TODO

1. the BFS energy calculation can only use the Turner1999 parameters, extend it to different parameters
2. ==18330== 208,848 bytes in 1 blocks are still reachable in loss record 1 of 1
   ==18330==    at 0x4C279F2: calloc (vg_replace_malloc.c:467)
   ==18330==    by 0x5099421: space (utils.c:45)
   ==18330==    by 0x509F40C: get_scaled_parameters (params.c:50)
   ==18330==    by 0x5097CD5: librna_read_param_file (rnalib.c:56)
   ==18330==    by 0x40CBFF: main (main.cc:1457)
3. the result list with -p is different from the one without -p (microstate and macrostate grammars yield different energy results)
4. ./RNAHeliCes ../examples/ires_picornaviridae.fa -u -k 2 -t 2 -r 2 ==> Segmentation fault 
5. integrate hienergy barrier tree function into hipath.cc
6. Write new hishape data structure for gap-file 

7. consider for rule 2, replace the map with hash_map
8. check if the record search used hash_map in rule 2 --> potential runtime improvement
9. ./RNAHeliCes: error while loading shared libraries: comp.so: cannot open shared object file: No such file or directory

10.     
     - src/libs/liblapack.a and src/libs/libblas.a are from Linear Algebra routines, these may be system dependent. If so, please reload them from Linear Algebra PACKage.

FF = g77
FLAG = -c

testeof.exe: deofcovcor.o deofpcs.o deoftotvar.o deof.o testeof.o
               $(FF) deofcovcor.o deofpcs.o deoftotvar.o deof.o testeof.o /usr/lib64/liblapack.a /usr/lib64/libblas.a 

sudo yum install libgfortran libf2c blas lapack

11. add option for rule1 in RNALocMin: -x [ --thresh ] [=arg(=10000)]   Specifiy a threshold value for initstem

12. NOTE current HiEAPath is dependant on RNAeval, so it causes problem. bind the program directly with library RNAeval

13.
The flag -std=c++0x gives you access to whatever c++11 functionality is implemented in your version of gcc. For random number distributions, c++11 has the header random. You do not need the tr1 namespace when using c++11.

The tr1 version of random is in include tr1/random, and everything there is under the std::tr1 namespace. To access this you do not need the c++0x flag.

To be clear:

For TR1 random numbers: #include <tr1/random> and use std::tr1::normal_distribution.

For c++11 random numbers: compile with flag c++0x, then #include <random> and use std::normal_distribution.



14. IMPORTANT TODO: using --minh doesn't work out of ./src directory
15. delete src/HiKinetics, since new version of HiKinetics exists under modified_software_and_scripts