[FIX] Fixing BAM position reading/writing.

Fixes issue #478 in seqan/seqan.

SeqAn's BAM I/O wrote the wrong values for the positions and template
lengths to BAM files.  This was caused by a misunderstanding of an older
version othe BAM file specification.
Merge branch 'hotfix/issue_478'
[DOC] Applying documentation changes from #481 to DDDoc