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Better documentation for ValidateVariants so that people realize it's used for strict validation of the VCF file. Added an option to turn off strict validation and an integration test to cover it.

This commit is contained in:
Eric Banks 2012-10-29 21:47:09 -04:00
parent 21fa5f70ca
commit b6a1967f12
2 changed files with 31 additions and 15 deletions
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15
public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/ValidateVariants.java
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@ -46,16 +46,20 @@ import java.util.Set;
/** /**
* Strictly validates a variants file. * Validates a VCF file with an extra strict set of criteria.
* *
* <p> * <p>
* ValidateVariants is a GATK tool that takes a VCF file and validates much of the information inside it. * ValidateVariants is a GATK tool that takes a VCF file and validates much of the information inside it.
* Checks include the correctness of the reference base(s), accuracy of AC & AN values, tests against rsIDs * In addition to standard adherence to the VCF specification, this tool performs extra checks to make ensure
* when a dbSNP file is provided, and that all alternate alleles are present in at least one sample. * the information contained within the file is correct. Checks include the correctness of the reference base(s),
* accuracy of AC & AN values, tests against rsIDs when a dbSNP file is provided, and that all alternate alleles
* are present in at least one sample.
*
* If you are looking simply to test the adherence to the VCF specification, use --validationType NONE.
* *
* <h2>Input</h2> * <h2>Input</h2>
* <p> * <p>
* A variant set to filter. * A variant set to validate.
* </p> * </p>
* *
* <h2>Examples</h2> * <h2>Examples</h2>
@ -79,10 +83,9 @@ public class ValidateVariants extends RodWalker<Integer, Integer> {
protected DbsnpArgumentCollection dbsnp = new DbsnpArgumentCollection(); protected DbsnpArgumentCollection dbsnp = new DbsnpArgumentCollection();
public enum ValidationType { public enum ValidationType {
ALL, REF, IDS, ALLELES, CHR_COUNTS ALL, REF, IDS, ALLELES, CHR_COUNTS, NONE
} }
@Hidden
@Argument(fullName = "validationType", shortName = "type", doc = "which validation type to run", required = false) @Argument(fullName = "validationType", shortName = "type", doc = "which validation type to run", required = false)
protected ValidationType type = ValidationType.ALL; protected ValidationType type = ValidationType.ALL;

31
public/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/ValidateVariantsIntegrationTest.java
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@ -33,6 +33,8 @@ import java.util.Arrays;
public class ValidateVariantsIntegrationTest extends WalkerTest { public class ValidateVariantsIntegrationTest extends WalkerTest {
protected static final String emptyMd5 = "d41d8cd98f00b204e9800998ecf8427e";
public static String baseTestString(String file, String type) { public static String baseTestString(String file, String type) {
return "-T ValidateVariants -R " + b36KGReference + " -L 1:10001292-10001303 --variant:vcf " + privateTestDir + file + " --validationType " + type; return "-T ValidateVariants -R " + b36KGReference + " -L 1:10001292-10001303 --variant:vcf " + privateTestDir + file + " --validationType " + type;
} }
@ -42,7 +44,7 @@ public class ValidateVariantsIntegrationTest extends WalkerTest {
WalkerTestSpec spec = new WalkerTestSpec( WalkerTestSpec spec = new WalkerTestSpec(
baseTestString("validationExampleGood.vcf", "ALL"), baseTestString("validationExampleGood.vcf", "ALL"),
0, 0,
Arrays.asList("d41d8cd98f00b204e9800998ecf8427e") Arrays.asList(emptyMd5)
); );
executeTest("test good file", spec); executeTest("test good file", spec);
