Basepairing Bern

[kclem]

Various improvements and bug fixes:

• Add param --plot_center to allow custom plots centered at a given point in plotCustomAllelePlot script (ecf23ef)
• All sub-CRISPResso runs are run with 1 process in Batch, WGS, Pooled, etc. Because we added multiprocessing capabilities to CRISPResso (the plotting part) we thought it would be slick for CRISPRessoPooled to run sqrt(n_processes) CRISPResso processes with sqrt(n_processes) processes each. Unfortunately, sqrt(n) isn't a really useful number for the number of processes people usually run (e.g. 2 or 3 or even 8), and a lot of the CRISPResso processing isn't enabled to take advantage of multiprocessing (e.g. the alignment step), so processes were being wasted. So we reverted back to having n_processes CRISPResso processes, each with 1 process. (a923a7c)
• Remove version checks for numpy and seaborn (90b43ea)
• Fix allele plotting error for plot 5 referring to uninitialized y_max variable (53197e6)
• Fix unicode errors for bam read/write (8196b6a)
• Convert columns in nucleotide count and modification tables to numeric for PE analysis (cabebbe)
• Make loggers module-specific so matplotlib debug doesn't get spewn out in the CRISPResso log (c2bdd96)
• Add unit tests (3e6c281)

Full Changelog: v2.2.5...v2.2.6

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This discussion was created from the release Basepairing Bern.