Fixed outpt stream of fine grained insert size stats
Added stats report and process registry plus signal handeling for the pipeline
Changed insert size range resolution
Added process cleanup
Added simple alignemnt parsing access
Added ability to keep junctions based on anotation even if coverage is too low and we only have a partial overlap
Integrated annotation based junction filtering for parial overlaps into pipeline
Fixed issue with calculating the stats in background
cp some documentation. This needs work