[DOC] Converting README to RST file.
[FIX] Adjusting samcat, bs_tools, and mason2 to fixed SAM/BAM.

Hash of hotfix was 2fae0b1d3270fc9bcb1cfa3b0c55b5c61d5e6ddb.
Merge pull request #573 from holtgrewe/hotfix/apps-to-new-sam-bam

[FIX] Adjusting samcat, bs_tools, and mason2 to fixed SAM/BAM.
[FIX] fixed #509
[FIX] fixed #519
Merge pull request #581 from weese/hotfix/trac-tickets

[FIX] fixed Hotfix/trac tickets
Merge pull request #505 from holtgrewe/feature/readme-update

[DOC] Converting README to RST file.
[FIX] Only attempt to run nosetests (for util/py_lib) if found.
Merge pull request #582 from holtgrewe/fix/notests-windows

[FIX] Only attempt to run nosetests (for util/py_lib) if found.
[INTERNAL] Yara: verbose output to cerr instead of cout
[DOC] Yara: improved the help
Merge pull request #590 from holtgrewe/fix/mason2-compile

[FIX] Mason2 did not compile with new stream module.
[FIX, CLI] Yara: pipe to stdout
[INTERNAL] Yara: options cleanup
[INTERNAL] Yara: bumped version to 0.9.1
[TEST] Yara: updated sam file
[CLI] Yara: removed options --no-header to output a headless SAM file
Merge pull request #592 from esiragusa/feature/yara/pipe

[FEATURE] Yara: output to stdout
[FIX] no header reordering if input is a single file
Merge branch 'develop' of github.com:seqan/seqan into feature/stream-fixes