zzh
/
gatk-3.8
1
0
Fork 0
Code Issues Pull Requests Packages Projects Releases Wiki Activity

Bug fix when specifying a JEXL expression for a field that doesn't exist: we should treat the whole expression as false, but we were rethrowing the JEXL exception in this case. Added integration test to cover this in SelectVariants

This commit is contained in:
Guillermo del Angel 2012-07-10 13:59:00 -04:00
parent d7bf74fb7e
commit 279dff9f81
2 changed files with 19 additions and 1 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

7
public/java/src/org/broadinstitute/sting/utils/variantcontext/VariantJEXLContext.java
View File

@ -268,7 +268,12 @@ class JEXLMap implements Map<VariantContextUtils.JexlVCMatchExp, Boolean> {
// treat errors as no match
jexl.put(exp, value == null ? false : value);
} catch (Exception e) {
throw new UserException.CommandLineException(String.format("Invalid JEXL expression detected for %s with message %s", exp.name, e.getMessage()));
// if exception happens because variable is undefined (i.e. field in expression is not present), evaluate to FALSE
// todo - might be safer if we explicitly checked for an exception type, but Apache's API doesn't seem to have that ability
if (e.getMessage().contains("undefined variable"))
jexl.put(exp,false);
else
throw new UserException.CommandLineException(String.format("Invalid JEXL expression detected for %s with message %s", exp.name, e.getMessage()));
}
}

13
public/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariantsIntegrationTest.java
View File

@ -70,6 +70,19 @@ public class SelectVariantsIntegrationTest extends WalkerTest {
executeTest("testComplexSelection--" + testfile, spec);
}
@Test
public void testNonExistingFieldSelection() {
String testfile = validationDataLocation + "test.filtered.maf_annotated.vcf";
WalkerTestSpec spec = new WalkerTestSpec(
baseTestString(" -env -ef -select 'foo!=0||DP>0' --variant " + testfile),
1,
Arrays.asList("44e77cea624cfff2b8acc3a4b30485cb") // should yield empty vcf because the foo!=0 will yield complete expression false
);
spec.disableShadowBCF();
executeTest("testNonExistingSelection--" + testfile, spec);
}
@Test
public void testSampleExclusion() {
String testfile = validationDataLocation + "test.filtered.maf_annotated.vcf";