Argument parsing, usage statement, and small improvements for countKmers

[standage]

I made a few changes to the countKmers script for my own use, and thought they might be useful for others as well.

• added option parsing so that users can configure cores, paths, etc from the command line without modifying the script
• added a usage statement so users can see options by running ./countKmers -h
• added an option for users to specify the FASTQ file extension; also, it autodetects whether the extension includes .gz or not and dynamically determines whether to use zcat or cat, again so users don't have to modify the script

I also updated README.md to reflect these changes, and the fact that Jellyfish 2 is a suitable alternative to the modified version of Jellyfish bundled with HAWK which seems to be giving some users issues.

[standage]

Rolled back the text about Jellyfish 2.

[atifrahman]

Thank you so much for your modifications! Incorporated a few. We are working on a few things. We will take care of the rest once that's done.