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Don't allow users to specify keys and IDs that contain angle brackets or equals signs (not allowed in VCF spec). 

* As reported here: http://gatkforums.broadinstitute.org/discussion/comment/4270#Comment_4270
  * This was a commit into the variant.jar; the changes here are a rev of that jar and handling of errors in VF
  * Added integration test to confirm failure with User Error
  * Removed illegal header line in KB test VCF that was causing related tests to fail.
This commit is contained in:
Eric Banks 2013-04-04 10:44:40 -05:00
parent 14bbba0980
commit 7897d52f32
4 changed files with 22 additions and 10 deletions
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8
protected/java/test/org/broadinstitute/sting/gatk/walkers/filters/VariantFiltrationIntegrationTest.java
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@ -47,6 +47,7 @@
package org.broadinstitute.sting.gatk.walkers.filters;
import org.broadinstitute.sting.WalkerTest;
import org.broadinstitute.sting.utils.exceptions.UserException;
import org.testng.annotations.Test;
import java.util.Arrays;
@ -106,6 +107,13 @@ public class VariantFiltrationIntegrationTest extends WalkerTest {
executeTest("test filter sites not in mask", spec3);
}
@Test
public void testIllegalFilterName() {
WalkerTestSpec spec = new WalkerTestSpec(
baseTestString() + " -filter 'DoC < 20 || FisherStrand > 20.0' -filterName 'foo < foo' --variant " + privateTestDir + "vcfexample2.vcf -L 1:10,020,000-10,021,000", 1,
UserException.class);
executeTest("test illegal filter name", spec);
}
@Test
public void testFilter1() {

22
public/java/src/org/broadinstitute/sting/gatk/walkers/filters/VariantFiltration.java
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@ -186,18 +186,22 @@ public class VariantFiltration extends RodWalker<Integer, Integer> {
if ( clusterWindow > 0 )
hInfo.add(new VCFFilterHeaderLine(CLUSTERED_SNP_FILTER_NAME, "SNPs found in clusters"));
for ( VariantContextUtils.JexlVCMatchExp exp : filterExps )
hInfo.add(new VCFFilterHeaderLine(exp.name, exp.exp.toString()));
for ( VariantContextUtils.JexlVCMatchExp exp : genotypeFilterExps )
hInfo.add(new VCFFilterHeaderLine(exp.name, exp.exp.toString()));
if ( genotypeFilterExps.size() > 0 )
hInfo.add(VCFStandardHeaderLines.getFormatLine(VCFConstants.GENOTYPE_FILTER_KEY));
if ( mask.isBound() ) {
if (filterRecordsNotInMask)
hInfo.add(new VCFFilterHeaderLine(MASK_NAME, "Doesn't overlap a user-input mask"));
else hInfo.add(new VCFFilterHeaderLine(MASK_NAME, "Overlaps a user-input mask"));
try {
for ( VariantContextUtils.JexlVCMatchExp exp : filterExps )
hInfo.add(new VCFFilterHeaderLine(exp.name, exp.exp.toString()));
for ( VariantContextUtils.JexlVCMatchExp exp : genotypeFilterExps )
hInfo.add(new VCFFilterHeaderLine(exp.name, exp.exp.toString()));
if ( mask.isBound() ) {
if (filterRecordsNotInMask)
hInfo.add(new VCFFilterHeaderLine(MASK_NAME, "Doesn't overlap a user-input mask"));
else hInfo.add(new VCFFilterHeaderLine(MASK_NAME, "Overlaps a user-input mask"));
}
} catch (IllegalArgumentException e) {
throw new UserException.BadInput(e.getMessage());
}
writer.writeHeader(new VCFHeader(hInfo, SampleUtils.getUniqueSamplesFromRods(getToolkit(), inputNames)));

BIN
settings/repository/org.broadinstitute/variant-1.85.1357.jar → settings/repository/org.broadinstitute/variant-1.88.1401.jar
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2
settings/repository/org.broadinstitute/variant-1.85.1357.xml → settings/repository/org.broadinstitute/variant-1.88.1401.xml
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@ -1,3 +1,3 @@
<ivy-module version="1.0">
<info organisation="org.broadinstitute" module="variant" revision="1.85.1357" status="integration" />
<info organisation="org.broadinstitute" module="variant" revision="1.88.1401" status="integration" />
</ivy-module>