fix: GenotypesTR to properly load repeat count instead of GT (#212)

CAST-genomics · May 16, 2023 · 93a4eb2 · 93a4eb2
1 parent 3740ec1
commit 93a4eb2
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Showing 4 changed files with 99 additions and 441 deletions.
diff --git a/haptools/clump.py b/haptools/clump.py
@@ -426,9 +426,9 @@ def ComputeExactLD(candidate_gt, index_gt, log):
 
 def _FilterGts(candidate_gt, index_gt, log):
     """
-    Filter invalid values from gts which is 255 since uint8 encodes -1 as 255
+    Filter invalid values from gts which is 254 since uint8 encodes -2 as 254
     """
-    valid_gts = (candidate_gt < 255) & (index_gt < 255)
+    valid_gts = (candidate_gt < 254) & (index_gt < 254)
     candidate_gt = candidate_gt[valid_gts]
     index_gt = index_gt[valid_gts]