finished pindel mod creation [iss13]
pindel mod runs insert size calculation if necessary
Merge branch 'master' of github.com:BauerLab/ngsane into iss13
Added some files to cleanup in tophat.sh
Bugfix dummy removal
Merge branch 'new_mods'
fix for unmapped reads
moved fix_tophat_unmapped_reads.pyto next checkpoint
 fix_tophat_unmapped_reads.py removed for thedebugdebugging
not used any longer
refactoring HiC mods
sampleconfig simplified
default simplified
redundant double code block removed
enable to specify Phred encoding
Phred encoding options simplified
Bugfix Phred detection
setupscript
MCR and chance updated
ami figure