[BAM]Implement: Realignment improvements
[BAM]Implement: Added configurable flags to realigner context
[BAM]Fix: Some fixes and tweaks in realignment
[BAM]Implement: Added version defines and --version option to realigner
[BAM]Bugfix: Start position to get score will be minor always than reference position
[BAM]Fix: Leak memory fixes
[BAM]Fix: Bugfixes
[BAM]Fix: Fixed bug when input buffer is empty during refilling (list is not correct updated)