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Forum: What are your "model" examples for bioinformatics programming?
5
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4.3 years ago
Dan D 6.8k
Tennessee

We've talked a lot about good practices 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

ADD COMMENTlink 4.3 years ago Dan D 6.8k • updated 4.3 years ago Pierre Lindenbaum 120k
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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...

ADD REPLYlink 4.3 years ago
Pierre Lindenbaum
120k
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0

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.

ADD REPLYlink 4.3 years ago
dariober
10k
Entering edit mode
0

"Minimum standards" has some good advice.

ADD REPLYlink 4.3 years ago
Brian Bushnell
16k
2
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4.3 years ago
Istvan Albert 80k
University Park, USA

Bedtools - best docs of all time

ADD COMMENTlink 4.3 years ago Istvan Albert 80k
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1

+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.

ADD REPLYlink 4.3 years ago
Pierre Lindenbaum
120k

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