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VDBWRAIR / samtools

GNU General Public License v2.0
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Matplotlib dependency #2

Open averagehat opened 9 years ago

averagehat commented 9 years ago

Currently bqd.py is dependent on matplotlib.lines.Line2D here This is currently the only use of matplotlib in this project, so it would be nice to drop it.

The functionality isn't being used within this package -- it's being used somewhere else in ngs_mapper

necrolyte2 commented 9 years ago

I'm not sure that bqd.py should even be part of the samtools project. bqd.py is really for ngs_mapper to build the graphics and it seems like almost all of its functionality will be gutted when we integrate this project into ngs_mapper

averagehat commented 9 years ago

My thinking is that bqd.py parses pileup output which samtools.py is also doing. Optimally bqd would use samtools.py's Mpileup class. At least the call from bqd should be through a python module. We would get pretty close to having all samtools functionality wrapped in a python module (no direct calls vi Popen), which is probably good.

averagehat commented 9 years ago

I'll remove bqd.py in the next push