fix --recover-var-ids line indexes for .bim

chrchang · Aug 14, 2023 · 27aa941 · 27aa941
1 parent 5ec081d
commit 27aa941
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Showing 2 changed files with 3 additions and 2 deletions.
diff --git a/2.0/plink2.cc b/2.0/plink2.cc
@@ -72,7 +72,7 @@ static const char ver_str[] = "PLINK v2.00a5"
 #elif defined(USE_AOCL)
   " AMD"
 #endif
-  " (13 Aug 2023)";
+  " (14 Aug 2023)";
 static const char ver_str2[] =
   // include leading space if day < 10, so character length stays the same
   ""

diff --git a/2.0/plink2_misc.cc b/2.0/plink2_misc.cc
@@ -778,6 +778,7 @@ PglErr RecoverVarIds(const char* fname, const uintptr_t* variant_include, const
       }
       strict_allele_order = (flags / kfRecoverVarIdsStrictBimOrder) & 1;
       line_iter = line_start;
+      --line_idx;
     }
     // Only nonzero if we're actually replacing existing IDs with the missing
     // ID in the conflict case.
@@ -802,7 +803,7 @@ PglErr RecoverVarIds(const char* fname, const uintptr_t* variant_include, const
     uintptr_t record_uidx = ~k0LU;  // deliberate overflow
     uint32_t cur_allele_ct = 2;
     for (; TextGetUnsafe2(&txs, &line_iter); line_iter = AdvPastDelim(line_iter, '\n')) {
-      if (!(line_idx % 1000000)) {
+      if ((!(line_idx % 1000000)) && line_idx) {
         printf("\r--recover-var-ids: %" PRIuPTR "m lines scanned.", line_idx / 1000000);
         fflush(stdout);
       }