[PKG] use both absolute(package) and relative importing, so one can still run tophat.py directly
[Tophat][ADD] --index-bam option
[Tophat][MOD] more comment
[PKG] modify _version.py generated description, new version format (-dirty) if there are unstaged files in repo.
[Tophat] reformat doctoring (possibly use Sphinx for documentation in near future)
[Tophat] complete comment-like documentation for function naming
[Tophat] show warns if run the tophat.py directly; show version in command-line help