Example commands do not work

[Jakob Nissen]

Copy pasting one of the examples from your README:

(bioinfo) [jakobnissen:cdhit]$ ../kma/kma –ipe ../VOF/200501_M03704_0228_000000000-CPYBD/V000034484* –o testout –t_db swine_kma_db -1t1
Invalid option: –ipe

It turns out your example uses a different version of the - symbol, which does not parse in my terminal.

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Furthermore, after having changed the - symbol to the correct one:

(bioinfo) [jakobnissen:cdhit]$ ../kma/kma -ipe ../VOF/200501_M03704_0228_000000000-CPYBD/V000034484* –o testout –t_db swine_kma_db -1t1
 Too few arguments handed

It appears the -1t1 flag does not work.

[ptlcc]

In this case I would go out on a limb and say there must be some hidden characters in the README, causing this behaviour when parsing the cmd-line.

I have removed these from the README.