[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/pigeonhole'
[DOC,FEATURE] Adding documentation built with Sphinx.
[FEATURE] Integrating Disqus into tutorial on readthedocs.org.
[DOC] Adding Dave's fixes and improvements to Sphinx manual.
[DOC] Merging more tutorial updates by Dave.
[DOC] Template updates.
[DOC] Disabling Disqus comments again to see whether they cause problems.
[FIX,DOC] Trying to tackle RTD issue with header/footer injection.
[FIX] Fix for layout.html.
[DOC] Trying to use page.html instead of layout.html...
[DOC] Removing "How To:" prefix in howtos.
[DOC] Fixing foldable spacing in CSS.
[DOC] Hiding genindex and search on start page.
[DOC] Updating requirements of seqansphinx.
[DOC] Adding attic for manual.
[DOC] Bug removal and improvements to the manual.
[DOC] Adding one more fragment link.
[DOC] Adding DOIs for references.
[DOC] Improvents to index.rst

* adding short summary what SeqAn is about
* fixing typo