Forum:What are your "model" examples for bioinformatics programming?
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5.9 years ago
Dan D 7.2k

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.

I'll start:

Picard - written in Java

Sickle - written in C++

Cutadapt - written in Python

github coding best practices RNA-Seq Forum • 2.0k views
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I'm a huge fan of picard/htsjdk, but it is not gold to me.  I don't like many things : parameters with annotations, a weird base class, stdin/stdout not  default, non standard way of setting parameters, not using interfaces in SamRecord, using getXXXX for boolean in SamRecord instead of isXXXX, etc...

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Somewhat off-topic... I find surprising that Java doesn't have a standard command line parser like argparse for python. There are a few libraries out there (I'm happy with argparse4j for that tiny bit of java I write) but none of them seems widely accepted. So many command line tools in java use their home made ways of parsing arguments.

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"Minimum standards" has some good advice.

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5.9 years ago

Bedtools - best docs of all time

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+1 for the doc, but I don't like the way sub-programs are initialized with the contructor. Everytime a new parameter is needed, you need to extend the C++ constructor, IMHO a "better" way would be to use  the builder pattern https://en.wikipedia.org/wiki/Builder_pattern . Bedtools *is* a great tool anyway.

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