[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.
Merge branch 'master' into develop

Conflicts:
	core/apps/samcat/tests/ex1_merged.bam
	core/apps/samcat/tests/run_tests.py
	core/tests/index/test_index_creation.cpp
	core/tests/index/test_index_creation.h
	extras/apps/bs_tools/bisar.h
	extras/apps/mason2/tests/simulator.out2.sam
	extras/apps/mason2/tests/simulator.out7.sam
Merge pull request #603 from holtgrewe/develop

Merging master into develop.