CODE
- new line added after each log message
- each command is printed on standard out
- header printed correctly in candidate file and added to final junction file
- small cosmetic changes in usage and eliminate one -h (was present twice)
- eliminate chrM in filtering script chimjunc_filter.awk
- eliminate indiv error files and put in main error file
- eliminate usage in stdout printed a second time at the end
- made lid not mandatory and if not specified call it myexp
- eliminate creation of FirstMapping directory
- compute quality offset inside chimpipe and therefore remove it from the options (means cannot be ignored anymore ...)
- infer library type inside chimpipe unless it is provided (BR)
- gtf2fasta.sh: $genome instead of $index everywhere
- similarity_bt_gnpairs.sh: remove number of threads as option and ask for 4
- ChimPipe.sh: add gene similarity matrix computing in case the file is not provided or present where it is expected

DOCUMENTATION
- changed long-help into full-help to reflect what is implemented