gma1 . Print (stdout, sl1, true, 60);
gma1 . Print (stdout, sl1, true, 60, & tg1);
int  main    (int argc, char * argv [])  {   ReadBank_t  read_bank;   Celera_Message_t  msg;   Read_t  read;   FILE  * input_fp;   vector <char *>  string_list, qual_list, tag;   vector <char *>  sl1, sl2;   vector <char *>  tg1, tg2;   vector <int>  offset;   vector <int>  ref, str_len;   vector <Range_t>  pos;   vector < vector <int> >  del_list;   Gapped_Multi_Alignment_t  gma, gma1, gma2;   vector <ID_Pair_t>  map;   vector <Unitig_Ref_t>  uni_list;   time_t  now;   int  contig_ct, cons_len;   now = time (NULL);   cerr << "Starting at " << ctime (& now) << endl;   Verbose = 1;   Parse_Command_Line (argc, argv);   cerr << "Read bank is " << Bank_Name << endl;   cerr << "Processing messages from file " << Tig_File_Name << endl;   cerr << "Map file is " << Map_File_Name << endl;   Load_ID_Map (map, Map_File_Name . c_str ());   Load_Unitigs (uni_list, Unitig_File_Name . c_str ());   input_fp = File_Open (Tig_File_Name . c_str (), "r");   read_bank . openStore (Bank_Name);   contig_ct = 0;   while  (msg . read (input_fp))     {      if  (msg . getMsgType () == CCO_MSG)          {           cerr << "Process contig " << msg . getAccession () << endl;           Get_Strings_And_Lengths               (string_list, qual_list, str_len, tag, msg, read_bank, map,                uni_list);           gma . Make_From_CCO_Msg (msg, str_len);           contig_ct ++;           if  (contig_ct == 1)               {                gma1 = gma;                Copy (sl1, string_list);                Copy (tg1, tag);               }           else if  (contig_ct == 2)               {                gma2 = gma;                Copy (sl2, string_list);                Copy (tg2, tag);               }          }     }   fclose (input_fp);   read_bank . closeStore ();   cout << endl << endl << "Contig #1" << endl;   gma1 . Print (stdout, sl1, true, 60);   gma2 . Reverse_Complement (sl2);   cout << endl << endl << "Contig #2 after reverse" << endl;   gma2 . Print (stdout, sl2, true, 60);{ int  i, n; n = tg1 . size (); for  (i = 0;  i < n;  i ++)   tg1 [i] [0] = 'a'; n = tg2 . size (); for  (i = 0;  i < n;  i ++)   tg2 [i] [0] = 'b';}   cons_len = gma2 . Ungapped_Consensus_Len ();//   gma1 . Partial_Merge (gma2, cons_len - 3731, cons_len - 2452, 1322, 2638,//        sl1, sl2, & tg1, & tg2);   gma1 . Partial_Merge (gma2, cons_len - 3731, cons_len - 2566, 1322, 2487,        sl1, sl2, & tg1, & tg2);   gma1 . Partial_Merge (gma2, cons_len - 2474, cons_len - 236, 3080, 5324,        sl1, sl2, & tg1, & tg2);   cout << endl << endl << "Contig #1 after merge" << endl;   gma1 . Print (stdout, sl1, true, 60, & tg1);#if  0   {    char  * s = "gacgttc";    char  * t = "ggactcc";    Alignment_t  ali;    Global_Align (s, 7, t, 0, 7, 2, -3, -2, -1, ali);    ali . Print (stdout, s, t);   }#endif   return  0;  }