From 66c205534216fdf7307a0104f48ffd097f56525f Mon Sep 17 00:00:00 2001
From: Ryan Amari <ramari16@gmail.com>
Date: Tue, 2 Jan 2024 09:23:19 -0800
Subject: [PATCH] Fix intersection/union of variant filters bug

---
 .../hpds/processing/GenomicProcessorNodeImpl.java   | 13 ++++++++++---
 1 file changed, 10 insertions(+), 3 deletions(-)

diff --git a/processing/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/processing/GenomicProcessorNodeImpl.java b/processing/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/processing/GenomicProcessorNodeImpl.java
index 9d2e4e39..e11a1be6 100644
--- a/processing/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/processing/GenomicProcessorNodeImpl.java
+++ b/processing/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/processing/GenomicProcessorNodeImpl.java
@@ -89,10 +89,16 @@ public BigInteger runGetPatientMask(DistributableQuery distributableQuery) {
                 List<VariantIndex> variantSets = getVariantsMatchingFilters(filter);
                 log.info("Found " + variantSets.size() + " groups of sets for patient identification");
                 if(!variantSets.isEmpty()) {
-                    // INTERSECT all the variant sets.
-                    intersectionOfInfoFilters = variantSets.get(0);
+                    // todo: and/or distinction missing
+                    VariantIndex unionOfVariantSets = new SparseVariantIndex(Set.of());
                     for(VariantIndex variantSet : variantSets) {
-                        intersectionOfInfoFilters = intersectionOfInfoFilters.intersection(variantSet);
+                        unionOfVariantSets = unionOfVariantSets.union(variantSet);
+                    }
+
+                    if (intersectionOfInfoFilters == null) {
+                        intersectionOfInfoFilters = unionOfVariantSets;
+                    } else {
+                        intersectionOfInfoFilters = intersectionOfInfoFilters.intersection(unionOfVariantSets);
                     }
                 } else {
                     // todo: create an empty variant index implementation
@@ -183,6 +189,7 @@ private List<VariantIndex> getVariantIndicesForCategoryFilter(Map.Entry<String,
         List<String> infoKeys = filterInfoCategoryKeys(values, infoStore);
 
         if(infoKeys.size()>1) {
+            // These should be ANDed
             return infoKeys.stream()
                     .map(key -> variantIndexCache.get(column, key))
                     .collect(Collectors.toList());