check if input file is compressed (gziped/bzip2ed) and open accordingly#130

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mdcao wants to merge 3 commits intotseemann:masterfrom mdcao:master

+88-4

Commits on Jul 15, 2015

check if input file is compressed (gziped/bzip2ed) and open accordingly
mdcao
committed

Commits on Apr 10, 2017

Merge https://github.com/tseemann/prokka
mdcao
committed

Commits on Apr 16, 2017

get alignment
mdcao
committed