Adding the some bisulfite related code needed for abismal but it might not stay here

Author: andrewdavidsmith

bisulfite_utils.hpp

@@ -23,6 +23,36 @@
 #include <string>
 #include <random>
 
+#include "sam_record.hpp"
+
+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;
+}
+
+inline bool
+is_t_rich(const sam_rec &sr) {
+  return samflags::check(sr.flags, bsflags::read_is_t_rich);
+}
+
+inline bool
+is_a_rich(const sam_rec &sr) {
+  return !samflags::check(sr.flags, bsflags::read_is_t_rich);
+}
+
+inline void
+set_t_rich(sam_rec &sr) {
+  samflags::set(sr.flags, bsflags::read_is_t_rich);
+}
+
+inline void
+set_a_rich(sam_rec &sr) {
+  samflags::unset(sr.flags, bsflags::read_is_t_rich);
+}
+
+
 void
 bisulfite_treatment(std::mt19937 &generator, std::string &seq,
                     double bs_rate = 1.0, double meth_rate = 0.0);