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root/gclib/tophat_cpp/bwt_map.h
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# Line 491 | Line 491
491    void end(bool end) { _end = end; }
492    
493    // this is for debugging purpose
494 <  bool check_editdist_consistency(const RefSequenceTable& rt);
494 >  bool check_editdist_consistency(const RefSequenceTable& rt, bool bDebug = false);
495    
496   private:
497    
# Line 625 | Line 625
625          ret.first->second.seq = seq;
626          ret.first->second.len = len;
627          ret.first->second.observation_order = _next_id;
628 <        //assert (_refid_to_hash.size() + 1 == _next_id);
628 >    //assert (_refid_to_hash.size() + 1 == _next_id);
629          _refid_to_name.push_back (name);
630                          
631          ++_next_id;
# Line 1196 | Line 1196
1196                      // when it comes to convert from qual in color to qual in bp,
1197                      // we need to fill in the two extream qual values using the adjacent qual values.
1198                      size_t qual_len = strlen(qual);
1199 <                    if (color && !color_out && qual_len > 2) {
1199 >                    if (color && qual_len > 2) {
1200                            qual[0] = qual[1];
1201                            qual[qual_len-1] = qual[qual_len-2];
1202                            }
# Line 1248 | Line 1248
1248                    const char* ref_name2,
1249                    const char* sequence,
1250                    const char* qualities,
1251 <                  bool from_bowtie = false);
1251 >                  bool from_bowtie = false,
1252 >                  const vector<string>* extra_fields = NULL);
1253  
1254  
1255   void extract_partial_hits(const BowtieHit& bh, const string& seq, const string& qual,
# Line 1260 | Line 1261
1261   */
1262   std::string print_cigar(const vector<CigarOp>& bh_cigar);
1263  
1264 + /**
1265 + * Calculate bowtie (1 or 2) related extra SAM fields such as
1266 + * AS:i (alignment score)
1267 + * MD:Z
1268 + * NM:i
1269 + * etc
1270 + */
1271 + void bowtie_sam_extra(const BowtieHit& bh, const RefSequenceTable& rt, vector<string>& fields);
1272 +
1273   #endif

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