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root/gclib/tophat_cpp/bwt_map.cpp
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# Line 955 | Line 955
955      if (!found) {
956          if (ofs>=l_len) {
957             found=true;
958 <           //inject new code here
958 >           //TODO:inject new code here, splitting existing code if necessary
959 >
960 >           continue;
961             }
962          else {
963             //not found yet, just copy these codes
964             splcigar.push_back(cigar[c]);
965             }
966         }
967 <    else { //found yet
968 <
967 >    else { //found already
968 >       //TODO: check this
969 >       splcigar.push_back(cigar[c]);
970         }
971          }
972   }

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