@ -53,7 +55,7 @@ public class ValidateVariantsIntegrationTest extends WalkerTest {
WalkerTestSpec spec = new WalkerTestSpec( WalkerTestSpec spec = new WalkerTestSpec(
baseTestString("validationExampleBad.vcf", "REF"), baseTestString("validationExampleBad.vcf", "REF"),
0, 0,
UserException.MalformedFile.class UserException.FailsStrictValidation.class
); );
executeTest("test bad ref base #1", spec); executeTest("test bad ref base #1", spec);
@ -64,7 +66,7 @@ public class ValidateVariantsIntegrationTest extends WalkerTest {
WalkerTestSpec spec = new WalkerTestSpec( WalkerTestSpec spec = new WalkerTestSpec(
baseTestString("validationExampleBad2.vcf", "REF"), baseTestString("validationExampleBad2.vcf", "REF"),
0, 0,
UserException.MalformedFile.class UserException.FailsStrictValidation.class
); );
executeTest("test bad ref base #2", spec); executeTest("test bad ref base #2", spec);
@ -75,7 +77,7 @@ public class ValidateVariantsIntegrationTest extends WalkerTest {
WalkerTestSpec spec = new WalkerTestSpec( WalkerTestSpec spec = new WalkerTestSpec(
baseTestString("validationExampleBad.vcf", "CHR_COUNTS"), baseTestString("validationExampleBad.vcf", "CHR_COUNTS"),
0, 0,
UserException.MalformedFile.class UserException.FailsStrictValidation.class
); );
executeTest("test bad chr counts #1", spec); executeTest("test bad chr counts #1", spec);
@ -86,7 +88,7 @@ public class ValidateVariantsIntegrationTest extends WalkerTest {
WalkerTestSpec spec = new WalkerTestSpec( WalkerTestSpec spec = new WalkerTestSpec(
baseTestString("validationExampleBad2.vcf", "CHR_COUNTS"), baseTestString("validationExampleBad2.vcf", "CHR_COUNTS"),
0, 0,
UserException.MalformedFile.class UserException.FailsStrictValidation.class
); );
executeTest("test bad chr counts #2", spec); executeTest("test bad chr counts #2", spec);
@ -97,7 +99,7 @@ public class ValidateVariantsIntegrationTest extends WalkerTest {
WalkerTestSpec spec = new WalkerTestSpec( WalkerTestSpec spec = new WalkerTestSpec(
baseTestString("validationExampleBad.vcf", "IDS") + " --dbsnp " + b36dbSNP129, baseTestString("validationExampleBad.vcf", "IDS") + " --dbsnp " + b36dbSNP129,
0, 0,
UserException.MalformedFile.class UserException.FailsStrictValidation.class
); );
executeTest("test bad RS ID", spec); executeTest("test bad RS ID", spec);
@ -108,7 +110,7 @@ public class ValidateVariantsIntegrationTest extends WalkerTest {
WalkerTestSpec spec = new WalkerTestSpec( WalkerTestSpec spec = new WalkerTestSpec(
baseTestString("validationExampleBad.vcf", "ALLELES"), baseTestString("validationExampleBad.vcf", "ALLELES"),
0, 0,
UserException.MalformedFile.class UserException.FailsStrictValidation.class
); );
executeTest("test bad alt allele", spec); executeTest("test bad alt allele", spec);
@ -119,18 +121,29 @@ public class ValidateVariantsIntegrationTest extends WalkerTest {
WalkerTestSpec spec = new WalkerTestSpec( WalkerTestSpec spec = new WalkerTestSpec(
baseTestString("validationExampleBad3.vcf", "REF"), baseTestString("validationExampleBad3.vcf", "REF"),
0, 0,
UserException.MalformedFile.class UserException.FailsStrictValidation.class
); );
executeTest("test bad ref allele in deletion", spec); executeTest("test bad ref allele in deletion", spec);
} }
@Test
public void testNoValidation() {
WalkerTestSpec spec = new WalkerTestSpec(
baseTestString("validationExampleBad.vcf", "NONE"),
0,
Arrays.asList(emptyMd5)
);
executeTest("test no validation", spec);
}
@Test @Test
public void testComplexEvents() { public void testComplexEvents() {
WalkerTestSpec spec = new WalkerTestSpec( WalkerTestSpec spec = new WalkerTestSpec(
baseTestString("complexEvents.vcf", "ALL"), baseTestString("complexEvents.vcf", "ALL"),
0, 0,
Arrays.asList("d41d8cd98f00b204e9800998ecf8427e") Arrays.asList(emptyMd5)
); );
executeTest("test validating complex events", spec); executeTest("test validating complex events", spec);