Entirely removing the instance variable of MappedRead that holds the per-base quality scores

Author: andrewdavidsmith

MappedRead.cpp

@@ -53,6 +53,7 @@ MappedRead::MappedRead(const string &line) {
       end = start + seq.length();
     }
     r = GenomicRegion(chrom, start, end, name, score, strand);
+    is >> scr;
   }
   else throw runtime_error("bad line in MappedRead file: " + line);
 }
@@ -62,5 +63,7 @@ MappedRead::tostring() const {
   std::ostringstream oss;
   oss << r; // no chaining for the << of GenomicRegion
   oss << '\t' << seq;
+  if (!scr.empty())
+    oss << '\t' << scr;
   return oss.str();
 }

MappedRead.hpp

@@ -30,6 +30,7 @@ struct MappedRead {
   explicit MappedRead(const std::string &line);
   GenomicRegion r;
   std::string seq;
+  std::string scr;
   std::string tostring() const;
 };