update CLI help #105
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update CLI help #105
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I updated the CLI help messages. And also
seedfor the build command (not used)-uuppercase flag in the build command. Looking at the code I realized that we are filtering for allowed characters and then convert them to uppercase when reading fastas. The allowed characters are uppercase. I therefore inverted the uppercase conversion and the filtering, so that also lowercase inputs should work.-xflag in the build command, which was not used so far.(Nb: the branch is based on the PR #103)