Added ht-seq-count

Uncomment GENCODEGTF variable in config file to run ht-seq-count
(Stranded & genes) with GencodeV14 annotations using tophatcuff.sh.

hugfre
permissions changed
Merge branch 'master' of github.com:Gurado/ngsane
Added --library-type to tophatcuff.sh

Added RNA_SEQ_LIBRARY_TYPE variable to tophatcuff_config.txt.

Added --libary-type to tophatcuff.sh to specify library type for
tophat, cufflinks and ht-seq-count
bug fix.

added missing ${ } to filename.
hicup plots in summary included
Merge branch 'master' of github.com:Gurado/ngsane
bugfix htseq-count
Merge branch 'master' of github.com:Gurado/ngsane
detect missing input data and provide useful error message
generate data from hicup to feed into  fit-hi-c
Bugfix hicup python script
Bugfix hicup (wip)
ignore pyc files
Bugfix hicup class scope (wip)
Bugfix populating the intervaltree
Bugfix sam parsing
adding veryverbose mode
Bugfix chattiness of hicup processing
Bugfix hicup read processing