GT-87 - initial hash based implementation for merging alignments with big sets of multi maps. implementation for templates still missing
GT-87 - hash based search also for templates
GT-87 fixed memory issue
Force subprocess termination on kill
GT-88 added check for empty lines
Removed the old SAM converter command, replaced with the new Converter
GT-90 - fixed the issue in the stats
Merge branch 'develop' of ssh://10.3.11.15:7999/gt/gemtools into develop
Write raw stats before json
Added missing check for GT-87
Merge branch 'develop' of ssh://fenris.ti00a1.pcb.ub.es:7999/gt/gemtools into develop
Added missing initialization for GT-87
GT-91 - added parameter to enable duplicate checks to the simple template/alignment insert method and restored default behaviour where it was used, except for gt.filter, where check parameter was added
GT-92 - added json library
GT-92 - added support for json library in Makefiles
GT-92 - added json output to stats and added json utility module
GT-91 - updated the python binding to use a gt.stats call
GT-93 - added json output support to gtf counter
Updated pipeline to ouptut json gtf stats
GT-95 - added counter for mapped_reads (counts per read not per template)