From 7e4a3f1027c2842c04448c233d9ef7fdcc375570 Mon Sep 17 00:00:00 2001
From: Ryan Amari <ramari16@gmail.com>
Date: Wed, 21 Feb 2024 21:23:40 -0500
Subject: [PATCH] ALS-5819: Save empty variant masks as null

---
 .../dbmi/avillach/hpds/data/genotype/VariableVariantMasks.java  | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/data/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/data/genotype/VariableVariantMasks.java b/data/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/data/genotype/VariableVariantMasks.java
index 5d8efd3d..09ecb30f 100644
--- a/data/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/data/genotype/VariableVariantMasks.java
+++ b/data/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/data/genotype/VariableVariantMasks.java
@@ -78,7 +78,7 @@ public VariableVariantMasks(char[][] maskValues) {
 
 	private VariantMask variantMaskFromRawString(String maskStringRaw) {
 		if (!maskStringRaw.contains("1")) {
-			return new VariantMaskSparseImpl(Set.of());
+			return null;
 		}
 
 		VariantMask variantMask;