Testing Mergin
Test Merge
Merge branch 'cfeatures' into test.merge

Conflicts:
	GEMTools/src/gt_stats.c
Modify macro GT_GET_PERCENTAGE
Merge branch 'develop' of ssh://fenris.ti00a1.pcb.ub.es:7999/gt/gemtools into test.merge

Conflicts:
	GEMTools/tools/gt.filter.c
file name cleanup for mac
Updated docs for scoring
Added gtf parser and filter tool
Scoring tables
added dirty filtering
revert back to old version and removed the score sorting
New features
Added template sorting by distance __ score
commit
Merge branch 'develop' of ssh://fenris.ti00a1.pcb.ub.es:7999/gt/gemtools into filtering
fixed the template sort by score and clean up teh gtf parsing
Cleanup annotation mapping
All SAM stuff and more...
Fixed compilation errors
Merge branch 'develop' of ssh://fenris.ti00a1.pcb.ub.es:7999/gt/gemtools into test.merge

Conflicts:
	GEMTools/src/Makefile
	GEMTools/src/gt_input_parser.c
	GEMTools/src/gt_string.c
	GEMTools/tools/Makefile
Cleanup