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SelectVariants JEXL filter fixes and refactor #8092

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merged 16 commits into from
Jan 7, 2023
Merged

SelectVariants JEXL filter fixes and refactor #8092

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7960a9d
select variants tests
takutosato Oct 24, 2022
5a651c2
clean up and add comment
takutosato Oct 24, 2022
3f1cb46
just a commit
takutosato Oct 3, 2022
8f00b6b
cleaned up
takutosato Oct 10, 2022
6e0bf02
add
takutosato Oct 16, 2022
298ebba
documentation
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8ae12bf
oops
takutosato Oct 16, 2022
027bc98
interim
takutosato Oct 24, 2022
aac4af6
integratttion test issues
takutosato Nov 14, 2022
9da35dc
all the tests
takutosato Nov 19, 2022
e93d9c2
some changes
takutosato Nov 28, 2022
94ff401
proofreading
takutosato Nov 28, 2022
615ac1a
ready
takutosato Nov 28, 2022
8d5db3e
David R review and optimizations from profiling
takutosato Jan 7, 2023
78c226d
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takutosato Jan 7, 2023
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2 changes: 2 additions & 0 deletions src/main/java/org/broadinstitute/hellbender/tools/walkers/filters/VariantFiltration.java
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Original file line number Diff line number Diff line change
Expand Up @@ -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);
}
Expand Down Expand Up @@ -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);
}
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