Fixing sim command parameter for require valid

src/abismal.cpp

@@ -1067,7 +1067,7 @@ struct paired_end_mapping_statistics {
     return oss.str();
   }
   NLOHMANN_DEFINE_TYPE_INTRUSIVE(paired_end_mapping_statistics, read_pair_stats,
-                                 end1_stats, end2_stats);
+                                 end1_stats, end2_stats)
 };
 
 static void

src/simreads.cpp

@@ -81,14 +81,15 @@ rand_double() -> double {  // ADS: in the interval [0, 1]
 static inline auto
 format_fastq_record(const std::string &name,
                     const std::string &read) -> std::string {
+  static constexpr auto assumed_quality_score = 63;
   assert(!name.empty());
   std::string s;
   s += '@';
   s += name;
   s += '\n';
   s += read;
   s += "\n+\n";
-  s += std::string(std::size(read), 'B');
+  s += std::string(std::size(read), assumed_quality_score);
   return s;
 }
 
@@ -283,7 +284,7 @@ sim_frag_position(const std::string &genome, const std::size_t frag_len,
   // NOLINTBEGIN(*-narrowing-conversions)
   the_frag = std::string(g_beg + the_posn, g_beg + the_posn + frag_len);
   while (require_valid &&
-         std::all_of(std::cbegin(the_frag), std::cend(the_frag), is_valid)) {
+         !std::all_of(std::cbegin(the_frag), std::cend(the_frag), is_valid)) {
     the_posn = simreads_random::rand() % lim;
     the_frag = std::string(g_beg + the_posn, g_beg + the_posn + frag_len);
   }