Added features to gt.filter
Merge branch 'develop' of ssh://fenris.ti00a1.pcb.ub.es:7999/gt/gemtools into test.merge

Conflicts:
	GEMTools/src/gt_stats.c
	GEMTools/tools/gt.filter.c
Added fileds
Added changes to gt.filter
Merge branches 'test.merge' and 'develop' into develop
Updated filtering
GT-68 - refactored the no_split distance method
GT-68 - added counter recalculation using the no_split distances
GT-68 added rnaseq parameter to gt.filter and do counter recalculation
removed missing function call
GT-68 - added rna-seq option to filter and added no_split counter recalculation
Merge branch 'filtering' into develop

Conflicts:
	GEMTools/src/gt_alignment_utils.c
	GEMTools/tools/gt.filter.c
GT-68 added various filtering options including the split map filter and
the annotation filter
GT-68 - fixed issue with split map consistency check
annotation filter
Fixed num_templates in stats
Bumped version to 1.6.2
Disable XS field calculations
Updated readme
Merge branch 'master' into develop

Conflicts:
	Makefile
	python/gem/commands.py
	python/gem/pipeline.py
	setup.py