fix multiallelic sample-filtering bug

chrchang · Nov 14, 2024 · 6287f6a · 6287f6a
1 parent 39d4f67
commit 6287f6a
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Showing 2 changed files with 7 additions and 6 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 v2.0.0-a.6.0"
+static const char ver_str[] = "PLINK v2.0.0-a.6.1"
 #ifdef NOLAPACK
   "NL"
 #elif defined(LAPACK_ILP64)
@@ -72,7 +72,7 @@ static const char ver_str[] = "PLINK v2.0.0-a.6.0"
 #elif defined(USE_AOCL)
   " AMD"
 #endif
-  " (11 Nov 2024)";
+  " (14 Nov 2024)";
 static const char ver_str2[] =
   // include leading space if day < 10, so character length stays the same
   ""
@@ -2719,7 +2719,6 @@ PglErr Plink2Core(const Plink2Cmdline* pcp, MakePlink2Flags make_plink2_flags, c
         }
 
         if (pcp->command_flags1 & kfCommand1MakePlink2) {
-          // todo: unsorted case (--update-chr, etc.)
           if (pcp->sort_vars_mode > kSortNone) {
             reterr = MakePlink2Vsort(sample_include, &pii, sex_nm, sex_male, pheno_cols, pheno_names, new_sample_idx_to_old, variant_include, variant_bps, variant_ids, allele_idx_offsets, allele_storage, allele_presents, allele_permute, pvar_qual_present, pvar_quals, pvar_filter_present, pvar_filter_npass, pvar_filter_storage, info_reload_slen? pvarname : nullptr, variant_cms, pcp->output_missing_pheno, pcp->legacy_output_missing_pheno, contig_lens, pcp->update_chr_flag, (make_plink2_flags & kfMakePgenWriterVer)? ver_str : nullptr, xheader_blen, info_flags, raw_sample_ct, sample_ct, pheno_ct, max_pheno_name_blen, raw_variant_ct, variant_ct, max_allele_ct, max_variant_id_slen, max_allele_slen, max_filter_slen, info_reload_slen, pcp->output_missing_geno_char, pcp->max_thread_ct, pcp->hard_call_thresh, pcp->dosage_erase_thresh, pcp->misc_flags, make_plink2_flags, (pcp->sort_vars_mode == kSortNatural), pcp->pvar_psam_flags, cip, xheader, chr_idxs, &simple_pgr, outname, outname_end);
           } else {

diff --git a/2.0/plink2_data.cc b/2.0/plink2_data.cc
@@ -5985,9 +5985,11 @@ THREAD_FUNC_DECL MakePgenThread(void* raw_arg) {
   uintptr_t* ac_flipped = nullptr;
   if (ctx->thread_write_mhc) {
     ExpandMhc(sample_ct, ctx->thread_write_mhc[tidx], &write_patch_01_set, &write_patch_01_vals, &write_patch_10_set, &write_patch_10_vals);
-    ac_remap = ctx->thread_ac_remap[tidx];
-    ac_rotate = ctx->thread_ac_rotate[tidx];
-    ac_flipped = ctx->thread_ac_flipped[tidx];
+    if (ctx->thread_ac_remap) {
+      ac_remap = ctx->thread_ac_remap[tidx];
+      ac_rotate = ctx->thread_ac_rotate[tidx];
+      ac_flipped = ctx->thread_ac_flipped[tidx];
+    }
   }
   uintptr_t* write_phasepresent = nullptr;
   uintptr_t* write_phaseinfo = nullptr;