also backport PglMultiallelicSparseToDense() remap bugfix

chrchang · Jul 4, 2024 · adfee42 · adfee42
1 parent bc6b5b6
commit adfee42
Showing 1 changed file with 3 additions and 0 deletions.
diff --git a/2.0/include/pgenlib_write.cc b/2.0/include/pgenlib_write.cc
@@ -1923,6 +1923,9 @@ void PglMultiallelicSparseToDense(const uintptr_t* __restrict genoarr, const uin
         const uintptr_t sample_idx = BitIter1(patch_01_set, &sample_idx_base, &cur_bits);
         const AlleleCode ac = remap[patch_01_vals[uii]];
         if (ac > remap0) {
+          // bugfix (4 Jul 2024): cannot assume wide_codes[2 * sample_idx] ==
+          // remap0.  It's remap1 when remap1 < remap0.
+          wide_codes[2 * sample_idx] = remap0;
           wide_codes[2 * sample_idx + 1] = ac;
         } else {
           wide_codes[2 * sample_idx] = ac;