Fix bucket index by sample

hms-dbmi · Mar 27, 2024 · 887dad2 · 887dad2
1 parent 5325ac0
commit 887dad2
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Showing 2 changed files with 6 additions and 7 deletions.
diff --git a/data/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/data/genotype/BucketIndexBySample.java b/data/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/data/genotype/BucketIndexBySample.java
@@ -99,15 +99,14 @@ public BucketIndexBySample(VariantStore variantStore, String storageDir) throws
 							// For each patient set the patientBucketCharMask entry to 0 or 1 if they have a variant in the bucket.
 
 							// todo: implement for variant explorer
-							/*int maxIndex = patientMaskForBucket[0].bitLength() - 1;
 							int indexOfBucket = Collections.binarySearch(bucketList, bucketKey) + 2; //patientBucketCharMasks has bookend bits
-							for(int x = 2;x<patientMaskForBucket[0].bitLength()-2;x++) {
-								if(patientMaskForBucket[0].testBit(maxIndex - x)) {  //testBit uses inverted indexes
-									patientBucketCharMasks[x-2][indexOfBucket] = '1';									
+							for(int x = 0; x < patientIds.size(); x++) {
+								if(patientMaskForBucket[0].testBit(x)) {
+									patientBucketCharMasks[x][indexOfBucket] = '1';
 								}else {
-									patientBucketCharMasks[x-2][indexOfBucket] = '0';
+									patientBucketCharMasks[x][indexOfBucket] = '0';
 								}
-							}*/
+							}
 						});
 			} else {
 				log.info("null entry for contig " + contig);

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
@@ -88,7 +88,7 @@ private VariantMask variantMaskFromRawString(String maskStringRaw) {
 		}
 
 		VariantMask variantMask;
-		BigInteger bitmask = new BigInteger(oneone + maskStringRaw + oneone, 2);
+		BigInteger bitmask = new BigInteger(oneone + new StringBuilder(maskStringRaw).reverse() + oneone, 2);
 		if (bitmask.bitCount() - 4 > VariableVariantMasks.SPARSE_VARIANT_THRESHOLD) {
 			variantMask = new VariantMaskBitmaskImpl(bitmask);
 		} else {