refmap.cpp

   1 /*
   2  * refmap.cpp
   3  *
   4  *  Created on: Aug 3, 2009
   5  *      Author: Ben Langmead
   6  */
   7
   8 #include <stdexcept>
   9 #include "refmap.h"
  10 #include "assert_helpers.h"
  11
  12 using namespace std;
  13
  14 /**
  15  * Given a refid,offset pair in the index space, transform it into the
  16  * reference coordinate space according to the reference mappings
  17  * provided by the user.
  18  */
  19 void ReferenceMap::map(U32Pair& h) const {
  20         if(h.first >= map_.size()) {
  21                 cerr << "Could not find a reference-map entry for reference "
  22                                   << h.first << " in map file \"" << fname_ << "\""
  23                                   << endl;
  24                 throw 1;
  25         }
  26         h.second += map_[h.first].second;
  27         h.first = map_[h.first].first;
  28 }
  29
  30 /**
  31  * Parse a reference-map file.
  32  */
  33 void ReferenceMap::parse() {
  34         ifstream in(fname_);
  35         if(!in.good() || !in.is_open()) {
  36                 cerr << "Could not open reference map file " << fname_ << endl;
  37                 throw 1;
  38         }
  39         int c;
  40         while((c = in.peek()) != EOF) {
  41                 if(c == '>') {
  42                         // This appears to be a name line
  43                         in.get(); // chop off the initial '>'
  44                         uint32_t off;
  45                         in >> off;
  46                         in.get(); // chop off tab
  47                         char buf[1024];
  48                         in.getline(buf, 1023);
  49                         if(parseNames_) {
  50                                 if(names_.size() <= off) names_.resize(off+1);
  51                                 names_[off] = string(buf);
  52                         }
  53                         continue;
  54                 }
  55                 uint32_t id, off;
  56                 in >> id >> off;
  57                 map_.resize(map_.size()+1);
  58                 map_.back().first = id;
  59                 map_.back().second = off;
  60                 while(isspace(in.peek())) in.get();
  61         }
  62         assert_eq(EOF, c);
  63         in.close();
  64 }