phased-r2 dosage-handling rework

chrchang · Oct 28, 2023 · 4345436 · 4345436
1 parent 3f93710
commit 4345436
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Showing 2 changed files with 1,084 additions and 1,049 deletions.
diff --git a/2.0/plink2.cc b/2.0/plink2.cc
@@ -72,7 +72,7 @@ static const char ver_str[] = "PLINK v2.00a6"
 #elif defined(USE_AOCL)
   " AMD"
 #endif
-  " (24 Oct 2023)";
+  " (27 Oct 2023)";
 static const char ver_str2[] =
   // include leading space if day < 10, so character length stays the same
   ""
@@ -2786,6 +2786,7 @@ PglErr Plink2Core(const Plink2Cmdline* pcp, MakePlink2Flags make_plink2_flags, c
         logerrputs("Error: --clump requires a sorted .pvar/.bim.  Retry this command after using\n--make-pgen/--make-bed + --sort-vars to sort your data.\n");
         goto Plink2Core_ret_INCONSISTENT_INPUT;
       }
+      // currently undergoing repairs
       reterr = ClumpReports(variant_include, cip, variant_bps, variant_ids, allele_idx_offsets, allele_storage, founder_info, sex_nm, sex_male, &(pcp->clump_info), raw_variant_ct, variant_ct, raw_sample_ct, founder_ct, nosex_ct, max_variant_id_slen, max_allele_slen, pcp->output_min_ln, pcp->max_thread_ct, pgr_alloc_cacheline_ct, &pgfi, &simple_pgr, outname, outname_end);
       if (unlikely(reterr)) {
         goto Plink2Core_ret_1;