gatk-3.8/public/java/test/org/broadinstitute/variant/vcf/VCFIntegrationTest.java

package org.broadinstitute.variant.vcf;

import org.broadinstitute.sting.WalkerTest;
import org.broadinstitute.sting.utils.exceptions.UserException;
import org.testng.annotations.Test;

import java.io.File;
import java.util.Arrays;
import java.util.List;

public class VCFIntegrationTest extends WalkerTest {

    @Test(enabled = true)
    public void testReadingAndWritingWitHNoChanges() {

        String md5ofInputVCF = "d991abe6c6a7a778a60a667717903be0";
        String testVCF = privateTestDir + "vcf4.1.example.vcf";

        String baseCommand = "-R " + b37KGReference + " --no_cmdline_in_header -o %s ";

        String test1 = baseCommand + "-T VariantAnnotator --variant " + testVCF + " -L " + testVCF;
        WalkerTestSpec spec1 = new WalkerTestSpec(test1, 1, Arrays.asList(md5ofInputVCF));
        List<File> result = executeTest("Test Variant Annotator with no changes", spec1).getFirst();

        String test2 = baseCommand + "-T VariantsToVCF --variant " + result.get(0).getAbsolutePath();
        WalkerTestSpec spec2 = new WalkerTestSpec(test2, 1, Arrays.asList(md5ofInputVCF));
        executeTest("Test Variants To VCF from new output", spec2);
    }

    @Test(enabled = true)
    public void testReadingAndWritingBreakpointAlleles() {
        String testVCF = privateTestDir + "breakpoint-example.vcf";

        String baseCommand = "-R " + b37KGReference + " --no_cmdline_in_header -o %s ";

        String test1 = baseCommand + "-T SelectVariants -V " + testVCF;
        WalkerTestSpec spec1 = new WalkerTestSpec(test1, 1, Arrays.asList("13329ba7360a8beb3afc02569e5a20c4"));
        executeTest("Test reading and writing breakpoint VCF", spec1);
    }

    @Test(enabled = true)
    public void testReadingLowerCaseBases() {
        String testVCF = privateTestDir + "lowercaseBases.vcf";

        String baseCommand = "-R " + b37KGReference + " --no_cmdline_in_header -o %s ";

        String test1 = baseCommand + "-T SelectVariants -V " + testVCF;
        WalkerTestSpec spec1 = new WalkerTestSpec(test1, 1, Arrays.asList("e0e308a25e56bde1c664139bb44ed19d"));
        executeTest("Test reading VCF with lower-case bases", spec1);
    }

    @Test(enabled = true)
    public void testReadingAndWriting1000GSVs() {
        String testVCF = privateTestDir + "1000G_SVs.chr1.vcf";

        String baseCommand = "-R " + b37KGReference + " --no_cmdline_in_header -o %s ";

        String test1 = baseCommand + "-T SelectVariants -V " + testVCF;
        WalkerTestSpec spec1 = new WalkerTestSpec(test1, 1, Arrays.asList("bdab26dd7648a806dbab01f64db2bdab"));
        executeTest("Test reading and writing 1000G Phase I SVs", spec1);
    }

    @Test
    public void testReadingAndWritingSamtools() {
        String testVCF = privateTestDir + "samtools.vcf";

        String baseCommand = "-R " + b37KGReference + " --no_cmdline_in_header -o %s ";

        String test1 = baseCommand + "-T SelectVariants -V " + testVCF;
        WalkerTestSpec spec1 = new WalkerTestSpec(test1, 1, Arrays.asList("38697c195e7abf18d95dcc16c8e6d284"));
        executeTest("Test reading and writing samtools vcf", spec1);
    }

    @Test
    public void testWritingSamtoolsWExBCFExample() {
        String testVCF = privateTestDir + "ex2.vcf";
        String baseCommand = "-R " + b36KGReference + " --no_cmdline_in_header -o %s ";
        String test1 = baseCommand + "-T SelectVariants -V " + testVCF;
        WalkerTestSpec spec1 = new WalkerTestSpec(test1, 1, Arrays.asList("e8f721ce81e4fdadba13c5291027057f"));
        executeTest("Test writing samtools WEx BCF example", spec1);
    }

    @Test(enabled = true)
    public void testReadingSamtoolsWExBCFExample() {
        String testVCF = privateTestDir + "ex2.bcf";
        String baseCommand = "-R " + b36KGReference + " --no_cmdline_in_header -o %s ";
        String test1 = baseCommand + "-T SelectVariants -V " + testVCF;
        WalkerTestSpec spec1 = new WalkerTestSpec(test1, 1, Arrays.asList("0439e2b4ccc63bb4ba7c283cd9ab1b25"));
        executeTest("Test reading samtools WEx BCF example", spec1);
    }

    //
    //
    // Tests to ensure that -U LENIENT_VCF_PROCESS
    //
    //

    @Test
    public void testFailingOnVCFWithoutHeaders() {
        runVCFWithoutHeaders("", "", IllegalStateException.class, false);
    }

    @Test
    public void testPassingOnVCFWithoutHeadersWithLenientProcessing() {
        runVCFWithoutHeaders("-U LENIENT_VCF_PROCESSING", "6de8cb7457154dd355aa55befb943f88", null, true);
    }

    private void runVCFWithoutHeaders(final String moreArgs, final String expectedMD5, final Class expectedException, final boolean disableBCF) {
        final String testVCF = privateTestDir + "vcfexample2.noHeader.vcf";
        final String baseCommand = "-R " + b37KGReference
                + " --no_cmdline_in_header -o %s "
                + "-T VariantsToVCF -V " + testVCF + " " + moreArgs;
        WalkerTestSpec spec1 = expectedException != null
                ? new WalkerTestSpec(baseCommand, 1, expectedException)
                : new WalkerTestSpec(baseCommand, 1, Arrays.asList(expectedMD5));
        if ( disableBCF )
            spec1.disableShadowBCF();
        executeTest("Test reading VCF without header lines with additional args " + moreArgs, spec1);
    }
}