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> especially in the Bioinformatics/Genomics space My first internship was re-writing a Perl program that parsed the output of `samtools mpileup`[0] into a C pr
by skulk 5y ago
> especially in the Bioinformatics/Genomics space
My first internship was re-writing a Perl program that parsed the output of `samtools mpileup`[0] into a C program that used htslib[1] to directly read the BAM file and extract the relevant data. This preprocessing (the Perl version) was the slowest part of the pipeline, even slower than the actual data analysis.
[0]: http://www.htslib.org/doc/samtools-mpileup.html http://www.htslib.org/doc/samtools-mpileup.html
[1]: http://www.htslib.org/ http://www.htslib.org/
- olliej 5y agooof I can't imagine converting perl string manipulation to C was fun. Did you try to replicate what the perl code was doing, or did you just redo the entire thing in a more C like way?
- thraxil 5y agoYeah, I feel like that was a pretty common workflow. Someone would get a new algorithm working in Perl, test it on fairly small datasets, maybe publish their paper, then some poor chump would have to carefully rewrite it in C to make it actually useful for real data. I was at a university, so our chumps were grad students. I'm sure interns were the industry equivalent :)