SelectVariants JEXL filter fixes and refactor (#8092)

SelectVariants improvements: more documentation, more tests, refactoring, a new argument --select-genotype.
broadinstitute · Jan 7, 2023 · 9f77b1f · 9f77b1f
1 parent 9ced727
commit 9f77b1f
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Showing 4 changed files with 592 additions and 104 deletions.
diff --git a/src/main/java/org/broadinstitute/hellbender/tools/walkers/filters/VariantFiltration.java b/src/main/java/org/broadinstitute/hellbender/tools/walkers/filters/VariantFiltration.java
@@ -403,6 +403,7 @@ private VariantContext filter(final VariantContext variant, final FeatureContext
         }
 
         for ( final JexlVCMatchExp exp : filterExps ) {
+            // Note that g is set to null since filterExps contains INFO-level filters
             if ( matchesFilter(vc, null, exp, invertFilterExpression) ) {
                 filters.add(exp.name);
             }
@@ -437,6 +438,7 @@ private List<String> getGenotypeFilters(final VariantContext vc, final Genotype
 
         // Add if expression filters the variant context
         for (final JexlVCMatchExp exp : genotypeFilterExps) {
+            // Give the genotype g to mathchesFilter enables JEXL matching on genotype fields
             if (matchesFilter(vc, g, exp, invertGenotypeFilterExpression)) {
                 filters.add(exp.name);
             }