mcieslik-mctp / epicode Goto Github PK

Hi,

In trying to install epicode, I noticed it fails complaining that pysam 0.7.5 does not exist. I checked for the listed versions, and 0.7.6 does exist, which I presume is close in functionality to 0.7.5.

Could you make the epicode dependencies point to pysam 0.7.6 instead of the non-existent 0.7.5?

Thanks

The command has a typo -bams instead of -bbams. Also it does not document that both bam file directories should have files with matching names.

should point to the scripts in the repo/scripts dir

R scripts require:

library(ggplot2)
library(reshape2)
library(stringr)
library(rjson)

should be documented

When provided unsorted .bam files the script dies with a series of uninformative errors. This would be better handled by first checking the input.

The run id sometimes starts with a - sign, which means that the files output by epicode will be prefixed by a dash. Since manipulating files prefixed with a - is very inconvenient and that this - sign little informative I suggest removing it systematically.

need to define a minimum set of bam files, maybe 4?