New FragmentStore SAM export

- changed the FragmentStore SAM I/O to fill BamAlignmentRecords and to the Bam I/O module
- It is now possible to easily define custom alignment functors if the FragmentStore contains only matches (no gaps)
- cleaned up some parts of the Bam I/O and FragmentStore module

This the 2nd revision of the review https://reviewboard.seqan.de/r/356/