, enforcing the same samples
{-1, HEADER_VCF, false}, // tests replacing with a new header, not enforcing the same samples
{-1, HEADER_VCF_WITH_EXTRA_SAMPLE, false}, // tests replacing with a new header with an extra sample, not enforcing the same samples
{-1, null, true}, // tests discovering the header lines from the VCF using all records
{2, null, true}, // tests that the MissingFilter FILTER is found (in the second record)
{Integer.MAX_VALUE, null, true} // tests discovering the header lines from the VCF using all records (with CHECK_FIRST_N_RECORDS set to infinity)
};
}
@Test(expectedExceptions=java.lang.IllegalStateException.class)
public void testMissingFilterNotInFirstNRecords() throws IOException {
// NB: the MissingFilter FILTER is in the second record, so not found in the first pass of the VCF
runFixVcfHeader(1, null, true);
}
@Test(expectedExceptions=PicardException.class)
public void testReplaceHeaderWithDifferentSamplesError() throws IOException {
runFixVcfHeader(-1, HEADER_VCF_WITH_EXTRA_SAMPLE, true);
}
}
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