ALS-5981: Fix off by one error in sparse mask creation

hms-dbmi · Mar 25, 2024 · a9afcd4 · a9afcd4
1 parent b0699f1
commit a9afcd4
Showing 1 changed file with 3 additions and 2 deletions.
diff --git a/.../src/main/java/edu/harvard/hms/dbmi/avillach/hpds/data/genotype/VariableVariantMasks.java b/.../src/main/java/edu/harvard/hms/dbmi/avillach/hpds/data/genotype/VariableVariantMasks.java
@@ -94,8 +94,9 @@ private VariantMask variantMaskFromRawString(String maskStringRaw) {
 			variantMask = new VariantMaskBitmaskImpl(bitmask);
 		} else {
 			Set<Integer> patientIndexes = new HashSet<>();
-			for(int i = 2; i < bitmask.bitLength() - 2; i++) {
-				if (bitmask.testBit(i)) {
+			for(int i = 0; i < bitmask.bitLength() - 4; i++) {
+				// i + 2 because the mask is padded with 2 bits on each end
+				if (bitmask.testBit(i + 2)) {
 					patientIndexes.add(i);
 				}
 			}