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LKremer / scbs

Python package with CLI for the analysis of single cell methylation data. Now known as MethSCAn: https://github.com/anders-biostat/MethSCAn
https://anders-biostat.github.io/MethSCAn/
GNU General Public License v3.0
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custom format specification #8

Closed simon-anders closed 2 years ago

simon-anders commented 2 years ago

For option '--input-format', column 4 is defined as follows:

 4. The column number that contains either unmethylated counts (u) or the total
                       coverage (c) followed by either 'm' or 'c', e.g. '4c' to denote that the 4th column
                       contains the coverage

Why do I have to suffix the number with 'm' and not 'u'?

LKremer commented 2 years ago

Good catch, this doesn't make sense. I think this is just an error in the help string, but before I change the help string I will write a basic test for this custom format stuff, to make sure everything is working as intended.

LKremer commented 2 years ago

Should be fixed now. You use 'u' now instead of 'm'.