extend nmax domains

from 32 to 64

src/Geno.cpp

@@ -3298,7 +3298,7 @@ void check_in_map_from_files_sets(bool const& keep, map <string, vector<int>>& m
 
 }
 
-void get_masks_info(const struct in_files* files, struct param* params, struct filter* filters, map<std::string, anno_name>& anno_map, std::map <std::string, std::map <std::string, uint32_t>>& regions, vector<maskinfo>& mask_map, std::vector <std::vector<string>>& mask_out, uint64& all_masks, vector<snp>& snpinfo, mstream& sout) {
+void get_masks_info(const struct in_files* files, struct param* params, struct filter* filters, map<std::string, anno_name>& anno_map, std::map <std::string, std::map <std::string, uint64>>& regions, vector<maskinfo>& mask_map, std::vector <std::vector<string>>& mask_out, uint64& all_masks, vector<snp>& snpinfo, mstream& sout) {
 
   // read annotation categories if specified
   if(params->w_anno_lab) read_anno_cat(files, params, anno_map, sout);
@@ -3370,12 +3370,12 @@ void read_anno_cat(const struct in_files* files, struct param* params, map<strin
   sout << "n_categories = " << lineread << endl;
 }
 
-void read_anno(struct param* params, const struct in_files* files, struct filter* filters, map<string, anno_name>& anno_map, std::map <std::string, std::map <std::string, uint32_t>>& regions, vector<snp>& snpinfo, mstream& sout) {
+void read_anno(struct param* params, const struct in_files* files, struct filter* filters, map<string, anno_name>& anno_map, std::map <std::string, std::map <std::string, uint64>>& regions, vector<snp>& snpinfo, mstream& sout) {
 
   int lineread = 0, col_cat = 2, nregions = 0;
   uint32_t snp_pos, ncat = 0, n_anno_read = 0;
   uint64 null_id = 0ULL;
-  uint32_t null_region = 0ULL;
+  uint64 null_region = 0ULL;
   double set_weight = 0;
   anno_name new_anno;
   annoinfo ainfo;
@@ -3447,7 +3447,7 @@ void read_anno(struct param* params, const struct in_files* files, struct filter
       // check if new set
       if (!in_map(gname, regions)){ // create new map with region for set
         BIT_SET(ainfo.regionid, 0); // set first bit
-        std::map <std::string, uint32_t> gene_region_map;
+        std::map <std::string, decltype(null_region)> gene_region_map;
         gene_region_map[tmp_str_vec[col_cat-1]] = ainfo.regionid;
         regions[gname] = gene_region_map;
         nregions++;

src/Geno.hpp

@@ -40,7 +40,7 @@
 #include "pgenlibr.h"
 
 struct annoinfo {
-  uint32_t regionid = 0ULL;
+  uint64 regionid = 0ULL;
   uint64 id = 0ULL;
 };
 
@@ -234,16 +234,16 @@ struct anno_name {
 struct maskinfo {
   std::string name, region_name = "";
   uint64 id = 0ULL;
-  uint32_t region = 0ULL;
+  uint64 region = 0ULL;
 };
 
 void read_setlist(const struct in_files*,struct param*,struct filter*,std::vector<std::vector<vset>>&,std::vector<snp>&,const uint64,const double,mstream&);
 void check_sets_include_exclude(bool const&,const struct in_files*,struct param*,struct filter*,std::vector<std::vector<vset>>&,mstream&);
 void check_in_map_from_files_sets(bool const&,std::map<std::string,std::vector<int>>&,std::vector<std::string> const&,bool const&,mstream&);
 
-void get_masks_info(const struct in_files*,struct param*,struct filter*,std::map<std::string,anno_name>&,std::map <std::string, std::map <std::string,uint32_t>>&,std::vector<maskinfo>&,std::vector<std::vector<std::string>>&,uint64&,std::vector<snp>&,mstream& sout);
+void get_masks_info(const struct in_files*,struct param*,struct filter*,std::map<std::string,anno_name>&,std::map <std::string, std::map <std::string,uint64>>&,std::vector<maskinfo>&,std::vector<std::vector<std::string>>&,uint64&,std::vector<snp>&,mstream& sout);
 void read_anno_cat(const struct in_files*,struct param*,std::map<std::string,anno_name>&,mstream& sout);
-void read_anno(struct param*,const struct in_files*,struct filter*,std::map<std::string,anno_name>&,std::map <std::string, std::map <std::string,uint32_t>>&,std::vector<snp>&,mstream& sout);
+void read_anno(struct param*,const struct in_files*,struct filter*,std::map<std::string,anno_name>&,std::map <std::string, std::map <std::string,uint64>>&,std::vector<snp>&,mstream& sout);
 void read_aafs(const double,const struct in_files*,struct filter*,std::vector<snp>&,bool const&,mstream& sout);
 bool check_singleton_column(std::string const&);
 void read_masks(const struct in_files*,struct param*,std::map<std::string,anno_name>&,std::vector<maskinfo>&,std::vector<std::vector<std::string>>&,uint64&,mstream& sout);

src/Masks.cpp

@@ -126,7 +126,7 @@ void GenoMask::setBins(struct param* params, mstream& sout){
 void GenoMask::prepMasks(int const& ntotal, const string& setID) {
 
   maskinfo tmp_region_mask;
-  std::map <std::string, uint32_t>::iterator itr;
+  std::map <std::string, decltype(tmp_region_mask.region)>::iterator itr;
 
   // make new set of masks if using set regions
   if(w_regions){ 

src/Masks.hpp

@@ -32,7 +32,7 @@ class GenoMask {
 
   public:
     std::map <std::string, anno_name> annotations; // store identifier as 1 byte vector
-    std::map <std::string, std::map <std::string, uint32_t>> regions; // store identifier as 1 byte vector
+    std::map <std::string, std::map <std::string, uint64>> regions; // store identifier as 1 byte vector
     std::vector <maskinfo> masks, base_masks;
     std::vector <std::vector <std::string>> mask_out, list_masks;//contains mask info
     Eigen::VectorXd aafs;

src/Regenie.hpp

@@ -345,7 +345,7 @@ struct param {
   bool set_select_list = false; // comma separated list of sets given
   bool keep_sets = false, rm_sets = false; // user specify to filter sets in analysis
   bool w_regions = false; // categorize by set regions 
-  uint max_cat = 64, nmax_regions = 32; // maximum number of annotations (to fit in uint64)
+  uint max_cat = 64, nmax_regions = 64; // maximum number of annotations (to fit in uint64)
   std::vector<std::string> mbins; // temporary object to store aaf bins
   bool mask_rule_max = true, mask_rule_comphet = false; // default use max to combine mask
   std::string mask_rule = "max";