Add support for when the genome reference contains IUPAC (e.g., R for A/G, Y for C/T, etc.) codes in them?

dohlee / metheor

:comet: Ultrafast DNA methylation heterogeneity calculation from bisulfite alignments (Lee et al., PLOS Computational Biology. 2023)

GNU General Public License v3.0

43 stars 8 forks source link

Closed litaifang closed 1 year ago

litaifang commented 1 year ago

Some versions of the human genome reference has IUPAC codes in them and may not be compatible with these https://github.com/dohlee/metheor/blob/master/src/tag.rs#L72. Wondering if you'd like to add support for these cases?

dohlee commented 1 year ago

Thank you for the suggestion. Fixed in https://github.com/dohlee/metheor/blob/master/src/tag.rs#L79. Would you update the package to version 0.1.5 and test it with your data? If it seems okay, I'll close this issue.

Best, Dohoon

litaifang commented 1 year ago

Thanks. Yep version 0.1.5 handles IUPAC now.