.sample loading, --ld chrX het-haploid

chrchang · Sep 22, 2023 · 5e420bb · 5e420bb
1 parent b0d5bb7
commit 5e420bb
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Showing 3 changed files with 5 additions and 3 deletions.
diff --git a/2.0/plink2.cc b/2.0/plink2.cc
@@ -44,7 +44,7 @@
 namespace plink2 {
 #endif
 
-static const char ver_str[] = "PLINK v2.00a4.8"
+static const char ver_str[] = "PLINK v2.00a4.9"
 #ifdef NOLAPACK
   "NL"
 #elif defined(LAPACK_ILP64)
@@ -72,7 +72,7 @@ static const char ver_str[] = "PLINK v2.00a4.8"
 #elif defined(USE_AOCL)
   " AMD"
 #endif
-  " (15 Sep 2023)";
+  " (22 Sep 2023)";
 static const char ver_str2[] =
   // include leading space if day < 10, so character length stays the same
   ""

diff --git a/2.0/plink2_import.cc b/2.0/plink2_import.cc
@@ -9437,7 +9437,8 @@ PglErr OxSampleToPsam(const char* samplename, const char* const_fid, const char*
     uintptr_t* col_first_pass_remaining;
     uintptr_t* col_nm;
     unsigned char* col_types;
-    if (unlikely(bigstack_alloc_w(col_ctl, &col_first_pass_remaining) ||
+    // bugfix (22 Sep 2023): forgot to 0-initialize col_first_pass_remaining
+    if (unlikely(bigstack_calloc_w(col_ctl, &col_first_pass_remaining) ||
                  bigstack_calloc_w(col_ctl, &col_nm) ||
                  bigstack_alloc_uc(col_ct, &col_types))) {
       goto OxSampleToPsam_ret_NOMEM;

diff --git a/2.0/plink2_ld.cc b/2.0/plink2_ld.cc
@@ -3222,6 +3222,7 @@ PglErr LdConsole(const uintptr_t* variant_include, const ChrInfo* cip, const cha
           BitvecInvmask(R_CAST(uintptr_t*, x_male_dosage_invmask), founder_dosagev_ct * kWordsPerVec, R_CAST(uintptr_t*, dosage_uhets[0]));
           const uint64_t invalid_uhethet_dosageprod = DosageUnsignedNomissDotprod(dosage_uhets[0], dosage_uhets[1], founder_dosagev_ct);
           unknown_hethet_d -= S_CAST(int64_t, invalid_uhethet_dosageprod) * kRecipDosageMidSq;
+          known_dotprod_d += u63tod(invalid_uhethet_dosageprod) * (kRecipDosageMidSq * 0.5);
         }
         x_male_nmajsums_d[0] = S_CAST(int64_t, x_male_nmaj_dosages[0]) * kRecipDosageMid;
         x_male_nmajsums_d[1] = S_CAST(int64_t, x_male_nmaj_dosages[1]) * kRecipDosageMid;