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JEXL update 

-- Update to 2.1.1 from 2.0
-- VariantFiltrationWalker now allows you to run with type unsafe selects, which all default to false when matching.  So "AF < 0.5" works even in the presence of multi-allelics now.
--
This commit is contained in:
Mark DePristo 2012-06-21 09:54:36 -04:00
parent 24dd8ee51b
commit 31ee8aa01a
3 changed files with 7 additions and 4 deletions
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2
ivy.xml
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@ -59,7 +59,7 @@
<!-- Commons Dependencies --> <!-- Commons Dependencies -->
<dependency org="org.apache.commons" name="commons-email" rev="1.2"/> <dependency org="org.apache.commons" name="commons-email" rev="1.2"/>
<dependency org="org.apache.commons" name="commons-jexl" rev="2.0"/> <dependency org="org.apache.commons" name="commons-jexl" rev="2.1.1"/>
<dependency org="commons-lang" name="commons-lang" rev="2.5"/> <dependency org="commons-lang" name="commons-lang" rev="2.5"/>
<dependency org="commons-logging" name="commons-logging" rev="1.1.1"/> <dependency org="commons-logging" name="commons-logging" rev="1.1.1"/>
<dependency org="commons-io" name="commons-io" rev="2.1"/> <dependency org="commons-io" name="commons-io" rev="2.1"/>

5
public/java/src/org/broadinstitute/sting/utils/variantcontext/VariantContextUtils.java
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@ -52,8 +52,9 @@ public class VariantContextUtils {
private final static boolean ASSUME_MISSING_FIELDS_ARE_STRINGS = false; private final static boolean ASSUME_MISSING_FIELDS_ARE_STRINGS = false;
static { static {
engine.setSilent(false); // will throw errors now for selects that don't evaluate properly engine.setSilent(true); // will throw errors now for selects that don't evaluate properly
engine.setLenient(false); engine.setLenient(true);
engine.setDebug(false);
} }
/** /**

4
public/java/src/org/broadinstitute/sting/utils/variantcontext/VariantJEXLContext.java
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@ -264,7 +264,9 @@ class JEXLMap implements Map<VariantContextUtils.JexlVCMatchExp, Boolean> {
// if the context is null, we need to create it to evaluate the JEXL expression // if the context is null, we need to create it to evaluate the JEXL expression
if (this.jContext == null) createContext(); if (this.jContext == null) createContext();
try { try {
jexl.put (exp, (Boolean) exp.exp.evaluate(jContext)); final Boolean value = (Boolean) exp.exp.evaluate(jContext);
// treat errors as no match
jexl.put(exp, value == null ? false : value);
} catch (Exception e) { } catch (Exception e) {
throw new UserException.CommandLineException(String.format("Invalid JEXL expression detected for %s with message %s", exp.name, e.getMessage())); throw new UserException.CommandLineException(String.format("Invalid JEXL expression detected for %s with message %s", exp.name, e.getMessage()));
} }