This was a nice twist on the usual complaints about code and documentation. A way to recognize good behavior and illustrate examples that are well done. I liked it.
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We’ve talked a lot about Minimum Standards For Bioinformatics Command Line Tools here, but I’m wondering what you consider to be “gold standard” examples of coding/programming that bioinformaticians should read to improve their own coding and understanding.
Picard – written in Java
Sickle – written in C++
Cutadapt – written in Python
Anyway, I thought it was a good idea to show the kind of behavior you want to encourage. Check out the chatter and add other good examples, if you have some.