TO DO:
o change optim parameter in main flipflop
o check everything ok on windows and os
o take care of all cpp warnings (isolasso+spams)


CHANGES IN VERSION 1.4.1
 --------------------------
    o [pre-processing] solve small issue of possibly duplicated read type, see getType in readgroup.cpp

CHANGES IN VERSION 1.3.9
--------------------------
    o [pre-processing] redefine extreme boundary of segments (first and last), see calculateBound in readgroup.cpp

CHANGES IN VERSION 1.3.7
--------------------------
    o solve non-portable flags issues, see Makevars 

CHANGES IN VERSION 1.3.5
--------------------------
    o solve compilation isue on Mavericks (using clang), see Makevars.

CHANGES IN VERSION 1.3.4
--------------------------
    o properly take into account 'S', 'X' and '=' characters (soft clipping, strict mismatch and match) in the CIGAR of the sam file


CHANGES IN VERSION 1.3.2
--------------------------
    o Solve small bugs in the graph construction
    o Update the optimization solver for refit. More accurate and faster!
    o Remove warnings from spams (to continue ...)


CHANGES IN VERSION 1.1.6
--------------------------

NEW FEATURES

    o Add 'expected.counts' in the output objects. 
      It gives the expected raw count (ie number of mapped fragments) for each predicted transcripts. 
      This information is also available in the output gtf file.


CHANGES IN VERSION 1.1.4
--------------------------

NEW FEATURES

    o Add a 'OnlyPreprocess' option for performing only the pre-processing step of the input sam file.  
    This step writes two files: one file named 'prefix.instance' and one other named 'prefix.totalnumread',
    where 'prefix' is the prefix of the input sam file.
    The 'prefix.instance' file can then be given to the option 'preprocess.instance'
    and the total number of mapped reads is stored in the 'prefix.totalnumread' file.

    o Allow to give 'NN' (total number of mapped fragments) even when using the sam file as input.
    This can be used to run flipflop in parallel on parsed sam files with the same NN constant. 


USER-LEVEL CHANGES

    o Handle '~' in input paths with path.expand function.

    o Give a more detailed R output with the read count.


MINOR CHANGES

    o Do not write individual Coverage into the pre-processing file anymore ie, the .instance file.
    (in practice comments lines in readgroup.cpp, part 'toStream')



CHANGES IN VERSION 1.1.2
--------------------------

BUG FIXES

    o Switch from GRangeList to a regular list as the number of metadata columns could not vary in GRangeList.