[FEATURE] Gustaf: infer del from nested inversions
[FEATURE] Gustaf: infer del from overlapping inversions
[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] Added READMEs for bs_tools.
[DOC] updated index fox
[DOC] documented property map interface of VS tree iterators
[FIX] fixed string tree index concept
[DOX] added missing <tt> tags and &lt; &gt; in Hannes documentation
Merge pull request #503 from weese/feature/dox-fixes

[DOC] index related dox fixes
Merge pull request #504 from holtgrewe/sphinx-manual

[DOC] Adding Sphinx manual for SeqAn master.
[DOC] Removing stray characters in I/O Overview
[FIX] Fixing reading and writing of comment lines in SAM headers.
Merge pull request #506 from seqan/hotfix/bam-comment-reading

[FIX] Fixing reading and writing of comment lines in SAM headers.
Merge branch 'hotfix/issue_478'
[DOC] Applying documentation changes from #481 to DDDoc
[DOC] Fixing doc bug of FileOpenMode #249
Merge branch 'feature/gustaf_sv_classification_invdel' of github.com:ktrappe/seqan into develop
Merge branch 'develop' of github.com:skrakau/seqan into develop
[DOC,FIX] Fixing bug in SequencesInDepth.rst