package org.broadinstitute.sting.gatk.walkers.variantutils;

import org.broadinstitute.sting.WalkerTest;
import org.junit.Test;

import java.util.Arrays;

public class SelectVariantsIntegrationTest extends WalkerTest {
    public static String baseTestString(String args) {
        return "-T SelectVariants -R " + b36KGReference + " -L 1 -o %s" + args;
    }

    @Test
    public void testComplexSelection() {
        String testfile = validationDataLocation + "test.filtered.maf_annotated.vcf";

        WalkerTestSpec spec = new WalkerTestSpec(
            baseTestString(" -sn A -sn [CDEH] -env -ef -select 'AF < 0.2' -B variant,VCF," + testfile),
            1,
            Arrays.asList("3a15628b5980031c629c0c33e7e60b40")
        );

        executeTest("testComplexSelection--" + testfile, spec);
    }
}

package org.broadinstitute.sting.gatk.walkers.variantutils;

import org.broadinstitute.sting.WalkerTest;
import org.junit.Test;

import java.util.Arrays;

public class SelectVariantsIntegrationTest extends WalkerTest {
    public static String baseTestString(String args) {
        return "-T SelectVariants -R " + b36KGReference + " -L 1 -o %s" + args;
    }

    @Test
    public void testComplexSelection() {
        String testfile = validationDataLocation + "test.filtered.maf_annotated.vcf";

        WalkerTestSpec spec = new WalkerTestSpec(
            baseTestString(" -sn A -sn '[CDEH]' -env -ef -select 'AF < 0.2' -B variant,VCF," + testfile),
            1,
            Arrays.asList("3a15628b5980031c629c0c33e7e60b40")
        );

        executeTest("testComplexSelection--" + testfile, spec);
    }
}

Put single quotes around the regex. This isn't strictly necessary through the integration test machinery, but *is* necessary at the console, and it's convenient to be able to cut and paste this.
Put single quotes around the regex.  This isn't strictly necessary through the integration test machinery, but *is* necessary at the console, and it's convenient to be able to cut and paste this.

git-svn-id: 4561c0a8f080806b19201efb9525134c00b76d40@3977 348d0f76-0448-11de-a6fe-93d51630548a
