From 2bbee443210e33536026d7f6760c09a1cff4ef05 Mon Sep 17 00:00:00 2001
From: Christopher Chang <chrchang523@gmail.com>
Date: Thu, 4 Jul 2024 14:33:00 -0700
Subject: [PATCH] backport nonref_flags elision

---
 2.0/plink2_data.cc | 20 ++++++++++++++++++++
 1 file changed, 20 insertions(+)

diff --git a/2.0/plink2_data.cc b/2.0/plink2_data.cc
index 2f27d9bb..22b3b548 100644
--- a/2.0/plink2_data.cc
+++ b/2.0/plink2_data.cc
@@ -6388,6 +6388,16 @@ PglErr MakePgenRobust(const uintptr_t* sample_include, const uint32_t* new_sampl
           nonref_flags_write = nullptr;
           nonref_flags_storage = 1;
         }
+      } else {
+        if (nonref_flags_write[0] & 1) {
+          if (AllBitsAreOne(nonref_flags_write, raw_variant_ct)) {
+            nonref_flags_write = nullptr;
+            nonref_flags_storage = 2;
+          }
+        } else if (AllWordsAreZero(nonref_flags_write, BitCtToWordCt(raw_variant_ct))) {
+          nonref_flags_write = nullptr;
+          nonref_flags_storage = 1;
+        }
       }
       snprintf(outname_end, kMaxOutfnameExtBlen, ".pgen");
       uintptr_t spgw_alloc_cacheline_ct;
@@ -7517,6 +7527,16 @@ PglErr MakePlink2NoVsort(const uintptr_t* sample_include, const PedigreeIdInfo*
           nonref_flags_write = nullptr;
           nonref_flags_storage = 1;
         }
+      } else {
+        if (nonref_flags_write[0] & 1) {
+          if (AllBitsAreOne(nonref_flags_write, raw_variant_ct)) {
+            nonref_flags_write = nullptr;
+            nonref_flags_storage = 2;
+          }
+        } else if (AllWordsAreZero(nonref_flags_write, BitCtToWordCt(raw_variant_ct))) {
+          nonref_flags_write = nullptr;
+          nonref_flags_storage = 1;
+        }
       }
       ctx.pwcs = &(mpgwp->pwcs[0]);
       ctx.thread_write_genovecs = nullptr;