setting read is a rich as 1 by default, to match the abismal standard

Author: guilhermesena1

bisulfite_utils.hpp

@@ -29,30 +29,29 @@ namespace bsflags {
   // ADS: this is our addition to the SAM flags, using the "free" bits
   /* 4096 0x1000 read is A-rich
    */
-  static const uint16_t read_is_t_rich = 0x1000;
+  static const uint16_t read_is_a_rich = 0x1000;
 }
 
 inline bool
 is_t_rich(const sam_rec &sr) {
-  return samflags::check(sr.flags, bsflags::read_is_t_rich);
+  return !samflags::check(sr.flags, bsflags::read_is_a_rich);
 }
 
 inline bool
 is_a_rich(const sam_rec &sr) {
-  return !samflags::check(sr.flags, bsflags::read_is_t_rich);
+  return samflags::check(sr.flags, bsflags::read_is_a_rich);
 }
 
 inline void
 set_t_rich(sam_rec &sr) {
-  samflags::set(sr.flags, bsflags::read_is_t_rich);
+  samflags::unset(sr.flags, bsflags::read_is_a_rich);
 }
 
 inline void
 set_a_rich(sam_rec &sr) {
-  samflags::unset(sr.flags, bsflags::read_is_t_rich);
+  samflags::set(sr.flags, bsflags::read_is_a_rich);
 }
 
-
 void
 bisulfite_treatment(std::mt19937 &generator, std::string &seq,
                     double bs_rate = 1.0, double meth_rate = 0.0);