[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
[Tophat] --index-bam now shows progress; fix program description
[Tophat] fix display project name
[Tophat][FIX] samtools command typo, no shell
[Tophat][FIX] correct samtools input filename and timestamp
[PKG] release 0.0.6
[Tophat][FIX] if a sample has completed already, no error will show.