Perl 6 - the future is here, just unevenly distributed

IRC log for #bioperl, 2015-02-18

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02:48 Topic for #bioperl is now Be patient! People chat here daily, but not necessarily the minute or hour you wandered in. Leave your IRC client connected. | http://bioperl.org/wiki/IRC#Getting_help | http://www.bioperl.org/wiki/Using_Git | nopaste to gist.github.com
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14:20 samb1 Hello, this looks interesting: http://biorxiv.org/content/early/2015/02/13/013011.full-text.pdf+html  :) would be nice if bioperl had more NGS stuff (or maybe it has but I've missed it) anyway, looking to get involved with the project and contribute to it as much as I can.. I work as a perl developer, currently in a very non-sciencey/corporate setting but started out several years ago as a molecular
14:20 samb1 biologist then did lots of bioinformatics stuff with my MSc (also did a year of a bioinformatics PhD then got distracted but might revive it!)
14:20 samb1 thought I'd introduce myself rather than lurking :)
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16:03 pyrimidine samb1: I agree, FWIW
16:04 pyrimidine samb1: part of the problem with NGS is getting decent performance (current state of classes for dealing w/FASTQ is terrible)
16:16 pyrimidine samb1: but... if someone wanted to, for instance, take that on as a project then it's cool w/ me
16:17 pyrimidine :)
16:17 pyrimidine or, as they say in the biz, 'well volunteered!'
16:21 samb1 yes that was a classic "someone should" comment I made :) ... well I plan to look into it and see how far I get... I looked at biojava it has fairly well defined classes for handling illumina data and such, but I'm a perl person mainly so would like to see it happen.. we'll see...
16:31 pyrimidine samb1: If you need a fast (e.g. XS-based) parser, I have a prototype here: https://github.com/cjfields/Bio-Kseq
16:32 pyrimidine samb1: works for FASTQ and FASTA.  Should be mem-leak free (I've tested this w/ several whole genome files).  Needs some scrubbing for a release.
16:34 pyrimidine samb1: if you do some refactoring, one key thing to avoid is inheritance (if possible).  That was IMHO the main bottleneck last I checked.
16:48 samb1 nice, I'll have a look :)
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